{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T10:16:40Z","timestamp":1790417800239,"version":"4.1.0"},"reference-count":73,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2022,1,18]],"date-time":"2022-01-18T00:00:00Z","timestamp":1642464000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Antimicrobial resistance (AMR) is a serious global health threat and extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales are a major contributor. This study aimed to gain a deeper insight into the AMR burden of wild animals. In total, 1595 fecal samples were collected by two systematic searches in Mecklenburg-Western Pomerania, north-east Germany. Samples were screened for ESBL-carrying Escherichia (E.) coli and isolates found were further analyzed using antimicrobial susceptibility testing and whole-genome sequencing. We found an estimated prevalence of 1.2% ESBL-producing E. coli in wild boar and 1.1% in wild ruminants. CTX-M-1 was the most abundant CTX-M type. We also examined fecal samples from wild boar and wild ruminants using shotgun metagenomics to gain insight into the resistome in wild animals. The latter revealed significantly lower normalized counts for AMR genes in wildlife samples compared to farm animals. The AMR gene levels were lower in wild ruminants than in wild boar. In conclusion, our study revealed a low prevalence of ESBL-producing E. coli and a low overall AMR gene burden in wild boar and wild ruminants, probably due to the secluded location of the search area.<\/jats:p>","DOI":"10.3390\/antibiotics11020123","type":"journal-article","created":{"date-parts":[[2022,1,18]],"date-time":"2022-01-18T08:09:20Z","timestamp":1642493360000},"page":"123","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":37,"title":["Genomic Analysis of ESBL-Producing E. coli in Wildlife from North-Eastern Germany"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8135-3814","authenticated-orcid":false,"given":"Timo","family":"Homeier-Bachmann","sequence":"first","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald\u2013Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1964-8600","authenticated-orcid":false,"given":"Anne K.","family":"Sch\u00fctz","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald\u2013Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7403-9755","authenticated-orcid":false,"given":"Sylvia","family":"Dreyer","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of International Animal Health\/One Health, 17493 Greifswald\u2013Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Glanz","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald\u2013Insel Riems, Germany"},{"name":"Wildlife Research Unit, Agricultural Centre Baden-W\u00fcrttemberg, 88326 Aulendorf, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2669-8799","authenticated-orcid":false,"given":"Katharina","family":"Schaufler","sequence":"additional","affiliation":[{"name":"Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany"},{"name":"Institute of Infection Medicine, Christian-Albrecht University and University Medical Center Schleswig-Holstein, 24118 Kiel, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7400-9409","authenticated-orcid":false,"given":"Franz J.","family":"Conraths","sequence":"additional","affiliation":[{"name":"Friedrich-Loeffler-Institut, Institute of Epidemiology, 17493 Greifswald\u2013Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,1,18]]},"reference":[{"key":"ref_1","unstructured":"WHO (2014). Antimicrobial Resistance Global Report on Surveillance, World Health Organization."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Verburg, I., Garcia-Cobos, S., Hernandez Leal, L., Waar, K., Friedrich, A.W., and Schmitt, H. (2019). Abundance and Antimicrobial Resistance of Three Bacterial Species Along a Complete Wastewater Pathway. Microorganisms, 7.","DOI":"10.3390\/microorganisms7090312"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Homeier-Bachmann, T., Heiden, S.E., Lubcke, P.K., Bachmann, L., Bohnert, J.A., Zimmermann, D., and Schaufler, K. (2021). Antibiotic-Resistant Enterobacteriaceae in Wastewater of Abattoirs. Antibiotics, 10.","DOI":"10.3390\/antibiotics10050568"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature10388","article-title":"Antibiotic Resistance Is Ancient","volume":"477","author":"King","year":"2011","journal-title":"Nature"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"627","DOI":"10.1016\/j.sapharm.2018.09.017","article-title":"Community Pharmacy Interventions to Improve Antibiotic Stewardship and Implications for Pharmacy Education: A Narrative Overview","volume":"15","author":"Bishop","year":"2019","journal-title":"Res. Soc. Adm. Pharm."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"135001","DOI":"10.1016\/j.scitotenv.2019.135001","article-title":"Wild Boar as a Reservoir of Antimicrobial Resistance","volume":"717","author":"Torres","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_7","unstructured":"EMA-ESVAC (2020). Sales of Veterinary Antimicrobial Agents in 31 European Countries in 2018, European Medicines Agency (EMA). Available online: https:\/\/www.ema.europa.eu\/en\/documents\/report\/sales-veterinary-antimicrobial-agents-31-european-countries-2018-trends-2010-2018-tenth-esvac-report_en.pdf."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Binsker, U., K\u00e4sbohrer, A., and Hammerl, J.A. (2021). Global Colistin Use: A Review of the Emergence of Resistant Enterobacterales and the Impact on Their Genetic Basis. FEMS Microbiol. Rev., fuab049.","DOI":"10.1093\/femsre\/fuab049"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"20140083","DOI":"10.1098\/rstb.2014.0083","article-title":"Antimicrobial Resistance in Humans, Livestock and the Wider Environment","volume":"370","author":"Woolhouse","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, Research, and Development of New Antibiotics: The Who Priority List of Antibiotic-Resistant Bacteria and Tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1007\/BF01641355","article-title":"Transferable Resistance to Cefotaxime, Cefoxitin, Cefamandole and Cefuroxime in Clinical Isolates of Klebsiella Pneumoniae and Serratia Marcescens","volume":"11","author":"Knothe","year":"1983","journal-title":"Infection"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"e00047-19","DOI":"10.1128\/CMR.00047-19","article-title":"Epidemiology of \u0392-Lactamase-Producing Pathogens","volume":"33","author":"Bush","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Huebner, N.O., Dittmann, K., Henck, V., Wegner, C., and Kramer, A. (2016). Epidemiology of Multidrug Resistant Bacterial Organisms and Clostridium Difficile in German Hospitals in 2014: Results from a Nationwide One-Day Point Prevalence of 329 German Hospitals. BMC Infect. Dis., 16.","DOI":"10.1186\/s12879-016-1756-z"},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Blaak, H., van Hoek, A.H.A.M., Hamidjaja, R.A., van der Plaats, R.Q.J., Kerkhof-de Heer, L., Husman, A.M.D., and Schets, F.M. (2015). Distribution, Numbers, Diversity of Esbl-Producing E. Coli in the Poultry Farm Environment. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0135402"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1089\/fpd.2015.1936","article-title":"Extended-Spectrum Beta-Lactamase, Ampc-Producing, Fluoroquinolone-Resistant Escherichia Coli in Retail Broiler Chicken Meat, Italy","volume":"12","author":"Ghodousi","year":"2015","journal-title":"Foodborne Pathog. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"138788","DOI":"10.1016\/j.scitotenv.2020.138788","article-title":"Antibiotic-Resistant Bacteria and Antimicrobial Residues in Wastewater and Process Water from German Pig Slaughterhouses and Their Receiving Municipal Wastewater Treatment Plants","volume":"727","author":"Savin","year":"2020","journal-title":"Sci. Total Environ."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"575391","DOI":"10.3389\/fmicb.2020.575391","article-title":"Colistin-Resistant Enterobacteriaceae Isolated from Process Waters and Wastewater from German Poultry and Pig Slaughterhouses","volume":"11","author":"Savin","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/s41426-018-0033-1","article-title":"Rapid Rise of the Esbl and Mcr-1 Genes in Escherichia Coli of Chicken Origin in China, 2008\u20132014","volume":"7","author":"Wu","year":"2018","journal-title":"Emerg. Microbes Infect."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.burns.2012.07.015","article-title":"Colistin in Burn Intensive Care: Back to the Future?","volume":"39","author":"Azzopardi","year":"2013","journal-title":"Burns"},{"key":"ref_20","unstructured":"World Health Organization\u2014AGISAR (2017). Critically Important Antimicrobials for Human Medicine, 5th Revision, World Health Organization."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Holtmann, A.R., Meemken, D., M\u00fcller, A., Seinige, D., B\u00fcttner, K., Failing, K., and Kehrenberg, C. (2021). Wild Boars Carry Extended-Spectrum \u0392-Lactamase- and Ampc-Producing Escherichia Coli. Microorganisms, 9.","DOI":"10.3390\/microorganisms9020367"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e00243-19","DOI":"10.1128\/AAC.00243-19","article-title":"Genomic and Functional Analysis of Emerging Virulent and Multidrug-Resistant Escherichia Coli Lineage Sequence Type 648","volume":"63","author":"Schaufler","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"fiv155","DOI":"10.1093\/femsec\/fiv155","article-title":"Clonal Spread and Interspecies Transmission of Clinically Relevant Esbl-Producing Escherichia Coli of St410--Another Successful Pandemic Clone?","volume":"92","author":"Schaufler","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e01167-19","DOI":"10.1128\/AAC.01167-19","article-title":"Wildlife Is Overlooked in the Epidemiology of Medically Important Antibiotic-Resistant Bacteria","volume":"63","author":"Dolejska","year":"2019","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/s41467-019-08853-3","article-title":"Global Monitoring of Antimicrobial Resistance Based on Metagenomics Analyses of Urban Sewage","volume":"10","author":"Hendriksen","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"147269","DOI":"10.1016\/j.scitotenv.2021.147269","article-title":"Prevalence of Multidrug-Resistant and Extended-Spectrum Beta-Lactamase-Producing Escherichia Coli in Urban Community Wastewater","volume":"785","author":"Schmiege","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"4406","DOI":"10.1038\/s41467-019-12111-x","article-title":"The Fecal Resistome of Dairy Cattle Is Associated with Diet During Nursing","volume":"10","author":"Liu","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Skar\u017cy\u0144ska, M., Leekitcharoenphon, P., Hendriksen, R.S., Aarestrup, F.M., and Wasyl, D. (2020). A Metagenomic Glimpse into the Gut of Wild and Domestic Animals: Quantification of Antimicrobial Resistance and More. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0242987"},{"key":"ref_29","unstructured":"World Health Organization (2019). Critically Important Antimicrobials for Human Medicine, World Health Organization. [6th rev. ed.]."},{"key":"ref_30","unstructured":"International Committee Unanimously Adopted the List of Antimicrobial Agents of Veterinary Importance (2018). Oie List of Antimicrobial Agents of Veterinary Importance, OIE\u2014World Organisation for Animal Health."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1111\/1758-2229.12019","article-title":"The Clermont Escherichia Coli Phylo-Typing Method Revisited: Improvement of Specificity and Detection of New Phylo-Groups","volume":"5","author":"Clermont","year":"2013","journal-title":"Environ. Microbiol. Rep."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1093\/jac\/dkx488","article-title":"Plasmids Carrying Antimicrobial Resistance Genes in Enterobacteriaceae","volume":"73","author":"Rozwandowicz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","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":"ref_34","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s13059-020-02014-2","article-title":"Ccmetagen: Comprehensive and Accurate Identification of Eukaryotes and Prokaryotes in Metagenomic Data","volume":"21","author":"Marcelino","year":"2020","journal-title":"Genome Biol."},{"key":"ref_35","first-page":"627821","article-title":"Wildlife as Sentinels of Antimicrobial Resistance in Germany?","volume":"7","author":"Alt","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1089\/mdr.2017.0148","article-title":"Antimicrobial Resistance in Escherichia Coli Isolated from Wild Animals in Poland","volume":"24","author":"Wasyl","year":"2018","journal-title":"Microb. Drug Resist."},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Formenti, N., Cal\u00f2, S., Parisio, G., Guarneri, F., Birbes, L., Pitozzi, A., Scali, F., Tonni, M., Guadagno, F., and Giovannini, S. (2021). Esbl\/Ampc-Producing Escherichia Coli in Wild Boar: Epidemiology and Risk Factors. Animals, 11.","DOI":"10.3390\/ani11071855"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1080\/01652176.2014.949391","article-title":"Acquired Antibiotic Resistance among Wild Animals: The Case of Iberian Lynx (Lynx Pardinus)","volume":"34","author":"Sousa","year":"2014","journal-title":"Vet. Q."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"e02227","DOI":"10.1128\/mBio.02227-15","article-title":"Antimicrobial Resistance in Agriculture","volume":"7","author":"Thanner","year":"2016","journal-title":"mBio"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Larsen, J., Raisen, C.L., Ba, X., Sadgrove, N.J., Padilla-Gonz\u00e1lez, G.F., Simmonds, M.S.J., Loncaric, I., Kerschner, H., Apfalter, P., and Hartl, R. (2022). Emergence of Methicillin Resistance Predates the Clinical Use of Antibiotics. Nature, 1\u20137.","DOI":"10.1038\/s41586-021-04265-w"},{"key":"ref_41","unstructured":"Deutscher Wetterdienst (2021, October 01). CDC\u2014Climate Data Center, Germany. Available online: https:\/\/cdc.dwd.de\/portal\/Offenbach."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"422","DOI":"10.3934\/microbiol.2020025","article-title":"Fecal Carriage of Esbl-Producing Escherichia Coli in Egyptian Patients Admitted to the Medical Research Institute Hospital, Alexandria University","volume":"6","author":"ElBaradei","year":"2020","journal-title":"AIMS Microbiol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s12223-015-0427-6","article-title":"Molecular Characterization of Bacteremic Escherichia Coli Isolates in Romania","volume":"61","author":"Usein","year":"2016","journal-title":"Folia Microbiol."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Ramos, S., Silva, V., Dapkevicius, M.L.E., Cani\u00e7a, M., Tejedor-Junco, M.T., Igrejas, G., and Poeta, P. (2020). Escherichia Coli as Commensal and Pathogenic Bacteria among Food-Producing Animals: Health Implications of Extended Spectrum \u0392-Lactamase (Esbl) Production. Animals, 10.","DOI":"10.3390\/ani10122239"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1912","DOI":"10.1128\/AAC.02756-15","article-title":"Kpc-Like Carbapenemase-Producing Enterobacteriaceae Colonizing Patients in Europe and Israel","volume":"60","author":"Baraniak","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"4814","DOI":"10.1128\/AAC.02573-14","article-title":"Comparative Genomics of an Inca\/C Multidrug Resistance Plasmid from Escherichia Coli and Klebsiella Isolates from Intensive Care Unit Patients and the Utility of Whole-Genome Sequencing in Health Care Settings","volume":"58","author":"Hazen","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e01689-18","DOI":"10.1128\/AAC.01689-18","article-title":"A Large, Refractory Nosocomial Outbreak of Klebsiella Pneumoniae Carbapenemase-Producing Escherichia Coli Demonstrates Carbapenemase Gene Outbreaks Involving Sink Sites Require Novel Approaches to Infection Control","volume":"62","author":"Decraene","year":"2018","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Tarabai, H., Wyrsch, E.R., Bitar, I., Dolejska, M., and Djordjevic, S.P. (2021). Epidemic Hi2 Plasmids Mobilising the Carbapenemase Gene Bla(Imp-4) in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia Coli St216 Colonising Silver Gulls. Microorganisms, 9.","DOI":"10.3390\/microorganisms9030567"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1016\/j.ijantimicag.2017.10.007","article-title":"Longitudinal Study on Antimicrobial Consumption and Resistance in Rabbit Farming","volume":"51","author":"Agnoletti","year":"2018","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.diagmicrobio.2016.03.008","article-title":"Community Fecal Carriage of Broad-Spectrum Cephalosporin-Resistant Escherichia Coli in Tunisian Children","volume":"87","author":"Ferjani","year":"2017","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1128\/AAC.01656-12","article-title":"Clonal Structure, Extended-Spectrum Beta-Lactamases, Acquired Ampc-Type Cephalosporinases of Escherichia Coli Populations Colonizing Patients in Rehabilitation Centers in Four Countries","volume":"57","author":"Izdebski","year":"2013","journal-title":"Antimicrob Agents Chemother"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"e00135-18","DOI":"10.1128\/CMR.00135-18","article-title":"Global Extraintestinal Pathogenic Escherichia Coli (Expec) Lineages","volume":"32","author":"Manges","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e00897-20","DOI":"10.1128\/mSystems.00897-20","article-title":"Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: A Systematic Review and Phylogenomic Analyses from a One Health Perspective","volume":"5","author":"Reta","year":"2020","journal-title":"Msystems"},{"key":"ref_54","unstructured":"Landesforst, M.V. (2022, January 05). \u201cLandesforst MV\u2014A Brief Profi Le\u201d. Available online: https:\/\/www.wald-mv.de\/Unser-Wald\/Wald%E2%80%93in%E2%80%93Zahlen\/?id=18071&processor=veroeff."},{"key":"ref_55","unstructured":"FAO (2021). The Fao Action Plan on Antimicrobial Resistance 2021\u20132025, FAO."},{"key":"ref_56","first-page":"4","article-title":"A Matter of Taste\u2014Wild Game Meat, the Consumption Thereof, Is Important in Germany\u2014and Should Be Worldwide","volume":"3","author":"Damm","year":"2021","journal-title":"Conserv. Frontlines"},{"key":"ref_57","doi-asserted-by":"crossref","unstructured":"Baym, M., Kryazhimskiy, S., Lieberman, T.D., Chung, H., Desai, M.M., and Kishony, R. (2015). Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes. PLoS ONE, 10.","DOI":"10.1101\/013771"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"Spades: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and Samtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q.D., Wortman, J., and Young, S.K. (2014). Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0112963"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"Checkm: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","article-title":"Open-Access Bacterial Population Genomics: Bigsdb Software, the Pubmlst.Org Website and Their Applications [Version 1; Peer Review: 2 Approved]","volume":"3","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"Vfdb 2019: A Comparative Pathogenomic Platform with an Interactive Web Interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic. Acids Res."},{"key":"ref_65","doi-asserted-by":"crossref","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":"ref_66","doi-asserted-by":"crossref","first-page":"D737","DOI":"10.1093\/nar\/gkt1252","article-title":"Bacmet: Antibacterial Biocide and Metal Resistance Genes Database","volume":"42","author":"Pal","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_67","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":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e00095-16","DOI":"10.1128\/mSystems.00095-16","article-title":"Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition","volume":"1","author":"Knudsen","year":"2016","journal-title":"Msystems"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"D574","DOI":"10.1093\/nar\/gkw1009","article-title":"Megares: An Antimicrobial Resistance Database for High Throughput Sequencing","volume":"45","author":"Lakin","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkz1010","article-title":"Megares 2.0: A Database for Classification of Antimicrobial Drug, Biocide and Metal Resistance Determinants in Metagenomic Sequence Data","volume":"48","author":"Doster","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1403","DOI":"10.1111\/1755-0998.12399","article-title":"Metaxa2: Improved Identification and Taxonomic Classification of Small and Large Subunit Rrna in Metagenomic Data","volume":"15","author":"Hartmann","year":"2015","journal-title":"Mol. Ecol. Resour."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2490","DOI":"10.1038\/ismej.2015.59","article-title":"Metagenomic and Network Analysis Reveal Wide Distribution and Co-Occurrence of Environmental Antibiotic Resistance Genes","volume":"9","author":"Li","year":"2015","journal-title":"ISME J."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Clausen, P.T.L.C., Aarestrup, F.M., and Lund, O. (2018). Rapid and Precise Alignment of Raw Reads against Redundant Databases with Kma. 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