{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T09:46:42Z","timestamp":1784800002006,"version":"3.55.0"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T00:00:00Z","timestamp":1568073600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T00:00:00Z","timestamp":1568073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"French ministry of agriculture and food EcoAntibio plan"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>To guarantee food safety, a better deciphering of ecology and adaptation strategies of bacterial pathogens such as <jats:italic>Salmonella<\/jats:italic> in food environments is crucial. The role of food processing conditions such as cleaning and disinfection procedures on antimicrobial resistance emergence should especially be investigated. In this work, the prevalence and antimicrobial resistance of <jats:italic>Salmonella<\/jats:italic> and the microbial ecology of associated surfaces communities were investigated in a pig slaughterhouse before and after cleaning and disinfection procedures. <jats:italic>Salmonella<\/jats:italic> were detected in 67% of samples and isolates characterization revealed the presence of 15 PFGE-patterns belonging to five serotypes: S.4,5,12:i:-, Rissen, Typhimurium, Infantis and Derby. Resistance to ampicillin, sulfamethoxazole, tetracycline and\/or chloramphenicol was detected depending on serotypes. 16S rRNA-based bacterial diversity analyses showed that <jats:italic>Salmonella<\/jats:italic> surface associated communities were highly dominated by the <jats:italic>Moraxellaceae<\/jats:italic> family with a clear site-specific composition suggesting a persistent colonization of the pig slaughterhouse. Cleaning and disinfection procedures did not lead to a modification of <jats:italic>Salmonella<\/jats:italic> susceptibility to antimicrobials in this short-term study but they tended to significantly reduce bacterial diversity and favored some genera such as <jats:italic>Rothia<\/jats:italic> and <jats:italic>Psychrobacter<\/jats:italic>. Such data participate to the construction of a comprehensive view of <jats:italic>Salmonella<\/jats:italic> ecology and antimicrobial resistance emergence in food environments in relation with cleaning and disinfection procedures.<\/jats:p>","DOI":"10.1038\/s41598-019-49464-8","type":"journal-article","created":{"date-parts":[[2019,9,10]],"date-time":"2019-09-10T10:04:12Z","timestamp":1568109852000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Impact of cleaning and disinfection procedures on microbial ecology and Salmonella antimicrobial resistance in a pig slaughterhouse"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7221-8944","authenticated-orcid":false,"given":"Arnaud","family":"Bridier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia","family":"Le Grandois","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie-H\u00e9l\u00e8ne","family":"Moreau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charleyne","family":"Pr\u00e9nom","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Le Roux","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carole","family":"Feurer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5721-8068","authenticated-orcid":false,"given":"Christophe","family":"Soumet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,9,10]]},"reference":[{"issue":"12","key":"49464_CR1","first-page":"228","volume":"15","author":"EFSA & ECDC","year":"2017","unstructured":"EFSA & ECDC. The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016. EFSA Journal 15(12), 228 (2017).","journal-title":"EFSA Journal"},{"key":"49464_CR2","unstructured":"Van Cauteren, D. et al. Estimation de la morbidit\u00e9 et de la mortalit\u00e9 li\u00e9es aux infections d\u2019origine alimentaire en France m\u00e9tropolitaine, 2008\u20132013. Bull. Epid\u00e9miol. Hebd. 1, 2\u201310, http:\/\/invs.santepubliquefrance.fr\/beh\/2018\/1\/2018_1_1.html (2018)."},{"key":"49464_CR3","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1017\/S0950268814001903","volume":"143","author":"LV De Knegt","year":"2015","unstructured":"De Knegt, L. V., Pires, S. M. & Hald, T. Attributing foodborne salmonellosis in humans to animal reservoirs in the European Union using a multi-country stochastic model. Epidemiol Infect 143, 1175\u20131186, https:\/\/doi.org\/10.1017\/S0950268814001903 (2015).","journal-title":"Epidemiol Infect"},{"key":"49464_CR4","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.fm.2017.03.017","volume":"71","author":"M Ronnqvist","year":"2018","unstructured":"Ronnqvist, M., Valttila, V., Ranta, J. & Tuominen, P. Salmonella risk to consumers via pork is related to the Salmonella prevalence in pig feed. Food Microbiol 71, 93\u201397, https:\/\/doi.org\/10.1016\/j.fm.2017.03.017 (2018).","journal-title":"Food Microbiol"},{"key":"49464_CR5","doi-asserted-by":"publisher","first-page":"899","DOI":"10.4315\/0362-028X.JFP-12-404","volume":"76","author":"H Arguello","year":"2013","unstructured":"Arguello, H., Alvarez-Ordonez, A., Carvajal, A., Rubio, P. & Prieto, M. Role of slaughtering in Salmonella spreading and control in pork production. J Food Prot 76, 899\u2013911, https:\/\/doi.org\/10.4315\/0362-028X.JFP-12-404 (2013).","journal-title":"J Food Prot"},{"key":"49464_CR6","doi-asserted-by":"publisher","first-page":"1022","DOI":"10.1111\/1541-4337.12283","volume":"16","author":"T M\u00f8retr\u00f8","year":"2017","unstructured":"M\u00f8retr\u00f8, T. & Langsrud, S. Residential Bacteria on Surfaces in the Food Industry and Their Implications for Food Safety and Quality. Comprehensive Reviews in Food Science and Food Safety 16, 1022\u20131041, https:\/\/doi.org\/10.1111\/1541-4337.12283 (2017).","journal-title":"Comprehensive Reviews in Food Science and Food Safety"},{"key":"49464_CR7","doi-asserted-by":"publisher","first-page":"841","DOI":"10.3389\/fmicb.2015.00841","volume":"6","author":"E Giaouris","year":"2015","unstructured":"Giaouris, E. et al. Intra- and inter-species interactions within biofilms of important foodborne bacterial pathogens. Front Microbiol 6, 841, https:\/\/doi.org\/10.3389\/fmicb.2015.00841 (2015).","journal-title":"Front Microbiol"},{"key":"49464_CR8","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1186\/1746-6148-6-48","volume":"6","author":"O Habimana","year":"2010","unstructured":"Habimana, O. et al. Micro ecosystems from feed industry surfaces: a survival and biofilm study of Salmonella versus host resident flora strains. BMC Vet Res 6, 48, https:\/\/doi.org\/10.1186\/1746-6148-6-48 (2010).","journal-title":"BMC Vet Res"},{"key":"49464_CR9","doi-asserted-by":"publisher","first-page":"1284","DOI":"10.3390\/ijerph15061284","volume":"15","author":"N Oloso","year":"2018","unstructured":"Oloso, N. et al. Antimicrobial Resistance in Food Animals and the Environment in Nigeria: A Review. International Journal of Environmental Research and Public Health 15, 1284 (2018).","journal-title":"International Journal of Environmental Research and Public Health"},{"key":"49464_CR10","doi-asserted-by":"publisher","first-page":"2643","DOI":"10.3390\/ijerph10072643","volume":"10","author":"C Verraes","year":"2013","unstructured":"Verraes, C. et al. Antimicrobial resistance in the food chain: a review. Int J Environ Res Public Health 10, 2643\u20132669, https:\/\/doi.org\/10.3390\/ijerph10072643 (2013).","journal-title":"Int J Environ Res Public Health"},{"key":"49464_CR11","doi-asserted-by":"publisher","first-page":"567","DOI":"10.3390\/antibiotics4040567","volume":"4","author":"AD Wales","year":"2015","unstructured":"Wales, A. D. & Davies, R. H. Co-Selection of Resistance to Antibiotics, Biocides and Heavy Metals, and Its Relevance to Foodborne Pathogens. Antibiotics (Basel) 4, 567\u2013604, https:\/\/doi.org\/10.3390\/antibiotics4040567 (2015).","journal-title":"Antibiotics (Basel)"},{"key":"49464_CR12","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1111\/jam.13247","volume":"121","author":"C Soumet","year":"2016","unstructured":"Soumet, C. et al. Reduced susceptibilities to biocides and resistance to antibiotics in food-associated bacteria following exposure to quaternary ammonium compounds. J Appl Microbiol 121, 1275\u20131281, https:\/\/doi.org\/10.1111\/jam.13247 (2016).","journal-title":"J Appl Microbiol"},{"key":"49464_CR13","doi-asserted-by":"publisher","first-page":"2241","DOI":"10.1093\/jac\/dkv109","volume":"70","author":"MA Webber","year":"2015","unstructured":"Webber, M. A. et al. Parallel evolutionary pathways to antibiotic resistance selected by biocide exposure. J Antimicrob Chemother 70, 2241\u20132248, https:\/\/doi.org\/10.1093\/jac\/dkv109 (2015).","journal-title":"J Antimicrob Chemother"},{"key":"49464_CR14","unstructured":"SCENIHR. Assessment of the Antibiotic Resistance Effects of Biocides Scientific Committee on Emerging and Newly Identified Health Risks, European commission (2009)."},{"key":"49464_CR15","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1046\/j.1365-2672.1999.00488.x","volume":"28","author":"C Soumet","year":"1999","unstructured":"Soumet, C. et al. Evaluation of a multiplex PCR assay for simultaneous identification of Salmonella sp., Salmonella enteritidis and Salmonella typhimurium from environmental swabs of poultry houses. Lett Appl Microbiol 28, 113\u2013117 (1999).","journal-title":"Lett Appl Microbiol"},{"key":"49464_CR16","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1016\/j.resmic.2009.10.002","volume":"161","author":"M Guibourdenche","year":"2010","unstructured":"Guibourdenche, M. et al. Supplement 2003\u20132007 (No. 47) to the White-Kauffmann-Le Minor scheme. Res Microbiol 161, 26\u201329, https:\/\/doi.org\/10.1016\/j.resmic.2009.10.002 (2010).","journal-title":"Res Microbiol"},{"key":"49464_CR17","unstructured":"Grimont P. A. D. & X., W. F. Antigenic formulae of the Salmonella serovars. Institut Pasteur & WHO Collaborating Centre for Reference and Research on Salmonella Paris, France (2007)."},{"key":"49464_CR18","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1089\/fpd.2006.3.59","volume":"3","author":"EM Ribot","year":"2006","unstructured":"Ribot, E. M. et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 3, 59\u201367, https:\/\/doi.org\/10.1089\/fpd.2006.3.59 (2006).","journal-title":"Foodborne Pathog Dis"},{"key":"49464_CR19","doi-asserted-by":"publisher","first-page":"1045","DOI":"10.1128\/JCM.43.3.1045-1050.2005","volume":"43","author":"SB Hunter","year":"2005","unstructured":"Hunter, S. B. et al. Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard. J Clin Microbiol 43, 1045\u20131050, https:\/\/doi.org\/10.1128\/JCM.43.3.1045-1050.2005 (2005).","journal-title":"J Clin Microbiol"},{"key":"49464_CR20","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1089\/fpd.2007.0090","volume":"4","author":"A Kerouanton","year":"2007","unstructured":"Kerouanton, A. et al. Pulsed-field gel electrophoresis subtyping database for foodborne Salmonella enterica serotype discrimination. Foodborne Pathog Dis 4, 293\u2013303, https:\/\/doi.org\/10.1089\/fpd.2007.0090 (2007).","journal-title":"Foodborne Pathog Dis"},{"key":"49464_CR21","doi-asserted-by":"publisher","first-page":"46","DOI":"10.2807\/esm.08.02.00401-en","volume":"8","author":"TM Peters","year":"2003","unstructured":"Peters, T. M. et al. The Salm-gene project - a European collaboration for DNA fingerprinting for food-related salmonellosis. Euro Surveill 8, 46\u201350 (2003).","journal-title":"Euro Surveill"},{"key":"49464_CR22","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1089\/fpd.2006.3.20","volume":"3","author":"TJ Barrett","year":"2006","unstructured":"Barrett, T. J., Gerner-Smidt, P. & Swaminathan, B. Interpretation of pulsed-field gel electrophoresis patterns in foodborne disease investigations and surveillance. Foodborne Pathog Dis 3, 20\u201331, https:\/\/doi.org\/10.1089\/fpd.2006.3.20 (2006).","journal-title":"Foodborne Pathog Dis"},{"key":"49464_CR23","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.3389\/fimmu.2017.01553","volume":"8","author":"E Jacouton","year":"2017","unstructured":"Jacouton, E., Chain, F., Sokol, H., Langella, P. & Bermudez-Humaran, L. G. Probiotic Strain Lactobacillus casei BL23 Prevents Colitis-Associated Colorectal Cancer. Front Immunol 8, 1553, https:\/\/doi.org\/10.3389\/fimmu.2017.01553 (2017).","journal-title":"Front Immunol"},{"key":"49464_CR24","doi-asserted-by":"publisher","first-page":"1287","DOI":"10.1093\/bioinformatics\/btx791","volume":"34","author":"F Escudie","year":"2018","unstructured":"Escudie, F. et al. FROGS: Find, Rapidly, OTUs with Galaxy Solution. Bioinformatics 34, 1287\u20131294, https:\/\/doi.org\/10.1093\/bioinformatics\/btx791 (2018).","journal-title":"Bioinformatics"},{"key":"49464_CR25","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","volume":"27","author":"T Magoc","year":"2011","unstructured":"Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957\u20132963, https:\/\/doi.org\/10.1093\/bioinformatics\/btr507 (2011).","journal-title":"Bioinformatics"},{"key":"49464_CR26","doi-asserted-by":"publisher","first-page":"e593","DOI":"10.7717\/peerj.593","volume":"2","author":"F Mahe","year":"2014","unstructured":"Mahe, F., Rognes, T., Quince, C., de Vargas, C. & Dunthorn, M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, e593, https:\/\/doi.org\/10.7717\/peerj.593 (2014).","journal-title":"PeerJ"},{"key":"49464_CR27","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","volume":"4","author":"T Rognes","year":"2016","unstructured":"Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584, https:\/\/doi.org\/10.7717\/peerj.2584 (2016).","journal-title":"PeerJ"},{"key":"49464_CR28","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nmeth.2276","volume":"10","author":"NA Bokulich","year":"2013","unstructured":"Bokulich, N. A. et al. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10, 57\u201359, https:\/\/doi.org\/10.1038\/nmeth.2276 (2013).","journal-title":"Nat Methods"},{"key":"49464_CR29","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","volume":"73","author":"Q Wang","year":"2007","unstructured":"Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261\u20135267, https:\/\/doi.org\/10.1128\/AEM.00062-07 (2007).","journal-title":"Appl Environ Microbiol"},{"key":"49464_CR30","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421, https:\/\/doi.org\/10.1186\/1471-2105-10-421 (2009).","journal-title":"BMC Bioinformatics"},{"key":"49464_CR31","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41, D590\u2013596, https:\/\/doi.org\/10.1093\/nar\/gks1219 (2013).","journal-title":"Nucleic Acids Res"},{"key":"49464_CR32","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8, e61217, https:\/\/doi.org\/10.1371\/journal.pone.0061217 (2013).","journal-title":"PLoS One"},{"key":"49464_CR33","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-6-r60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol 12, R60, https:\/\/doi.org\/10.1186\/gb-2011-12-6-r60 (2011).","journal-title":"Genome Biol"},{"key":"49464_CR34","doi-asserted-by":"publisher","first-page":"1513","DOI":"10.1017\/S095026881700036X","volume":"145","author":"S Bonardi","year":"2017","unstructured":"Bonardi, S. Salmonella in the pork production chain and its impact on human health in the European Union. Epidemiol Infect 145, 1513\u20131526, https:\/\/doi.org\/10.1017\/S095026881700036X (2017).","journal-title":"Epidemiol Infect"},{"key":"49464_CR35","doi-asserted-by":"publisher","first-page":"6151","DOI":"10.4081\/ijfs.2016.6151","volume":"5","author":"P Di Ciccio","year":"2016","unstructured":"Di Ciccio, P. et al. Microbiological contamination in Three Large-Scale Pig Slaughterhouses in Northern Italy. Ital J Food Saf 5, 6151, https:\/\/doi.org\/10.4081\/ijfs.2016.6151 (2016).","journal-title":"Ital J Food Saf"},{"key":"49464_CR36","doi-asserted-by":"crossref","first-page":"19580","DOI":"10.2807\/ese.15.22.19580-en","volume":"15","author":"KL Hopkins","year":"2010","unstructured":"Hopkins, K. L. et al. Multiresistant Salmonella enterica serovar 4,[5],12:i:- in Europe: a new pandemic strain? Euro Surveill 15, 19580 (2010).","journal-title":"Euro Surveill"},{"key":"49464_CR37","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1126\/science.aar3777","volume":"360","author":"S Baker","year":"2018","unstructured":"Baker, S., Thomson, N., Weill, F. X. & Holt, K. E. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science 360, 733\u2013738, https:\/\/doi.org\/10.1126\/science.aar3777 (2018).","journal-title":"Science"},{"key":"49464_CR38","doi-asserted-by":"publisher","first-page":"1187","DOI":"10.1017\/S0950268803001171","volume":"131","author":"T Hald","year":"2003","unstructured":"Hald, T., Wingstrand, A., Swanenburg, M., von Altrock, A. & Thorberg, B. M. The occurrence and epidemiology of Salmonella in European pig slaughterhouses. Epidemiol Infect 131, 1187\u20131203 (2003).","journal-title":"Epidemiol Infect"},{"key":"49464_CR39","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.ijfoodmicro.2011.08.025","volume":"151","author":"F Piras","year":"2011","unstructured":"Piras, F., Brown, D. J., Meloni, D., Mureddu, A. & Mazzette, R. Investigation of Salmonella enterica in Sardinian slaughter pigs: prevalence, serotype and genotype characterization. Int J Food Microbiol 151, 201\u2013209, https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2011.08.025 (2011).","journal-title":"Int J Food Microbiol"},{"key":"49464_CR40","doi-asserted-by":"publisher","first-page":"274","DOI":"10.4315\/0362-028X-72.2.274","volume":"72","author":"UG Barron","year":"2009","unstructured":"Barron, U. G. et al. Estimation of prevalence of Salmonella on pig carcasses and pork joints, using a quantitative risk assessment model aided by meta-analysis. J Food Prot 72, 274\u2013285 (2009).","journal-title":"J Food Prot"},{"key":"49464_CR41","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/S0168-1605(97)01267-1","volume":"36","author":"BR Berends","year":"1997","unstructured":"Berends, B. R., Van Knapen, F., Snijders, J. M. & Mossel, D. A. Identification and quantification of risk factors regarding Salmonella spp. on pork carcasses. Int J Food Microbiol 36, 199\u2013206 (1997).","journal-title":"Int J Food Microbiol"},{"key":"49464_CR42","doi-asserted-by":"publisher","first-page":"2326","DOI":"10.4315\/0362-028X-72.11.2326","volume":"72","author":"A Letellier","year":"2009","unstructured":"Letellier, A. et al. Risk factors at slaughter associated with presence of Salmonella on hog carcasses in Canada. J Food Prot 72, 2326\u20132331 (2009).","journal-title":"J Food Prot"},{"key":"49464_CR43","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1016\/j.vetmic.2015.03.014","volume":"177","author":"HB Kim","year":"2015","unstructured":"Kim, H. B. & Isaacson, R. E. The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing. Veterinary Microbiology 177, 242\u2013251, https:\/\/doi.org\/10.1016\/j.vetmic.2015.03.014 (2015).","journal-title":"Veterinary Microbiology"},{"key":"49464_CR44","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-22692-0","volume":"8","author":"J Quan","year":"2018","unstructured":"Quan, J. et al. A global comparison of the microbiome compositions of three gut locations in commercial pigs with extreme feed conversion ratios. Scientific Reports 8, 4536, https:\/\/doi.org\/10.1038\/s41598-018-22692-0 (2018).","journal-title":"Scientific Reports"},{"key":"49464_CR45","doi-asserted-by":"publisher","unstructured":"Holman, D. B., Brunelle, B. W., Trachsel, J. & Allen, H. K. Meta-analysis To Define a Core Microbiota in the Swine Gut. mSystems 2, https:\/\/doi.org\/10.1128\/mSystems.00004-17 (2017).","DOI":"10.1128\/mSystems.00004-17"},{"key":"49464_CR46","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-30932-6","volume":"8","author":"D Crespo-Piazuelo","year":"2018","unstructured":"Crespo-Piazuelo, D. et al. Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions. Sci Rep 8, 12727, https:\/\/doi.org\/10.1038\/s41598-018-30932-6 (2018).","journal-title":"Sci Rep"},{"key":"49464_CR47","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/1746-6148-10-69","volume":"10","author":"JS Weese","year":"2014","unstructured":"Weese, J. S., Slifierz, M., Jalali, M. & Friendship, R. Evaluation of the nasal microbiota in slaughter-age pigs and the impact on nasal methicillin-resistant Staphylococcus aureus (MRSA) carriage. BMC Vet Res 10, 69, https:\/\/doi.org\/10.1186\/1746-6148-10-69 (2014).","journal-title":"BMC Vet Res"},{"key":"49464_CR48","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.fm.2014.04.015","volume":"45","author":"A Bridier","year":"2015","unstructured":"Bridier, A. et al. Biofilm-associated persistence of food-borne pathogens. Food Microbiol 45, 167\u2013178, https:\/\/doi.org\/10.1016\/j.fm.2014.04.015 (2015).","journal-title":"Food Microbiol"},{"key":"49464_CR49","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/j.ijfoodmicro.2014.04.021","volume":"181","author":"MR Gantzhorn","year":"2014","unstructured":"Gantzhorn, M. R., Pedersen, K., Olsen, J. E. & Thomsen, L. E. Biocide and antibiotic susceptibility of Salmonella isolates obtained before and after cleaning at six Danish pig slaughterhouses. Int J Food Microbiol 181, 53\u201359, https:\/\/doi.org\/10.1016\/j.ijfoodmicro.2014.04.021 (2014).","journal-title":"Int J Food Microbiol"},{"key":"49464_CR50","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.fm.2015.04.010","volume":"51","author":"L Lavilla Lerma","year":"2015","unstructured":"Lavilla Lerma, L., Benomar, N., Casado Munoz Mdel, C., Galvez, A. & Abriouel, H. Correlation between antibiotic and biocide resistance in mesophilic and psychrotrophic Pseudomonas spp. isolated from slaughterhouse surfaces throughout meat chain production. Food Microbiol 51, 33\u201344, https:\/\/doi.org\/10.1016\/j.fm.2015.04.010 (2015).","journal-title":"Food Microbiol"},{"issue":"7","key":"49464_CR51","doi-asserted-by":"publisher","first-page":"ftw094","DOI":"10.1093\/femspd\/ftw094","volume":"74","author":"Damien Costa","year":"2016","unstructured":"Costa, D. et al. Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants. Pathog Dis 74, https:\/\/doi.org\/10.1093\/femspd\/ftw094 (2016).","journal-title":"Pathogens and Disease"},{"key":"49464_CR52","doi-asserted-by":"publisher","unstructured":"Forbes, S. et al. Formulation of Biocides Increases Antimicrobial Potency and Mitigates the Enrichment of Nonsusceptible Bacteria in Multispecies Biofilms. Appl Environ Microbiol 83, https:\/\/doi.org\/10.1128\/AEM.03054-16 (2017).","DOI":"10.1128\/AEM.03054-16"},{"key":"49464_CR53","doi-asserted-by":"publisher","unstructured":"Bertelli, C. et al. Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms. Frontiers in Microbiology 9, https:\/\/doi.org\/10.3389\/fmicb.2018.02520 (2018).","DOI":"10.3389\/fmicb.2018.02520"},{"key":"49464_CR54","doi-asserted-by":"publisher","first-page":"320","DOI":"10.2166\/wst.2018.289","volume":"78","author":"K Reynolds-Clausen","year":"2018","unstructured":"Reynolds-Clausen, K., Surridge-Talbot, K., Botes, M. & Eugene Cloete, T. Bacterial species diversity as an indicator of dibromonitrilopropionamide (DBNPA) biocide efficacy. Water Science and Technology 78, 320\u2013328, https:\/\/doi.org\/10.2166\/wst.2018.289 (2018).","journal-title":"Water Science and Technology"},{"key":"49464_CR55","doi-asserted-by":"publisher","first-page":"2113","DOI":"10.3389\/fmicb.2018.02113","volume":"9","author":"L Jiang","year":"2018","unstructured":"Jiang, L. et al. Effect of Different Disinfectants on Bacterial Aerosol Diversity in Poultry Houses. Front Microbiol 9, 2113, https:\/\/doi.org\/10.3389\/fmicb.2018.02113 (2018).","journal-title":"Front Microbiol"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-49464-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-49464-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-49464-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T13:25:20Z","timestamp":1671283520000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-49464-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,10]]},"references-count":55,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["49464"],"URL":"https:\/\/doi.org\/10.1038\/s41598-019-49464-8","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,10]]},"assertion":[{"value":"26 December 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 August 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"12947"}}