{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T20:16:42Z","timestamp":1790367402906,"version":"4.1.0"},"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T00:00:00Z","timestamp":1531958400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Cybec Foundation"},{"name":"Australian Government Research Training Program"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0201031","type":"journal-article","created":{"date-parts":[[2018,7,19]],"date-time":"2018-07-19T14:37:07Z","timestamp":1532011027000},"page":"e0201031","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":27,"title":["Salmonella spp. transmission in a vertically integrated poultry operation: Clustering and diversity analysis using phenotyping (serotyping, phage typing) and genotyping (MLVA)"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5550-3834","authenticated-orcid":true,"given":"Helen Kathleen","family":"Crabb","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4740-9404","authenticated-orcid":true,"given":"Joanne Lee","family":"Allen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanne Maree","family":"Devlin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3239-1419","authenticated-orcid":true,"given":"Simon Matthew","family":"Firestone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Colin Reginald","family":"Wilks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James Rudkin","family":"Gilkerson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,7,19]]},"reference":[{"issue":"2","key":"ref1","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.cmi.2015.12.004","article-title":"Salmonellosis: the role of poultry meat","volume":"22","author":"P Antunes","year":"2016","journal-title":"Clin Microbiol Infect"},{"issue":"6","key":"ref2","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1093\/ps\/78.6.848","article-title":"Risk factors associated with Salmonella Typhimurium infection in Danish broiler flocks","volume":"78","author":"MN Skov","year":"1999","journal-title":"Poult Sci"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1016\/S0167-5877(99)00002-1","article-title":"Risk factors for <italic>Salmonella enterica<\/italic> subsp. <italic>enterica<\/italic> contamination in French broiler-chicken flocks at the end of the rearing period","volume":"39","author":"N Rose","year":"1999","journal-title":"Prev Vet Med"},{"issue":"1","key":"ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0167-5877(99)00016-1","article-title":"Generalised linear mixed models analysis of risk factors for contamination of Danish broiler flocks with <italic>Salmonella<\/italic> Typhimurium","volume":"40","author":"M Chri\u00e9l","year":"1999","journal-title":"Prev Vet Med"},{"issue":"5","key":"ref5","doi-asserted-by":"crossref","first-page":"742","DOI":"10.4315\/0362-028X-65.5.742","article-title":"Serotype tracking through integrated broiler chicken operations","volume":"65","author":"JS Bailey","year":"2002","journal-title":"J Food Prot"},{"issue":"7\u20138","key":"ref6","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1111\/j.1863-2378.2009.01263.x","article-title":"Inter-relationships of <italic>Salmonella<\/italic> status of flock and grow-out environment at sequential segments in broiler production and processing","volume":"57","author":"VV Volkova","year":"2010","journal-title":"Zoonoses and Public Health"},{"issue":"8","key":"ref7","first-page":"1413","article-title":"A study of the dissemination of salmonellosis in a commercial broiler chicken operation","volume":"30","author":"GK Morris","year":"1969","journal-title":"Am J Vet Res"},{"issue":"3","key":"ref8","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.3382\/ps.0531114","article-title":"Transmission of <italic>Salmonella<\/italic> through an integrated poultry organisation","volume":"53","author":"BS Bains","year":"1974","journal-title":"Poult Sci"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"957","DOI":"10.3382\/ps.0550957","article-title":"Dissemination of <italic>Salmonella<\/italic> serotypes from raw feed ingredients to chicken carcases","volume":"55","author":"MA MacKenzie","year":"1976","journal-title":"Poult Sci"},{"issue":"10","key":"ref10","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1111\/j.1751-0813.1971.tb02029.x","article-title":"A study of the epizootology and control of <italic>Salmonella<\/italic> Typhimurium infection in a commercial poultry organisation","volume":"47","author":"CAW Jackson","year":"1971","journal-title":"Aust Vet J"},{"issue":"5","key":"ref11","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.3382\/ps.2013-03558","article-title":"Prevalence and characterization of <italic>Salmonella<\/italic> species in entire steps of a single integrated broiler supply chain in Korea","volume":"93","author":"SW Choi","year":"2014","journal-title":"Poult Sci"},{"issue":"4","key":"ref12","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1292\/jvms.69.399","article-title":"Characterization of <italic>Salmonella<\/italic> spp. isolated from an integrated broiler chicken operation in Korea","volume":"69","author":"YJ Lee","year":"2007","journal-title":"J Vet Med Sci"},{"issue":"2","key":"ref13","doi-asserted-by":"crossref","first-page":"155","DOI":"10.4142\/jvs.2007.8.2.155","article-title":"Dissemination and tracking of <italic>Salmonella<\/italic> spp. in integrated broiler operation","volume":"8","author":"A Kim","year":"2007","journal-title":"J Vet Sci"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1080\/00071660120109872","article-title":"Use of molecular fingerprinting to assist the understanding of the epidemiology of <italic>Salmonella<\/italic> contamination within broiler production","volume":"43","author":"E Liebana","year":"2010","journal-title":"Br Poult Sci"},{"key":"ref15","unstructured":"Biosecurity Australia. Generic Import Risk Analysis Report for Chicken Meat: Final Report. Bioscurity Australia, Canberra, Australia 2008."},{"issue":"3","key":"ref16","first-page":"E213","article-title":"Monitoring the incidence and causes of diseases potentially transmitted by food in Australia: Annual report of the OzFoodNet network, 2010","volume":"36","year":"2012","journal-title":"Commun Dis Intell"},{"issue":"5","key":"ref17","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.fm.2017.03.008","article-title":"The use of social network analysis to examine the transmission of <italic>Salmonella<\/italic> spp. within a vertically integrated broiler enterprise","volume":"71","author":"HK Crabb","year":"2018","journal-title":"Food Microbiology"},{"key":"ref18","unstructured":"Food Regulation Standing Committee. Australian Standard for construction of premises and hygienic production of poultry meat for human consumption: AS 4465: 2005 FRSC Technical Report No 12006."},{"key":"ref19","article-title":"Model Code of Practice for the Welfare of Animals: Domestic Poultry","volume":"83","year":"2002"},{"key":"ref20","article-title":"NSW\/VIC Accreditation program for the control of <italic>Salmonella<\/italic> Enteritidis","author":"G Arzey","year":"2002"},{"key":"ref21","unstructured":"FSANZ. Primary Production and Processing Standard for Poultry Meat.: Food Standards Australia New Zealand; 2012."},{"key":"ref22","unstructured":"Research ethics and integrity. Animal ethics and welfare Victoria, Australia: The University of Melbourne; 2017. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/staff.unimelb.edu.au\/research\/ethics-integrity\/animal-ethics\" xlink:type=\"simple\">https:\/\/staff.unimelb.edu.au\/research\/ethics-integrity\/animal-ethics<\/ext-link>."},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0167-5877(97)00081-0","article-title":"A new probability formula for surveys to substantiate freedom from disease","volume":"34","author":"AR Cameron","year":"1998","journal-title":"Prev Vet Med"},{"key":"ref24","first-page":"228","article-title":"Veterinary Epidemiology","author":"M Thrusfield","year":"2007"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1016\/j.prevetmed.2004.07.003","article-title":"A practical approach to calculate sample size for herd prevalence surveys","volume":"65","author":"RW Humphry","year":"2004","journal-title":"Prev Vet Med"},{"key":"ref26","article-title":"EU Interlaboratory comparison study veterinary XIV (2011); Detection of <italic>Salmonella<\/italic> in chicken faeces","author":"AFA Kuijpers","year":"2011"},{"key":"ref27","article-title":"EU Interlaboratory comparison study primary production XVI (2013): Detection of <italic>Salmonella<\/italic> in chicken faeces adhering to boot socks","author":"AFA Kuijpers","year":"2014"},{"key":"ref28","article-title":"EU Interlaboratory comparison study animal feed II (2012); Detection of <italic>Salmonella<\/italic> in chicken feed","author":"AFA Kuijpers","year":"2012"},{"issue":"2","key":"ref29","doi-asserted-by":"crossref","first-page":"513","DOI":"10.2307\/1589943","article-title":"A comparison of culturing drag swabs and litter for identification of infections with <italic>Salmonella<\/italic> spp in commercial chicken flocks","volume":"25","author":"DJ Kingston","year":"1981","journal-title":"Avian Dis"},{"issue":"4","key":"ref30","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1093\/japr\/14.4.694","article-title":"Recovery and genetic similarity of <italic>Salmonella<\/italic> from broiler house drag swabs versus surgical shoe covers","volume":"14","author":"BA McCrea","year":"2005","journal-title":"Journal of Applied Poultry Research"},{"key":"ref31","unstructured":"Standards Australia. Australian Standard 5013.10\u20132009. Food Microbiological Method 10: Microbiology of food and animal feeding stuffs\u2014Horizontal method for the detection of Salmonella spp. (ISO 6579:2002, MOD). Sydney, Australia: SAI Global; 2009."},{"issue":"8","key":"ref32","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1007\/s11274-009-0025-3","article-title":"Detection of <italic>Salmonella enterica<\/italic> serovar Typhimurium by selective amplification of <italic>fliC<\/italic>, <italic>fliB<\/italic>, <italic>iroB<\/italic>, <italic>rfbJ<\/italic>, STM2755, STM4497 genes by polymerase chain reaction in a monoplex and multiplex format","volume":"25","author":"M Shanmugasundaram","year":"2009","journal-title":"World Journal of Microbiology and Biotechnology"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1099\/mic.0.047001-0","article-title":"Phenotypic and molecular characterization of Salmonella enterica serovar Sofia, an avirulent species in Australian poultry","volume":"157","author":"E Gan","year":"2011","journal-title":"Microbiology-Sgm"},{"key":"ref34","article-title":"Antigenic formulae of the <italic>Salmonella<\/italic> serovars, 9th Edition","author":"PAD Grimont","year":"2007"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1017\/S0022172400056187","article-title":"Bacteriophage-typing designations of <italic>Salmonella<\/italic> Typhimurium","volume":"78","author":"ES Anderson","year":"1977","journal-title":"Journal of Hygiene, Cambridge"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1016\/j.mimet.2004.06.014","article-title":"Multiple-locus variable-number tandem-repeats analysis of <italic>Salmonella enterica<\/italic> subsp. <italic>enterica<\/italic> serovar Typhimurium using PCR multiplexing and multicolor capillary electrophoresis","volume":"59","author":"B-A Lindstedt","year":"2004","journal-title":"J Microbiol Methods"},{"issue":"2","key":"ref37","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1071\/NB07116","article-title":"Using MLVA to type strains of <italic>Salmonella<\/italic> Typhimurium in New South Wales","volume":"19","author":"G, L. Gilbert","year":"2008","journal-title":"New South Wales public health bulletin"},{"key":"ref38","unstructured":"Heuzenroeder MW, Ross IL, Hocking H, Davos D, Young CC, Morgan G. An integrated typing service for the surveillance of Salmonella in chickens. Molecular and classical typing of Salmonella populations in chickens. Project No PRJ-003419. ACT, Australia: Rural Industries Research and Development Corporation; 2013. p. 1\u201365."},{"issue":"4","key":"ref39","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1111\/j.1472-765X.2007.02220.x","article-title":"Novel PCR assay for identification of <italic>Salmonella enterica<\/italic> serovar Infantis","volume":"45","author":"G Kardos","year":"2007","journal-title":"Lett Appl Microbiol"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1128\/AEM.69.1.290-296.2003","article-title":"Multicenter validation of the analytical accuracy of <italic>Salmonella<\/italic> PCR: towards an International Standard","volume":"69","author":"B Malorny","year":"2003","journal-title":"Appl Environ Microbiol"},{"key":"ref41","article-title":"R: A language and environment for statistical computing","year":"2016"},{"key":"ref42","unstructured":"Oksansen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. 2.4\u20134 ed. Cran.R-project.org: Cran.R-project.org; 2017."},{"key":"ref43","first-page":"207","article-title":"A manual and software for common statistical methods for ecological and biodiversity studies","author":"R Kindt","year":"2005"},{"issue":"1","key":"ref44","first-page":"1","article-title":"FactoMineR: An R package for Multivariate Analysis","volume":"25","author":"S Le","year":"2008","journal-title":"Journal of Statistical Software"},{"key":"ref45","unstructured":"Kassambara A, Mundt F. factoextra: Extract and visualize the results of multivariate data analyses. 1.0.05.999 ed. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.sthda.com\/english\/rpkgs\/factoextra2017\" xlink:type=\"simple\">http:\/\/www.sthda.com\/english\/rpkgs\/factoextra2017<\/ext-link>."},{"key":"ref46","unstructured":"Suzuki R, Shimodaira H. pvclust: Hierarchical clustering with p-values via multiscale bootstrap. 2.0\u20130 ed: Cran-R-project; 2015."},{"key":"ref47","unstructured":"Chen H. VennDiagram: Generate high-resolution venn and euler plots. R package v 1.6.17. Cran.R-Project2016."},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1093\/bioinformatics\/btw582","article-title":"PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods","volume":"33","author":"M Nascimento","year":"2017","journal-title":"Bioinformatics"},{"issue":"5","key":"ref49","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1128\/JB.186.5.1518-1530.2004","article-title":"eBURST: Inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data","volume":"186","author":"EJ Feil","year":"2004","journal-title":"J Bacteriol"},{"issue":"Supplement 3","key":"ref50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1469-0691.2007.01786.x","article-title":"Guidelines for the validation and application of typing methods for use in bacterial epidemiology","volume":"13","author":"A van Belkum","year":"2007","journal-title":"Clin Microbiol Infect"},{"key":"ref51","article-title":"Applied Epidemiology in Victoria","author":"Z Cutcher","year":"2015"},{"key":"ref52","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4419-7976-6","article-title":"Numerical Ecology with R","author":"D Borcard","year":"2011"},{"issue":"2","key":"ref53","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1111\/j.1461-0248.2004.00707.x","article-title":"A new statistical approach for assessing similarity of species composition with incidence and abundance data","volume":"8","author":"A Chao","year":"2005","journal-title":"Ecology Letters"},{"issue":"6","key":"ref54","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1111\/j.1541-0420.2005.00489.x","article-title":"Abundence-based similarity indices and their estimation when there are sunseen species in samples","volume":"62","author":"A Chao","year":"2006","journal-title":"Biometrics"},{"issue":"2","key":"ref55","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1007\/s004420100716","article-title":"Ecologically meaningful transformations for ordination of species data","volume":"129","author":"P Legendre","year":"2001","journal-title":"Oecologia"},{"key":"ref56","first-page":"1007","article-title":"Numerical Ecology","author":"P Legendre","year":"2012"},{"key":"ref57","first-page":"155","article-title":"Practical guide to principal component methods in R","author":"A Kassambara","year":"2017"},{"key":"ref58","unstructured":"Powling J. National Enteric Pathogens Surveillance Scheme Non-human Annual Report 2013. The University of Melbourne, Australia: Microbiological Diagnostic Unit, 2014."},{"issue":"4","key":"ref59","doi-asserted-by":"crossref","first-page":"707","DOI":"10.4315\/0362-028X-72.4.707","article-title":"Do microbial interactions and cultivation media decrease the accuracy of <italic>Salmonella<\/italic> surveillance systems and outbreak investigations?","volume":"72","author":"R Singer","year":"2009","journal-title":"J Food Prot"},{"issue":"1","key":"ref60","first-page":"27","article-title":"A Review: Principles of <italic>Salmonella<\/italic> Isolation","volume":"46","author":"RWS Harvey","year":"1979","journal-title":"J Appl Microbiol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1177\/104063870001200203","article-title":"A statistical model for assessing sample size for bacterial colony selection: a case study of <italic>Escherischia coli<\/italic> and avian cellulitis","volume":"12","author":"R Singer","year":"2000","journal-title":"J Vet Diagn Invest"},{"issue":"3","key":"ref62","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1017\/S0022172400045939","article-title":"The examination of samples infected with multiple <italic>Salmonella<\/italic> serotypes","volume":"65","author":"RWS Harvey","year":"1967","journal-title":"J Hyg (Lond)"},{"key":"ref63","unstructured":"IMVS. Australian Salmonella Reference Centre: Monthly Report\u2014January 2011. Adelaide, South Australia: IMVS Pathology,; 2011. p. 7."},{"issue":"1","key":"ref64","first-page":"66","article-title":"Practical evaluation of molecular subtyping and phage typing in outbreaks of infection due to <italic>Salmonella<\/italic> enterica serotype Typhimurium","volume":"33","author":"NJ Jeoffreys","year":"2001","journal-title":"Pathology (Phila)"},{"issue":"3","key":"ref65","doi-asserted-by":"crossref","first-page":"583","DOI":"10.2307\/1592082","article-title":"Transmission of <italic>Salmonella<\/italic> Typhimurium during hatching of broiler chicks","volume":"38","author":"JA Cason","year":"1994","journal-title":"Avian Dis"},{"issue":"16","key":"ref66","doi-asserted-by":"crossref","first-page":"3036","DOI":"10.1128\/JB.01820-14","article-title":"Analysis of <italic>Salmonella enterica<\/italic> serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons","volume":"196","author":"K Dimovski","year":"2014","journal-title":"J Bacteriol"},{"issue":"12","key":"ref67","doi-asserted-by":"crossref","first-page":"e84055","DOI":"10.1371\/journal.pone.0084055","article-title":"MLVA as a tool for public health surveillance of human <italic>Salmonella<\/italic> Typhimurium: Prospective study in Belgium and evaluation of MLVA loci stability","volume":"8","author":"V Wuyts","year":"2013","journal-title":"PLoS ONE"},{"issue":"9","key":"ref68","doi-asserted-by":"crossref","first-page":"3058","DOI":"10.1128\/JCM.00715-07","article-title":"Stability of multiple-locus variable-number tandem repeats in <italic>Salmonella enterica<\/italic> serovar Typhimurium","volume":"45","author":"KL Hopkins","year":"2007","journal-title":"J Clin Microbiol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0201031","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T15:11:23Z","timestamp":1540221083000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0201031"}},"subtitle":[],"editor":[{"given":"Anderson de Souza","family":"Sant\u2019Ana","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,7,19]]},"references-count":68,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2018,7,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0201031","relation":{"is-supplemented-by":[{"id-type":"doi","id":"10.17504\/protocols.io.n6pdhdn","asserted-by":"object"},{"id-type":"doi","id":"10.17504\/protocols.io.n6sdhee","asserted-by":"object"}]},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,7,19]]}}}