{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T02:06:17Z","timestamp":1774922777953,"version":"3.50.1"},"reference-count":77,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T00:00:00Z","timestamp":1712880000000},"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>The rise of antibiotic resistance in the food chain is influenced by the use of antimicrobial agents, such as antibiotics, metals, and biocides, throughout the entire farm-to-fork continuum. Besides, non-clinical reservoirs potentially contribute to the transmission of critical pathogens such as multidrug-resistant (MDR) <jats:italic>Klebsiella pneumoniae<\/jats:italic>. However, limited knowledge exists about the population structure and genomic diversity of <jats:italic>K. pneumoniae<\/jats:italic> circulating in conventional poultry production. We conducted a comprehensive characterization of <jats:italic>K. pneumoniae<\/jats:italic> across the whole chicken production chain (7 farms; 14 flocks + environment + meat, 56 samples; 2019\u20132022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features of <jats:italic>K. pneumoniae<\/jats:italic> were characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive for <jats:italic>K. pneumoniae<\/jats:italic> with a significant increase (<jats:italic>p<\/jats:italic>\u2009&amp;lt;\u20090.05) from early (<jats:italic>n<\/jats:italic>\u2009=\u20091\/14) to pre-slaughter (<jats:italic>n<\/jats:italic>\u2009=\u200911\/14) stages, most (<jats:italic>n<\/jats:italic>\u2009=\u20096\/7) persisting in chicken meat batches. Colistin-resistant <jats:italic>K. pneumoniae<\/jats:italic> rates were low (4%-<jats:italic>n<\/jats:italic>\u2009=\u20091\/24 positive samples), while most samples carried MDR strains (67%-<jats:italic>n<\/jats:italic>\u2009=\u200916\/24) and copper-tolerant isolates (63%-<jats:italic>n<\/jats:italic>\u2009=\u200915\/24, with <jats:italic>sil<\/jats:italic> and <jats:italic>pco<\/jats:italic> gene clusters; MIC<jats:sub>CuSO4<\/jats:sub>\u2009\u2265\u200916\u2009mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity against <jats:italic>K. pneumoniae<\/jats:italic> (MIC\/MBC range\u2009=\u20094\u201364\u2009mg\/L) from representative strains independently of the presence or absence of genes linked to QACs tolerance. A polyclonal <jats:italic>K. pneumoniae<\/jats:italic> population, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chicken\u2019s lifecycle at the farm (ST29-KL124, ST11-KL106, ST15-KL19, ST1228-KL38), until the meat (ST1-KL19, ST11-KL111, ST6405-KL109, and ST6406-CG147-KL111), or over years (ST631-49 KL109, ST6651-KL107, ST6406-CG147-KL111). Notably, some lineages were identical to those from human clinical isolates. WGS also revealed F-type multireplicon plasmids carrying <jats:italic>sil<\/jats:italic>\u2009+\u2009<jats:italic>pco<\/jats:italic> (copper) co-located with <jats:italic>qacE<\/jats:italic>\u03941\u2009\u00b1\u2009<jats:italic>qacF<\/jats:italic> (QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverse <jats:italic>K. pneumoniae<\/jats:italic> clones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencing <jats:italic>K. pneumoniae<\/jats:italic> persistence and dissemination within poultry production, contributing to improved food safety risk management. This study underscores the significance of understanding the interplay between antimicrobial control strategies and non-clinical sources to effectively address the spread of antimicrobial resistance.<\/jats:p>","DOI":"10.3389\/fmicb.2024.1365011","type":"journal-article","created":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T04:13:55Z","timestamp":1712895235000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":17,"title":["Decoding Klebsiella pneumoniae in poultry chain: unveiling genetic landscape, antibiotic resistance, and biocide tolerance in non-clinical reservoirs"],"prefix":"10.3389","volume":"15","author":[{"given":"Joana","family":"Mour\u00e3o","sequence":"first","affiliation":[]},{"given":"Mafalda","family":"Magalh\u00e3es","sequence":"additional","affiliation":[]},{"given":"Marisa","family":"Ribeiro-Almeida","sequence":"additional","affiliation":[]},{"given":"Andreia","family":"Rebelo","sequence":"additional","affiliation":[]},{"given":"Carla","family":"Novais","sequence":"additional","affiliation":[]},{"given":"Lu\u00edsa","family":"Peixe","sequence":"additional","affiliation":[]},{"given":"\u00c2ngela","family":"Novais","sequence":"additional","affiliation":[]},{"given":"Patr\u00edcia","family":"Antunes","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2024,4,12]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/j.jhin.2012.03.003","article-title":"Klebsiella pneumoniae susceptibility to biocides and its association with cepA, qac\u0394E and qacE efflux pump genes and antibiotic resistance","volume":"81","author":"Abuzaid","year":"2012","journal-title":"J. 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