{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T20:07:24Z","timestamp":1793218044784,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pbio.3003848","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000}}],"reference-count":75,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:00:00Z","timestamp":1781222400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["805046"],"award-info":[{"award-number":["805046"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016190","name":"Trond Mohn stiftelse","doi-asserted-by":"publisher","award":["TMS2021TMT09"],"award-info":[{"award-number":["TMS2021TMT09"]}],"id":[{"id":"10.13039\/100016190","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016190","name":"Trond Mohn stiftelse","doi-asserted-by":"publisher","award":["TMS2020TMT11"],"award-info":[{"award-number":["TMS2020TMT11"]}],"id":[{"id":"10.13039\/100016190","id-type":"DOI","asserted-by":"publisher"}]},{"name":"ERA-Net: JPI-AMR","award":["NFR333432"],"award-info":[{"award-number":["NFR333432"]}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>\n                    Antimicrobial resistance (AMR) is a substantial and growing global health burden. Understanding, and predicting, its evolution in specific pathogens will help responses across scales from individual patient cases to large-scale policy. Here, we use global data on AMR features, predicted from 47k\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    genomes, with hypercubic transition path sampling to infer the evolutionary pathways by which AMR features in\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    (KpAMR) are acquired across 102 countries, territories, and areas. We identify \u201cglobally consistent\u201d evolutionary behaviors that hold across countries, and \u201cglobally divergent\u201d behaviors including carbapenem and fluoroquinolone resistance that vary across countries. We show how these divergent dynamics covary both with public health superregion and drug use policy, and reveal competing evolutionary pathways within and between countries. Using newly sequenced data across several decades from sub-Saharan Africa, we show that this inferred global roadmap of KpAMR evolution successfully predicts prospective evolutionary dynamics. Together, we hope that the ability to characterize and predict evolutionary dynamics of AMR acquisition, connected to socio-economic and drug policy predictors, will help strengthen our understanding of AMR evolution worldwide.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003848","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T17:44:56Z","timestamp":1781286296000},"page":"e3003848","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Evolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniae"],"prefix":"10.1371","volume":"24","author":[{"given":"Olav N. L.","family":"Aga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sabrina J.","family":"Moyo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joel","family":"Manyahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Upendo","family":"Kibwana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iren H.","family":"L\u00f6hr","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nina","family":"Langeland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f8rn","family":"Blomberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8559-3519","authenticated-orcid":true,"given":"Iain G.","family":"Johnston","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"issue":"10325","key":"pbio.3003848.ref001","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Antimicrobial Resistance Collaborators","year":"2022","journal-title":"Lancet"},{"issue":"10459","key":"pbio.3003848.ref002","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","article-title":"Global burden of bacterial antimicrobial resistance 1990-2021: a systematic analysis with forecasts to 2050","volume":"404","author":"GBD 2021 Antimicrobial Resistance Collaborators","year":"2024","journal-title":"Lancet"},{"issue":"6","key":"pbio.3003848.ref003","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41579-019-0315-1","article-title":"Population genomics of Klebsiella pneumoniae","volume":"18","author":"KL Wyres","year":"2020","journal-title":"Nat Rev Microbiol"},{"key":"pbio.3003848.ref004","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.mib.2018.04.004","article-title":"Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria","volume":"45","author":"KL Wyres","year":"2018","journal-title":"Curr Opin Microbiol"},{"key":"pbio.3003848.ref005","doi-asserted-by":"crossref","DOI":"10.1093\/cid\/ciab784","article-title":"Rapid genomic characterization and global surveillance of Klebsiella using pathogenwatch","volume":"73","author":"S Argim\u00f3n","year":"2021","journal-title":"Clin Infect Dis"},{"issue":"1","key":"pbio.3003848.ref006","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1186\/s13073-025-01466-0","article-title":"A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs","volume":"17","author":"MAK Hetland","year":"2025","journal-title":"Genome Med"},{"issue":"27","key":"pbio.3003848.ref007","article-title":"Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health","volume":"112","author":"KE Holt","year":"2015","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pbio.3003848.ref008","doi-asserted-by":"crossref","first-page":"7251","DOI":"10.1038\/s41467-022-34312-7","article-title":"Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance","volume":"13","author":"P Munk","year":"2022","journal-title":"Nat Commun"},{"issue":"6","key":"pbio.3003848.ref009","doi-asserted-by":"crossref","DOI":"10.1128\/mbio.00488-25","article-title":"Evolutionary accumulation modeling in AMR: machine learning to infer and predict evolutionary dynamics of multi-drug resistance","volume":"16","author":"J Renz","year":"2025","journal-title":"mBio"},{"issue":"3","key":"pbio.3003848.ref010","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1111\/eva.12753","article-title":"Evolutionary epidemiology models to predict the dynamics of antibiotic resistance","volume":"12","author":"F Blanquart","year":"2019","journal-title":"Evol Appl"},{"key":"pbio.3003848.ref011","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.39435","article-title":"The distribution of antibiotic use and its association with antibiotic resistance","volume":"7","author":"SW Olesen","year":"2018","journal-title":"Elife"},{"issue":"7","key":"pbio.3003848.ref012","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1008010","article-title":"Population structure across scales facilitates coexistence and spatial heterogeneity of antibiotic-resistant infections","volume":"16","author":"MS Krieger","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"pbio.3003848.ref013","article-title":"On the evolutionary ecology of multidrug resistance in bacteria","volume":"15","author":"with the Maela Pneumococcal Collaboration","year":"2019","journal-title":"PLoS Pathog"},{"issue":"3","key":"pbio.3003848.ref014","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/ng.2878","article-title":"Evolution and transmission of drug-resistant tuberculosis in a Russian population","volume":"46","author":"N Casali","year":"2014","journal-title":"Nat Genet"},{"key":"pbio.3003848.ref015","article-title":"A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling","author":"IG Johnston","year":"2024","journal-title":"bioRxiv"},{"issue":"24","key":"pbio.3003848.ref016","doi-asserted-by":"crossref","first-page":"5457","DOI":"10.1093\/bioinformatics\/btac710","article-title":"EvAM-Tools: tools for evolutionary accumulation and cancer progression models","volume":"38","author":"R Diaz-Uriarte","year":"2022","journal-title":"Bioinformatics"},{"key":"pbio.3003848.ref017","article-title":"Reconstructing disease histories in huge discrete state spaces","author":"R Schill","year":"2024","journal-title":"KI - K\u00fcnstliche Intelligenz"},{"issue":"6","key":"pbio.3003848.ref018","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1038\/s41576-024-00803-0","article-title":"A phylogenetic approach to comparative genomics","volume":"26","author":"AE Dewar","year":"2025","journal-title":"Nat Rev Genet"},{"issue":"1","key":"pbio.3003848.ref019","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1093\/sysbio\/syu070","article-title":"The unsolved challenge to phylogenetic correlation tests for categorical characters","volume":"64","author":"WP Maddison","year":"2015","journal-title":"Syst Biol"},{"issue":"9","key":"pbio.3003848.ref020","article-title":"HyperTraPS-CT: inference and prediction for accumulation pathways with flexible data and model structures","volume":"20","author":"ONL Aga","year":"2024","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pbio.3003848.ref021","article-title":"HyperTraPS: inferring probabilistic patterns of trait acquisition in evolutionary and disease progression pathways","volume":"10","author":"SF Greenbury","year":"2020","journal-title":"Cell Syst"},{"issue":"2","key":"pbio.3003848.ref022","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.cels.2016.01.013","article-title":"Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention","volume":"2","author":"IG Johnston","year":"2016","journal-title":"Cell Syst"},{"issue":"1","key":"pbio.3003848.ref023","doi-asserted-by":"crossref","first-page":"3676","DOI":"10.1038\/s41467-023-39400-w","article-title":"Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees","volume":"14","author":"XG Luo","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3003848.ref024","article-title":"HyperHMM: efficient inference of evolutionary and progressive dynamics on hypercubic transition graphs","volume":"39","author":"MT Moen","year":"2023","journal-title":"Bioinformatics"},{"issue":"1","key":"pbio.3003848.ref025","doi-asserted-by":"crossref","first-page":"4188","DOI":"10.1038\/s41467-021-24448-3","article-title":"A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex","volume":"12","author":"MMC Lam","year":"2021","journal-title":"Nat Commun"},{"key":"pbio.3003848.ref026","unstructured":"Becker RA, Wilks AR, Brownrigg R, Minka TP, Deckmyn A. maps: draw geographical maps. R Package Version. 2018."},{"issue":"1","key":"pbio.3003848.ref027","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"SK Gupta","year":"2014","journal-title":"Antimicrob Agents Chemother"},{"issue":"10","key":"pbio.3003848.ref028","first-page":"001294","article-title":"Diversity, functional classification and genotyping of SHV \u03b2-lactamases in Klebsiella pneumoniae","volume":"10","author":"KK Tsang","year":"2024","journal-title":"Microb Genom"},{"issue":"8","key":"pbio.3003848.ref029","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/molbev\/msm118","article-title":"Mutational reversions during adaptive protein evolution","volume":"24","author":"MA DePristo","year":"2007","journal-title":"Mol Biol Evol"},{"issue":"5770","key":"pbio.3003848.ref030","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1126\/science.1123539","article-title":"Darwinian evolution can follow only very few mutational paths to fitter proteins","volume":"312","author":"DM Weinreich","year":"2006","journal-title":"Science"},{"key":"pbio.3003848.ref031","article-title":"Extracting useful information about reversible evolutionary processes from irreversible evolutionary accumulation models","author":"IG Johnston","year":"2026","journal-title":"arXiv"},{"key":"pbio.3003848.ref032","doi-asserted-by":"crossref","first-page":"62306","DOI":"10.1109\/ACCESS.2025.3558392","article-title":"A picture guide to cancer progression and evolutionary accumulation models: systematic critique, plausible interpretations, and alternative uses","volume":"13","author":"R Diaz-Uriarte","year":"2025","journal-title":"IEEE Access"},{"issue":"2","key":"pbio.3003848.ref033","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1093\/sysbio\/syac066","article-title":"Reducing the biases in false correlations between discrete characters","volume":"72","author":"JD Boyko","year":"2023","journal-title":"Syst Biol"},{"key":"pbio.3003848.ref034","doi-asserted-by":"crossref","first-page":"13816","DOI":"10.1109\/ACCESS.2025.3527715","article-title":"Clustering large-scale biomedical data to model dynamic accumulation processes in disease progression and anti-microbial resistance evolution","volume":"13","author":"KA Dauda","year":"2025","journal-title":"IEEE Access"},{"issue":"1","key":"pbio.3003848.ref035","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1038\/s44259-023-00014-3","article-title":"Profile and resistance levels of 136 integron resistance genes","volume":"1","author":"A Hip\u00f3lito","year":"2023","journal-title":"NPJ Antimicrob Resist"},{"key":"pbio.3003848.ref036","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1051\/vetres:2001123","article-title":"Resistance to trimethoprim and sulfonamides","volume":"32","author":"O Sk\u00f6ld","year":"2001","journal-title":"Vet Res"},{"key":"pbio.3003848.ref037","volume-title":"Global antimicrobial resistance and use surveillance system (GLASS) report 2022","year":"2022"},{"key":"pbio.3003848.ref038","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1471-2334-7-43","article-title":"Antimicrobial resistance predicts death in Tanzanian children with bloodstream infections: a prospective cohort study","volume":"7","author":"B Blomberg","year":"2007","journal-title":"BMC Infect Dis"},{"key":"pbio.3003848.ref039","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.3389\/fmicb.2020.02118","article-title":"Bacteraemia, malaria, and case fatality among children hospitalized with fever in Dar es Salaam, Tanzania","volume":"11","author":"SJ Moyo","year":"2020","journal-title":"Front Microbiol"},{"issue":"12","key":"pbio.3003848.ref040","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0145632","article-title":"Prevalence and antimicrobial resistance of microbes causing bloodstream infections in Unguja, Zanzibar","volume":"10","author":"A Onken","year":"2015","journal-title":"PLoS One"},{"issue":"4","key":"pbio.3003848.ref041","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pntd.0012132","article-title":"Predominance of multidrug-resistant Salmonella Typhi genotype 4.3.1 with low-level ciprofloxacin resistance in Zanzibar","volume":"18","author":"A Onken","year":"2024","journal-title":"PLoS Negl Trop Dis"},{"issue":"2","key":"pbio.3003848.ref042","doi-asserted-by":"crossref","DOI":"10.1093\/jacamr\/dlaf026","article-title":"National consumption of antimicrobials in Tanzania: 2020-2022","volume":"7","author":"S Mapunjo","year":"2025","journal-title":"JAC Antimicrob Resist"},{"issue":"10","key":"pbio.3003848.ref043","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.3390\/antibiotics10101249","article-title":"National antibiotics utilization trends for human use in Tanzania from 2010 to 2016 inferred from Tanzania Medicines and Medical Devices Authority Importation Data","volume":"10","author":"RZ Sangeda","year":"2021","journal-title":"Antibiotics (Basel)"},{"key":"pbio.3003848.ref044","doi-asserted-by":"crossref","first-page":"62306","DOI":"10.1109\/ACCESS.2025.3558392","article-title":"A picture guide to cancer progression and monotonic accumulation models: evolutionary assumptions, plausible interpretations, and alternative uses","volume":"13","author":"R Diaz-Uriarte","year":"2025","journal-title":"IEEE Access"},{"issue":"11","key":"pbio.3003848.ref045","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1086\/430005","article-title":"Estimating HIV evolutionary pathways and the genetic barrier to drug resistance","volume":"191","author":"N Beerenwinkel","year":"2005","journal-title":"J Infect Dis"},{"issue":"7","key":"pbio.3003848.ref046","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/j.tim.2015.02.009","article-title":"Collateral sensitivity of antibiotic-resistant microbes","volume":"23","author":"C P\u00e1l","year":"2015","journal-title":"Trends Microbiol"},{"issue":"4","key":"pbio.3003848.ref047","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1128\/jb.64.4.489-499.1952","article-title":"Genetic studies on microbial cross resistance to toxic agents i","volume":"64","author":"W Szybalski","year":"1952","journal-title":"J Bacteriol"},{"issue":"1","key":"pbio.3003848.ref048","doi-asserted-by":"crossref","first-page":"4731","DOI":"10.1038\/s41467-024-49122-2","article-title":"\u03b2-lactamase expression induces collateral sensitivity in Escherichia coli","volume":"15","author":"C Herencias","year":"2024","journal-title":"Nat Commun"},{"issue":"10219","key":"pbio.3003848.ref049","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/S0140-6736(19)32989-7","article-title":"Global, regional, and national sepsis incidence and mortality, 1990\u20132017: analysis for the Global Burden of Disease Study","volume":"395","author":"KE Rudd","year":"2020","journal-title":"Lancet"},{"issue":"2","key":"pbio.3003848.ref050","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0089142","article-title":"A system to automatically classify and name any individual genome-sequenced organism independently of current biological classification and nomenclature","volume":"9","author":"H Marakeby","year":"2014","journal-title":"PLoS One"},{"issue":"7","key":"pbio.3003848.ref051","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msac135","article-title":"A dual barcoding approach to bacterial strain nomenclature: genomic taxonomy of Klebsiella pneumoniae strains","volume":"39","author":"M Hennart","year":"2022","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pbio.3003848.ref052","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/bioinformatics\/btz513","article-title":"Modelling cancer progression using Mutual Hazard Networks","volume":"36","author":"R Schill","year":"2020","journal-title":"Bioinformatics"},{"issue":"4","key":"pbio.3003848.ref053","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"Phangorn: phylogenetic analysis in R","volume":"27","author":"KP Schliep","year":"2011","journal-title":"Bioinformatics"},{"key":"pbio.3003848.ref054","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.00961","article-title":"Phenotypic landscape inference reveals multiple evolutionary paths to C4 photosynthesis","volume":"2","author":"BP Williams","year":"2013","journal-title":"Elife"},{"issue":"2","key":"pbio.3003848.ref055","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"S Kurtz","year":"2004","journal-title":"Genome Biol"},{"issue":"7","key":"pbio.3003848.ref056","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1128\/JB.00043-12","article-title":"Complete genome sequence of Klebsiella pneumoniae subsp. pneumoniae HS11286, a multidrug-resistant strain isolated from human sputum","volume":"194","author":"P Liu","year":"2012","journal-title":"J Bacteriol"},{"key":"pbio.3003848.ref057","first-page":"1409","article-title":"A statistical method for evaluating systematic relationships","volume":"38","author":"RR Sokal","year":"1958","journal-title":"Univ Kansas Sci Bull"},{"key":"pbio.3003848.ref058","volume-title":"R: A language and environment for statistical computing","author":"R Core Team","year":"2022"},{"issue":"4","key":"pbio.3003848.ref059","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"N Saitou","year":"1987","journal-title":"Mol Biol Evol"},{"issue":"3","key":"pbio.3003848.ref060","doi-asserted-by":"crossref","first-page":"034003","DOI":"10.1088\/1742-5468\/ad3197","article-title":"Evolutionary accessibility of random and structured fitness landscapes","volume":"2024","author":"J Krug","year":"2024","journal-title":"J Stat Mech"},{"issue":"3","key":"pbio.3003848.ref061","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1007\/s00285-023-01882-z","article-title":"Accessibility percolation on Cartesian power graphs","volume":"86","author":"B Schmiegelt","year":"2023","journal-title":"J Math Biol"},{"issue":"11","key":"pbio.3003848.ref062","article-title":"Whole-genome sequencing to identify drivers of carbapenem-resistant Klebsiella pneumoniae transmission within and between regional long-term acute-care hospitals","volume":"63","author":"JH Han","year":"2019","journal-title":"Antimicrob Agents Chemother"},{"issue":"11","key":"pbio.3003848.ref063","first-page":"2246","article-title":"Global phylogeography and genomic epidemiology of carbapenem-resistant blaOXA-232\u2013carrying Klebsiella pneumoniae sequence type 15 lineage","volume":"29","author":"Y Wu","year":"2023","journal-title":"Emerg Infect Dis"},{"issue":"1","key":"pbio.3003848.ref064","doi-asserted-by":"crossref","first-page":"8495","DOI":"10.1038\/s41467-023-44285-w","article-title":"Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients","volume":"14","author":"L Aguilar-Bultet","year":"2023","journal-title":"Nat Commun"},{"key":"pbio.3003848.ref065","volume-title":"combination Matrix Axis for \u2018ggplot2\u2019 to Create \u2018UpSet\u2019 Plots","author":"C Ahlmann-Eltze","year":"2025"},{"issue":"28","key":"pbio.3003848.ref066","doi-asserted-by":"crossref","first-page":"848","DOI":"10.21105\/joss.00848","article-title":"countrycode: an R package to convert country names and country codes","volume":"3","author":"V Arel-Bundock","year":"2018","journal-title":"JOSS"},{"issue":"1","key":"pbio.3003848.ref067","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting linear mixed-effects models using lme4","volume":"67","author":"D Bates","year":"2015","journal-title":"J Stat Soft"},{"key":"pbio.3003848.ref068","doi-asserted-by":"crossref","unstructured":"Clarke E, Sherrill-Mix S, Dawson C. ggbeeswarm: categorical scatter (violin point) plots. 2016. Available from: https:\/\/cir.nii.ac.jp\/crid\/1360019690351052672","DOI":"10.32614\/CRAN.package.ggbeeswarm"},{"issue":"7825","key":"pbio.3003848.ref069","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/s41586-020-2649-2","article-title":"Array programming with NumPy","volume":"585","author":"CR Harris","year":"2020","journal-title":"Nature"},{"key":"pbio.3003848.ref070","unstructured":"Kassambara A. Ggpubr: \u201cggplot2\u201d based publication ready plots. R Package Version 0.4. 0, 438. 2020."},{"issue":"2","key":"pbio.3003848.ref071","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1111\/j.2041-210X.2011.00169.x","article-title":"phytools: an R package for phylogenetic comparative biology (and other things)","volume":"3","author":"LJ Revell","year":"2011","journal-title":"Methods Ecol Evol"},{"key":"pbio.3003848.ref072","unstructured":"Slowikowski K. ggrepel: automatically position non-overlapping text labels with \u2018ggplot2\u2019. R package version 0.9. 1, 2021. 2021."},{"key":"pbio.3003848.ref073","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: elegant graphics for data analysis","author":"H Wickham","year":"2016"},{"issue":"43","key":"pbio.3003848.ref074","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"H Wickham","year":"2019","journal-title":"JOSS"},{"key":"pbio.3003848.ref075","unstructured":"Wickham H, Fran\u00e7ois R, Henry L, M\u00fcller K, Vaughan D. Dplyr: a grammar of data manipulation. R package version 1.1. 2. Computer Software. 2023."}],"updated-by":[{"DOI":"10.1371\/journal.pbio.3003848","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T00:00:00Z","timestamp":1781740800000}}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003848","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,18]],"date-time":"2026-06-18T17:53:56Z","timestamp":1781805236000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003848"}},"subtitle":[],"editor":[{"given":"J. Arjan G. M.","family":"de Visser","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,6,12]]},"references-count":75,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2026,6,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3003848","relation":{},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,12]]}}}