{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:48:20Z","timestamp":1760060900188,"version":"build-2065373602"},"reference-count":43,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2023,10,18]],"date-time":"2023-10-18T00:00:00Z","timestamp":1697587200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Food Microbiology"],"published-print":{"date-parts":[[2024,4]]},"DOI":"10.1016\/j.fm.2023.104403","type":"journal-article","created":{"date-parts":[[2023,10,18]],"date-time":"2023-10-18T11:46:17Z","timestamp":1697629577000},"page":"104403","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii"],"prefix":"10.1016","volume":"118","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8559-1660","authenticated-orcid":false,"given":"Balaji","family":"Sundararaman","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karen","family":"Shapiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Packham","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lauren E.","family":"Camp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rachel S.","family":"Meyer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Beth","family":"Shapiro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard E.","family":"Green","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/j.fm.2023.104403_bib1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.fm.2023.104403_bib2","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1017\/S0950268899002113","article-title":"Potential contamination of drinking water with Toxoplasma gondii oocysts","volume":"122","author":"Aramini","year":"1999","journal-title":"Epidemiol. Infect."},{"key":"10.1016\/j.fm.2023.104403_bib3","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1111\/tbed.14214","article-title":"Epidemiological study of toxoplasmosis outbreaks in Brazil","volume":"69","author":"Balbino","year":"2022","journal-title":"Transbound. Emerg. Dis."},{"key":"10.1016\/j.fm.2023.104403_bib4","doi-asserted-by":"crossref","first-page":"2230","DOI":"10.1128\/JCM.00486-15","article-title":"Rapid whole-genome sequencing of Mycobacterium tuberculosis isolates directly from clinical samples","volume":"53","author":"Brown","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib5","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1089\/fpd.2019.2662","article-title":"Use of whole-genome sequencing for food safety and public health in the United States","volume":"16","author":"Brown","year":"2019","journal-title":"Foodb. Pathog. Dis."},{"key":"10.1016\/j.fm.2023.104403_bib6","doi-asserted-by":"crossref","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.fm.2023.104403_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.fawpar.2020.e00096","article-title":"Application of next generation sequencing for detection of protozoan pathogens in shellfish","volume":"21","author":"DeMone","year":"2020","journal-title":"Food Waterborne Parasitol"},{"key":"10.1016\/j.fm.2023.104403_bib8","doi-asserted-by":"crossref","DOI":"10.1016\/j.ijfoodmicro.2021.109315","article-title":"A metabarcoding approach for detecting protozoan pathogens in wild oysters from Prince Edward Island, Canada","volume":"360","author":"DeMone","year":"2021","journal-title":"Int. J. Food Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib9","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1186\/s42522-020-00015-6","article-title":"Novel opportunities for NGS-based one health surveillance of foodborne viruses","volume":"2","author":"Desdouits","year":"2020","journal-title":"One Health Outlook"},{"key":"10.1016\/j.fm.2023.104403_bib10","doi-asserted-by":"crossref","DOI":"10.1016\/j.vetpar.2020.109296","article-title":"Recent epidemiologic and clinical importance of Toxoplasma gondii infections in marine mammals: 2009-2020","volume":"288","author":"Dubey","year":"2020","journal-title":"Vet. Parasitol."},{"key":"10.1016\/j.fm.2023.104403_bib11","doi-asserted-by":"crossref","first-page":"3565","DOI":"10.1128\/JCM.01066-15","article-title":"Utility of whole-genome sequencing of Escherichia coli O157 for outbreak detection and epidemiological surveillance","volume":"53","author":"Holmes","year":"2015","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib12","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1101\/gr.5969107","article-title":"MEGAN analysis of metagenomic data","volume":"17","author":"Huson","year":"2007","journal-title":"Genome Res."},{"key":"10.1016\/j.fm.2023.104403_bib13","doi-asserted-by":"crossref","first-page":"806","DOI":"10.1136\/bmj.4.5686.806-b","article-title":"Life cycle of toxoplasma gondii","volume":"4","author":"Hutchison","year":"1969","journal-title":"Br. Med. J."},{"key":"10.1016\/j.fm.2023.104403_bib14","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1093\/cid\/ciw242","article-title":"Implementation of nationwide real-time whole-genome sequencing to enhance listeriosis outbreak detection and investigation","volume":"63","author":"Jackson","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"10.1016\/j.fm.2023.104403_bib15","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1128\/JCM.03617-13","article-title":"Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli","volume":"52","author":"Joensen","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib16","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1093\/jhered\/esab012","article-title":"A fast and efficient single-stranded genomic library preparation method optimized for ancient DNA","volume":"112","author":"Kapp","year":"2021","journal-title":"J. Hered."},{"key":"10.1016\/j.fm.2023.104403_bib17","doi-asserted-by":"crossref","DOI":"10.1016\/j.fm.2021.103816","article-title":"Quantification of viable protozoan parasites on leafy greens using molecular methods","volume":"99","author":"Kim","year":"2021","journal-title":"Food Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib18","article-title":"World health organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis","volume":"12","author":"Kirk","year":"2015","journal-title":"PLoS Med."},{"key":"10.1016\/j.fm.2023.104403_bib19","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.fawpar.2016.01.001","article-title":"Detection of Cyclospora cayetanensis, Cryptosporidium spp., and Toxoplasma gondii on imported leafy green vegetables in Canadian survey","volume":"2","author":"Lalonde","year":"2016","journal-title":"Food and Waterborne Parasitol."},{"key":"10.1016\/j.fm.2023.104403_bib20","first-page":"770","article-title":"Rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations","volume":"5","author":"Law","year":"2014","journal-title":"Front. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib21","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.fm.2023.104403_bib22","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms10147","article-title":"Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes","volume":"7","author":"Lorenzi","year":"2016","journal-title":"Nat. Commun."},{"key":"10.1016\/j.fm.2023.104403_bib23","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet j"},{"key":"10.1016\/j.fm.2023.104403_bib24","series-title":"CRC Handbook of Marine Mammal Medicine","article-title":"Protozoan parasites of marine mammals","author":"Miller","year":"2018"},{"key":"10.1016\/j.fm.2023.104403_bib25","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES.2017.22.23.30544","article-title":"PulseNet International: vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance","volume":"22","author":"Nadon","year":"2017","journal-title":"Euro Surveill."},{"key":"10.1016\/j.fm.2023.104403_bib26","doi-asserted-by":"crossref","DOI":"10.1111\/1755-0998.12895","article-title":"Minimizing polymerase biases in metabarcoding","author":"Nichols","year":"2018","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.fm.2023.104403_bib27","doi-asserted-by":"crossref","first-page":"129","DOI":"10.4103\/0301-4738.25839","article-title":"Outbreak of ocular toxoplasmosis in Coimbatore, India","volume":"54","author":"Palanisamy","year":"2006","journal-title":"Indian J. Ophthalmol."},{"key":"10.1016\/j.fm.2023.104403_bib28","doi-asserted-by":"crossref","first-page":"ofac344","DOI":"10.1093\/ofid\/ofac344","article-title":"Changing diagnostic testing practices for foodborne pathogens, foodborne diseases active surveillance network, 2012-2019","volume":"9","author":"Ray","year":"2022","journal-title":"Open Forum Infect. Dis."},{"key":"10.1016\/j.fm.2023.104403_bib29","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1128\/CMR.05013-11","article-title":"Epidemiology of and diagnostic strategies for toxoplasmosis","volume":"25","author":"Robert-Gangneux","year":"2012","journal-title":"Clin. Microbiol. Rev."},{"key":"10.1016\/j.fm.2023.104403_bib30","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.fm.2023.104403_bib31","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1111\/j.1365-2672.2012.05384.x","article-title":"PCR inhibitors - occurrence, properties and removal","volume":"113","author":"Schrader","year":"2012","journal-title":"J. Appl. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib32","doi-asserted-by":"crossref","DOI":"10.1016\/j.fawpar.2019.e00049","article-title":"Environmental transmission of Toxoplasma gondii: oocysts in water, soil and food","volume":"15","author":"Shapiro","year":"2019","journal-title":"Food Waterborne Parasitol"},{"key":"10.1016\/j.fm.2023.104403_bib33","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.diagmicrobio.2008.07.009","article-title":"Evaluation of loop-mediated isothermal amplification for detection of Toxoplasma gondii in water samples and comparative findings by polymerase chain reaction and immunofluorescence test (IFT)","volume":"62","author":"Sotiriadou","year":"2008","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"10.1016\/j.fm.2023.104403_bib34","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41576-019-0119-1","article-title":"Ancient pathogen genomics as an emerging tool for infectious disease research","volume":"20","author":"Spyrou","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.fm.2023.104403_bib35","doi-asserted-by":"crossref","first-page":"5844","DOI":"10.1073\/pnas.1203190109","article-title":"Globally diverse Toxoplasma gondii isolates comprise six major clades originating from a small number of distinct ancestral lineages","volume":"109","author":"Su","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"year":"2023","series-title":"A hybridization target enrichment approach for pathogen genomics. mBio","author":"Sundararaman","key":"10.1016\/j.fm.2023.104403_bib43"},{"key":"10.1016\/j.fm.2023.104403_bib36","doi-asserted-by":"crossref","DOI":"10.7717\/peerj.8213","article-title":"VCF2PopTree: a client-side software to construct population phylogeny from genome-wide SNPs","volume":"7","author":"Subramanian","year":"2019","journal-title":"PeerJ"},{"key":"10.1016\/j.fm.2023.104403_bib37","doi-asserted-by":"crossref","first-page":"509","DOI":"10.15585\/mmwr.mm6917a1","article-title":"Preliminary incidence and trends of infections with pathogens transmitted commonly through food - foodborne diseases active surveillance network, 10 U.S. Sites, 2016-2019","volume":"69","author":"Tack","year":"2020","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"10.1016\/j.fm.2023.104403_bib38","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/s13073-014-0104-4","article-title":"Stopping outbreaks with real-time genomic epidemiology","volume":"6","author":"Tang","year":"2014","journal-title":"Genome Med."},{"key":"10.1016\/j.fm.2023.104403_bib39","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1016\/j.pt.2013.06.001","article-title":"Toxoplasma oocysts as a public health problem","volume":"29","author":"Torrey","year":"2013","journal-title":"Trends Parasitol."},{"key":"10.1016\/j.fm.2023.104403_bib40","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1159\/000235639","article-title":"The era of genomic epidemiology","volume":"33","author":"Traynor","year":"2009","journal-title":"Neuroepidemiology"},{"key":"10.1016\/j.fm.2023.104403_bib41","doi-asserted-by":"crossref","first-page":"4035","DOI":"10.1128\/AEM.70.7.4035-4039.2004","article-title":"Evaluation of a strategy for Toxoplasma gondii oocyst detection in water","volume":"70","author":"Villena","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"10.1016\/j.fm.2023.104403_bib42","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1101\/gr.262816.120","article-title":"Third-generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants","volume":"31","author":"Xia","year":"2021","journal-title":"Genome Res."}],"container-title":["Food Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0740002023001909?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0740002023001909?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T19:17:56Z","timestamp":1760037476000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0740002023001909"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,4]]},"references-count":43,"alternative-id":["S0740002023001909"],"URL":"https:\/\/doi.org\/10.1016\/j.fm.2023.104403","relation":{},"ISSN":["0740-0020"],"issn-type":[{"type":"print","value":"0740-0020"}],"subject":[],"published":{"date-parts":[[2024,4]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Whole genome enrichment approach for genomic surveillance of Toxoplasma gondii","name":"articletitle","label":"Article Title"},{"value":"Food Microbiology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.fm.2023.104403","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 The Authors. Published by Elsevier Ltd.","name":"copyright","label":"Copyright"}],"article-number":"104403"}}