{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T04:34:46Z","timestamp":1784694886421,"version":"3.55.0"},"reference-count":43,"publisher":"Elsevier BV","issue":"2-3","license":[{"start":{"date-parts":[[2022,2,1]],"date-time":"2022-02-01T00:00:00Z","timestamp":1643673600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,2,1]],"date-time":"2022-02-01T00:00:00Z","timestamp":1643673600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,9,15]],"date-time":"2021-09-15T00:00:00Z","timestamp":1631664000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100006229","name":"Oak Ridge Institute for Science and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006229","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000015","name":"U.S. Department of Energy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000015","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007917","name":"Agricultural Research Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007917","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006225","name":"Oak Ridge Associated Universities","doi-asserted-by":"publisher","award":["DE-SC0014664"],"award-info":[{"award-number":["DE-SC0014664"]}],"id":[{"id":"10.13039\/100006225","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["International Journal for Parasitology"],"published-print":{"date-parts":[[2022,2]]},"DOI":"10.1016\/j.ijpara.2021.08.002","type":"journal-article","created":{"date-parts":[[2021,9,17]],"date-time":"2021-09-17T10:43:50Z","timestamp":1631875430000},"page":"145-155","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":5,"title":["Trich-tracker \u2013 a practical tool to trace Trichinella spiralis transmission based on rapid, cost-effective sampling of genome-wide genetic variation"],"prefix":"10.1016","volume":"52","author":[{"given":"Ewa","family":"Bilska-Zaj\u0105c","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Benjamin","family":"Rosenthal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ijpara.2021.08.002_b0005","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nrg.2015.28","article-title":"Harnessing the power of RADseq for ecological and evolutionary genomics","volume":"17","author":"Andrews","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.ijpara.2021.08.002_b0010","doi-asserted-by":"crossref","first-page":"e3376","DOI":"10.1371\/journal.pone.0003376","article-title":"Rapid SNP discovery and genetic mapping using sequenced RAD markers","volume":"3","author":"Baird","year":"2008","journal-title":"PLoS ONE"},{"key":"10.1016\/j.ijpara.2021.08.002_b0015","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.ijppaw.2019.07.009","article-title":"Intraspecific genetic variation in Trichinella spiralis and Trichinella britovi populations circulating in different geographical regions of Poland","volume":"10","author":"Bilska-Zaj\u0105c","year":"2019","journal-title":"Int J Parasitol Parasites Wildl"},{"key":"10.1016\/j.ijpara.2021.08.002_b0020","doi-asserted-by":"crossref","first-page":"109052","DOI":"10.1016\/j.vetpar.2020.109052","article-title":"Diversity of Trichinella species in relation to the host species and geographical location","volume":"279","author":"Bilska-Zaj\u0105c","year":"2020","journal-title":"Vet. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0025","doi-asserted-by":"crossref","unstructured":"Bilska-Zajac, E., Tonanzi, D., Pozio, E., R\u00f3\u017cycki, M., Cencek, T., Thompson, P., Rosenthal, M., La Rosa, G., 2021. Genetic evidence substantiates transmission of Trichinella spiralis from one swine farm to another. Parasites Vectors 14, 359 (2021).","DOI":"10.1186\/s13071-021-04861-9"},{"key":"10.1016\/j.ijpara.2021.08.002_b0030","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10592-018-1134-z","article-title":"Comparing inferences derived from microsatellite and RADseq datasets: a case study involving threatened bull trout","volume":"20","author":"Bohling","year":"2019","journal-title":"Conserv. Genet."},{"key":"10.1016\/j.ijpara.2021.08.002_b0035","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.fawpar.2018.01.001","article-title":"Foodborne parasites: Outbreaks and outbreak investigations. A meeting report from the European network for foodborne parasites (Euro-FBP)","volume":"10","author":"Cacci\u00f2","year":"2018","journal-title":"Food Waterborne Parasitol"},{"key":"10.1016\/j.ijpara.2021.08.002_b0040","doi-asserted-by":"crossref","first-page":"3124","DOI":"10.1111\/mec.12354","article-title":"Stacks: an analysis tool set for population genomics","volume":"22","author":"Catchen","year":"2013","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0045","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.exppara.2018.06.004","article-title":"Cryptosporidium genotyping in Europe: the current status and processes for a harmonised multi-locus genotyping scheme","volume":"191","author":"Chalmers","year":"2018","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0050","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1007\/s12686-011-9548-7","article-title":"STRUCTURE HARVESTER: a website and program for visual-izing STRUCTURE output and implementing the Evanno method","volume":"4","author":"Earl","year":"2012","journal-title":"Conser. Genet. Resour."},{"key":"10.1016\/j.ijpara.2021.08.002_b0055","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1111\/j.1365-294X.2005.02553.x","article-title":"Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study","volume":"14","author":"Evanno","year":"2005","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0060","first-page":"217","article-title":"Commission implementing regulation (EU) 2015\/1375 of 10 August 2015 laying down specific rules on official controls for Trichinella in meat","volume":"2015","author":"Commission","year":"2015","journal-title":"Off. J. Eur. Union"},{"key":"10.1016\/j.ijpara.2021.08.002_b0065","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1111\/zph.12148","article-title":"Trichinellosis outbreak caused by meat from a wild boar hunted in an Italian region considered to be at negligible risk for Trichinella","volume":"62","author":"Fichi","year":"2015","journal-title":"Zoonoses Public Health"},{"key":"10.1016\/j.ijpara.2021.08.002_b0070","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1128\/CMR.00075-13","article-title":"Whole-genome sequencing in outbreak analysis","volume":"28","author":"Gilchrist","year":"2015","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.ijpara.2021.08.002_b0075","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s41564-018-0296-2","article-title":"Tracking virus outbreaks in the twenty-first century","volume":"4","author":"Grubaugh","year":"2019","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0080","doi-asserted-by":"crossref","unstructured":"Harilal, D., Ramaswamy, S., Loney, T., Suwaidi, H.A., Khansaheb, H., Alkhaja, A., Varghese, R., Deesi, Z., Nowotny, N., Alsheikh-Ali, A., Abou Tayoun, A., 2020. SARS-CoV-2 whole genome amplification and sequencing for effective population-based surveillance and control of viral transmission. Clin Chem 66, 1450-1458.","DOI":"10.1093\/clinchem\/hvaa187"},{"key":"10.1016\/j.ijpara.2021.08.002_b0085","doi-asserted-by":"crossref","unstructured":"Hoberg, E.P., Brooks, D. R., 2008. A macroevolutionary mosaic: Episodic host\u2010switching, geographical colonization and diversification in complex host\u2013parasite systems. J. Biogeography 35, 1533\u20131550.","DOI":"10.1111\/j.1365-2699.2008.01951.x"},{"key":"10.1016\/j.ijpara.2021.08.002_b0090","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2021.08.002_b0095","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1007\/s00436-007-0527-6","article-title":"Trichinella spiralis reinfection: macrophage activity in BALB\/c mice","volume":"101","author":"Ko\u0142odziej-Soboci\u0144ska","year":"2007","journal-title":"Parasitol. Res."},{"key":"10.1016\/j.ijpara.2021.08.002_b0100","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1016\/j.meegid.2012.01.008","article-title":"Development of a single larva microsatellite analysis to investigate the population structure of Trichinella spiralis","volume":"12","author":"La Rosa","year":"2012","journal-title":"Infect Genet Evol"},{"key":"10.1016\/j.ijpara.2021.08.002_b0105","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1186\/s13071-018-2939-9","article-title":"Multilocus genotype analysis outlines distinct histories for Trichinella britovi in the neighboring Mediterranean islands of Corsica and Sardinia","volume":"11","author":"La Rosa","year":"2018","journal-title":"Parasit Vectors"},{"key":"10.1016\/j.ijpara.2021.08.002_b0110","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1016\/j.ijpara.2017.12.007","article-title":"Rare but evolutionarily consequential outcrossing in a highly inbred zoonotic parasite","volume":"48","author":"La Rosa","year":"2018","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0115","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ijpara.2021.08.002_b0120","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ijpara.2021.08.002_b0125","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1016\/j.tube.2014.04.005","article-title":"Whole-genome sequencing to detect recent transmission of Mycobacterium tuberculosis in settings with a high burden of tuberculosis","volume":"94","author":"Luo","year":"2014","journal-title":"Tuberculosis (Edinb)"},{"key":"10.1016\/j.ijpara.2021.08.002_b0130","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/0014-4894(86)90044-5","article-title":"Trichinella spiralis: antifecundity and antinewborn larvae immunity in swine","volume":"62","author":"Marti","year":"1986","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0135","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.vetpar.2010.10.058","article-title":"Investigation of an outbreak of Taenia saginata cysts (cysticercus bovis) in dairy cattle from two farms","volume":"176","author":"McFadden","year":"2011","journal-title":"Vet. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0140","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.ijpara.2014.08.010","article-title":"Mitochondrial genomes of Trichinella species and genotypes - a basis for diagnosis, and systematic and epidemiological explorations","volume":"44","author":"Mohandas","year":"2014","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0145","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/0014-4894(85)90090-6","article-title":"Trichinella spiralis: acquired immunity in swine","volume":"59","author":"Murrell","year":"1985","journal-title":"Exp. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0150","doi-asserted-by":"crossref","first-page":"3193","DOI":"10.1111\/mec.14792","article-title":"These aren't the loci you'e looking for: principles of effective SNP filtering for molecular ecologists","volume":"27","author":"O'Leary","year":"2018","journal-title":"Mol. Ecol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0155","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.vetpar.2007.07.002","article-title":"World distribution of Trichinella spp. infections in animals and humans","volume":"149","author":"Pozio","year":"2007","journal-title":"Vet. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0160","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1093\/genetics\/155.2.945","article-title":"Inference of population structure using multilocus genotype data","volume":"155","author":"Pritchard","year":"2000","journal-title":"Genetics"},{"key":"10.1016\/j.ijpara.2021.08.002_b0165","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.AME-0001-2018","article-title":"Advances in molecular epidemiology of infectious diseases: definitions, approaches, and scope of the field","volume":"6","author":"Riley","year":"2018","journal-title":"Microbiol Spectr"},{"key":"10.1016\/j.ijpara.2021.08.002_b0170","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1038\/nprot.2017.123","article-title":"Deriving genotypes from RAD-seq short-read data using Stacks","volume":"12","author":"Rochette","year":"2017","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.ijpara.2021.08.002_b0175","doi-asserted-by":"crossref","first-page":"799","DOI":"10.1016\/j.meegid.2008.07.008","article-title":"Human dispersal of Trichinella spiralis in domesticated pigs","volume":"8","author":"Rosenthal","year":"2008","journal-title":"Infect Genet Evol"},{"key":"10.1016\/j.ijpara.2021.08.002_b0180","doi-asserted-by":"crossref","first-page":"218","DOI":"10.3389\/fgene.2020.00218","article-title":"Comparing the performance of microsatellites and RADseq in population genetic studies: analysis of data for pike (Esox lucius) and a synthesis of previous studies","volume":"11","author":"Sunde","year":"2020","journal-title":"Front. Genet."},{"key":"10.1016\/j.ijpara.2021.08.002_b0185","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1186\/s12936-019-2880-1","article-title":"Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa","volume":"18","author":"Tessema","year":"2019","journal-title":"Malar. J."},{"key":"10.1016\/j.ijpara.2021.08.002_b0190","doi-asserted-by":"crossref","first-page":"104705","DOI":"10.1016\/j.meegid.2021.104705","article-title":"Divergence at mitochondrial and ribosomal loci indicates the split between Asian and European populations of Trichinella spiralis occurred prior to swine domestication","volume":"88","author":"Thompson","year":"2021","journal-title":"Infect Genet Evol"},{"key":"10.1016\/j.ijpara.2021.08.002_b0195","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1016\/j.ijpara.2013.06.007","article-title":"Parasite zoonoses and wildlife: One Health, spillover and human activity","volume":"43","author":"Thompson","year":"2013","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0200","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1016\/j.pt.2019.07.002","article-title":"Foodborne parasites in Europe: present status and future trends","volume":"35","author":"Trevisan","year":"2019","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0205","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.meegid.2017.07.004","article-title":"A step forward in the understanding of the presence and expansion of Echinococcus multilocularis in Eastern Europe using microsatellite EmsB genotyping in Poland","volume":"54","author":"Umhang","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0210","doi-asserted-by":"crossref","first-page":"1859","DOI":"10.1016\/S0020-7519(99)00107-1","article-title":"A multiplex PCR for unequivocal differentiation of all encapsulated and non-encapsulated genotypes of Trichinella","volume":"29","author":"Zarlenga","year":"1999","journal-title":"Int. J. Parasitol."},{"key":"10.1016\/j.ijpara.2021.08.002_b0215","doi-asserted-by":"crossref","first-page":"756","DOI":"10.1645\/14-622.1","article-title":"Anthropogenics: human influence on global and genetic homogenization of parasite populations","volume":"100","author":"Zarlenga","year":"2014","journal-title":"J. Parasitol."}],"container-title":["International Journal for Parasitology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0020751921002629?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0020751921002629?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T14:07:19Z","timestamp":1758118039000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0020751921002629"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2]]},"references-count":43,"journal-issue":{"issue":"2-3","published-print":{"date-parts":[[2022,2]]}},"alternative-id":["S0020751921002629"],"URL":"https:\/\/doi.org\/10.1016\/j.ijpara.2021.08.002","relation":{},"ISSN":["0020-7519"],"issn-type":[{"value":"0020-7519","type":"print"}],"subject":[],"published":{"date-parts":[[2022,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Trich-tracker \u2013 a practical tool to trace Trichinella spiralis transmission based on rapid, cost-effective sampling of genome-wide genetic variation","name":"articletitle","label":"Article Title"},{"value":"International Journal for Parasitology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ijpara.2021.08.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s). Published by Elsevier Ltd on behalf of Australian Society for Parasitology.","name":"copyright","label":"Copyright"}]}}