{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T17:05:07Z","timestamp":1785431107683,"version":"3.56.0"},"reference-count":187,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T00:00:00Z","timestamp":1780012800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    The emergence of antimicrobial-resistant and livestock-associated\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    represents a serious public health concern, necessitating comprehensive genomic investigations. Bacterial strains were isolated from different domestic animals located in KwaZulu-Natal and Eastern Cape Provinces in South Africa. Antibiotic susceptibility testing was performed using the Kirby\u2013Bauer disk diffusion method. Biofilm formation and hypermucoviscosity were investigated. Genomic DNA of the isolates was extracted, and whole-genome sequencing was performed using an Illumina MiSeq platform. Here, we report the isolation, molecular detection, virulence and antimicrobial resistance (AMR) determinants, as well as phylogenetic analyses of 16\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    strains using whole-genome sequence (WGS) analysis. Ten\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    strains, three\n                    <jats:italic>Klebsiella variicola<\/jats:italic>\n                    and three\n                    <jats:italic>Klebsiella aerogenes<\/jats:italic>\n                    were detected. The assembled contigs were analyzed for AMR and virulence genes, K and O types, and multi-locus sequence type (MLST). To compare the sequenced strains to other previously sequenced\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    species, a distance-based phylogeny method was used to confirm the taxonomic designation of the 16\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    genomes in an extended context of 169 genomes from the different\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    species. Genomic analysis identified several antibiotic resistance genes conferring resistance to beta-lactams (\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>SHV-11-like<\/jats:sub>\n                    <jats:italic>, bla<\/jats:italic>\n                    <jats:sub>SHV-40\/56\/79\/85\/89-like<\/jats:sub>\n                    <jats:italic>, bla<\/jats:italic>\n                    <jats:sub>SHV-110\/81-like<\/jats:sub>\n                    <jats:italic>, bla<\/jats:italic>\n                    <jats:sub>SHV-119<\/jats:sub>\n                    <jats:italic>, bla<\/jats:italic>\n                    <jats:sub>SHV-164\/59-like<\/jats:sub>\n                    , and\n                    <jats:italic>bla<\/jats:italic>\n                    <jats:sub>LEN-16-like<\/jats:sub>\n                    ), quinolones (\n                    <jats:italic>oqxA, oqxA-like, oqxB<\/jats:italic>\n                    ,\n                    <jats:italic>oqxB<\/jats:italic>\n                    -like), tetracyclines [\n                    <jats:italic>tet(A)<\/jats:italic>\n                    ], and fosfomycin (\n                    <jats:italic>fosA<\/jats:italic>\n                    -like). All isolates harbored genes conferring resistance to at least three antibiotic classes, thus classifying them as multidrug-resistant (MDR). Nine sequence types (ST-76, ST-128, ST-494, ST-617, ST-2465, ST-4039, ST-5470, ST-5478, and ST-5497) were identified using the MLST\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    scheme in the\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    collection. The latter three STs are being reported for the first time in the current study. MLST analysis revealed that the three\n                    <jats:italic>K. variicola<\/jats:italic>\n                    isolates belonged to ST-696 using the MLST\n                    <jats:italic>K. variicola<\/jats:italic>\n                    scheme. Although no hypervirulent strains were identified, the 16\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    isolates were\n                    <jats:italic>in vitro<\/jats:italic>\n                    biofilm producers and contained one to five intact prophages. The detection of MDR\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    highlights the critical significance of genomic surveillance in monitoring the dissemination of antimicrobial resistance in livestock pathogens and within the food chain. The report of novel sequence types (ST-5470, ST-5478, and ST-5497) in\n                    <jats:italic>K. pneumoniae<\/jats:italic>\n                    present new allelic profiles, indicating the ongoing evolution and diversification within the species.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2026.1752622","type":"journal-article","created":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T10:32:52Z","timestamp":1780050772000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Phenotypic and genome-based characterization of Klebsiella species from different One Health sources in South Africa reveals the presence of multidrug-resistant isolates"],"prefix":"10.3389","volume":"17","author":[{"given":"Mohamed E.","family":"El Zowalaty","sequence":"first","affiliation":[{"name":"School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bibek","family":"Lamichhane","sequence":"additional","affiliation":[{"name":"Department of Veterinary Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky","place":["Lexington, KY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Falgenhauer","sequence":"additional","affiliation":[{"name":"Hessian State Office for Health and Care, Department II.1 Health and Infection Protection, State Laboratory for Human Medicine","place":["Dillenburg, Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Yeop","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, College of Veterinary Medicine, Konkuk University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel C.","family":"Eze","sequence":"additional","affiliation":[{"name":"School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal","place":["Durban, South Africa"]},{"name":"Department of Chemistry, Louisiana State University","place":["Baton Rouge, LA, United States"]},{"name":"Department of Medical Laboratory Science, College of Health Sciences, Idaho State University","place":["Pocatello, ID, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean G.","family":"Young","sequence":"additional","affiliation":[{"name":"Department of Health Data Science and Biostatistics, Peter O\u2019Donnell Jr. School of Public Health, The University of Texas Southwestern Medical Center","place":["Dallas, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asmaa","family":"Saleh","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University","place":["Riyadh, Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen","family":"Forsythe","sequence":"additional","affiliation":[{"name":"Foodmicrobe.com Ltd.","place":["Nottingham, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver T.","family":"Zishiri","sequence":"additional","affiliation":[{"name":"Discipline of Genetics, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal","place":["Durban, South Africa"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dong-Hun","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, College of Veterinary Medicine, Konkuk University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ji-Yeon","family":"Hyeon","sequence":"additional","affiliation":[{"name":"Department of Veterinary Medicine, College of Veterinary Medicine, Konkuk University","place":["Seoul, Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yosra A.","family":"Helmy","sequence":"additional","affiliation":[{"name":"Department of Veterinary Science, Martin-Gatton College of Agriculture, Food and Environment, University of Kentucky","place":["Lexington, KY, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,29]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1016\/j.psj.2025.104855","article-title":"Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both no-antibiotics-ever (NAE) and conventional broiler complexes","volume":"104","author":"Adhikari","year":"2025","journal-title":"Poult. 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Microbiol."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1111\/zph.12612","article-title":"Carriage of carbapenemase-and extended-spectrum cephalosporinase-producing Escherichia coli and Klebsiella pneumoniae in humans and livestock in rural Cambodia; gender and age differences and detection of blaOXA-48 in humans","volume":"66","author":"Atterby","year":"2019","journal-title":"Zoonoses Public Health"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"181","DOI":"10.3390\/membranes10080181","article-title":"Polymyxins and bacterial membranes: A review of antibacterial activity and mechanisms of resistance","volume":"10","author":"Ayoub","year":"2020","journal-title":"Membranes"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1017\/s0195941700062603","article-title":"Habitat association of Klebsiella species","volume":"6","author":"Bagley","year":"1985","journal-title":"Infect. Control."},{"key":"ref10","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1007\/s00284-021-02472-2","article-title":"Genome-wide identification and analysis of chromosomally integrated putative prophages associated with clinical Klebsiella pneumoniae strains","volume":"78","author":"Baliga","year":"2021","journal-title":"Curr. Microbiol."},{"key":"ref11","doi-asserted-by":"publisher","first-page":"e0220484","DOI":"10.1371\/journal.pone.0220484","article-title":"International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda","volume":"15","author":"Ball","year":"2020","journal-title":"PLoS One"},{"key":"ref12","doi-asserted-by":"publisher","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":"ref13","doi-asserted-by":"publisher","first-page":"10610","DOI":"10.1038\/s41598-019-46998-9","article-title":"Molecular epidemiology of Klebsiella variicola obtained from different sources","volume":"9","author":"Barrios-Camacho","year":"2019","journal-title":"Sci. Rep."},{"key":"ref190","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-25679-0","article-title":"Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae","author":"Bharatham","year":"2021","journal-title":"Nat. Commun."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1812","DOI":"10.3201\/eid2011.140206","article-title":"Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups","volume":"20","author":"Bialek-Davenet","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e0191958","DOI":"10.1371\/journal.pone.0191958","article-title":"Emergence of Klebsiella pneumoniae subspecies pneumoniae as a cause of septicaemia in pigs in England","volume":"13","author":"Bidewell","year":"2018","journal-title":"PLoS One"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e04210-23","DOI":"10.1128\/spectrum.04210-23","article-title":"Klebsiella pneumoniae arms itself: poultry food chain drives spread and evolution of mcr-1.26-IncX4 plasmids","volume":"12","author":"Binsker","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"275","DOI":"10.3969\/j.issn.1673-7555.2013.26.224","article-title":"An investigation of food poisoning caused by Klebsiella pneumoniae","volume":"8","author":"Bi","year":"2013","journal-title":"Chin. Pract. Med."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"e000369","DOI":"10.1099\/mgen.0.000369","article-title":"Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae","volume":"6","author":"Bleriot","year":"2020","journal-title":"Microb. Genom."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"110049","DOI":"10.1016\/j.ijfoodmicro.2022.110049","article-title":"Detection of carbapenemase-and ESBL-producing Klebsiella pneumoniae from bovine bulk milk and comparison with clinical human isolates in Italy","volume":"387","author":"Bonardi","year":"2023","journal-title":"Int. J. 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