{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T21:43:44Z","timestamp":1790804624899,"version":"4.1.0"},"reference-count":62,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,5,5]],"date-time":"2023-05-05T00:00:00Z","timestamp":1683244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["ZA 697\/6\u20131"],"award-info":[{"award-number":["ZA 697\/6\u20131"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Extended spectrum beta-lactamases (ESBL) are frequently found in Enterobacterales isolates from Western Africa. However, information on the molecular epidemiology of regional ESBL-positive Enterobacterales strains is scarce. In order to provide epidemiological information, ESBL-positive <jats:italic>Escherichia coli<\/jats:italic> isolates from stool samples of European soldiers with diarrhea deployed to a field camp in Mali were subjected to whole-genome sequencing (Illumina MiSeq and Oxford Nanopore MinION) and antimicrobial susceptibility testing. With two exemptions, sequence-based analysis suggested an absence of transmission events between soldiers as indicated by a high genetic diversity of isolates and sequence types, confirming previous rep-PCR results. Third-generation cephalosporin resistance was associated with the presence of <jats:italic>bla<\/jats:italic><jats:sub>CTX-M-15<\/jats:sub> genes with (<jats:italic>n<\/jats:italic>\u2009=\u200914) and without (<jats:italic>n<\/jats:italic>\u2009=\u20095) co-occurring <jats:italic>bla<\/jats:italic><jats:sub>TEM-1b<\/jats:sub> genes. Between 0 and 6 virulence and resistance plasmids per isolate were recorded. The detected resistance plasmids could be categorized into five types, which, in turn, share different sequence-identical segments, representing particular antimicrobial resistance gene-associated mobile genetic elements (MGEs). Phenotypic resistance rates within the 19 assessed isolates that showed distinguishable colony morphologies were 94.7% (18\/19) against ampicillin-sulbactam and trimethoprim\/sulfamethoxazole, 68.4% (13\/19) against moxifloxacin, 31.6% (6\/19) against ciprofloxacin, 42.1% (8\/19) against gentamicin, 31.6% (6\/19) against tobramycin, and 21.1% (4\/19) against piperacillin-tazobactam and fosfomycin. Virulence-associated genes mediating infectious gastroenteritis were rarely detected. The gene <jats:italic>aggR<\/jats:italic>, which is characteristic for enteroaggregative <jats:italic>E. coli<\/jats:italic>, was only detected in one single isolate. In summary, we found a variety of different strains and clonal lineages of ESBL-carrying <jats:italic>E. coli.<\/jats:italic> Transmission either between soldiers or from common contaminated sources was demonstrated in two cases and played only a minor role in this military field camp, while there were indications that resistance gene bearing MGEs had been exchanged between antimicrobial resistance gene-(ARG-)carrying plasmids.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1169829","type":"journal-article","created":{"date-parts":[[2023,5,5]],"date-time":"2023-05-05T05:49:59Z","timestamp":1683265799000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":9,"title":["Molecular epidemiology of enterically colonizing Escherichia coli with resistance against third-generation cephalosporins isolated from stool samples of European soldiers with concomitant diarrhea on deployment in Western African Mali"],"prefix":"10.3389","volume":"14","author":[{"given":"Katharina","family":"Hoffmann","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Riediger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aljoscha","family":"Tersteegen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pauline","family":"Marquardt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sascha","family":"Kahlfu\u00df","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Achim J.","family":"Kaasch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ralf Matthias","family":"Hagen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hagen","family":"Frickmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas E.","family":"Zautner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,5,5]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.jgar.2020.03.009","article-title":"Implementation of antimicrobial stewardship programmes in African countries: a systematic literature review","volume":"22","author":"Akpan","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"2748","DOI":"10.1093\/jac\/dkab212","article-title":"dfrA trimethoprim resistance genes found in gram-negative bacteria: compilation and unambiguous numbering","volume":"76","author":"Ambrose","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/S1473-3099(16)30319-X","article-title":"Import and spread of extended-spectrum \u03b2-lactamase-producing Enterobacteriaceae by international travellers (COMBAT study): a prospective, multicentre cohort study","volume":"17","author":"Arcilla","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1017\/ice.2022.187","article-title":"Serratia marcescens outbreak in a neonatal intensive care unit associated with contaminated donor milk","volume":"5","author":"Bechmann","year":"2022","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"2271","DOI":"10.1093\/jac\/dkr307","article-title":"Salmonella carriage in adopted children from Mali: 2001-08","volume":"66","author":"Boisram\u00e9-Gastrin","year":"2011","journal-title":"J. Antimicrob. Chemother."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1128\/CMR.14.4.933-951.2001","article-title":"Extended-spectrum beta-lactamases in the 21st century: characterization, epidemiology, and detection of this important resistance threat","volume":"14","author":"Bradford","year":"2001","journal-title":"Clin. Microbiol. Rev."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"642","DOI":"10.1097\/01.inf.0000130951.85974.79","article-title":"Invasive pneumococcal infections among hospitalized children in Bamako","volume":"23","author":"Campbell","year":"2004","journal-title":"Mali. Pediatr. Infect. Dis J."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"3895","DOI":"10.1128\/AAC.02412-14","article-title":"In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing","volume":"58","author":"Carattoli","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/s41579-020-0416-x","article-title":"The population genetics of pathogenic Escherichia coli","volume":"19","author":"Denamur","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci. Rep."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s40779-018-0166-5","article-title":"Infectious diseases during the European Union training mission Mali (EUTM MLI)\u2014a four-year experience","volume":"5","author":"Frickmann","year":"","journal-title":"Mil. Med. Res."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2018\/9395420","article-title":"Resistant gram-negative Bacteria and diagnostic point-of-care options for the field setting during military operations","volume":"2018","author":"Frickmann","year":"","journal-title":"Biomed. Res. Int."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"573904","DOI":"10.1155\/2015\/573904","article-title":"Surveillance of food- and smear-transmitted pathogens in European soldiers with diarrhea on deployment in the tropics: experience from the European Union training Mission (EUTM) Mali","volume":"2015","author":"Frickmann","year":"2015","journal-title":"Biomed. Res. Int."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"e0162129","DOI":"10.1371\/journal.pone.0162129","article-title":"Low enteric colonization with multidrug-resistant pathogens in soldiers returning from deployments-experience from the years 2007-2015","volume":"11","author":"Frickmann","year":"2016","journal-title":"PLoS One"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"D851","DOI":"10.1093\/nar\/gkx1068","article-title":"RefSeq: an update on prokaryotic genome annotation and curation","volume":"46","author":"Haft","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1556\/1886.2015.00037","article-title":"\u03b2-Lactamases encoded by blaCTX-M Group I genes as determinants of resistance of ESBL-positive Enterobacteriaceae in European soldiers in tropical Mali","volume":"5","author":"Hagen","year":"2015","journal-title":"Eur. J. Microbiol. Immunol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"O109","DOI":"10.1111\/1469-0691.12339","article-title":"Prevalence and characterization of extended-spectrum \u03b2-lactamase-producing clinical Salmonella enterica isolates in Dakar, Senegal, from 1999 to 2009","volume":"20","author":"Harrois","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1016\/j.ijid.2021.06.024","article-title":"Prevalence of cervical HPV infection, sexually transmitted infections and associated antimicrobial resistance in women attending cervical cancer screening in Mali","volume":"108","author":"Jary","year":"2021","journal-title":"Int. J. Infect. Dis."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"294","DOI":"10.1038\/nbt.2522","article-title":"Updating benchtop sequencing performance comparison","volume":"31","author":"J\u00fcnemann","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"837","DOI":"10.1093\/cid\/ciu957","article-title":"Antimicrobials increase travelers' risk of colonization by extended-spectrum betalactamase-producing Enterobacteriaceae","volume":"60","author":"Kantele","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"Koren","year":"2017","journal-title":"Genome Res."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"D1020","DOI":"10.1093\/nar\/gkaa1105","article-title":"RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation","volume":"49","author":"Li","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1021\/acsinfecdis.5b00129","article-title":"Crystal structures of trimethoprim-resistant DfrA1 rationalize potent inhibition by Propargyl-linked Antifolates","volume":"2","author":"Lombardo","year":"2016","journal-title":"ACS Infect. Dis."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.ijmm.2014.12.001","article-title":"Colonization with extended-spectrum beta-lactamase-producing and carbapenemase-producing Enterobacteriaceae in international travelers returning to Germany","volume":"305","author":"L\u00fcbbert","year":"2015","journal-title":"Int. J. Med. Microbiol."},{"key":"ref29","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1055\/s-0043-105251","article-title":"Tropenmediziner der Bundeswehr: Einsatzerfahrungen in Mali","volume":"24","author":"Maa\u00dfen","year":"2017","journal-title":"Flugmed. Tropenmed. Reisemed."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"e01269","DOI":"10.1128\/JCM.01269-20","article-title":"In silico genotyping of Escherichia coli isolates for Extraintestinal virulence genes by use of whole-genome sequencing data","volume":"58","author":"Malberg Tetzschner","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"141","DOI":"10.11604\/pamj.2020.37.141.22716","article-title":"Tuberculosis and HIV coinfection complicated by nosocomial infection caused by Klebsiella pneumoniae: about 4 cases in a Department of Infectious diseases in Mali","volume":"37","author":"Meli","year":"2020","journal-title":"Pan Afr. Med. J."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"466","DOI":"10.1186\/1471-2334-13-466","article-title":"Predominance of Klebsiella pneumoniae ST14 carrying CTX-M-15 causing neonatal sepsis in Tanzania","volume":"13","author":"Mshana","year":"2013","journal-title":"BMC Infect. Dis."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1815272","DOI":"10.1080\/16549716.2020.1815272","article-title":"Prevalence of multidrug-, extensive drug-, and pandrug-resistant commensal Escherichia coli isolated from healthy humans in community settings in low- and middle-income countries: a systematic review and meta-analysis","volume":"12","author":"Nkansa-Gyamfi","year":"2019","journal-title":"Glob. Health Action"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2021\/5153237","article-title":"Genetic determinants of resistance among ESBL-producing Enterobacteriaceae in community and hospital settings in east, central, and southern Africa: A systematic review and Meta-analysis of prevalence","volume":"2021","author":"Onduru","year":"2021","journal-title":"Can. J. Infect. Dis. Med. Microbiol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"2448","DOI":"10.3390\/microorganisms10122448","article-title":"Molecular epidemiology of Escherichia coli with resistance against third-generation Cephalosporines isolated from deployed German soldiers-A retrospective assessment after deployments to the African Sahel region and other sites between 2007 and 2016","volume":"10","author":"Pankok","year":"","journal-title":"Microorganisms"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"689","DOI":"10.3390\/antibiotics11050689","article-title":"Epidemiology of plasmids in Escherichia coli and Klebsiella pneumoniae with acquired extended Spectrum Beta-lactamase genes isolated from chronic wounds in Ghana","volume":"11","author":"Pankok","year":"","journal-title":"Antibiotics"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1016\/0140-6736(91)91511-R","article-title":"Long-acting chloramphenicol versus intravenous ampicillin for treatment of bacterial meningitis","volume":"338","author":"P\u00e9coul","year":"1991","journal-title":"Lancet"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1038\/nature17672","article-title":"Interconnected microbiomes and resistomes in low-income human habitats","volume":"533","author":"Pehrsson","year":"2016","journal-title":"Nature"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e000206","DOI":"10.1099\/mgen.0.000206","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genom."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/s41467-019-08529-y","article-title":"Collateral sensitivity constrains resistance evolution of the CTX-M-15 \u03b2-lactamase","volume":"10","author":"Rosenkilde","year":"2019","journal-title":"Nat. Commun."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"3962","DOI":"10.1128\/JB.01947-07","article-title":"The carriage population of Staphylococcus aureus from Mali is composed of a combination of pandemic clones and the divergent Panton-valentine leukocidin-positive genotype ST152","volume":"190","author":"Ruimy","year":"2008","journal-title":"J. Bacteriol."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/cid\/civ333","article-title":"High rate of acquisition but short duration of carriage of multidrug-resistant Enterobacteriaceae after travel to the tropics","volume":"61","author":"Rupp\u00e9","year":"2015","journal-title":"Clin. Infect. Dis."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.3855\/jidc.7536","article-title":"Prevalence of ESBL-producing Enterobacteriaceae isolated from blood cultures in Mali","volume":"10","author":"Sangare","year":"2016","journal-title":"J. Infect. Dev. Ctries."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1016\/j.medmal.2015.08.003","article-title":"Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from blood cultures in Africa","volume":"45","author":"Sangare","year":"2015","journal-title":"Med. Mal. Infect."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1684\/mst.2017.0681","article-title":"Prevalence of extended-spectrum beta-lactamase phenotypes in enterobacteria isolated from blood cultures of patients at admission to the University Hospital of Bamako","volume":"27","author":"Sangar\u00e9","year":"2017","journal-title":"Med. Sante Trop."},{"key":"ref46","doi-asserted-by":"publisher","first-page":"e0172652","DOI":"10.1371\/journal.pone.0172652","article-title":"Very high prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in bacteriemic patients hospitalized in teaching hospitals in Bamako","volume":"12","author":"Sangare","year":"2017","journal-title":"PLoS One"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1054\/drup.2000.0146","article-title":"Sulfonamide resistance: mechanisms and trends","volume":"3","author":"Sk\u00f6ld","year":"2000","journal-title":"Drug Resist. Updat."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1128","DOI":"10.1126\/science.1176950","article-title":"Functional characterization of the antibiotic resistance reservoir in the human microflora","volume":"325","author":"Sommer","year":"2009","journal-title":"Science"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/s13059-018-1540-z","article-title":"SKESA: strategic k-mer extension for scrupulous assemblies","volume":"19","author":"Souvorov","year":"2018","journal-title":"Genome Biol."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1097\/01.inf.0000164768.28135.0d","article-title":"Burden of invasive disease caused by Haemophilus influenzae type b in Bamako, Mali: impetus for routine infant immunization with conjugate vaccine","volume":"24","author":"Sow","year":"2005","journal-title":"Pediatr. Infect. Dis. J."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1093\/jac\/dkq068","article-title":"Intrafamilial transmission of extended-spectrum-beta-lactamase-producing Escherichia coli and Salmonella enterica Babelsberg among the families of internationally adopted children","volume":"65","author":"Tand\u00e9","year":"2010","journal-title":"J. Antimicrob. Chemother."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"472","DOI":"10.3201\/eid1503.071637","article-title":"Extended-spectrum beta-lactamase-producing Enterobacteriaceae in a Malian orphanage","volume":"15","author":"Tand\u00e9","year":"2009","journal-title":"Emerg. Infect. Dis."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"taab138","DOI":"10.1093\/jtm\/taab138","article-title":"TaqMan Array card testing of participant-collected stool smears to determine the pathogen-specific epidemiology of travellers' diarrhoea","volume":"29","author":"Tisdale","year":"2022","journal-title":"J. Travel Med."},{"key":"ref55","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1111\/j.1600-0463.2011.02766.x","article-title":"Antimicrobial susceptibility to parenteral and oral agents in a largely polyclonal collection of CTX-M-14 and CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae","volume":"119","author":"Titelman","year":"2011","journal-title":"APMIS"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"615649","DOI":"10.3389\/fmed.2021.615649","article-title":"Antimicrobial resistance in Enterobacterales and its contribution to Sepsis in sub-saharan Africa","volume":"8","author":"Tompkins","year":"2021","journal-title":"Front. Med."},{"key":"ref57","doi-asserted-by":"publisher","first-page":"2817","DOI":"10.3389\/fmicb.2019.02817","article-title":"IS26-mediated transfer of blaNDM-1 as the Main route of resistance transmission during a polyclonal, multispecies outbreak in a German hospital","volume":"10","author":"Weber","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"2138","DOI":"10.12688\/f1000research.21782.4","article-title":"Benchmarking of long-read assemblers for prokaryote whole genome sequencing","volume":"8","author":"Wick","year":"2019","journal-title":"F1000Res"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e1009802","DOI":"10.1371\/journal.pcbi.1009802","article-title":"Polypolish: short-read polishing of long-read bacterial genome assemblies","volume":"18","author":"Wick","year":"2022","journal-title":"PLoS Comput. Biol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"2764","DOI":"10.1093\/jac\/dkx217","article-title":"PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens","volume":"72","author":"Zankari","year":"2017","journal-title":"J. Antimicrob. Chemother."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref62","doi-asserted-by":"publisher","first-page":"7538","DOI":"10.1111\/1462-2920.15783","article-title":"Fitness cost and compensation mechanism of sulfonamide resistance genes (sul1, sul2, and sul3) in Escherichia coli","volume":"23","author":"Zhou","year":"2021","journal-title":"Environ. 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