Jukka Corander

• Pöntinen, Anna Kaarina; Trung, Nguyen Vinh; Mallawaarachchi, Sudaraka; Gladstone, Rebecca Ashley; Kuronen, Juri & Samuelsen, Ørjan [Show all 15 contributors for this article] (2026). Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage. Microbial Genomics. 12(9). doi: 10.1099/mgen.0.001795. Full text in Research Archive
• Vumbaca, Michela; Biffignandi, Gherard Batisti; Cavanna, Caterina; Bellinzona, Greta; Corbella, Marta & Mileto, Irene [Show all 10 contributors for this article] (2026). Genomic Characterization of Candida spp. Highlights a Persistent, Azole-Resistant C. parapsilosis Clone Circulating in a Tertiary Care Hospital During the First COVID-19 Wave. Mycopathologia. ISSN 0301-486X. 191(2). doi: 10.1007/s11046-026-01070-9. Full text in Research Archive Show summary

  Yeasts belonging to the Candida genus typically reside on the mucosal surface and within the respiratory and gastrointestinal tract as commensals. Under conditions of host vulnerability, they can act as opportunistic pathogens, leading to various forms of candidiasis, including candidemia. Such infections can be particularly problematic when caused by isolates that exhibit resistance to antifungal drugs, which are becoming more prevalent in many regions. One hundred and seven samples of Candida spp. were isolated from patients with candidemia in the hospital San Matteo in Pavia (Italy) over a period of 6 years, from 2015 to the first COVID wave in spring 2020. In order to understand the epidemiology of Candida infections in this hospital setting, the isolates were whole-genome sequenced, confirming that most belonged to C. parapsilosis and C. albicans. Comparative genomics revealed that isolates of C. albicans were genomically diverse, indicative of repeated introductions in the hospital from the community. C. parapsilosis isolates on the other hand belonged to two groups of highly similar isolates, representing strains capable of long-term persistence in the hospital. All isolates of the main persistent group were resistant to fluconazoleresulting from the Y132F substitution in ERG11 and the N455D substitution in UPC2, while presenting variable levels of resistance to voriconazole and itraconazole. Interestingly, with the exception of the single isolate susceptible to both voriconazole and itraconazole, all the 61 isolates presented one unreported missense mutation in MRR1 (S1907C).

• Gladstone, Rebecca Ashley; Pesonen, Maiju; Pöntinen, Anna Kaarina; Mäklin, Tommi; MacAlasdair, Neil Zhang Nian Zhong & Thorpe, Harry [Show all 17 contributors for this article] (2026). Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli. Nature Microbiology. doi: 10.1038/s41564-026-02283-w. Full text in Research Archive Show summary

  Bacterial polysaccharide capsules contribute to antigenic diversity and immune evasion. Escherichia coli infections, including those caused by extraintestinal pathogenic E. coli (ExPEC), cause substantial antimicrobial resistance-associated morbidity and mortality. However, much-needed genotypic methods for E. coli capsule typing to aid epidemiological analysis and therapeutic design are lacking. Here we describe the curation of an in silico typing database for group 2 and 3 ATP-binding cassette transporter-dependent capsule (K) loci from 18,185 kps-positive E. coli genomes from all continents and its application to carriage and ExPEC disease cohorts. Capsules K1, K5 and K2 were the most common types in European BSIs, and together with K100 and K52 they were responsible for 58% of multidrug resistance, with differing associations with invasiveness. Homologous recombination, insertion sequences and plasmids were associated with capsular gene exchange. These findings improve understanding of capsule epidemiology and evolution to inform future diagnostic and therapeutic strategies to combat ExPEC infections.

• Blomstedt, Paul; Mesquita, Diego; Rivasplata, Omar; Lintusaari, Jarno; Sivula, Tuomas & Corander, Jukka [Show all 7 contributors for this article] (2026). Meta-Analysis of Bayesian Analyses. Bayesian Analysis. ISSN 1936-0975. 21(1), p. 229–254. doi: 10.1214/24-BA1465. Full text in Research Archive
• Ross, Theodor Anton; Pöntinen, Anna Kaarina; Holsbø, Einar; Samuelsen, Ørjan; Hegstad, Kristin & Kampffmeyer, Michael [Show all 8 contributors for this article] (2026). Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types. Microbial Genomics. 12(1). doi: 10.1099/mgen.0.001608. Full text in Research Archive
• Gibbon, Marjorie J.; Couto, Natacha; Cozens, Keira; Habib, Samia; Cowley, Lauren & Aanensen, David M. [Show all 20 contributors for this article] (2026). Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis. Lancet Microbe. 7(2). doi: 10.1016/j.lanmic.2025.101236. Full text in Research Archive Show summary

  Background Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both virulence factors and antimicrobial resistance genes (ARGs) have raised serious public health concerns. The aim of this study is to describe the global diversity of plasmids carrying iuc3 (a key virulence factor in K pneumoniae associated with pigs and clinical isolates) from diverse settings, and their role in the emergence of convergent strains through hybridisation with plasmids carrying ARGs. Methods This population genomic analysis study was designed to describe both the global and local diversity of iuc3-carrying plasmids from diverse sources, and the co-occurrence of iuc3 with ARGs. We used all 4148 Klebsiella spp isolates from two large One-Health studies (SpARK, Italy, and OH-DART, Thailand), including 191 Klebsiella isolates from pigs, 635 from clinical isolates, 1040 from hospital and community carriage, and 2282 from other sources. Short-read sequencing of Klebsiella isolates was performed as part of the SpARK study. We sequenced Klebsiella isolates from the OH-DART (MicrobesNG, Birmingham, UK; HiSeq and NovaSeq, Illumina San Diego, CA, USA; GridION, Oxford Nanopore Technologies, Oxford, UK) and SpARK (MinION or GridION, Oxford Nanopore Technologies, Oxford, UK) studies. We also retrieved plasmid sequences carrying iuc3 from the National Centre for Biotechnology Information (NCBI). To ascertain the degree of diversity, evolutionary dynamics, and structuring across ecological and geographical axes, we detected ARGs and virulence loci, analysed clustering patterns and generated approximate maximum-likelihood phylogenetic trees. Findings We identified 48 K pneumoniae isolates with iuc3 in the SpARK data and 79 in the OH-DART data. Three (2·4%) of these 127 isolates were from clinical sources, 73 (57·5%) were from pig or pork meat. iuc3 isolates corresponded to multiple (n=47) host sequence types (STs), with ST35, ST45, ST881, ST25, and ST967 harbouring iuc3 in both datasets. We generated hybrid assemblies for 44 (SpARK) and 36 (OH-DART) isolates, plus a single iuc3 isolate from Germany. 53 (65·4%) of these isolates were from pigs, three (3·7%) from clinical sources, and 25 (30·9%) from other sources. There were an additional 48 iuc3 positive isolates from our collections for which only short read data was available. A single iuc3-positive Klebsiella oxytoca isolate from a pig farm was detected in the SpARK data, which was also sequenced. We identified 330 iuc3-positive isolates and 58 iuc3-carrying plasmid assemblies from NCBI, of which 83 (21·4%) were from clinical sources, 120 from pigs (30·9%), and 185 (47·7%) from other sources or of unknown provenance. These isolates were from K pneumoniae except two isolates of Klebsiella quasipneumoniae subsp similipneumoniae and one of Enterobacter hormaechei. The combined dataset of 517 iuc3 plasmids ranged in size from 110 375 bp to 365 580 bp and mostly corresponded to multiple IncFIB(K) and IncFII replicon types. We found seven convergent K pneumoniae plasmids in the Thai data: six from fresh markets and one from a neighbouring hospital. These plasmids emerged through the hybridisation of cocirculating iuc3 plasmids and plasmids encoding extended-spectrum β-lactamases (ESBLs), although none of these seven plasmids carried genes encoding carbapenemases. We also identified putative cocirculating parental plasmids carrying iuc3 and ESBL-encoding genes. Clustering and phylogenetic analysis resolved the iuc3 plasmid sequences into three groups, which were consistent using both complete plasmid sequences (n=139) and short-read data (n=517). In the complete plasmid sequence data, 66 strains contained group 1 plasmids, 38 strains contained group 2 plasmids, and 35 strains contained group 3 plasmids. Group 3 plasmids are mostly carried by isolates circulating in hospitals throughout Asia, with occasional examples in Europe and elsewhere, and carry multiple ARGs and potential virulence factors. By contrast, group 1 plasmids are commonly carried by porcine isolates in Europe, and group 2 are a heterogeneous mixture of geographical and ecological sources. Interpretation Plasmid hybridisation occurs frequently outside of the health-care environment and can lead to the convergence of resistance and virulence traits. Generating complete plasmid sequences from regional population-scale samples facilitates the identification of convergent plasmids and their putative parental plasmids. Three robust groups of iuc3 plasmids were resolved, which show both epidemiological and geographical differences; one of these groups was associated with clinical isolates in Asia and warrants targeted plasmid surveillance.

• Fisher, Lewis W.S.; Thorpe, Harry; Sassera, Davide; Corander, Jukka & Bryant, Josephine M. (2025). High frequency body site translocation of nosocomial Pseudomonas aeruginosa. Nature Communications. 16(1). doi: 10.1038/s41467-025-66088-x. Full text in Research Archive Show summary

  Pseudomonas aeruginosa is an important nosocomial pathogen which can cause serious infections across diverse anatomic locations. Infections can spread within an individual to different body sites, but the rate and directionality of this process is unknown. Here, we explore within-host diversity as well as the body site translocation dynamics using de-convoluted metagenomic P. aeruginosa reads from 256 hospital patients sampled at both respiratory and gut sites. Of the 84 patients where P. aeruginosa genomes could be recovered, there were 27 cases where the same P. aeruginosa clone was detected across multiple body sites. Using a simulation approach, we find that the majority of body site sharing is likely due to within-patient translocation of clones rather than independent acquisition from the hospital environment. Using ancestral reconstruction, we predict that most clones likely occupied a respiratory niche, and that the probable direction of clone transmission is lung-to-gut. Analysis of within-patient variation highlights strong enrichment of mutations in genes associated with antimicrobial resistance, irrespective of sample type. We report significantly more translocation than has been previously reported and highlight that lower respiratory tract infections can result in persistent gut colonisation of P. aeruginosa, a major risk factor for sepsis in vulnerable patients.

• Ojala, Fanni; Pesonen, Henri; Gladstone, Rebecca Ashley; Mäklin, Tommi; Tonkin-Hill, Gerry & Marttinen, Pekka [Show all 7 contributors for this article] (2025). Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones. Nature Communications. 16(1). doi: 10.1038/s41467-025-65301-1. Full text in Research Archive Show summary

  Abstract Extra-intestinal pathogenic Escherichia coli ubiquitously colonize the human gut and represent clinically the most significant bacterial species causing urinary tract infections and bacteremia. During the last two decades clades of the ST131 lineage have spread globally, but it remains unknown how their transmission dynamics compare to the basic reproduction numbers ( R 0 ) for viral pandemics. We develop a compartmental model for asymptomatic gut colonization and onward transmission coupled with an epidemiological observation model and fit it on the major ST131 clades. Our results indicate that the ST131-A transmission potential ( R 0 = 1.47) can be comparable to pandemic influenza viruses, while the significantly lower transmissibility of ST131-C1 ( R 0 = 1.18) and ST131-C2 ( R 0 = 1.13) suggests that their dissemination has been aided by antibiotic selection pressure and healthcare facilities. Our results provide an advance in understanding the relative transmissibility of these opportunistic pathogens.

• MacAlasdair, Neil Zhang Nian Zhong; Pöntinen, Anna Kaarina; Ling, Clare; Mallawaarachchi, Sudaraka; Thaipadungpanit, Janjira & Nosten, Francois H. [Show all 11 contributors for this article] (2025). Genetic population structure of Haemophilus influenzae at local and global scales. Nature Microbiology. 10(12), p. 3136–3147. doi: 10.1038/s41564-025-02171-9. Full text in Research Archive Show summary

  Haemophilus influenzae is an opportunistic bacterial pathogen that causes both non-invasive and invasive disease in humans. Although the H. influenzae type b vaccine can reduce invasive disease, it is not effective against non-b serotypes or unencapsulated non-typeable H. influenzae (NTHi). The genetic population structure of H. influenzae , especially NTHi, which is typically prevalent in lower- and middle-income countries, is unclear. Here we whole-genome sequenced 4,474 isolates of H. influenzae from an unvaccinated paediatric carriage and pneumonia cohort from the Maela camp for displaced persons in northwestern Thailand. Despite no H. influenzae type b immunization, serotype b was uncommon, whereas 92.4% of the isolates were NTHi. Most multidrug-resistant lineages were NTHi, and there were no lineages enriched among disease samples. Incorporating 5,976 published genomes revealed a highly admixed population structure, low core genome nucleotide diversity and evidence of pervasive negative selection. Our findings expand our understanding of this major pathogen in lower- and middle-income countries and at a global scale.

• Kuronen, Juri; Corander, Jukka & Pensar, Johan (2025). Learning pairwise Markov network structures using correlation neighborhoods. Communications in Statistics - Simulation and Computation. ISSN 0361-0918. doi: 10.1080/03610918.2025.2602032. Full text in Research Archive Show summary

  Markov networks are widely studied and used throughout multivariate statistics and computer science. In particular, the problem of learning the structure of Markov networks from data without invoking chordality assumptions in order to retain expressiveness of the model class has been given a considerable attention in the recent literature, where numerous constraint-based or score-based methods have been introduced. Here we develop a new search algorithm for the network score-optimization that has several computational advantages and scales well to high-dimensional data sets. The key observation behind the algorithm is that the neighborhood of a variable can be efficiently captured using local penalized likelihood ratio (PLR) tests by exploiting an exponential decay of correlations across the neighborhood with an increasing graph-theoretic distance from the focus node. The candidate neighborhoods are then processed by a two-stage hill-climbing (HC) algorithm. Our approach, termed fully as PLRHC-BIC0.5, compares favorably against the state-of-the-art methods in all our experiments spanning both low- and high-dimensional networks and a wide range of sample sizes. An efficient implementation of PLRHC-BIC0.5 is freely available from the URL: https://github.com/jurikuronen/plrhc.

• Winkler, Andrea Sylvia; Mburu, Christina Brux; Carabin, Hélène; Neves, Carlos Goncalo Rolhas Fernandes Das; Häsler, Barbara & Zinsstag, Jakob [Show all 40 contributors for this article] (2025). The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems. The Lancet. ISSN 0140-6736. 406(10502), p. 501–570. doi: 10.1016/s0140-6736(25)00627-0. Full text in Research Archive
• Ross, Theodor Anton; Janice, Jessin; Alonso, Sergio Arredondo; Löhr, Iren Høyland; Holsbø, Einar & Corander, Jukka [Show all 9 contributors for this article] (2025). Enterococcus lactis is ecologically and genetically distinct from the major opportunistic pathogen Enterococcus faecium. Microbial Genomics. 11(6), p. 1–14. doi: 10.1099/mgen.0.001420. Full text in Research Archive
• Wang, Meng; Jin, Longyang; Wang, Ruobing; Wang, Qi; Wang, Shuyi & Wu, Xingyu [Show all 9 contributors for this article] (2025). KpnK48 clone driving hypervirulent carbapenem-resistant Escherichia coli epidemics: Insights into its evolutionary trajectory similar to Klebsiella pneumoniae. Drug resistance updates. ISSN 1368-7646. 81. doi: 10.1016/j.drup.2025.101243. Full text in Research Archive Show summary

  Aims Hypervirulent and carbapenem-resistant pathogens posed a significant and growing threat to global public health. This study focused on the rapid spread of a hypervirulent carbapenem-resistant E. coli (hv-CREC) subclone and its genomic resembles with hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP), driven by recombination impacting both chromosomal and plasmid gene content. Methods A multicenter molecular epidemiological study was conducted on 653 CREC clinical isolates collected across China (2013–2022), integrated with public genomic data. Pangenome-wide and phylogeographical analyses were performed to uncover recombination events, define the epidemic clone, and trace its evolutionary history. Growth advantage and virulence were evaluated through competition assays and Galleria mellonella infection models. Results Sequence types (ST) 167, ST410, ST617, and ST361 collectively accounted for 53.8 % (351/653) of the CREC isolates, with ST167 showing a sharp increase in prevalence after 2017. Among these, subclone named KpnK48 emerged as the primary driver of the increase in ST167 CREC prevalence. Traced to a European origin, KpnK48 rapidly expanded globally, particularly in China. The remarkable success of KpnK48 could plausibly be attributed to enhanced survival and virulence, driven by the acquisition of a ∼492 kb recombinant genomic region which mirrored the genomic architecture underlying the hv-CRKP ST11-K64 clone, reflecting a Klebsiella-like evolutionary path. Additionally, plasmid shift in KpnK48 clone from the prevalent NDM-IncX3 plasmid to Klebsiella-common NDM-IncF plasmid expanded its resistance spectrum and virulence gene repertoire, likely further amplifying its pathogenicity and success. Conclusions The KpnK48 subclone combined the features of hypervirulence and carbapenem resistance, bridging genomic traits of E. coli and K. pneumoniae, signifying a broader evolutionary trend with profound global health implications.

• Alonso, Sergio Arredondo; Pöntinen, Anna Kaarina; Gama, João Alves; Gladstone, Rebecca Ashley; Harms, Klaus & Tonkin-Hill, Gerry [Show all 23 contributors for this article] (2025). Plasmid-driven strategies for clone success in Escherichia coli. Nature Communications. 16, p. 1–15. doi: 10.1038/s41467-025-57940-1. Full text in Research Archive
• Pesonen, Henri & Corander, Jukka (2025). Stratified distance space improves the efficiency of sequential samplers for approximate Bayesian computation. Computational Statistics & Data Analysis. ISSN 0167-9473. 207. doi: 10.1016/j.csda.2025.108141. Full text in Research Archive Show summary

  Approximate Bayesian computation (ABC) methods are standard tools for inferring parameters of complex models when the likelihood function is analytically intractable. A popular approach to improving the poor acceptance rate of the basic rejection sampling ABC algorithm is to use sequential Monte Carlo (ABC SMC) to produce a sequence of proposal distributions adapting towards the posterior, instead of generating values from the prior distribution of the model parameters. Proposal distribution for the subsequent iteration is typically obtained from a weighted set of samples, often called particles, of the current iteration of this sequence. Current methods for constructing these proposal distributions treat all the particles equivalently, regardless of the corresponding value generated by the sampler, which may lead to inefficiency when propagating the information across iterations of the algorithm. To improve sampler efficiency, a modified approach called stratified distance ABC SMC is introduced. The algorithm stratifies particles based on their distance between the corresponding synthetic and observed data, and then constructs distinct proposal distributions for all the strata. Taking into account the distribution of distances across the particle space leads to substantially improved acceptance rate of the rejection sampling. It is shown that further efficiency could be gained by using a newly proposed stopping rule for the sequential process based on the stratified posterior samples and these advances are demonstrated by several examples.

• Thomas, Owen Matthew Truscott; Sá-Leão, Raquel; Lencastre, Hermínia de; Kaski, Samuel; Corander, Jukka & Pesonen, Henri (2025). Misspecification-robust likelihood-free inference in high dimensions. Computational statistics (Zeitschrift). ISSN 0943-4062. 40, p. 4399–4439. doi: 10.1007/s00180-025-01607-4. Full text in Research Archive Show summary

  Likelihood-free inference for simulator-based statistical models has developed rapidly from its infancy to a useful tool for practitioners. However, models with more than a handful of parameters still generally remain a challenge for the Approximate Bayesian Computation (ABC) based inference. To advance the possibilities for performing likelihood-free inference in higher dimensional parameter spaces, we introduce an extension of the popular Bayesian optimisation based approach to approximate discrepancy functions in a probabilistic manner which lends itself to an efficient exploration of the parameter space. Our approach achieves computational scalability for higher dimensional parameter spaces by using separate acquisition functions, discrepancies, and associated summary statistics for distinct subsets of the parameters. The efficient additive acquisition structure is combined with exponentiated loss-likelihood to provide a misspecification-robust characterisation of posterior distributions for subsets of model parameters. The method successfully performs computationally efficient inference in a moderately sized parameter space and compares favourably to existing modularised ABC methods. We further illustrate the potential of this approach by fitting a bacterial transmission dynamics model to a real data set, which provides biologically coherent results on strain competition in a 30-dimensional parameter space.

• Järvenpää, Marko Juhani & Corander, Jukka (2024). Approximate Bayesian inference from noisy likelihoods with Gaussian process emulated MCMC. Journal of machine learning research. ISSN 1532-4435. 25(366), p. 1–55. doi: https:/jmlr.org/beta/papers/v25/21-0421.html. Full text in Research Archive Show summary

  We present a framework for approximate Bayesian inference intended for a situation where only a limited number of noisy log-likelihood evaluations can be obtained due to constraints on the available computational budget, which is becoming increasingly common for expensive simulator-based models. We model the log-likelihood function using a Gaussian process (GP) and our main methodological innovation is to apply this model to emulate the progression that an exact Metropolis-Hastings (MH) sampler would take if it was applicable. Informative log-likelihood evaluation locations are selected using a sequential experimental design strategy until the MH accept/reject decisions are performed with sufficient level of accuracy based on a prespecified error tolerance criterion. The resulting approximate sampler is conceptually simple and shown to be sample-efficient. It is also more robust compared with earlier “Bayesian optimisation-like” methods tailored for approximate Bayesian inference, which generally assume a global surrogate model across the parameter space that can be challenging to fit well. We discuss some theoretical aspects and various interpretations of the resulting approximate MH sampler, and demonstrate its benefits in the context of Bayesian and generalised Bayesian likelihood-free inference for simulator-based statistical models.

• Mikkola, Petrus; Martin, Osvaldo A.; Chandramouli, Suyog; Hartmann, Marcelo; Pla, Oriol Abril & Thomas, Owen Matthew Truscott [Show all 12 contributors for this article] (2024). Prior Knowledge Elicitation: The Past, Present, and Future. Bayesian Analysis. ISSN 1936-0975. 19(4), p. 1129–1161. doi: 10.1214/23-BA1381. Full text in Research Archive Show summary

  Specification of the prior distribution for a Bayesian model is a central part of the Bayesian workflow for data analysis, but it is often difficult even for statistical experts. In principle, prior elicitation transforms domain knowledge of various kinds into well-defined prior distributions, and offers a solution to the prior specification problem. In practice, however, we are still fairly far from having usable prior elicitation tools that could significantly influence the way we build probabilistic models in academia and industry. We lack elicitation methods that integrate well into the Bayesian workflow and perform elicitation efficiently in terms of costs of time and effort. We even lack a comprehensive theoretical framework for understanding different facets of the prior elicitation problem. Why are we not widely using prior elicitation? We analyse the state of the art by identifying a range of key aspects of prior knowledge elicitation, from properties of the modelling task and the nature of the priors to the form of interaction with the expert. The existing prior elicitation literature is reviewed and categorized in these terms. This allows recognizing under-studied directions in prior elicitation research, finally leading to a proposal of several new avenues to improve prior elicitation methodology.

• Calland, Jessica Kate; Pesonen, Maiju; Mehat, Jai; Pascoe, Ben; Haydon, David J. & Lourenco, Jose [Show all 14 contributors for this article] (2024). Genomic tailoring of autogenous poultry vaccines to reduce Campylobacter from farm to fork. npj Vaccines. 9(1). doi: 10.1038/s41541-024-00879-z. Full text in Research Archive Show summary

  Campylobacter is a leading cause of food-borne gastroenteritis worldwide, linked to the consumption of contaminated poultry meat. Targeting this pathogen at source, vaccines for poultry can provide short-term caecal reductions in Campylobacter numbers in the chicken intestine. However, this approach is unlikely to reduce Campylobacter in the food chain or human incidence. This is likely as vaccines typically target only a subset of the high genomic strain diversity circulating among chicken flocks, and rapid evolution diminishes vaccine efficacy over time. To address this, we used a genomic approach to develop a whole-cell autogenous vaccine targeting isolates harbouring genes linked to survival outside of the host. We hyper-immunised a whole major UK breeder farm to passively target offspring colonisation using maternally-derived antibody. Monitoring progeny, broiler flocks revealed a near-complete shift in the post-vaccination Campylobacter population with an ~50% reduction in isolates harbouring extra-intestinal survival genes and a significant reduction of Campylobacter cells surviving on the surface of meat. Based on these findings, we developed a logistic regression model that predicted that vaccine efficacy could be extended to target 65% of a population of clinically relevant strains. Immuno-manipulation of poultry microbiomes towards less harmful commensal isolates by competitive exclusion, has major potential for reducing pathogens in the food production chain.

• Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Pesonen, Henri; Pesonen, Maiju; Cleon, Francois Pierre Alexandre & Parcell, Benjamin J [Show all 14 contributors for this article] (2024). Modulation of multidrug-resistant clone success in Escherichia coli populations: a longitudinal, multi-country, genomic and antibiotic usage cohort study. Lancet Microbe. 5(2), p. e142–e150. doi: 10.1016/S2666-5247(23)00292-6. Full text in Research Archive Show summary

  Background The effect of antibiotic usage on the success of multidrug-resistant (MDR) clones in a population remains unclear. With this genomics-based molecular epidemiology study, we aimed to investigate the contribution of antibiotic use to Escherichia coli clone success, relative to intra-strain competition for colonisation and infection.<p> <p>Methods We sequenced all the available E coli bloodstream infection isolates provided by the British Society for Antimicrobial Chemotherapy (BSAC) from 2012 to 2017 (n=718) and combined these with published data from the UK (2001–11; n=1090) and Norway (2002–17; n=3254). Defined daily dose (DDD) data from the European Centre for Disease Prevention and Control (retrieved on Sept 21, 2021) for major antibiotic classes (β-lactam, tetracycline, macrolide, sulfonamide, quinolone, and non-penicillin β-lactam) were used together with sequence typing, resistance profiling, regression analysis, and non-neutral Wright–Fisher simulation-based modelling to enable systematic comparison of resistance levels, clone success, and antibiotic usage between the UK and Norway. <p>Findings Sequence type (ST)73, ST131, ST95, and ST69 accounted for 892 (49⋅3%) of 1808 isolates in the BSAC collection. In the UK, the proportion of ST69 increased between 2001–10 and 2011–17 (p=0⋅0004), whereas the proportions of ST73 and ST95 did not vary between periods. ST131 expanded quickly after its emergence in 2003 and its prevalence remained consistent throughout the study period (apart from a brief decrease in 2009–10). The extended-spectrum β-lactamase (ESBL)-carrying, globally disseminated MDR clone ST131–C2 showed overall greater success in the UK (154 [56⋅8%] of 271 isolates in 2003–17) compared with Norway (51 [18⋅3%] of 278 isolates in 2002–17; p<0⋅0001). DDD data indicated higher total use of antimicrobials in the UK, driven mainly by the class of non-penicillin β-lactams, which were used between 2⋅7-times and 5⋅1-times more in the UK per annum (ratio mean 3⋅7 [SD 0⋅8]). This difference was associated with the higher success of the MDR clone ST131–C2 (pseudo-R² 69⋅1%). A non-neutral Wright–Fisher model replicated the observed expansion of non-MDR and MDR sequence types under higher DDD regimes. <p>Interpretation Our study indicates that resistance profiles of contemporaneously successful clones can vary substantially, warranting caution in the interpretation of correlations between aggregate measures of resistance and antibiotic usage. Our study further suggests that in countries with low-to-moderate use of antibiotics, such as the UK and Norway, the extent of non-penicillin β-lactam use modulates rather than determines the success of widely disseminated MDR ESBL-carrying E coli clones. Detailed understanding of underlying causal drivers of success is important for improved control of resistant pathogens.

• Taylor, Aidan J.; Yahara, Koji; Pascoe, Ben; Ko, Seungwon; Mageiros, Leonardos & Mourkas, Evangelos [Show all 23 contributors for this article] (2024). Epistasis, core-genome disharmony, and adaptation in recombining bacteria. mBio. ISSN 2161-2129. 15(6), p. e0058124–e0058124. doi: 10.1128/mbio.00581-24. Full text in Research Archive
• Paganini, Julian A.; Kerkvliet, Jesse J.; Vader, Lisa; Plantinga, Nienke L.; Meneses, Rodrigo & Corander, Jukka [Show all 9 contributors for this article] (2024). PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli. Microbial Genomics. 10(2). doi: 10.1099/mgen.0.001193. Full text in Research Archive Show summary

  Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-based tool that bins plasmid-predicted contigs into distinct plasmid predictions. Gplas2 is more effective at recovering plasmids with large sequencing coverage variations and can be combined with the output of any binary classifier. The combination of plasmidEC with gplas2 showed a high completeness (median=0.818) and F1-Score (median=0.812) when reconstructing ARG plasmids and exceeded the binning capacity of the reference-based method MOB-suite. In the absence of long-read data, our method offers an excellent alternative to reconstruct ARG plasmids in E. coli.

• Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka & Johannessen, Mona Susan [Show all 7 contributors for this article] (2024). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Frontiers in Cellular and Infection Microbiology. doi: 10.3389/fcimb.2024.1326730. Full text in Research Archive Show summary

  <p><i>Introduction:</i> Improved understanding of <i>Staphylococcus aureus</i> throat colonization in the presence of other co-existing microbes is important for mapping <i>S. aureus</i> adaptation to the human throat, and recurrence of infection. Here, we explore the responses triggered by the encounter between two common throat bacteria, <i>S. aureus</i> and <i>Streptococcus anginosus</i>, to identify genes in <i>S. aureus</i> that are important for colonization in the presence of human tonsillar epithelial cells and <i>S. anginosus</i>, and further compare this transcriptome with the genes expressed in <i>S. aureus</i> as only bacterium. <p><i>Methods:</i> We performed an in vitro co-culture experiment followed by RNA sequencing to identify interaction-induced transcriptional alterations and differentially expressed genes (DEGs), followed by gene enrichment analysis. <p><i>Results and discussion:</i> A total of 332 and 279 significantly differentially expressed genes with p-value < 0.05 and log2 FoldChange (log2FC) ≥ |2| were identified in <i>S. aureus</i> after 1 h and 3 h co-culturing, respectively. Alterations in expression of various <i>S. aureus</i> survival factors were observed when co-cultured with <i>S. anginosus</i> and tonsillar cells. The serine-aspartate repeat-containing protein D (sdrD) involved in adhesion, was for example highly upregulated in <i>S. aureus</i> during co-culturing with <i>S. anginosus</i> compared to <i>S. aureus</i> grown in the absence of <i>S. anginosus</i>, especially at 3 h. Several virulence genes encoding secreted proteins were also highly upregulated only when <i>S. aureus</i> was co-cultured with <i>S. anginosus</i> and tonsillar cells, and iron does not appear to be a limiting factor in this environment. These findings may be useful for the development of interventions against <i>S. aureus</i> throat colonization and could be further investigated to decipher the roles of the identified genes in the host immune response in context of a throat commensal landscape.

• Kuronen, Juri; Horsfield, Samuel T.; Pöntinen, Anna Kaarina; Mallawaarachchi, Sudaraka; Alonso, Sergio Arredondo & Thorpe, Harry [Show all 14 contributors for this article] (2024). Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Genome Research. ISSN 1088-9051. 34(7), p. 1081–1088. doi: 10.1101/gr.278485.123. Full text in Research Archive Show summary

  Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance, and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable high-accuracy long-read sequencing technologies. To exploit this opportunity, we introduce a phenotype- and alignment-free method for discovering coselected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact colored de Bruijn graph to approximate the intragenome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens Streptococcus pneumoniae and Enterococcus faecalis.

• Belman, Sophie; Pesonen, Henri; Croucher, Nicholas J.; Bentley, Stephen D. & Corander, Jukka (2024). Estimating between-country migration in pneumococcal populations. G3: Genes, Genomes, Genetics. 14(6), p. 1–11. doi: 10.1093/g3journal/jkae058. Full text in Research Archive Show summary

  Streptococcus pneumoniae (the pneumococcus) is a globally distributed, human obligate opportunistic bacterial pathogen which, although often carried commensally, is also a significant cause of invasive disease. Apart from multi-drug resistant and virulent clones, the rate and direction of pneumococcal dissemination between different countries remains largely unknown. The ability for the pneumococcus to take a foothold in a country depends on existing population configuration, the extent of vaccine implementation, as well as human mobility since it is a human obligate bacterium. To shed light on its international movement, we used extensive genome data from the Global Pneumococcal Sequencing project and estimated migration parameters between multiple countries in Africa. Data on allele frequencies of polymorphisms at housekeeping-like loci for multiple different lineages circulating in the populations of South Africa, Malawi, Kenya, and The Gambia were used to calculate the fixation index (⁠⁠) between countries. We then further used these summaries to fit migration coalescent models with the likelihood-free inference algorithms available in the ELFI software package. Synthetic datawere additionally used to validate the inference approach. Our results demonstrate country-pair specific migration patterns and heterogeneity in the extent of migration between different lineages. Our approach demonstrates that coalescent models can be effectively used for inferring migration rates for bacterial species and lineages provided sufficiently granular population genomics surveillance data. Further, it can demonstrate the connectivity of respiratory disease agents between countries to inform intervention policy in the longer term.

• Arachchi, Sudaraka Mallawa; Tonkin-Hill, Gerry; Pöntinen, Anna Kaarina; Calland, Jessica Kate; Gladstone, Rebecca Ashley & Alonso, Sergio Arredondo [Show all 13 contributors for this article] (2024). Detecting co-selection through excess linkage disequilibrium in bacterial genomes. NAR Genomics and Bioinformatics. 6(2). doi: 10.1093/nargab/lqae061. Full text in Research Archive Show summary

  Population genomics has revolutionized our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here, we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.

• Pol, Sreymom; Kallonen, Teemu; Mäklin, Tommi; Sar, Poda; Hopkins, Jill & Soeng, Sona [Show all 11 contributors for this article] (2024). Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing. mBio. ISSN 2161-2129. 15(6). doi: 10.1128/mbio.00784-24. Full text in Research Archive Show summary

  The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1–2, range 1–4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%–98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data.

• Thorpe, Harry; Pesonen, Maiju; Corbella, Marta; Pesonen, Henri; Gaiarsa, Stefano & Boinett, Christine J [Show all 28 contributors for this article] (2024). Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. Lancet Microbe. 5(10). doi: 10.1016/S2666-5247(24)00113-7. Full text in Research Archive Show summary

  Background Nosocomial infections pose a considerable risk to patients who are susceptible, and this is particularly acute in intensive care units when hospital-associated bacteria are endemic. During the first wave of the COVID-19 pandemic, the surge of patients presented a significant obstacle to the effectiveness of infection control measures. We aimed to assess the risks and extent of nosocomial pathogen transmission under a high patient burden by designing a novel bacterial pan-pathogen deep-sequencing approach that could be integrated with standard clinical surveillance and diagnostics workflows. Methods We did a prospective cohort study in a region of northern Italy that was severely affected by the first wave of the COVID-19 pandemic. Inpatients on both ordinary and intensive care unit (ICU) wards at the San Matteo hospital, Pavia were sampled on multiple occasions to identify bacterial pathogens from respiratory, nasal, and rectal samples. Diagnostic samples collected between April 7 and May 10, 2020 were cultured on six different selective media designed to enrich for Acinetobacter baumannii, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae, and DNA from each plate with positive growth was deep sequenced en masse. We used mSWEEP and mGEMS to bin sequencing reads by sequence cluster for each species, followed by mapping with snippy to generate high quality alignments. Antimicrobial resistance genes were detected by use of ARIBA and CARD. Estimates of hospital transmission were obtained from pairwise bacterial single nucleotide polymorphism distances, partitioned by within-patient and between-patient samples. Finally, we compared the accuracy of our binned Acinetobacter baumannii genomes with those obtained by single colony whole-genome sequencing of isolates from the same hospital. Findings We recruited patients from March 1 to May 7, 2020. The pathogen population among the patients was large and diverse, with 2148 species detections overall among the 2418 sequenced samples from the 256 patients. In total, 55 sequence clusters from key pathogen species were detected at least five times. The antimicrobial resistance gene prevalence was correspondingly high, with key carbapenemase and extended spectrum ß-lactamase genes detected in at least 50 (40%) of 125 patients in ICUs. Using high-resolution mapping to infer transmission, we established that hospital transmission was likely to be a significant mode of acquisition for each of the pathogen species. Finally, comparison with single colony Acinetobacter baumannii genomes showed that the resolution offered by deep sequencing was equivalent to single-colony sequencing, with the additional benefit of detection of co-colonisation of highly similar strains. Interpretation Our study shows that a culture-based deep-sequencing approach is a possible route towards improving future pathogen surveillance and infection control at hospitals. Future studies should be designed to directly compare the accuracy, cost, and feasibility of culture-based deep sequencing with single colony whole-genome sequencing on a range of bacterial species. Funding Wellcome Trust, European Research Council, Academy of Finland Flagship program, Trond Mohn Foundation, and Research Council of Norway.

• Tsang, Kara K.; Lam, Margaret M C; Wick, Ryan R.; Wyres, Kelly L.; Bachman, Michael & Baker, Stephen [Show all 74 contributors for this article] (2024). Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae. Microbial Genomics. 10(10). doi: 10.1099/mgen.0.001294. Full text in Research Archive Show summary

  Interpreting the phenotypes of bla_SHV alleles in Klebsiella pneumoniae genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla_SHV alleles or additional plasmid-borne bla_SHV alleles that have extended-spectrum β-lactamase (ESBL) activity and/ or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases [e.g. the National Center for Biotechnology Information (NCBI) Reference Gene Catalog and the β-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from K. pneumoniae genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific aa substitutions. We then systematically assigned SHV alleles to functional classes (WT, ESBL and BLI resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with the current assignments in the NCBI’s Reference Gene Catalog and/or BLDB (21 to WT, 12 to ESBL and 4 to BLI resistant). Phylogenetic and comparative genomic analyses support that (i) SHV-1 (encoded by bla_SHV-1 ) is the ancestral chromosomal variant, (ii) ESBL- and BLI-resistant variants have evolved multiple times through parallel substitution mutations, (iii) ESBL variants are mostly mobilized to plasmids and (iv) BLI-resistant variants mostly result from mutations in chromosomal bla_SHV. We used matched genome–phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 K. pneumoniae isolates carrying one or more bla_SHV alleles but no other acquired β-lactamases to assess genotype–phenotype relationships for bla_SHV. This collection includes human, animal and environmental isolates collected between 2001 and 2021 from 24 countries. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, whilst most omega-loop substitutions do not. Our data also provide support for the WT assignment of 67 protein variants, including 8 that were noted in public databases as ESBL. These eight variants were reclassified as WT because they lack ESBL-associated mutations, and our phenotype data support susceptibility to third-generation cephalosporins (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164 and SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping K. pneumoniae), whereby known and novel bla_SHV alleles are classified based on causative mutations. Kleborate v2.4.1 was updated to include ten novel protein variants from the KlebNET-GSP dataset and all alleles in public databases as of November 2023. This study demonstrates the power of sharing AMR phenotypes alongside genome data to improve the understanding of resistance mechanisms.

• Štrumbelj, Erik; Bouchard-Côté, Alexandre; Corander, Jukka; Gelman, Andrew; Rue, Håvard & Murray, Lawrence [Show all 9 contributors for this article] (2024). Past, Present and Future of Software for Bayesian Inference. Statistical Science. ISSN 0883-4237. 39(1), p. 46–61. doi: 10.1214/23-STS907. Full text in Research Archive
• Khawaja, Tamim; Mäklin, Tommi; Kallonen, Teemu; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina & Mero, Sointu [Show all 13 contributors for this article] (2024). Deep sequencing of Escherichia coli exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications. 15(1). doi: 10.1038/s41467-024-49591-5. Full text in Research Archive Show summary

  Multi-drug resistant (MDR) E. coli constitute a major public health burden globally, reaching the highest prevalence in the global south yet frequently flowing with travellers to other regions. However, our comprehension of the entire genetic diversity of E. coli colonising local populations remains limited. We quantified this diversity, its associated antimicrobial resistance (AMR), and assessed the impact of antibiotic use by recruiting 494 outpatients and 423 community dwellers in the Punjab province, Pakistan. Rectal swab and stool samples were cultured on CLED agar and DNA extracted from plate sweeps was sequenced en masse to capture both the genetic and AMR diversity of E. coli. We assembled 5,247 E. coli genomes from 1,411 samples, displaying marked genetic diversity in gut colonisation. Compared with high income countries, the Punjabi population generally showed a markedly different distribution of genetic lineages and AMR determinants, while use of antibiotics elevated the prevalence of well-known globally circulating MDR clinical strains. These findings implicate that longitudinal multi-regional genomics-based surveillance of both colonisation and infections is a prerequisite for developing mechanistic understanding of the interplay between ecology and evolution in the maintenance and dissemination of (MDR) E. coli

• Pascoe, Ben; Futcher, Georgina; Pensar, Johan; Bayliss, Sion C.; Mourkas, Evangelos & Calland, Jessica Kate [Show all 21 contributors for this article] (2024). Machine learning to attribute the source of Campylobacter infections in the United States: A retrospective analysis of national surveillance data. Journal of Infection. ISSN 0163-4453. 89(5). doi: 10.1016/j.jinf.2024.106265. Full text in Research Archive Show summary

  Objectives Integrating pathogen genomic surveillance with bioinformatics can enhance public health responses by identifying risk and guiding interventions. This study focusses on the two predominant Campylobacter species, which are commonly found in the gut of birds and mammals and often infect humans via contaminated food. Rising incidence and antimicrobial resistance (AMR) are a global concern, and there is an urgent need to quantify the main routes to human infection. Methods During routine US national surveillance (2009–2019), 8856 Campylobacter genomes from human infections and 16,703 from possible sources were sequenced. Using machine learning and probabilistic models, we target genetic variation associated with host adaptation to attribute the source of human infections and estimate the importance of different disease reservoirs. Results Poultry was identified as the primary source of human infections, responsible for an estimated 68% of cases, followed by cattle (28%), and only a small contribution from wild birds (3%) and pork sources (1%). There was also evidence of an increase in multidrug resistance, particularly among isolates attributed to chickens. Conclusions National surveillance and source attribution can guide policy, and our study suggests that interventions targeting poultry will yield the greatest reductions in campylobacteriosis and spread of AMR in the US. Data availability All sequence reads were uploaded and shared on NCBI’s Sequence Read Archive (SRA) associated with BioProjects; PRJNA239251 (CDC / PulseNet surveillance), PRJNA287430 (FSIS surveillance), PRJNA292668 & PRJNA292664 (NARMS) and PRJNA258022 (FDA surveillance). Publicly available genomes, including reference genomes and isolates sampled worldwide from wild birds are associated with BioProject accessions: PRJNA176480, PRJNA177352, PRJNA342755, PRJNA345429, PRJNA312235, PRJNA415188, PRJNA524300, PRJNA528879, PRJNA529798, PRJNA575343, PRJNA524315 and PRJNA689604. Contiguous assemblies of all genome sequences compared are available at Mendeley data (assembled C. coli genomes doi: 10.17632/gxswjvxyh3.1; assembled C. jejuni genomes doi: 10.17632/6ngsz3dtbd.1) and individual project and accession numbers can be found in Supplementary tables S1 and S2, which also includes pubMLST identifiers for assembled genomes. Figshare (10.6084/m9.figshare.20279928). Interactive phylogenies are hosted on microreact separately for C. jejuni (https://microreact.org/project/pascoe-us-cjejuni) and C. coli (https://microreact.org/project/pascoe-us-ccoli).

• Pereira, Ana P.; Antunes, Patrícia; Bierge, Paula; Willems, Rob J.L.; Corander, Jukka & Coque, Teresa M. [Show all 10 contributors for this article] (2023). Unraveling Enterococcus susceptibility to quaternary ammonium compounds: genes, phenotypes, and the impact of environmental conditions. Microbiology spectrum. 11(5). doi: 10.1128/spectrum.02324-23. Full text in Research Archive Show summary

  Quaternary ammonium compounds (QACs) have been extensively used in the community, healthcare facilities, and food chain, in concentrations between 20 and 30,000 mg/L. Enterococcus faecalis and Enterococcus faecium are ubiquitous in these settings and are recognized as nosocomial pathogens worldwide, but QACs’ activity against strains from diverse epidemiological and genomic backgrounds remained largely unexplored. We evaluated the role of Enterococcus isolates from different sources, years, and clonal lineages as hosts of QACs tolerance genes and their susceptibility to QACs in optimal, single-stress and cross-stress growth conditions. Only 1% of the Enterococcus isolates included in this study and 0.5% of publicly available Enterococcus genomes carried qacA/B, qacC, qacG, qacJ, qacZ, qrg, bcrABC or oqxAB genes, shared with >60 species of Bacillota, Pseudomonadota, Actinomycetota, or Spirochaetota. These genes were generally found within close proximity of antibiotics and/or metals resistance genes. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) of benzalkonium chloride (BC) and didecyldimethylammonium chloride ranged between 0.5 and 4 mg/L (microdilution: 37°C/20 h/pH = 7/aerobiosis) for 210 E. faecalis and E. faecium isolates (two isolates carrying qacZ). Modified growth conditions (e.g., 22°C/pH = 5) increased MICBC/MBCBC (maximum of eightfold and MBCBC = 16 mg/L) and changed bacterial growth kinetics under BC toward later stationary phases in both species, including in isolates without QACs tolerance genes. In conclusion, Enterococcus are susceptible to in-use QACs concentrations and rarely carry QACs tolerance genes. However, their potential gene exchange with different microbiota, the decreased susceptibility to QACs under specific environmental conditions, and the presence of subinhibitory QACs concentrations in various settings may contribute to the selection of particular strains and, thus, require a One Health strategy to maintain QACs effectiveness.

• Alonso, Sergio Arredondo; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Gama, João Alves; Schürch, Anita C. & Lanza, Val F. [Show all 10 contributors for this article] (2023). Mge-cluster: a reference-free approach for typing bacterial plasmids. NAR Genomics and Bioinformatics. 5(3). doi: 10.1093/nargab/lqad066. Full text in Research Archive Show summary

  Extrachromosomal elements of bacterial cells such as plasmids are notorious for their importance in evolution and adaptation to changing ecology. However, high-resolution population-wide analysis of plasmids has only become accessible recently with the advent of scalable long-read sequencing technology. Current typing methods for the classification of plasmids remain limited in their scope which motivated us to develop a computationally efficient approach to simultaneously recognize novel types and classify plasmids into previously identified groups. Here, we introduce mge-cluster that can easily handle thousands of input sequences which are compressed using a unitig representation in a de Bruijn graph. Our approach offers a faster runtime than existing algorithms, with moderate memory usage, and enables an intuitive visualization, classification and clustering scheme that users can explore interactively within a single framework. Mge-cluster platform for plasmid analysis can be easily distributed and replicated, enabling a consistent labelling of plasmids across past, present, and future sequence collections. We underscore the advantages of our approach by analysing a population-wide plasmid data set obtained from the opportunistic pathogen Escherichia coli, studying the prevalence of the colistin resistance gene mcr-1.1 within the plasmid population, and describing an instance of resistance plasmid transmission within a hospital environment.

• Calland, Jessica Kate; Haukka, Kaisa; Kpordze, Stephen W; Brusah, Atanyiwoen; Corbella, Marta & Merla, Cristina [Show all 13 contributors for this article] (2023). Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study. Lancet Microbe. 4(11), p. e943–e952. doi: 10.1016/S2666-5247(23)00208-2. Full text in Research Archive Show summary

  Background One Health approaches to address the increasing threat of antimicrobial resistance (AMR) are gaining attention. However, data on the distribution and movement of bacteria and their AMR-associated genes between clinical and non-clinical sources are scarce, especially from low-income and middle-income countries. We aimed to analyse Klebsiella isolates from various sources in Ghana and compare the prevalence of AMR with datasets from two other countries. Methods We conducted a cross-sectional genomic One Health study. Multiple clinical, environmental, and animal sources were sampled from 78 locations (eg, hospitals, residential areas, and farms) in and around Tamale, Ghana. Clinical samples were collected through routine screening and in cases of suspected infection between March 15 and Sept 15, 2019, and samples from the wider environment were collected during a dedicated sampling effort between the dates of Aug 19, 2018, and Sept 26, 2019. Sampling locations were approximately evenly distributed from the centre of the city and steadily outwards to capture both rural and urban locations. Samples with positive growth for Klebsiella were included. Isolates of Klebsiella were obtained from the samples using Simmons citrate agar medium and characterised by antimicrobial susceptibility testing and whole-genome sequencing. A comparative analysis with Klebsiella population surveys from Pavia, Italy, and Tromsø, Norway, was performed. AMR-associated and virulence genes were detected, and the population distribution of these genes was studied. Findings Of 957 samples collected around Tamale, Ghana, 620 were positive for Klebsiella spp. 573 Klebsiella isolates were successfully sequenced, of which 370 were Klebsiella pneumoniae. Only two hospital isolates were carbapenem-resistant. Extended-spectrum β-lactamase (ESBL) genes were relatively common among the Ghanaian clinical isolates but rare in the environmental samples. Prevalence of ESBL genes in human—hospital disease samples was 64% (14 of 22 isolates) in Ghana and 44% (four of nine isolates) in Italy, and prevalence in human—hospital carriage samples was 7% (eight of 107) in Ghana and 13% (54 of 428) in Italy; the prevalence was higher in human—hospital disease samples than in human—hospital carriage samples in both countries, and prevalence across both samples in both countries was higher than in Norway. Ghanaian isolates showed evidence of high recombination rates (recombination events compared with point mutations [r/m] 9·455) and a considerable accessory gene overlap with isolates from Italy and Norway. Interpretation Although several AMR-associated gene classes were observed relatively frequently in non-clinical sources, ESBL, carbapenemase, and virulence genes were predominantly present only in hospital samples. These results suggest that interventions should be focused on clinical settings to have the greatest effect on the prevalence and dissemination of AMR-associated genes. Funding European Research Council (742158), Academy of Finland EuroHPC grant, Trond Mohn Foundation (BATTALION grant), and Wellcome Trust.

• Connor, Christopher H.; Zucoloto, Amanda Z.; Munnoch, John T.; Yu, Ian-Ling; Corander, Jukka & Hoskisson, Paul A. [Show all 8 contributors for this article] (2023). Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract. PLoS Biology. ISSN 1544-9173. 21(10). doi: 10.1371/journal.pbio.3002329. Full text in Research Archive Show summary

  Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E . coli . Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E . coli ST131 is capable of out-competing and displacing non-MDR E . coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E . coli strains, challenge with MDR E . coli either by oral gavage or co-housing with MDR E . coli colonised mice results in displacement and dominant intestinal colonisation by MDR E . coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E . coli , we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E . coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E . coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E . coli via carriage and spread.

• Chaguza, Chrispin; Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Freitas, Ana R. & Novais, Carla [Show all 12 contributors for this article] (2023). The population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection. Microbiology spectrum. 11(6), p. e0020123–e0020123. doi: 10.1128/spectrum.00201-23. Full text in Research Archive Show summary

  Enterococcus faecalis is a commensal bacterium of the human gastrointestinal tract that causes opportunistic infections. The E. faecalis genetic changes associated with pathogenicity, particularly gut-to-bloodstream translocation, remain poorly understood. Here, we performed a genome-wide association study (GWAS) of 736 whole-genome sequences of fecal and bloodstream E. faecalis isolates from hospitalized and nonhospitalized individuals, respectively, to identify E. faecalis genetic signatures associated with the patient’s hospitalization status and body isolation source. We found that infection by hospitalization status and extraintestinal infection are heritable traits, with ~40% and ~30% of their variation explained by E. faecalis genetics, respectively. Furthermore, a GWAS using linear mixed models did not pinpoint any clear overrepresentation of individual genetic changes by hospitalization status or body isolation source after controlling for the population structure. However, we observed elevated signals in a genomic region containing a prophage element. However, the lineages themselves and their associated virulence factors and antibiotic resistance genes showed variable frequency among blood and fecal isolates and in hospitalized and nonhospitalized individuals. Altogether, our findings indicate that E. faecalis infection by hospitalization status and body sites is partially influenced by the overall genetic background of the isolates and antibiotic resistance patterns rather than genetic variation at individual loci, which suggests a greater role of other host and environmental factors and ultimately the opportunistic pathogenic lifestyle of this versatile host generalist bacterium.

• Yang, Zhirong; Chen, Yuwei; Sedov, Denis; Kaski, Samuel & Corander, Jukka (2023). Stochastic Cluster Embedding. Statistics and computing. ISSN 0960-3174. 33(12). doi: 10.1007/s11222-022-10186-z. Full text in Research Archive Show summary

  Neighbor embedding (NE) aims to preserve pairwise similarities between data items and has been shown to yield an effective principle for data visualization. However, even the best existing NE methods such as stochastic neighbor embedding (SNE) may leave large-scale patterns hidden, for example clusters, despite strong signals being present in the data. To address this, we propose a new cluster visualization method based on the Neighbor Embedding principle. We first present a family of Neighbor Embedding methods that generalizes SNE by using non-normalized Kullback–Leibler divergence with a scale parameter. In this family, much better cluster visualizations often appear with a parameter value different from the one corresponding to SNE. We also develop an efficient software that employs asynchronous stochastic block coordinate descent to optimize the new family of objective functions. Our experimental results demonstrate that the method consistently and substantially improves the visualization of data clusters compared with the state-of-the-art NE approaches. The code of our method is publicly available at https://github.com/rozyangno/sce.

• Tonkin-Hill, Gerry; Corander, Jukka & Parkhill, Julian (2023). Challenges in prokaryote pangenomics. Microbial Genomics. 9(5). doi: 10.1099/mgen.0.001021. Full text in Research Archive Show summary

  Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.

• Tonkin-Hill, Gerry; Gladstone, Rebecca Ashley; Pöntinen, Anna Kaarina; Alonso, Sergio Arredondo; Bentley, Stephen D. & Corander, Jukka (2023). Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Genome Research. ISSN 1088-9051. 33(1), p. 129–140. doi: 10.1101/gr.277340.122. Full text in Research Archive Show summary

  Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.

• Snaith, Ann E.; Dunn, Steven J.; Moran, Robert A.; Newton, Paul N.; Dance, David A. B. & Davong, Viengmon [Show all 10 contributors for this article] (2023). The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microbial Genomics. 9(5). doi: 10.1099/mgen.0.001000. Full text in Research Archive Show summary

  Increased colonization by antimicrobial-resistant organisms is closely associated with international travel. This study investigated the diversity of mobile genetic elements involved with antimicrobial resistance (AMR) gene carriage in extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli that colonized travellers to Laos. Long-read sequencing was used to reconstruct complete plasmid sequences from 48 isolates obtained from the daily stool samples of 23 travellers over a 3 week period. This method revealed a collection of 105 distinct plasmids, 38.1 % (n=40) of which carried AMR genes. The plasmids in this population were diverse, mostly unreported and included 38 replicon types, with F-type plasmids (n=23) the most prevalent amongst those carrying AMR genes. Fine-scale analysis of all plasmids identified numerous AMR gene contexts and emphasized the importance of IS elements, specifically members of the IS6/IS26 family, in the evolution of complex multidrug resistance regions. We found a concerning convergence of ESBL and colistin resistance determinants, with three plasmids from two different F-type lineages carrying blaCTX-M and mcr genes. The extensive diversity seen here highlights the worrying probability that stable new vehicles for AMR will evolve in E. coli populations that can disseminate internationally through travel networks.

• Picchini, Umberto; Simola, Umberto & Corander, Jukka (2023). Sequentially Guided MCMC Proposals for Synthetic Likelihoods and Correlated Synthetic Likelihoods. Bayesian Analysis. ISSN 1936-0975. 18(4), p. 1099–1129. doi: 10.1214/22-BA1305. Full text in Research Archive
• Rebelo, Andreia; Duarte, Bárbara; Ferreira, Carolina; Mourão, Joana; Ribeiro, Sofia & Freitas, Ana R. [Show all 12 contributors for this article] (2023). Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids. International journal of food microbiology. ISSN 0168-1605. 384. doi: 10.1016/j.ijfoodmicro.2022.109981. Full text in Research Archive Show summary

  Poultry meat has been a vehicle of antibiotic resistant bacteria and genes. Yet, the diversity of selective pressures associated with their maintenance in the poultry-production chain remains poorly explored. We evaluated the susceptibility of Enterococcus spp. from chicken meat collected 20 years apart to antibiotics, metals, acidic pH and peracetic acid-PAA. Contemporary chicken-meat samples (n = 53 batches, each including a pool of neck skin from 10 single carcasses) were collected in a slaughterhouse facility using PAA as disinfectant (March–August 2018, North of Portugal). Broilers were raised in intensive farms (n = 29) using CuSO4 and organic acids as feed additives. Data were compared with that of 67 samples recovered in the same region during 1999–2001. All 2018 samples had multidrug resistant-MDR isolates, with >45 % carrying Enterococcus faecalis, Enterococcus faecium or Enterococcus gallinarum resistant to tetracycline, erythromycin, ampicillin, quinupristin-dalfopristin, ciprofloxacin, chloramphenicol or aminoglycosides. Resistance rates were similar (P > 0.05) to those of 1999–2001 samples for all but five antibiotics. The decrease of samples carrying vancomycin-resistant isolates from 46 % to 0 % between 1999-2001 and 2018 was the most striking difference. Isolates from both periods were similarly susceptible to acid pH [minimum-growth pH (4.5-5.0), minimum-survival pH (3.0-4.0)] and to PAA (MIC90 = 100–120 mg/L/MBC90 = 140–160 mg/L; below concentrations used in slaughterhouse). Copper tolerance genes (tcrB and/or cueO) were respectively detected in 21 % and 4 % of 2018 and 1999-2001 samples. The tcrB gene was only detected in E. faecalis (MICCuSO4 > 12 mM), and their genomes were compared with other international ones of chicken origin (PATRIC database), revealing a polyclonal population and a plasmid or chromosomal location for tcrB. The tcrB plasmids shared diverse genetic modules, including multiple antimicrobial resistance genes (e.g. to tetracyclines, chloramphenicol, macrolide-lincosamide-streptogramin B-MLSB, aminoglycosides, bacitracin, coccidiostats). When in chromosome, the tcrB gene was co-located closely to merA (mercury) genes. Chicken meat remains an important vehicle of MDR Enterococcus spp. able to survive under diverse stresses (e.g. copper, acid) potentially contributing to these bacteria maintenance and flux among animal-environment-humans.

• Petazzoni, Greta; Bellinzona, Greta; Merla, Cristina; Corbella, Marta; Monzillo, Vincenzina & Samuelsen, Ørjan [Show all 10 contributors for this article] (2023). The COVID-19 Pandemic Sparked off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital. Microbiology spectrum. 11(2). doi: 10.1128/spectrum.04505-22. Full text in Research Archive Show summary

  Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems, and the sequence analysis attributed this to the carbapenemase gene blaOXA-23. Virulence factor screening unveiled that all strains carried determinants for biofilm formation, while plasmid analysis revealed the presence of two plasmids, one of which was ~100 kbp long and encoded a phage sequence. A core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and the local surveillance program. All strains belonged to the globally disseminated sequence type 2 (ST2) clone and were mainly divided into two clades. Isolates from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of A. baumannii in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in reduced attention to infection prevention and control practices.<p> <p><b>IMPORTANCE</b>: The COVID-19 pandemic, especially during the first wave, posed a great challenge to the hospital management and generally promoted nosocomial pathogen dissemination. MDR A. baumannii can easily spread and persist for a long time on surfaces, causing outbreaks in health care settings. Infection prevention and control practices, epidemiological surveillance, and microbiological screening are fundamental in order to control such outbreaks. Here, we sequenced the genomes of 96 isolates from an outbreak of MDR A. baumannii strains using both short- and long-read technology in order to reconstruct the outbreak events in fine detail. The sequence data demonstrated that two endemic clones of MDR A. baumannii were the source of this large hospital outbreak during the first COVID-19 pandemic wave, confirming the effect of COVID-19 emergency disrupting the protection provided by the use of the standard prevention procedures.

• Mai, The Tien; Lees, John A; Gladstone, Rebecca Ashley & Corander, Jukka (2023). Inferring the heritability of bacterial traits in the era of machine learning. Bioinformatics Advances. 3(1). doi: 10.1093/bioadv/vbad027. Full text in Research Archive Show summary

  Quantification of heritability is a fundamental desideratum in genetics, which allows an assessment of the contribution of additive genetic variation to the variability of a trait of interest. The traditional computational approaches for assessing the heritability of a trait have been developed in the field of quantitative genetics. However, the rise of modern population genomics with large sample sizes has led to the development of several new machine learning-based approaches to inferring heritability. In this article, we systematically summarize recent advances in machine learning which can be used to infer heritability. We focus on an application of these methods to bacterial genomes, where heritability plays a key role in understanding phenotypes such as antibiotic resistance and virulence, which are particularly important due to the rising frequency of antimicrobial resistance. By designing a heritability model incorporating realistic patterns of genome-wide linkage disequilibrium for a frequently recombining bacterial pathogen, we test the performance of a wide spectrum of different inference methods, including also GCTA. In addition to the synthetic data benchmark, we present a comparison of the methods for antibiotic resistance traits for multiple bacterial pathogens. Insights from the benchmarking and real data analyses indicate a highly variable performance of the different methods and suggest that heritability inference would likely benefit from tailoring of the methods to the specific genetic architecture of the target organism.

• Alonso, Sergio Arredondo; Blundell-Hunter, George; Fu, Zuyi; Gladstone, Rebecca Ashley; Fillol-Salom, Alfred & Loraine, Jessica [Show all 25 contributors for this article] (2023). Evolutionary and functional history of the Escherichia coli K1 capsule. Nature Communications. 14(1). doi: 10.1038/s41467-023-39052-w. Full text in Research Archive Show summary

  Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.

• Simola, U.; Bonfanti, A.; Dumusque, X.; Cisewski-Kehe, J.; Kaski, S. & Corander, Jukka (2022). Accounting for stellar activity signals in radial-velocity data by using change point detection techniques. Astronomy and Astrophysics (A & A). ISSN 0004-6361. 664. doi: 10.1051/0004-6361/202142941. Full text in Research Archive Show summary

  Context. Active regions on the photosphere of a star have been the major obstacle for detecting Earth-like exoplanets using the radial velocity (RV) method. A commonly employed solution for addressing stellar activity is to assume a linear relationship between the RV observations and the activity indicators along the entire time series, and then remove the estimated contribution of activity from the variation in RV data (overall correction method). However, since active regions evolve on the photosphere over time, correlations between the RV observations and the activity indicators will correspondingly be anisotropic. Aims. We present an approach that recognizes the RV locations where the correlations between the RV and the activity indicators significantly change in order to better account for variations in RV caused by stellar activity. Methods. The proposed approach uses a general family of statistical breakpoint methods, often referred to as change point detection (CPD) algorithms; several implementations of which are available in R and python. A thorough comparison is made between the breakpoint-based approach and the overall correction method. To ensure wide representativity, we use measurements from real stars that have different levels of stellar activity and whose spectra have different signal-to-noise ratios. Results. When the corrections for stellar activity are applied separately to each temporal segment identified by the breakpoint method, the corresponding residuals in the RV time series are typically much smaller than those obtained by the overall correction method. Consequently, the generalized Lomb–Scargle periodogram contains a smaller number of peaks caused by active regions. The CPD algorithm is particularly effective when focusing on active stars with long time series, such as α Cen B. In that case, we demonstrate that the breakpoint method improves the detection limit of exoplanets by 74% on average with respect to the overall correction method. Conclusions. CPD algorithms provide a useful statistical framework for estimating the presence of change points in a time series. Since the process underlying the RV measurements generates anisotropic data by its intrinsic properties, it is natural to use CPD to obtain cleaner signals from RV data. We anticipate that the improved exoplanet detection limit may lead to a widespread adoption of such an approach. Our test on the HD 192310 planetary system is encouraging, as we confirm the presence of the two hosted exoplanets and we determine orbital parameters consistent with the literature, also providing much more precise estimates for HD 192310 c. Key words: techniques: radial velocities / methods: data analysis / stars: activity / planetary systems

• Corander, Jukka; Hanage, William P & Pensar, Johan (2022). Causal discovery for the microbiome. Lancet Microbe. 3(11), p. e881–e887. doi: 10.1016/S2666-5247(22)00186-0. Full text in Research Archive Show summary

  Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.

• Lees, John A.; Tonkin-Hill, Gerry; Yang, Zhirong & Corander, Jukka (2022). Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Philosophical Transactions of the Royal Society of London. Biological Sciences. ISSN 0962-8436. 377(1861). doi: 10.1098/rstb.2021.0237. Full text in Research Archive Show summary

  In less than a decade, population genomics of microbes has progressed fromthe effort of sequencing dozens of strains to thousands, or even tens of thou-sands of strains in a single study. There are now hundreds of thousands ofgenomes available even for a single bacterial species, and the number of gen-omes is expected to continue to increase at an accelerated pace given theadvances in sequencing technology and widespread genomic surveillanceinitiatives. This explosion of data calls for innovative methods to enablerapid exploration of the structure of a population based on different datamodalities, such as multiple sequence alignments, assemblies and estimatesof gene content across different genomes. Here, we present Mandrake, anefficient implementation of a dimensional reduction method tailored forthe needs of large-scale population genomics. Mandrake is capable of visua-lizing population structure from millions of whole genomes, and weillustrate its usefulness with several datasets representing major pathogens.Our method is freely available both as an analysis pipeline (https://github.com/johnlees/mandrake) and as a browser-based interactive application(https://gtonkinhill.github.io/mandrake-web/).This article is part of a discussion meeting issue‘Genomic populationstructures of microbial pathogens’.1. IntroductionAdvances in DNA sequencing technology have recently made whole-genomesequencing both affordable and scalable enough for routine use in pathogensurveillance by research organizations and public health agencies around theworld [1,2]. A striking example of this is genomic surveillance of the SARS-CoV-2 virus for which over one million genome sequences became availablein just 15 months after its initial discovery [3]. To shed light on population geno-mic data at this scale calls for new tools that can be used for rapid exploration ofthe structure among the samples, with particular emphasis on detecting clustersof similar sequences [4,5]. In this paper, we explore and extend a class ofmethods that aims to reduce the dimensionality of such data to only two dimen-sions, in a manner that supports ready visualization and identification ofclusters.© 2022 The Authors. Published by the Royal Society under the terms of the Creative Commons AttributionLicense http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the originalauthor and source are credited.

• Aushev, Alexander; Pesonen, Henri Eerikki; Heinonen, Markus; Corander, Jukka & Kaski, Samuel (2022). Likelihood-free inference with deep Gaussian processes. Computational Statistics & Data Analysis. ISSN 0167-9473. 174. doi: 10.1016/j.csda.2022.107529. Full text in Research Archive Show summary

  Surrogate models have been successfully used in likelihood-free inference to decrease the number of simulator evaluations. The current state-of-the-art performance for this task has been achieved by Bayesian Optimization with Gaussian Processes (GPs). While this combination works well for unimodal target distributions, it is restricting the flexibility and applicability of Bayesian Optimization for accelerating likelihood-free inference more generally. This problem is addressed by proposing a Deep Gaussian Process (DGP) surrogate model that can handle more irregularly behaved target distributions. The experiments show how DGPs can outperform GPs on objective functions with multimodal distributions and maintain a comparable performance in unimodal cases. At the same time, DGPs generally require much fewer data to achieve the same level of performance as neural density and kernel mean embedding alternatives. This confirms that DGPs as surrogate models can extend the applicability of Bayesian Optimization for likelihood-free inference (BOLFI), while only adding computational overhead that remains negligible for computationally intensive simulators.

• Tonkin-Hill, Gerry; Ling, Clare; Chaguza, Chrispin; Salter, Susannah J.; Hinfonthong, Pattaraporn & Nikolaou, Elissavet [Show all 15 contributors for this article] (2022). Pneumococcal within-host diversity during colonization, transmission and treatment. Nature Microbiology. 7(11), p. 1791–1804. doi: 10.1038/s41564-022-01238-1. Full text in Research Archive Show summary

  Characterizing the genetic diversity of pathogens within the host promises to greatly improve surveillance and reconstruction of transmission chains. For bacteria, it also informs our understanding of inter-strain competition and how this shapes the distribution of resistant and sensitive bacteria. Here we study the genetic diversity of Streptococcus pneumoniae within 468 infants and 145 of their mothers by deep sequencing whole pneumococcal populations from 3,761 longitudinal nasopharyngeal samples. We demonstrate that deep sequencing has unsurpassed sensitivity for detecting multiple colonization, doubling the rate at which highly invasive serotype 1 bacteria were detected in carriage compared with gold-standard methods. The greater resolution identified an elevated rate of transmission from mothers to their children in the first year of the child’s life. Comprehensive treatment data demonstrated that infants were at an elevated risk of both the acquisition and persistent colonization of a multidrug-resistant bacterium following antimicrobial treatment. Some alleles were enriched after antimicrobial treatment, suggesting that they aided persistence, but generally purifying selection dominated within-host evolution. Rates of co-colonization imply that in the absence of treatment, susceptible lineages outcompeted resistant lineages within the host. These results demonstrate the many benefits of deep sequencing for the genomic surveillance of bacterial pathogens.

• Kičiatovas, Dovydas; Guo, Qingli; Kailas, Miika; Pesonen, Henri; Corander, Jukka & Kaski, Samuel [Show all 8 contributors for this article] (2022). Identification of multiplicatively acting modulatory mutational signatures in cancer. BMC Bioinformatics. 23. doi: 10.1186/s12859-022-05060-8. Full text in Research Archive Show summary

  Background A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framework, that can be used to build such understanding. They capture somatic mutation patterns and at best identify their causes. Most studies in this context have focused on an inherently additive analysis, e.g. by non-negative matrix factorization, where the mutations within a cancer sample are explained by a linear combination of independent mutational signatures. However, other recent studies show that the mutational signatures exhibit non-additive interactions. Results We carefully analysed such additive model fits from the PCAWG study cataloguing mutational signatures as well as their activities across thousands of cancers. Our analysis identified systematic and non-random structure of residuals that is left unexplained by the additive model. We used hierarchical clustering to identify cancer subsets with similar residual profiles to show that both systematic mutation count overestimation and underestimation take place. We propose an extension to the additive mutational signature model—multiplicatively acting modulatory processes—and develop a maximum-likelihood framework to identify such modulatory mutational signatures. The augmented model is expressive enough to almost fully remove the observed systematic residual patterns. Conclusion We suggest the modulatory processes biologically relate to sample specific DNA repair propensities with cancer or tissue type specific profiles. Overall, our results identify an interesting direction where to expand signature analysis.

• Pereira, Ana P.; Antunes, Patrícia; Willems, Rob; Corander, Jukka; Coque, Teresa M. & Peixe, Luísa [Show all 8 contributors for this article] (2022). Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiology spectrum. 10(4). doi: 10.1128/spectrum.01176-22. Full text in Research Archive Show summary

  Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization’s list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.

• Li, Nien-Kung; Corander, Jukka; Grad, Yonatan H. & Chang, Hsiao-Han (2022). Discovering recent selection forces shaping the evolution of dengue viruses based on polymorphism data across geographic scales. Virus Evolution. 8(2). doi: 10.1093/ve/veac108. Full text in Research Archive
• Mäklin, Tommi; Thorpe, Harry Arthur Frank Wright; Pöntinen, Anna Kaarina; Gladstone, Rebecca Ashley; Shao, Yan & Pesonen, Maiju [Show all 12 contributors for this article] (2022). Strong pathogen competition in neonatal gut colonisation. Nature Communications. 13(1). doi: 10.1038/s41467-022-35178-5. Full text in Research Archive Show summary

  Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.

• Thorpe, Harry Arthur Frank Wright; Booton, Ross; Kallonen, Teemu; Gibbon, Marjorie J.; Couto, Natacha & Passet, Virginie [Show all 21 contributors for this article] (2022). A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology. 7, p. 2054–2067. doi: 10.1038/s41564-022-01263-0. Full text in Research Archive Show summary

  Abstract The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.

• Mallawaarachchi, Sudaraka; Tonkin-Hill, Gerry; Croucher, Nicholas J.; Turner, Paul; Speed, Doug & Corander, Jukka [Show all 7 contributors for this article] (2022). Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. NAR Genomics and Bioinformatics. 4(1). doi: 10.1093/nargab/lqac011. Full text in Research Archive Show summary

  Whole-genome sequencing has facilitated genome-wide analyses of association, prediction and heritability in many organisms. However, such analyses in bacteria are still in their infancy, being limited by difficulties including genome plasticity and strong population structure. Here we propose a suite of methods including linear mixed models, elastic net and LD-score regression, adapted to bacterial traits using innovations such as frequency-based allele coding, both insertion/deletion and nucleotide testing and heritability partitioning. We compare and validate our methods against the current state-of-art using simulations, and analyse three phenotypes of the major human pathogen Streptococcus pneumoniae, including the first analyses of minimum inhibitory concentrations (MIC) for penicillin and ceftriaxone. We show that the MIC traits are highly heritable with high prediction accuracy, explained by many genetic associations under good population structure control. In ceftriaxone MIC, this is surprising because none of the isolates are resistant as per the inhibition zone criteria. We estimate that half of the heritability of penicillin MIC is explained by a known drug-resistance region, which also contributes a quarter of the ceftriaxone MIC heritability. For the within-host carriage duration phenotype, no associations were observed, but the moderate heritability and prediction accuracy indicate a moderately polygenic trait.

• Hal, Sebastiaan J van; Willems, Rob J L; Gouliouris, Theodore; Ballard, Susan A; Coque, Teresa M & Hammerum, Anette M [Show all 16 contributors for this article] (2022). The interplay between community and hospital Enterococcus faecium clones within health-care settings: a genomic analysis. Lancet Microbe. 3(2), p. e133–e141. doi: 10.1016/S2666-5247(21)00236-6. Full text in Research Archive Show summary

  Background The genomic relationships among Enterococcus faecium isolates are the subject of ongoing research that seeks to clarify the origins of observed lineages and the extent of horizontal gene transfer between them, and to robustly identify links between genotypes and phenotypes. E faecium is considered to form distinct groups—A and B—corresponding to isolates derived from patients who were hospitalised (A) and isolates from humans in the community (B). The additional separation of A into the so-called clades A1 and A2 remains an area of uncertainty. We aimed to investigate the relationships between A1 and non-A1 groups and explore the potential role of non-A1 isolates in shaping the population structure of hospital E faecium. Methods We collected short-read sequence data from invited groups that had previously published E faecium genome data. This hospital-based isolate collection could be separated into three groups (or clades, A1, A2, and B) by augmenting the study genomes with published sequences derived from human samples representing the previously defined genomic clusters. We performed phylogenetic analyses, by constructing maximum-likelihood phylogenetic trees, and identified historical recombination events. We assessed the pan-genome, did resistome analysis, and examined the genomic data to identify mobile genetic elements. Each genome underwent chromosome painting by use of ChromoPainter within FineSTRUCTURE software to assess ancestry and identify hybrid groups. We further assessed highly admixed regions to infer recombination directionality. Findings We assembled a collection of 1095 hospital E faecium sequences from 34 countries, further augmented by 33 published sequences. 997 (88%) of 1128 genomes clustered as A1, 92 (8%) as A2, and 39 (4%) as B. We showed that A1 probably emerged as a clone from within A2 and that, because of ongoing gene flow, hospital isolates currently identified as A2 represent a genetic continuum between A1 and community E faecium. This interchange of genetic material between isolates from different groups results in the emergence of hybrid genomes between clusters. Of the 1128 genomes, 49 (4%) hybrid genomes were identified: 33 previously labelled as A2 and 16 previously labelled as A1. These interactions were fuelled by a directional pattern of recombination mediated by mobile genetic elements. By contrast, the contribution of B group genetic material to A1 was limited to a few small regions of the genome and appeared to be driven by genomic sweep events. Interpretation A2 and B isolates coming into the hospital form an important reservoir for ongoing A1 adaptation, suggesting that effective long-term control of the effect of E faecium could benefit from strategies to reduce these genomic interactions, such as a focus on reducing the acquisition of hospital A1 strains by patients entering the hospital.

• Pesonen, Henri; Simola, Umberto; Luque, Alvaro Kohn; Vuollekoski, Henri; Lai, Xiaoran & Frigessi, Arnoldo [Show all 11 contributors for this article] (2022). ABC of the future. International Statistical Review. ISSN 0306-7734. doi: 10.1111/insr.12522. Full text in Research Archive Show summary

  Approximate Bayesian computation (ABC) has advanced in two decades from a seminal idea to a practically applicable inference tool for simulator-based statistical models, which are becoming increasingly popular in many research domains. The computational feasibility of ABC for practical applications has been recently boosted by adopting techniques from machine learning to build surrogate models for the approximate likelihood or posterior and by the introduction of a general-purpose software platform with several advanced features, including automated parallelisation. Here we demonstrate the strengths of the advances in ABC by going beyond the typical benchmark examples and considering real applications in astronomy, infectious disease epidemiology, personalised cancer therapy and financial prediction. We anticipate that the emerging success of ABC in producing actual added value and quantitative insights in the real world will continue to inspire a plethora of further applications across different fields of science, social science and technology.

• Pöntinen, Anna Kaarina; Top, Janetta; Alonso, Sergio Arredondo; Tonkin-Hill, Gerry; Freitas, Ana R. & Novais, Carla [Show all 21 contributors for this article] (2021). Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nature Communications. 12. doi: 10.1038/s41467-021-21749-5. Full text in Research Archive Show summary

  Abstract Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the “modern hospital” era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.

• Harrow, Gabrielle L.; Lees, John A.; Hanage, William P.; Lipsitch, Marc; Corander, Jukka & Colijn, Caroline [Show all 7 contributors for this article] (2021). Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. The ISME Journal. ISSN 1751-7362. 15, p. 1523–1538. doi: 10.1038/s41396-020-00867-w. Full text in Research Archive Show summary

  Abstract Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.

• Chewapreecha, Claire; Pensar, Johan; Chattagul, Supaksorn; Pesonen, Maiju; Sangphukieo, Apiwat & Boonklang, Phumrapee [Show all 18 contributors for this article] (2021). Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. Molecular Biology and Evolution (MBE). ISSN 0737-4038. 39(1). doi: 10.1093/molbev/msab306. Full text in Research Archive Show summary

  Abstract The soil bacterium Burkholderia pseudomallei is the causative agent of melioidosis and a significant cause of human morbidity and mortality in many tropical and subtropical countries. The species notoriously survives harsh environmental conditions but the genetic architecture for these adaptations remains unclear. Here we employed a powerful combination of genome-wide epistasis and co-selection studies (2,011 genomes), condition-wide transcriptome analyses (82 diverse conditions), and a gene knockout assay to uncover signals of “co-selection”—that is a combination of genetic markers that have been repeatedly selected together through B. pseudomallei evolution. These enabled us to identify 13,061 mutation pairs under co-selection in distinct genes and noncoding RNA. Genes under co-selection displayed marked expression correlation when B. pseudomallei was subjected to physical stress conditions, highlighting the conditions as one of the major evolutionary driving forces for this bacterium. We identified a putative adhesin (BPSL1661) as a hub of co-selection signals, experimentally confirmed a BPSL1661 role under nutrient deprivation, and explored the functional basis of co-selection gene network surrounding BPSL1661 in facilitating the bacterial survival under nutrient depletion. Our findings suggest that nutrient-limited conditions have been the common selection pressure acting on this species, and allelic variation of BPSL1661 may have promoted B. pseudomallei survival during harsh environmental conditions by facilitating bacterial adherence to different surfaces, cells, or living hosts.

• Suotsalo, Kimmo; Xu, Yingying; Corander, Jukka & Pensar, Johan (2021). High-dimensional structure learning of sparse vector autoregressive models using fractional marginal pseudo-likelihood. Statistics and computing. ISSN 0960-3174. 31(73). doi: 10.1007/s11222-021-10049-z. Full text in Research Archive Show summary

  Abstract Learning vector autoregressive models from multivariate time series is conventionally approached through least squares or maximum likelihood estimation. These methods typically assume a fully connected model which provides no direct insight to the model structure and may lead to highly noisy estimates of the parameters. Because of these limitations, there has been an increasing interest towards methods that produce sparse estimates through penalized regression. However, such methods are computationally intensive and may become prohibitively time-consuming when the number of variables in the model increases. In this paper we adopt an approximate Bayesian approach to the learning problem by combining fractional marginal likelihood and pseudo-likelihood. We propose a novel method, PLVAR, that is both faster and produces more accurate estimates than the state-of-the-art methods based on penalized regression. We prove the consistency of the PLVAR estimator and demonstrate the attractive performance of the method on both simulated and real-world data.

• Alonso, Sergio Arredondo; Top, Janetta; Corander, Jukka; Willems, Rob J. L. & Schürch, Anita C. (2021). Mode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals. Genome Medicine. 13(1), p. 1–18. doi: 10.1186/s13073-020-00825-3. Full text in Research Archive Show summary

  Background Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or by Tn1546 transposition between different genomic locations. Methods We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012–2015). Genomic information regarding clonality and Tn1546 characterization was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination. Results On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant. In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination. Conclusions In related VRE cases, the dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.

• Kantele, Anu; Kuenzli, Esther; Dunn, Steven; Dance, David A.B.; Newton, Paul N. & Davong, Viengmon [Show all 14 contributors for this article] (2021). Dynamics of intestinal multidrug-resistant bacteria colonisation contracted by visitors to a high-endemic setting: a prospective, daily, real-time sampling study. Lancet Microbe. 2(4), p. e151–e158. doi: 10.1016/S2666-5247(20)30224-X. Full text in Research Archive Show summary

  Background Antimicrobial resistance is highly prevalent in low-income and middle-income countries. International travel contributes substantially to the global spread of intestinal multidrug-resistant Gram-negative bacteria. Hundreds of millions of annual visitors to low-income and middle-income countries are all exposed to intestinal multidrug-resistant Gram-negative bacteria resulting in 30–70% of them being colonised at their return. The colonisation process in high-exposure environments is poorly documented because data have only been derived from before travel and after travel sampling. We characterised colonisation dynamics by exploring daily stool samples while visiting a low-income and middle-income countries. Methods In this prospective, daily, real-time sampling study 20 European visitors to Laos volunteered to provide daily stool samples and completed daily questionnaires for 22 days. Samples were initially assessed at Mahosot Hospital, Vientiane, Laos, for acquisition of extended-spectrum β-lactamase-producing (ESBL) Gram-negative bacteria followed by whole-genome sequencing of isolates at MicrobesNG, University of Birmingham, Birmingham, UK. The primary outcome of the study was to obtain data on the dynamics of intestinal multidrug-resistant bacteria acquisition. Findings Between Sept 18 and Sept 20, 2015, 23 volunteers were recruited, of whom 20 (87%) European volunteers were included in the final study population. Although colonisation rates were 70% at the end of the study, daily sampling revealed that all participants had acquired ESBL-producing Gram-negative bacteria at some point during the study period; the colonisation status varied day by day. Whole-genome sequencing analysis ascribed the transient pattern of colonisation to sequential acquisition of new strains, resulting in a loss of detectable colonisation by the initial multidrug-resistant Gram-negative strains. 19 (95%) participants acquired two to seven strains. Of the 83 unique strains identified (53 Escherichia coli, 10 Klebsiella spp, and 20 other ESBL-producing Gram-negative bacteria), some were shared by as many as four (20%) participants. Interpretation To our knowledge, this is the first study to characterise in real-time the dynamics of acquiring multidrug-resistant Gram-negative bacterial colonisation during travel. Our data show multiple transient colonisation events indicative of constant microbial competition and suggest that travellers are exposed to a greater burden of multidrug-resistant bacteria than previously thought. The data emphasise the need for preventing travellers' diarrhoea and limiting antibiotic use, addressing the two major factors predisposing colonisation. Funding The Finnish Governmental Subsidy for Health Science Research, The Scandinavian Society for Antimicrobial Chemotherapy, the Sigrid Jusélius Foundation, Biotechnology and Biological Sciences Research Council; Wellcome Trust, Medical Research Council; The Royal Society; Joint Programming Initiative on Antimicrobial Resistance, and European Research Council.

• Hal, Sebastiaan J. van; Willems, Rob J.L.; Gouliouris, Theodore; Ballard, Susan A.; Coque, Teresa M. & Hammerum, Anette M. [Show all 21 contributors for this article] (2021). The global dissemination of hospital clones of Enterococcus faecium. Genome Medicine. 13(52). doi: 10.1186/s13073-021-00868-0. Full text in Research Archive Show summary

  <i>Background</i> - The hospital-adapted A1 group of <i>Enterococcus faecium</i> remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood.<br><br> <i>Methods</i> - A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of <i>Enterococcus faecium</i> was assembled (<i>n</i> = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes.<br><br> <i>Results</i> - Two main modes of genomic evolution continue to shape <i>E. faecium</i>: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes.<br><br> <i>Conclusions</i> - The ability of A1 <i>E. faecium</i> to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.

• MacAlasdair, Neil; Pesonen, Maiju; Brynildsrud, Ola Brønstad; Eldholm, Vegard; Kristiansen, Paul Arne & Corander, Jukka [Show all 8 contributors for this article] (2021). The effect of recombination on the evolution of a population of Neisseria meningitidis. Genome Research. ISSN 1088-9051. 31(7), p. 1258–1268. doi: 10.1101/gr.264465.120. Full text in Research Archive Show summary

  Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal genomes is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated with routine pathogen transmission. Here, we fill this knowledge gap by a detailed analysis of 2839 meningococcal genomes obtained through a carriage study of over 50,000 samples collected systematically in Burkina Faso, West Africa, before, during, and after the serogroup A vaccine rollout, 2009–2012. Our findings indicate that the meningococcal genome is highly dynamic, with highly recombinant loci and frequent gene sharing across deeply separated lineages in a structured population. Furthermore, our findings illustrate how population structure can correlate with genome flexibility, as some lineages in Burkina Faso are orders of magnitude more recombinant than others. We also examine the effect of selection on the population, in particular how it is correlated with recombination. We find that recombination principally acts to prevent the accumulation of deleterious mutations, although we do also find an example of recombination acting to speed the adaptation of a gene. In general, we show the importance of recombination in the evolution of a geographically expansive population with deep population structure in a short timescale. This has important consequences for our ability to both foresee the outcomes of vaccination programs and, using surveillance data, predict when lineages of the meningococcus are likely to become a public health concern.

• Mai, The Tien; Turner, Paul & Corander, Jukka (2021). Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting. BMC Bioinformatics. 22(1). doi: 10.1186/s12859-021-04079-7. Full text in Research Archive Show summary

  Background Heritability is a central measure in genetics quantifying how much of the variability observed in a trait is attributable to genetic differences. Existing methods for estimating heritability are most often based on random-effect models, typically for computational reasons. The alternative of using a fixed-effect model has received much more limited attention in the literature. Results In this paper, we propose a generic strategy for heritability inference, termed as “boosting heritability”, by combining the advantageous features of different recent methods to produce an estimate of the heritability with a high-dimensional linear model. Boosting heritability uses in particular a multiple sample splitting strategy which leads in general to a stable and accurate estimate. We use both simulated data and real antibiotic resistance data from a major human pathogen, Sptreptococcus pneumoniae, to demonstrate the attractive features of our inference strategy. Conclusions Boosting is shown to offer a reliable and practically useful tool for inference about heritability.

• Gladstone, Rebecca Ashley; McNally, Alan; Pöntinen, Anna Kaarina; Tonkin-Hill, Gerry; Lees, John A. & Skytén, Kusti Onni [Show all 29 contributors for this article] (2021). Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. Lancet Microbe. 2(7), p. e331–e341. doi: 10.1016/S2666-5247(21)00031-8. Full text in Research Archive Show summary

  Background The clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology. Methods This was a longitudinal, E coli population, genomic, cohort study that sampled isolates from 22 512 E coli bloodstream infections included in the Norwegian surveillance programme on resistant microbes (NORM) from 2002 to 2017. 15 of 22 laboratories were able to share their isolates, and the first 22·5% of isolates from each year were requested. We used whole genome sequencing to infer the population structure (PopPUNK), and we investigated the clade composition of the dominant multidrug resistant clonal complex (CC)131 using genetic markers previously reported for sequence type (ST)131, effective population size (BEAST), and presence of determinants of antimicrobial resistance (ARIBA, PointFinder, and ResFinder databases) over time. We compared these features between the 2002–10 and 2011–17 time periods. We also compared our results with those of a longitudinal study from the UK done between 2001 and 2011. Findings Of the 3500 isolates requested from the participating laboratories, 3397 (97·1%) were received, of which 3254 (95·8%) were successfully sequenced and included in the analysis. A significant increase in the number of multidrug resistant CC131 isolates from 71 (5·6%) of 1277 in 2002–10 to 207 (10·5%) of 1977 in 2011–17 (p<0·0001), was the largest clonal expansion. CC131 was the most common clone in extended-spectrum β-lactamase (ESBL)-positive isolates (75 [58·6%] of 128) and fluoroquinolone non-susceptible isolates (148 [39·2%] of 378). Within CC131, clade A increased in prevalence from 2002, whereas the global multidrug resistant clade C2 was not observed until 2007. Multiple de-novo acquisitions of both blaCTX-M ESBL-encoding genes in clades A and C1 and gain of phenotypic fluoroquinolone non-susceptibility across the clade A phylogeny were observed. We estimated that exponential increases in the effective population sizes of clades A, C1, and C2 occurred in the mid-2000s, and in clade B a decade earlier. The rate of increase in the estimated effective population size of clade A (Ne=3147) was nearly ten-times that of C2 (Ne=345), with clade A over-represented in Norwegian CC131 isolates (75 [27·0%] of 278) compared with the UK study (8 [5·4%] of 147 isolates). Interpretation The early and sustained establishment of predominantly antimicrobial susceptible CC131 clade A isolates, relative to multidrug resistant clade C2 isolates, suggests that resistance is not necessary for clonal success. However, even in the low antibiotic use setting of Norway, resistance to important antimicrobial classes has rapidly been selected for in CC131 clade A isolates. This study shows the importance of genomic surveillance in uncovering the complex ecology underlying multidrug resistance dissemination and competition, which have implications for the design of strategies and interventions to control the spread of high-risk multidrug resistant clones.

• Wee, Bryan A.; Alves, Joana; Lindsay, Diane S. J.; Klatt, Ann-Brit; Sargison, Fiona A. & Cameron, Ross L. [Show all 13 contributors for this article] (2021). Population analysis of Legionella pneumophila reveals a basis for resistance to complement-mediated killing. Nature Communications. 12(1). doi: 10.1038/s41467-021-27478-z. Full text in Research Archive Show summary

  Abstract Legionella pneumophila is the most common cause of the severe respiratory infection known as Legionnaires’ disease. However, the microorganism is typically a symbiont of free-living amoeba, and our understanding of the bacterial factors that determine human pathogenicity is limited. Here we carried out a population genomic study of 902  L. pneumophila isolates from human clinical and environmental samples to examine their genetic diversity, global distribution and the basis for human pathogenicity. We find that the capacity for human disease is representative of the breadth of species diversity although some clones are more commonly associated with clinical infections. We identified a single gene ( lag-1 ) to be most strongly associated with clinical isolates. lag-1 , which encodes an O -acetyltransferase for lipopolysaccharide modification, has been distributed horizontally across all major phylogenetic clades of L. pneumophila by frequent recent recombination events. The gene confers resistance to complement-mediated killing in human serum by inhibiting deposition of classical pathway molecules on the bacterial surface. Furthermore, acquisition of lag-1 inhibits complement-dependent phagocytosis by human neutrophils, and promoted survival in a mouse model of pulmonary legionellosis. Thus, our results reveal L. pneumophila genetic traits linked to disease and provide a molecular basis for resistance to complement-mediated killing.

• Gladstone, Rebecca Ashley; Siira, Lotta; Brynildsrud, Ola Brønstad; Vestrheim, Didrik Frimann; Turner, Paul & Clarke, S.C. [Show all 21 contributors for this article] (2021). International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease. Vaccine. ISSN 0264-410X. 40(7), p. 1054–1060. doi: 10.1016/j.vaccine.2021.10.046. Full text in Research Archive Show summary

  Background: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them. Methods: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating. Results: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017. Conclusion: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

• Calland, Jessica K.; Pascoe, Ben; Bayliss, Sion; Mourkas, Evangelos; Berthenet, Elvire & Thorpe, Harry Arthur Frank Wright [Show all 12 contributors for this article] (2021). Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages. PLoS Genetics. ISSN 1553-7390. 17(9). doi: 10.1371/journal.pgen.1009829. Full text in Research Archive Show summary

  Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10 −6 s/s/y) and Campylobacter jejuni (3.4 x 10 −6 s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.

• Mäklin, Tommi; Kallonen, Teemu; David, Sophia; Boinett, Christine J.; Pascoe, Ben & Meric, Guillaume [Show all 13 contributors for this article] (2021). High-resolution sweep metagenomics using fast probabilistic inference [version 1; peer review: 1 approved, 1 approved with reservations]. Wellcome Open Research. 5(14). doi: 10.12688/WELLCOMEOPENRES.15639.2. Full text in Research Archive Show summary

  Determining the composition of bacterial communities beyond the level of a genus or species is challenging because of the considerable overlap between genomes representing close relatives. Here, we present the mSWEEP pipeline for identifying and estimating the relative sequence abundances of bacterial lineages from plate sweeps of enrichment cultures. mSWEEP leverages biologically grouped sequence assembly databases, applying probabilistic modelling, and provides controls for false positive results. Using sequencing data from major pathogens, we demonstrate significant improvements in lineage quantification and detection accuracy. Our pipeline facilitates investigating cultures comprising mixtures of bacteria, and opens up a new field of plate sweep metagenomics.

• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Show all 19 contributors for this article] (2021). Genome evolution and the emergence of pathogenicity in avian Escherichia coli. Nature Communications. 12(1). doi: 10.1038/s41467-021-20988-w. Full text in Research Archive Show summary

  Abstract Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

• Corander, Jukka; Remes, Ulpu Maria Vilhelmiina & Koski, Timo (2021). On the Jensen-Shannon divergence and the variation distance for categorical probability distributions. Kybernetika (Praha). ISSN 0023-5954. 57(6), p. 879–907. doi: 10.14736/kyb-2021-6-0879. Full text in Research Archive
• Horesh, Gal; Taylor-Brown, Alyce; McGimpsey, Stephanie; Lassalle, Florent; Corander, Jukka & Heinz, Eva [Show all 7 contributors for this article] (2021). Different evolutionary trends form the twilight zone of the bacterial pan-genome. Microbial Genomics. 7(9). doi: 10.1099/MGEN.0.000670. Full text in Research Archive Show summary

  The pan-genome is defined as the combined set of all genes in the gene pool of a species. Pan-genome analyses have been very useful in helping to understand different evolutionary dynamics of bacterial species: an open pan-genome often indicates a free-living lifestyle with metabolic versatility, while closed pan-genomes are linked to host-restricted, ecologically specialized bacteria. A detailed understanding of the species pan-genome has also been instrumental in tracking the phylodynamics of emerging drug resistance mechanisms and drug-resistant pathogens. However, current approaches to analyse a species’ pan-genome do not take the species population structure into account, nor do they account for the uneven sampling of different lineages, as is commonplace due to over-sampling of clinically relevant representatives. Here we present the application of a population structure-aware approach for classifying genes in a pan-genome based on within-species distribution. We demonstrate our approach on a collection of 7500 Escherichia coli genomes, one of the most-studied bacterial species and used as a model for an open pan-genome. We reveal clearly distinct groups of genes, clustered by different underlying evolutionary dynamics, and provide a more biologically informed and accurate description of the species’ pan-genome.

• Gibbon, Marjorie J.; Couto, Natacha; David, Sophia; Barden, Ruth; Standerwick, Richard & Jagadeesan, Kishore Kumar [Show all 17 contributors for this article] (2021). A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microbial Genomics. 7(3). doi: 10.1099/mgen.0.000509. Full text in Research Archive Show summary

  Klebsiella species occupy a wide range of environmental and animal niches, and occasionally cause opportunistic infections that are resistant to multiple antibiotics. In particular, Klebsiella pneumoniae (Kpne) has gained notoriety as a major nosocomial pathogen, due principally to the rise in non-susceptibility to carbapenems and other beta-lactam antibiotics. Whilst it has been proposed that the urban water cycle facilitates transmission of pathogens between clinical settings and the environment, the level of risk posed by resistant Klebsiella strains in hospital wastewater remains unclear. We used whole genome sequencing (WGS) to compare Klebsiella species in contemporaneous samples of wastewater from an English hospital and influent to the associated wastewater treatment plant (WWTP). As we aimed to characterize representative samples of Klebsiella communities, we did not actively select for antibiotic resistance (other than for ampicillin), nor for specific Klebsiella species. Two species, Kpne and K. ( Raoultella ) ornithinolytica (Korn), were of equal dominance in the hospital wastewater, and four other Klebsiella species were present in low abundance in this sample. In contrast, despite being the species most closely associated with healthcare settings, Kpne was the dominant species within the WWTP influent. In total, 29 % of all isolates harboured the bla OXA-48 gene on a pOXA-48-like plasmid, and these isolates were almost exclusively recovered from the hospital wastewater. This gene was far more common in Korn (68 % of isolates) than in Kpne (3.4 % of isolates). In general plasmid-borne, but not chromosomal, resistance genes were significantly enriched in the hospital wastewater sample. These data implicate hospital wastewater as an important reservoir for antibiotic-resistant Klebsiella , and point to an unsuspected role of species within the Raoultella group in the maintenance and dissemination of plasmid-borne bla OXA-48. This article contains data hosted by Microreact.

• Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva & Thomson, Nicholas R. (2021). A comprehensive and high-quality collection of escherichia coli genomes and their genes. Microbial Genomics. 7(2), p. 1–15. doi: 10.1099/mgen.0.000499. Full text in Research Archive Show summary

  Escherichia coli is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well-studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 E. coli and Shigella genomes to provide a single, uniform, high-quality dataset. Shigella were included as they are considered specialized pathovars of E. coli . We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.

• Mäklin, Tommi; Kallonen, Teemu; Alanko, Jarno; Samuelsen, Ørjan; Hegstad, Kristin & Mäkinen, Veli [Show all 9 contributors for this article] (2021). Bacterial genomic epidemiology with mixed samples. Microbial Genomics. 7(11), p. 1–18. doi: 10.1099/MGEN.0.000691. Full text in Research Archive Show summary

  Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, opening the possibility to sequence all colonies on selective plates with a single DNA extraction and sequencing step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on single-colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.

• Alonso, Sergio Arredondo; Pöntinen, Anna Kaarina; Cleon, Francois Pierre Alexandre; Gladstone, Rebecca Ashley; Schürch, Anita C. & Johnsen, Pål Jarle [Show all 8 contributors for this article] (2021). A high-throughput multiplexing and selection strategy to complete bacterial genomes. GigaScience. 10(12), p. 1–13. doi: 10.1093/gigascience/giab079. Full text in Research Archive Show summary

  Background: Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. Results: Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. Conclusions: The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis.

• Biffignandi, Gherard Batisti; Gibbon, Marjorie J.; Corbella, Marta; Thorpe, Harry Arthur Frank Wright; Merla, Cristina & Castelli, Michele [Show all 13 contributors for this article] (2021). Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae. G3: Genes, Genomes, Genetics. 11(2). doi: 10.1093/g3journal/jkab019. Full text in Research Archive Show summary

  Abstract During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”

• Top, Janetta; Arredondo-Alonso, Sergio; Schürch, Anita C.; Puranen, Santeri; Pesonen, Maiju & Pensar, Johan [Show all 8 contributors for this article] (2020). Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium. Microbial Genomics. 6(12), p. 1–8. doi: 10.1099/mgen.0.000488. Full text in Research Archive Show summary

  Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.

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• Mäklin, Tommi; Taira, Aurora; Alonso, Sergio Arredondo; Shao, Yan; Stratton, Michael R & Lawley, Trevor D [Show all 8 contributors for this article] (2025). Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli. Lancet Microbe. 6(5). doi: 10.1016/j.lanmic.2024.101015. Full text in Research Archive Show summary

  Biomedical research has implicated the bacterial metabolite colibactin as a causal risk factor for several cancer types, in particular, colorectal cancer. Colibactin has been known to drive tumorigenesis by inducing double-strand breaks in the DNA of epithelial cells exposed to colibactin-producing bacteria. Some phylogroup B2 Escherichia coli secrete colibactin during interbacterial warfare, concomitantly exposing the host to an increasing risk of DNA damage. This Personal View reviews the current knowledge about the cancer–colibactin interface and summarises metagenomics-based and population-genomics-based surveys to show that the prevalence of dominant colibactin-producing lineages of E coli varies considerably across geographical regions. The prevalence is further strongly associated with the age-standardised incidences of colorectal cancer, bladder cancer, and prostate cancer, suggesting that the degree of colibactin exposure in a population might contribute to the geographical variation of these cancers. Our observations provide a strong impetus for further research and the development of novel interventions to reduce the risks for colibactin-related cancers.

• Angchagun, Kesorn; Boonklang, Phumrapee; Chomkatekaew, Chalita; Pakdeerat, Sukritpong; Wongsuwan, Gumphol & Amornchai, Premjit [Show all 25 contributors for this article] (2023). BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection. Wellcome Open Research. 8. doi: 10.12688/wellcomeopenres.19809.2. Full text in Research Archive
• Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka & Johannessen, Mona Susan [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Full text in Research Archive
• Hanssen, Anne-Merethe Christiansen; Ajayi, Clément; Johannessen, Mona Susan; Julin, Kjersti; Pesonen, Maiju & Corander, Jukka [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Full text in Research Archive
• Bastakoti, Srijana; Pesonen, maiju; Ajayi, Clément; Julin, Kjersti; Johannessen, Mona Susan & Corander, Jukka [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Full text in Research Archive
• Bastakoti, Srijana; Pesonen, Maiju; Ajayi, Clément; Julin, Kjersti; Corander, Jukka & Johannessen, Mona Susan [Show all 7 contributors for this article] (2023). Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells. Full text in Research Archive
• Congo-Ouedraogo, M.; Poncin, T.; Sangaré, L.; Mérimèche, M.; Braille, A. & Jacquier, H. [Show all 13 contributors for this article] (2022). Genomic and antimicrobial resistance analyses of Neisseria gonorrhoeae isolates, Burkina Faso, 2018–2019. Journal of the European Academy of Dermatology and Venereology. ISSN 0926-9959. doi: 10.1111/jdv.18037. Full text in Research Archive
• Järvenpää, Marko Juhani & Corander, Jukka (2022). On predictive inference for intractable models via approximate Bayesian computation. Statistics and computing. ISSN 0960-3174. 33(2). doi: 10.1007/s11222-022-10163-6. Full text in Research Archive
• Ross, Theodor Anton; Pöntinen, Anna Kaarina; Janice, Jessin; Holsbø, Einar; Corander, Jukka & Hegstad, Kristin [Show all 7 contributors for this article] (2022). Leveraging machine learning for finding novel putative virulence factors in Enterococcus faecium. Full text in Research Archive
• Kloos, Julia Maria; Jänisch, Lea; Pöntinen, Anna Kaarina; Samuelsen, Ørjan; Johnsen, Pål Jarle & Corander, Jukka [Show all 7 contributors for this article] (2022). Different metabolic proficiency among dominant ExPEC lineages. Full text in Research Archive
• Corander, Jukka (2022). A conversation with Elja Arjas (Helsinki, November 2021 and March 2022). [Journal]. Scandinavian Journal of Statistics. doi: 10.1111/sjos.12612. Full text in Research Archive Show summary

  Statistics as an independent scientific discipline is relatively young in Finland. Its active history stretches back roughly a century, with the past 50 years signifying a period of growth. Few other academics such as Elja Arjas, now professor emeritus at University of Helsinki, have played a prominent role in establishing statistics in Finland. This conversation tries to illuminate how this came to happen and what was needed to push statistics as a discipline to a firmer ground. We do not have a looking glass at our disposal but will nevertheless also try make some predictions about the future.

• Gladstone, Rebecca Ashley; McNally, Alan; Johnsen, Pål Jarle; Samuelsen, Ørjan & Corander, Jukka (2021). Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection – Authors’ reply. Lancet Microbe. 2(10), p. e493–e493. doi: 10.1016/S2666-5247(21)00176-2. Full text in Research Archive
• Mageiros, Leonardos; Meric, Guillaume; Bayliss, Sion; Pensar, Johan; Pascoe, Ben & Mourkas, Evangelos [Show all 19 contributors for this article] (2021). Author Correction: Genome evolution and the emergence of pathogenicity in avian Escherichia coli (Nature Communications, (2021), 12, 1, (765), 10.1038/s41467-021-20988-w). Nature Communications. 12(1). doi: 10.1038/s41467-021-22238-5. Full text in Research Archive
• Corander, Jukka (2020). Adaptive Approximate Bayesian Computation tolerance selection. Bayesian Analysis. ISSN 1936-0975. doi: 10.1214/20-BA1211. Full text in Research Archive
• Corander, Jukka (2020). Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies. BMC Genomics. doi: 10.1186/s12864-020-06990-4. Full text in Research Archive Show summary

  Background Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. Results In this work, we improved the genome assemblies of the three Old World camel species – domestic dromedary and Bactrian camel, and the two-humped wild camel – via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex. Conclusions The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with a combined role of population history and differential exposures to pathogens, and consequent different selective pressures.

• Corander, Jukka (2020). Genomic signatures of domestication in Old World camels. Communications Biology. doi: 10.1038/s42003-020-1039-5. Full text in Research Archive
• Corander, Jukka (2020). Improved prediction of bacterial genotype-phenotype associations using interpretable pangenome-spanning regressions. mBio. ISSN 2161-2129. doi: 10.1128/mBio.01344-20. Full text in Research Archive
• Corander, Jukka (2020). gplas: a comprehensive tool for plasmid analysis using short-read graphs. Bioinformatics. ISSN 1367-4803. doi: 10.1093/bioinformatics/btaa233. Full text in Research Archive

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