{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T17:54:15Z","timestamp":1791914055490,"version":"4.3.4"},"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fleming Fund, SeqAfrica project","award":["FF RGR2 FF25"],"award-info":[{"award-number":["FF RGR2 FF25"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:sec id=\"sec001\">\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>\n                      Antimicrobial resistance (AMR) is a growing concern within the One Health framework. This study characterized AMR in\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      and\n                      <jats:italic>Klebsiella<\/jats:italic>\n                      spp. isolated from livestock fecal samples across commercial and communal farms in Namibia.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec002\">\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>About 140 fecal samples were collected from cattle, sheep, and chickens on farms in Namibia. Isolates were identified using the VITEK\u00ae 2 system and MALDI-ToF mass spectrometry. Antimicrobial susceptibility testing was performed using the Kirby\u2013Bauer disc diffusion method against nine antibiotics. Genomic DNA was extracted and subjected to whole-genome sequencing (WGS) using Illumina NextSeq 2000 platform.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec003\">\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      AMR genes were identified using ResFinder and Abricate, plasmid-associated replicons using plasmid analysis tools, and virulence-associated genes using VirulenceFinder. Phenotypic analyses showed resistance to \u03b2-lactams, tetracyclines, aminoglycosides, and fluoroquinolones among the tested isolates. WGS identified diverse resistance determinants and sequence types, including\n                      <jats:italic>E. coli<\/jats:italic>\n                      ST101 and ST1431,\n                      <jats:italic>K. oxytoca<\/jats:italic>\n                      ST2, and\n                      <jats:italic>K. pneumoniae<\/jats:italic>\n                      ST22. Multiple plasmid replicons were detected; however, their presence alone does not establish that individual resistance genes were plasmid-borne or that horizontal gene transfer occurred.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec id=\"sec004\">\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study provides the first genomic evidence of livestock-associated AMR in Namibia, identifying resistance determinants and multidrug-resistant\n                      <jats:italic>E. coli<\/jats:italic>\n                      and\n                      <jats:italic>Klebsiella spp.<\/jats:italic>\n                      in the sampled livestock population. The findings provide baseline genomic data for AMR surveillance and support strengthened antimicrobial stewardship and One Health monitoring. The concurrent detection of chromosomal resistance-associated mutations and diverse plasmid replicons illustrates the complexity of resistance mechanisms, although the present short-read data do not establish the direct physical linkage of individual ARGs to plasmids. These findings highlight the need for coordinated surveillance across animal, human, and environmental health sectors in Namibia.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1371\/journal.pone.0359106","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T17:37:36Z","timestamp":1791913056000},"page":"e0359106","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Phenotypic and genomic characterization of antimicrobial resistance in Escherichia coli and Klebsiella spp. from livestock in Namibia"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-5205-7225","authenticated-orcid":true,"given":"Loide N.","family":"Nangolo","sequence":"first","affiliation":[{"name":"Natural Resources and Applied Sciences, Namibia University of Science and Technology","place":["Windhoek, Namibia"],"department":["Department of 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FastQC: a quality control tool for high throughput sequence data. Babraham Institute, Cambridge, United Kingdom [Internet]. 2010."},{"issue":"15","key":"pone.0359106.ref011","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"issue":"5","key":"pone.0359106.ref012","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":"A Bankevich","year":"2012","journal-title":"J Comput Biol"},{"issue":"8","key":"pone.0359106.ref013","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: quality assessment tool for genome assemblies","volume":"29","author":"A Gurevich","year":"2013","journal-title":"Bioinformatics"},{"issue":"8","key":"pone.0359106.ref014","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"J Robertson","year":"2018","journal-title":"Microb Genom"},{"key":"pone.0359106.ref015","author":"T Seemann","year":"2015"},{"issue":"3","key":"pone.0359106.ref016","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gku1196","article-title":"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins","volume":"43","author":"NJ Croucher","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pone.0359106.ref017","article-title":"SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments","volume":"2","author":"AJ Page","year":"2016","journal-title":"Microb Genom"},{"issue":"2","key":"pone.0359106.ref018","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/molbev\/msz240","article-title":"Treeio: An R package for phylogenetic tree input and output with richly annotated and associated data","volume":"37","author":"L-G Wang","year":"2020","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pone.0359106.ref019","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: An r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"G Yu","year":"2016","journal-title":"Methods Ecol Evol"},{"issue":"14","key":"pone.0359106.ref020","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"T Seemann","year":"2014","journal-title":"Bioinformatics"},{"issue":"22","key":"pone.0359106.ref021","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"AJ Page","year":"2015","journal-title":"Bioinformatics"},{"issue":"1","key":"pone.0359106.ref022","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"issue":"1","key":"pone.0359106.ref023","doi-asserted-by":"crossref","first-page":"15108","DOI":"10.1038\/s41598-021-93970-7","article-title":"Genomic evolution of antimicrobial resistance in Escherichia coli","volume":"11","author":"P Leekitcharoenphon","year":"2021","journal-title":"Sci Rep"},{"issue":"11","key":"pone.0359106.ref024","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.3390\/antibiotics11111535","article-title":"Mini-review: Antibiotic-resistant escherichia coli from farm animal-associated sources","volume":"11","author":"C Xu","year":"2022","journal-title":"Antibiotics (Basel)"},{"key":"pone.0359106.ref025","article-title":"Antibiotic resistance in the food chain: A developing country-perspective","author":"LL Founou","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"5","key":"pone.0359106.ref026","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00549-23","article-title":"Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales","volume":"11","author":"OO Ikhimiukor","year":"2023","journal-title":"Microbiol Spectr"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0359106","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T17:37:40Z","timestamp":1791913060000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0359106"}},"subtitle":[],"editor":[{"given":"Md. 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