{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T22:27:31Z","timestamp":1784240851796,"version":"3.55.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2022,12,15]],"date-time":"2022-12-15T00:00:00Z","timestamp":1671062400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The silent pandemic of antimicrobial resistance (AR) has been on the rise for the past decades. It is essential to determine the burden of AR in animal farms that spreads leading to human exposure. A total of 100 samples including soil, litter, animal excreta, and wastewater were collected from seven conventional and one organic farm in Egypt. The prevalence of extended-spectrum \u03b2-lactamase-producing Escherichia coli (ESBL-producing E. coli), fluoroquinolone-resistant E. coli, fluoroquinolone-resistant Salmonella, and vancomycin-resistant enterococci (VRE) was determined in studied farms. Conventional farms had a higher prevalence of antimicrobial-resistant bacteria than the organic farm (73.81%\u00a0vs. 18.75%, P\u00a0&amp;lt;\u00a0.001). In conventional farms 21.43% of samples yielded mixed isolates; however, in the organic farm, only single isolates of ESBL-producing E. coli were detected. The most prevalent ESBL-production gene was blaTEM (82.14%), followed by blaCTX-M (48.22%), and blaSHV (19.64%), either alone or in combination with another gene. The most prevalent fluoroquinolone-resistance genes were qnrS (82.69%) and qnrB (42.30%), either alone or in combination with another gene(s). A total of five VRE isolates harbored vanA gene (83.33%), none carried vanB gene, and one isolate was negative for both genes. The studied conventional livestock farms had significantly higher rates of serious AR threats than the organic farm.<\/jats:p>","DOI":"10.1093\/lambio\/ovac048","type":"journal-article","created":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T13:41:01Z","timestamp":1712583661000},"source":"Crossref","is-referenced-by-count":4,"title":["Prevalence of antimicrobial-resistant bacteria in conventional vs. organic livestock farms in Egypt: a cross-sectional comparative study"],"prefix":"10.1093","volume":"76","author":[{"given":"Nada","family":"ElSayed","sequence":"first","affiliation":[{"name":"Microbiology Department, High Institute of Public Health, Alexandria University , 165 El-Horreya Avenue 21646 , El-Hadara, Alexandria, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laila","family":"El-Attar","sequence":"additional","affiliation":[{"name":"Microbiology Department, High Institute of Public Health, Alexandria University , 165 El-Horreya Avenue 21646 , El-Hadara, Alexandria, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8260-0111","authenticated-orcid":false,"given":"Amira","family":"Amine","sequence":"additional","affiliation":[{"name":"Microbiology Department, High Institute of Public Health, Alexandria University , 165 El-Horreya Avenue 21646 , El-Hadara, Alexandria, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,12,15]]},"reference":[{"key":"2024040813405515700_bib1","first-page":"1","article-title":"Extended-spectrum \u03b2-lactamases and\/or carbapenemases-producing Enterobacteriaceae isolated from retail chicken meat in Zagazig, Egypt","volume":"10","author":"Abdallah","year":"2015","journal-title":"PLoS ONE"},{"key":"2024040813405515700_bib2","doi-asserted-by":"crossref","first-page":"18637","DOI":"10.1038\/s41598-020-75608-2","article-title":"High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh","volume":"10","author":"Ahmed","year":"2020","journal-title":"Sci Rep"},{"key":"2024040813405515700_bib3","first-page":"93","article-title":"Detection of vancomycin resistance in enterococci isolated from poultry","volume":"18","author":"Ahmed","year":"2020","journal-title":"Nat Sci"},{"key":"2024040813405515700_bib4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.11604\/pamj-oh.2020.1.3.22325","article-title":"Antimicrobial resistance among commensal enteric bacteria isolated from healthy cattle in Libya","volume":"1","author":"Almshawt","year":"2020","journal-title":"PAMJ One Health"},{"key":"2024040813405515700_bib5","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1111\/lam.13106","article-title":"Molecular characterization of virulence and antibiotic resistance genes among Salmonella serovars isolated from broilers in Egypt","volume":"68","author":"Ammar","year":"2018","journal-title":"Lett Appl Microbiol"},{"key":"2024040813405515700_bib14","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/S0140-6736(21)02724-0","article-title":"Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis","volume":"399","author":"Antimicrobial Resistance Collaborators","year":"2022","journal-title":"Lancet"},{"key":"2024040813405515700_bib6","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fmicb.2016.01020","article-title":"Surveillance of extended-spectrum beta-lactamase-producing Escherichia coli in dairy cattle farms in the Nile Delta, Egypt","volume":"7","author":"Braun","year":"2016","journal-title":"Front Microbiol"},{"key":"2024040813405515700_bib9","doi-asserted-by":"crossref","DOI":"10.15620\/cdc:82532","article-title":"Antibiotic resistance threats in the United States, 2019","author":"Centers for Disease Control and Prevention","year":"2019"},{"key":"2024040813405515700_bib10","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1099\/jmm.0.064428-0","article-title":"Development and evaluation of a multiplex PCR for eight plasmid-mediated quinolone-resistance determinants","volume":"62","author":"Ciesielczuk","year":"2013","journal-title":"J Med Microbiol"},{"key":"2024040813405515700_bib11","article-title":"Methods for dilution antimicrobial susceptibility tests for bacteria that grow aerobically","volume-title":"CLSI Standard M07","author":"CLSI-M07","year":"2018"},{"key":"2024040813405515700_bib12","article-title":"Performance standards for antimicrobial susceptibility testing (M100)","volume-title":"CLSI Standard M07","author":"CLSIM100","year":"2020"},{"key":"2024040813405515700_bib13","doi-asserted-by":"crossref","first-page":"1318","DOI":"10.1128\/AAC.33.8.1318","article-title":"Cross-resistance to fluoroquinolones in multiple antibiotic-resistant (Mar) Escherichia coli selected by tetracycline or chloramphenicol: decreased drug accumulation associated with membrane changes in addition to OmpF reduction","volume":"33","author":"Cohen","year":"1989","journal-title":"Antimicrob Agents Chemother"},{"key":"2024040813405515700_bib16","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1007\/s10661-014-4218-3","article-title":"Veterinary antibiotic resistance, residues, and ecological risks in environmental samples obtained from poultry farms, Egypt","volume":"187","author":"Dahshan","year":"2015","journal-title":"Environ Monit Assess"},{"key":"2024040813405515700_bib17","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1016\/S1473-3099(19)30273-7","article-title":"Extended-spectrum \u03b2-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and Scotland: an epidemiological surveillance and typing study\u2019","volume":"19","author":"Day","year":"2019","journal-title":"Lancet Infect Dis"},{"key":"2024040813405515700_bib18","article-title":"Reflection paper on the use of macrolides, lincosamides and streptogramins (MLS) in food-producing animals in the European Union: development of resistance and impact on human and animal health Committee for Medicinal Products for Veterinary Use (CVMP)","author":"European Medicines Agency","year":"2011"},{"key":"2024040813405515700_bib20","doi-asserted-by":"crossref","first-page":"571958","DOI":"10.3389\/fmicb.2020.571958","article-title":"Complete genomic analysis of VRE from a cattle feedlot: focus on 2 antibiotic resistance","volume":"11","author":"Foka","year":"2020","journal-title":"Front Microbiol"},{"key":"2024040813405515700_bib21","article-title":"Principles of organic production: livestock and livestock products","author":"Food and Agriculture Organization","year":"2001"},{"key":"2024040813405515700_bib22","doi-asserted-by":"crossref","first-page":"9001","DOI":"10.3168\/jds.2016-11134","article-title":"Prevalence and risk factors for extended-spectrum \u03b2-lactamase- and AmpC-producing Escherichia coli in dairy farms","volume":"99","author":"Gonggrijp","year":"2016","journal-title":"J Dairy Sci"},{"key":"2024040813405515700_bib23","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1111\/j.1469-0691.2011.03497.x","article-title":"Dutch patients, retail chicken meat and poultry share the same ESBL genes, plasmids and strains","volume":"17","author":"Hall","year":"2011","journal-title":"Clin Microbiol Infect"},{"key":"2024040813405515700_bib24","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1111\/j.1469-0691.2012.03829.x","article-title":"Enterococci of animal origin and their significance for public health","volume":"18","author":"Hammerum","year":"2012","journal-title":"Clin Microbiol Infect"},{"key":"2024040813405515700_bib25","volume-title":"Kirby-Bauer Disk Diffusion Susceptibility Test Protocol","author":"Hudzicki","year":"2016"},{"key":"2024040813405515700_bib26","volume-title":"The Annual Poultry Guide: (Poultry: Middle East and South Africa)","author":"Ibrahim","year":"2019"},{"key":"2024040813405515700_bib27","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.mimet.2014.04.009","article-title":"Single-nucleotide polymorphism PCR for the detection of Mycoplasma pneumoniae and determination of macrolide resistance in respiratory samples","volume":"102","author":"Ji","year":"2014","journal-title":"J Microbiol Methods"},{"key":"2024040813405515700_bib28","first-page":"43","article-title":"Molecular characterisation of extended-spectrum \u03b2-lactamase-producing Escherichia coli and Salmonella isolated from poultry and poultry products in Egypt","volume":"24","author":"Kamel","year":"2021","journal-title":"Bulg Journal Vet Med"},{"key":"2024040813405515700_bib29","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13756-020-0697-x","article-title":"Antimicrobial use and resistance in food-producing animals and the environment: an African perspective","volume":"9","author":"Kimera","year":"2020","journal-title":"Antimicrob Resist Infect Cont"},{"key":"2024040813405515700_bib30","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1007\/s11694-016-9355-7","article-title":"Occurrence, genetic characterization and antimicrobial resistance of extended spectrum \u03b2-lactamase producing Escherichia coli isolated from S\u00fcrk samples, a traditional Turkish cheese","volume":"10","author":"K\u00fcrekci","year":"2016","journal-title":"J Food Measur Character"},{"key":"2024040813405515700_bib31","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1177\/003335491212700103","article-title":"A review of antibiotic use in food animals: perspective, policy, and potential","volume":"127","author":"Landers","year":"2012","journal-title":"Pub Health Rep"},{"key":"2024040813405515700_bib32","article-title":"Feeding details, feeding list","author":"Mazraaty","year":"2021"},{"key":"2024040813405515700_bib33","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2019\/4318306","article-title":"Antimicrobial resistance factors of extended-spectrum beta-lactamases producing Escherichia coli and Klebsiella pneumoniae isolated from cattle farms and raw beef in North-West Province, South Africa","volume":"2019","author":"Montso","year":"2019","journal-title":"Biomed Res Int"},{"key":"2024040813405515700_bib34","doi-asserted-by":"crossref","first-page":"104755","DOI":"10.1016\/j.prevetmed.2019.104755","article-title":"Differences in antimicrobial resistance of commensal Escherichia coli isolated from caecal contents of organically and conventionally raised broilers in Austria, 2010\u20132014 and 2016","volume":"171","author":"Much","year":"2019","journal-title":"Prev Vet Med"},{"key":"2024040813405515700_bib35","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1016\/j.ijantimicag.2019.03.001","article-title":"Comparing the selective and co-selective effects of different antimicrobials in bacterial communities","volume":"53","author":"Murray","year":"2019","journal-title":"Int J Antimicrob Agents"},{"key":"2024040813405515700_bib37","doi-asserted-by":"crossref","first-page":"5900","DOI":"10.3382\/ps\/pez337","article-title":"Plasmid-mediated quinolone resistance in Escherichia coli isolates from commercial broiler chickens and selection of fluoroquinolone-resistant mutants","volume":"98","author":"Nishikawa","year":"2019","journal-title":"Poult Sci"},{"key":"2024040813405515700_bib39","doi-asserted-by":"crossref","first-page":"9692","DOI":"10.3390\/ijerph120809692","article-title":"Prevalence of antimicrobial resistant and virulent Salmonella spp. in treated effluent and receiving aquatic milieu of wastewater treatment plants in Durban, South Africa","volume":"12","author":"Odjadjare","year":"2015","journal-title":"Int J Environ Res Pub Health"},{"key":"2024040813405515700_bib40","doi-asserted-by":"crossref","first-page":"418","DOI":"10.14202\/vetworld.2019.418-423","article-title":"Multidrug-resistant enterobacteria colonize commercial day-old broiler chicks in Nigeria","volume":"12","author":"Okorafor","year":"2019","journal-title":"Veter World"},{"key":"2024040813405515700_bib41","doi-asserted-by":"crossref","first-page":"108391","DOI":"10.1016\/j.ijfoodmicro.2019.108391","article-title":"Antibiotic-resistant commensal Escherichia coli are less frequently isolated from poultry raised using non-conventional management systems than from conventional broiler","volume":"214","author":"Pesciaroli","year":"2020","journal-title":"Int J Food Microbiol"},{"key":"2024040813405515700_bib42","doi-asserted-by":"crossref","first-page":"e0238939","DOI":"10.1371\/journal.pone.0238939","article-title":"Association between the use of colistin for short-term treatment of Gram-negative bacterial infections and the emergence of colistin-resistant Enterobacteriaceae in swine from selected swine farms in Thailand","volume":"15","author":"Poolperm","year":"2020","journal-title":"PLoS ONE"},{"key":"2024040813405515700_bib43","first-page":"1687","article-title":"Antibiotic resistance in faecal bacteria (Escherichia coli, Enterococcus spp.) in feral pigeons","volume":"109","author":"Radimersky","year":"2010","journal-title":"J Appl Microbiol"},{"key":"2024040813405515700_bib44","first-page":"587","article-title":"Streptogramins for the treatment of infections caused by Gram-positive pathogens","volume":"18","author":"Reissier","year":"2020","journal-title":"Expert Rev Anti Infect Ther"},{"key":"2024040813405515700_bib45","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1093\/jac\/dkl046","article-title":"In vitro activity of temocillin against extended spectrum \u03b2-lactamase-producing Escherichia coli","volume":"57","author":"Rodriguez-Villalobos","year":"2006","journal-title":"J Antimicrob Chemother"},{"key":"2024040813405515700_bib46","first-page":"886","article-title":"Phenotypic characterization of extended-spectrum-beta-lactamase producing E. coli from healthy individuals, patients, sewage sludge, cattle, chickens and raw meat","volume":"33","author":"Saleem","year":"2017","journal-title":"Pakistan J Med Sci"},{"key":"2024040813405515700_bib47","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.scitotenv.2013.12.005","article-title":"Lower prevalence of antibiotic-resistant Salmonella on large-scale U.S. conventional poultry farms that transitioned to organic practices","volume":"476-477","author":"Sapkota","year":"2014","journal-title":"Sci Total Environ"},{"key":"2024040813405515700_bib48","volume-title":"Wastewater Sampling","author":"Simpson","year":"2017"},{"key":"2024040813405515700_bib50","volume-title":"Bailey & Scott's Diagnostic Microbiology","author":"Tille","year":"2017","edition":"14th edn"},{"key":"2024040813405515700_bib51","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1159\/000361011","article-title":"High prevalence of cross-resistance to aminoglycosides in fluoroquinolone-resistant Escherichia coli clinical isolates","volume":"59","author":"Tsukamoto","year":"2014","journal-title":"Chemotherapy"},{"key":"2024040813405515700_bib52","doi-asserted-by":"crossref","first-page":"5649","DOI":"10.1073\/pnas.1503141112","article-title":"Global trends in antimicrobial use in food animals","volume":"112","author":"Van\u00a0Boeckel","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2024040813405515700_bib53","doi-asserted-by":"crossref","first-page":"1278","DOI":"10.1093\/jac\/dkr084","article-title":"International collaborative study on the occurrence of plasmid-mediated quinolone resistance in Salmonella enterica and Escherichia coli isolated from animals, humans, food and the environment in 13 European countries","volume":"66","author":"Veldman","year":"2011","journal-title":"J Antimicrob Chemother"},{"key":"2024040813405515700_bib54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/AEM.01682-17","article-title":"Impact of \u201craised without antibiotics\u201d beef cattle production practices on occurrences of antimicrobial resistance","volume":"83","author":"Vikram","year":"2017","journal-title":"Appl Environ Microbiol"},{"key":"2024040813405515700_bib55","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0147363","article-title":"Carbapenem-resistant bacteria recovered from faeces of dairy cattle in the high plains region of the USA","volume":"11","author":"Webb","year":"2016","journal-title":"PLoS ONE"},{"key":"2024040813405515700_bib56","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/nprot.2007.521","article-title":"Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances","volume":"3","author":"Wiegand","year":"2008","journal-title":"Nat Protoc"},{"key":"2024040813405515700_bib57","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/microorganisms8020261","article-title":"Phenotypic and genotypic traits of vancomycin-resistant enterococci from healthy food-producing animals","volume":"8","author":"Wist","year":"2020","journal-title":"Microorganisms"},{"key":"2024040813405515700_bib58","article-title":"Antimicrobial resistance in the food chain","author":"World Health Organization","year":"2017"},{"key":"2024040813405515700_bib59","article-title":"Prioritization of pathogens to guide discovery, research and development of new antibiotics for drug-resistant bacterial infections, including tuberculosis","author":"World Health Organization","year":"2017"},{"key":"2024040813405515700_bib60","doi-asserted-by":"crossref","first-page":"e0185326","DOI":"10.1371\/journal.pone.0185326","article-title":"Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China","volume":"12","author":"Yassin","year":"2017","journal-title":"PLoS ONE"},{"key":"2024040813405515700_bib61","first-page":"1","article-title":"Learning from agriculture : understanding low-dose antimicrobials as drivers of resistome expansion","volume":"5","author":"You","year":"2014","journal-title":"Front Microbiol"},{"key":"2024040813405515700_bib62","doi-asserted-by":"crossref","first-page":"12582","DOI":"10.3390\/ijerph111212582","article-title":"Multiresistant bacteria isolated from chicken meat in Austria","volume":"11","author":"Zarfel","year":"2014","journal-title":"Int J Environ Res Public Health"},{"key":"2024040813405515700_bib63","doi-asserted-by":"crossref","first-page":"3435","DOI":"10.1073\/pnas.1222743110","article-title":"Diverse and abundant antibiotic resistance genes in Chinese swine farms","volume":"110","author":"Zhu","year":"2013","journal-title":"Proc Natl Acad Sci"}],"container-title":["Letters in Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/lambio\/article-pdf\/76\/1\/ovac048\/55388651\/ovac048.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/lambio\/article-pdf\/76\/1\/ovac048\/55388651\/ovac048.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T13:41:43Z","timestamp":1712583703000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/lambio\/article\/doi\/10.1093\/lambio\/ovac048\/6912250"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,15]]},"references-count":56,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1,23]]}},"URL":"https:\/\/doi.org\/10.1093\/lambio\/ovac048","relation":{},"ISSN":["1472-765X"],"issn-type":[{"value":"1472-765X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,1]]},"published":{"date-parts":[[2022,12,15]]},"article-number":"ovac048"}}