{"id":"https://openalex.org/W3205964546","doi":"https://doi.org/10.3389/fmicb.2021.763669","title":"Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing","display_name":"Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing","publication_year":2021,"publication_date":"2021-10-18","ids":{"openalex":"https://openalex.org/W3205964546","doi":"https://doi.org/10.3389/fmicb.2021.763669","mag":"3205964546","pmid":"https://pubmed.ncbi.nlm.nih.gov/34733267","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/8558520"},"language":"en","primary_location":{"id":"doi:10.3389/fmicb.2021.763669","doi":"https://doi.org/10.3389/fmicb.2021.763669","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fmicb.2021.763669","pdf_url":null,"source":{"id":"https://openalex.org/S2484704948","display_name":"Frontiers in Microbiology","issn_l":"1664-302X","issn":["1664-302X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Microbiology","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/fmicb.2021.763669","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089294584","display_name":"Laura M. Carroll","orcid":"https://orcid.org/0000-0002-3677-0192","observed_orcids":["https://orcid.org/0000-0002-3677-0192"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Laura M. Carroll","raw_affiliation_strings":["Department of Food Science, Cornell University, Ithaca, New York, USA","Department of Food Science, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048218430","display_name":"Ariel J. Buehler","orcid":"https://orcid.org/0000-0003-0267-778X","observed_orcids":["https://orcid.org/0000-0003-0267-778X"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ariel J. Buehler","raw_affiliation_strings":["Department of Food Science, Cornell University, Ithaca, New York, USA","Department of Food Science, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016572389","display_name":"Ahmed Gaballa","orcid":"https://orcid.org/0000-0002-0246-4701","observed_orcids":["https://orcid.org/0000-0002-0246-4701"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ahmed Gaballa","raw_affiliation_strings":["Department of Food Science, Cornell University, Ithaca, New York, USA","Department of Food Science, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046831891","display_name":"Julie D. Siler","orcid":"https://orcid.org/0000-0003-3833-5802","observed_orcids":["https://orcid.org/0000-0003-3833-5802"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julie D. Siler","raw_affiliation_strings":["Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA","Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016508919","display_name":"Kevin J. Cummings","orcid":"https://orcid.org/0000-0003-3327-596X","observed_orcids":["https://orcid.org/0000-0003-3327-596X"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin J. Cummings","raw_affiliation_strings":["Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA","Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Rachel A. Cheng","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachel A. Cheng","raw_affiliation_strings":["Department of Food Science, Cornell University, Ithaca, New York, USA","Department of Food Science, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082217142","display_name":"Martin Wiedmann","orcid":"https://orcid.org/0000-0002-4168-5662","observed_orcids":["https://orcid.org/0000-0002-4168-5662"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Martin Wiedmann","raw_affiliation_strings":["Department of Food Science, Cornell University, Ithaca, New York, USA","Department of Food Science, Cornell University, Ithaca, NY, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, New York, USA","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Food Science, Cornell University, Ithaca, NY, United States","institution_ids":["https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5089294584"],"corresponding_institution_ids":["https://openalex.org/I205783295"],"apc_list":{"value":2950,"currency":"USD","value_usd":2950},"apc_paid":{"value":2950,"currency":"USD","value_usd":2950},"fwci":2.0102,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.84804454,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"12","issue":null,"first_page":"763669","last_page":"763669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10486","display_name":"Salmonella and Campylobacter epidemiology","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10943","display_name":"Escherichia coli research studies","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11688","display_name":"Microbial infections and disease research","score":0.0,"subfield":{"id":"https://openalex.org/subfields/2404","display_name":"Microbiology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/salmonella-enterica","display_name":"Salmonella enterica","score":0.9980000257492065},{"id":"https://openalex.org/keywords/dairy-cows","display_name":"dairy cattle","score":0.7950000166893005},{"id":"https://openalex.org/keywords/microevolution","display_name":"microevolution","score":0.8920000195503235},{"id":"https://openalex.org/keywords/antimicrobial-resistance","display_name":"antimicrobial resistance","score":0.9539999961853027},{"id":"https://openalex.org/keywords/antimicrobial-resistance-determinants","display_name":"antimicrobial resistance determinants","score":0.8309999704360962},{"id":"https://openalex.org/keywords/minimum-inhibitory-concentration-prediction","display_name":"minimum inhibitory concentration prediction","score":0.8059999942779541},{"id":"https://openalex.org/keywords/beta-lactamase","display_name":"beta-lactamase","score":0.8100000023841858},{"id":"https://openalex.org/keywords/blacmy","display_name":"blaCMY","score":0.8389999866485596},{"id":"https://openalex.org/keywords/blactx-m","display_name":"blaCTX-M","score":0.9940000176429749},{"id":"https://openalex.org/keywords/zoonotic-foodborne-pathogens","display_name":"zoonotic foodborne pathogens","score":0.7300000190734863},{"id":"https://openalex.org/keywords/whole-genome-phylogeny","display_name":"whole-genome phylogeny","score":0.8460000157356262}],"concepts":[{"id":"https://openalex.org/C2779607309","wikidata":"https://www.wikidata.org/wiki/Q2264864","display_name":"Salmonella enterica","level":4,"score":0.7981293201446533},{"id":"https://openalex.org/C11710620","wikidata":"https://www.wikidata.org/wiki/Q680054","display_name":"Microevolution","level":3,"score":0.7823041081428528},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7066518068313599},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5876420140266418},{"id":"https://openalex.org/C2781065037","wikidata":"https://www.wikidata.org/wiki/Q150839","display_name":"Salmonella","level":3,"score":0.5853187441825867},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.5755596160888672},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5037152171134949},{"id":"https://openalex.org/C2776977481","wikidata":"https://www.wikidata.org/wiki/Q2915","display_name":"Dairy cattle","level":2,"score":0.445875883102417},{"id":"https://openalex.org/C150903083","wikidata":"https://www.wikidata.org/wiki/Q7108","display_name":"Biotechnology","level":1,"score":0.433858722448349},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3285835087299347},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27099427580833435},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.21121814846992493},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.12111032009124756},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.11621329188346863},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.10603556036949158}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.3389/fmicb.2021.763669","doi":"https://doi.org/10.3389/fmicb.2021.763669","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fmicb.2021.763669","pdf_url":null,"source":{"id":"https://openalex.org/S2484704948","display_name":"Frontiers in Microbiology","issn_l":"1664-302X","issn":["1664-302X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Microbiology","raw_type":"journal-article"},{"id":"doi:10.1101/2021.08.20.457169","doi":"https://doi.org/10.1101/2021.08.20.457169","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2021.08.20.457169","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2021/08/21/2021.08.20.457169.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:europepmc.org:7450356","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8558520","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8558520","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8558520","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Front Microbiol","raw_type":"Text"},{"id":"pmid:34733267","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34733267","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in microbiology","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:d28c0743513d4bf690f46143f42429c9","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/d28c0743513d4bf690f46143f42429c9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Microbiology, Vol 12 (2021)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fmicb.2021.763669","doi":"https://doi.org/10.3389/fmicb.2021.763669","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fmicb.2021.763669","pdf_url":null,"source":{"id":"https://openalex.org/S2484704948","display_name":"Frontiers in Microbiology","issn_l":"1664-302X","issn":["1664-302X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","jufo-1","ki-jl-1","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Microbiology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.9208999872207642},{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.428600013256073}],"study_designs":[],"awards":[{"id":"https://openalex.org/G4989108295","display_name":null,"funder_award_id":"DGE-1650441","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G633020919","display_name":null,"funder_award_id":"N01AI30054","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7031722743","display_name":"Graduate Research Fellowship Program (GRFP)","funder_award_id":"1650441","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8229174675","display_name":null,"funder_award_id":"DGE-165-0441","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3205964546.pdf","grobid_xml":"https://content.openalex.org/works/W3205964546.grobid-xml"},"referenced_works_count":172,"referenced_works":["https://openalex.org/W220770808","https://openalex.org/W1089143458","https://openalex.org/W1483214510","https://openalex.org/W1587026990","https://openalex.org/W1596062789","https://openalex.org/W1605984840","https://openalex.org/W1688810545","https://openalex.org/W1779315825","https://openalex.org/W1831050183","https://openalex.org/W1845997799","https://openalex.org/W1957469265","https://openalex.org/W1968783265","https://openalex.org/W1971873666","https://openalex.org/W1972145956","https://openalex.org/W1973192023","https://openalex.org/W1974599898","https://openalex.org/W1975339800","https://openalex.org/W1977678315","https://openalex.org/W1983102293","https://openalex.org/W1984289559","https://openalex.org/W1992828939","https://openalex.org/W2000315035","https://openalex.org/W2026062398","https://openalex.org/W2038416870","https://openalex.org/W2044920068","https://openalex.org/W2058550226","https://openalex.org/W2059945137","https://openalex.org/W2063558597","https://openalex.org/W2066271947","https://openalex.org/W2069364310","https://openalex.org/W2074604023","https://openalex.org/W2094939159","https://openalex.org/W2095680943","https://openalex.org/W2096093282","https://openalex.org/W2097583215","https://openalex.org/W2099053943","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2105245948","https://openalex.org/W2105829810","https://openalex.org/W2106578986","https://openalex.org/W2107772251","https://openalex.org/W2108234281","https://openalex.org/W2108996658","https://openalex.org/W2109684694","https://openalex.org/W2111647009","https://openalex.org/W2112364185","https://openalex.org/W2112821341","https://openalex.org/W2116041602","https://openalex.org/W2117029130","https://openalex.org/W2117801354","https://openalex.org/W2118048521","https://openalex.org/W2118327902","https://openalex.org/W2118688136","https://openalex.org/W2120902911","https://openalex.org/W2121788088","https://openalex.org/W2122082385","https://openalex.org/W2122673596","https://openalex.org/W2123186607","https://openalex.org/W2127971944","https://openalex.org/W2128501349","https://openalex.org/W2128591134","https://openalex.org/W2128599926","https://openalex.org/W2129733478","https://openalex.org/W2131271579","https://openalex.org/W2132743040","https://openalex.org/W2134852597","https://openalex.org/W2136430672","https://openalex.org/W2138076738","https://openalex.org/W2138505176","https://openalex.org/W2140628770","https://openalex.org/W2142678478","https://openalex.org/W2143325926","https://openalex.org/W2143773368","https://openalex.org/W2145466384","https://openalex.org/W2147571700","https://openalex.org/W2150131459","https://openalex.org/W2151409320","https://openalex.org/W2151723211","https://openalex.org/W2153432740","https://openalex.org/W2155630536","https://openalex.org/W2161163382","https://openalex.org/W2161417515","https://openalex.org/W2162494851","https://openalex.org/W2164030271","https://openalex.org/W2165446840","https://openalex.org/W2165460624","https://openalex.org/W2168874401","https://openalex.org/W2189510244","https://openalex.org/W2218703360","https://openalex.org/W2287849783","https://openalex.org/W2295598076","https://openalex.org/W2318876458","https://openalex.org/W2322358787","https://openalex.org/W2340172603","https://openalex.org/W2394763400","https://openalex.org/W2415911133","https://openalex.org/W2423976053","https://openalex.org/W2432815617","https://openalex.org/W2460324897","https://openalex.org/W2469308171","https://openalex.org/W2513408189","https://openalex.org/W2513727910","https://openalex.org/W2544493586","https://openalex.org/W2557776122","https://openalex.org/W2582743722","https://openalex.org/W2583363792","https://openalex.org/W2592466705","https://openalex.org/W2604119841","https://openalex.org/W2614081736","https://openalex.org/W2623602852","https://openalex.org/W2624675983","https://openalex.org/W2726286722","https://openalex.org/W2729278855","https://openalex.org/W2743399464","https://openalex.org/W2747242995","https://openalex.org/W2753422859","https://openalex.org/W2767841410","https://openalex.org/W2775142379","https://openalex.org/W2778001471","https://openalex.org/W2782085461","https://openalex.org/W2789843538","https://openalex.org/W2795440218","https://openalex.org/W2796887402","https://openalex.org/W2801159594","https://openalex.org/W2809783422","https://openalex.org/W2810196595","https://openalex.org/W2810427827","https://openalex.org/W2811208756","https://openalex.org/W2883251903","https://openalex.org/W2895950305","https://openalex.org/W2898580681","https://openalex.org/W2901954177","https://openalex.org/W2903435924","https://openalex.org/W2904597931","https://openalex.org/W2923223796","https://openalex.org/W2925227700","https://openalex.org/W2936404759","https://openalex.org/W2944063377","https://openalex.org/W2949848068","https://openalex.org/W2951342755","https://openalex.org/W2951464304","https://openalex.org/W2951830743","https://openalex.org/W2952311913","https://openalex.org/W2952620784","https://openalex.org/W2952668074","https://openalex.org/W2964449978","https://openalex.org/W2967125766","https://openalex.org/W2968322804","https://openalex.org/W2975983989","https://openalex.org/W2983910950","https://openalex.org/W2996646588","https://openalex.org/W2999532268","https://openalex.org/W3006688339","https://openalex.org/W3007951356","https://openalex.org/W3009876791","https://openalex.org/W3014666387","https://openalex.org/W3014989991","https://openalex.org/W3015505532","https://openalex.org/W3019693505","https://openalex.org/W3037230961","https://openalex.org/W3082639302","https://openalex.org/W3102476541","https://openalex.org/W3174993126","https://openalex.org/W3197563078","https://openalex.org/W4211177544","https://openalex.org/W4232096031","https://openalex.org/W4242289937","https://openalex.org/W4242318543","https://openalex.org/W4250392946","https://openalex.org/W4399648713","https://openalex.org/W6869345919"],"related_works":["https://openalex.org/W3014666387","https://openalex.org/W4389056585","https://openalex.org/W6976761642","https://openalex.org/W4378516381","https://openalex.org/W4379051973","https://openalex.org/W2770895766","https://openalex.org/W2394763400","https://openalex.org/W6910980913","https://openalex.org/W7097518108","https://openalex.org/W4388794807"],"abstract_inverted_index":{"Abstract":[0],"Livestock":[1],"represent":[2],"a":[3,179,216],"possible":[4],"reservoir":[5],"for":[6,196,235],"facilitating":[7],"the":[8,11,31,65,74,77,81,127,154,186,243,291,313,320,323,329,345],"transmission":[9],"of":[10,69,76,85,101,182,185,218,227,242,248,250,294,316,322,333],"zoonotic":[12,337],"foodborne":[13],"pathogen":[14,72],"Salmonella":[15,42,155,318],"enterica":[16],"to":[17,28,40,63,111],"humans;":[18],"there":[19],"is":[20],"also":[21],"concern":[22],"that":[23,204,265],"strains":[24,43],"can":[25],"acquire":[26],"resistance":[27,104],"antimicrobials":[29],"in":[30,87,95,131,148,163,335],"farm":[32,325],"environment.":[33],"Here,":[34],"we":[35],"use":[36],"whole-genome":[37,156],"sequencing":[38],"(WGS)":[39],"characterize":[41],"(":[44,254],"n":[45],"=":[46],"128)":[47],"isolated":[48],"from":[49],"healthy":[50],"dairy":[51],"cattle":[52],"and":[53,67,83,109,116,138,162,222,231,245,285,300,326,331,339],"their":[54,340],"associated":[55,270,341],"environments":[56],"on":[57,207],"13":[58],"New":[59],"York":[60],"State":[61],"farms":[62],"assess":[64],"diversity":[66],"microevolution":[68,244],"this":[70],"important":[71],"at":[73,319,344],"level":[75],"individual":[78,272,324],"herd.":[79],"Additionally,":[80],"accuracy":[82,210],"concordance":[84,168],"multiple":[86,279],"silico":[88,96,132,149,164,172,240],"tools":[89,108],"are":[90],"assessed,":[91],"including:":[92],"(i)":[93],"two":[94],"serotyping":[97,133,137],"tools,":[98],"(ii)":[99],"combinations":[100],"five":[102,112],"antimicrobial":[103,119],"(AMR)":[105],"determinant":[106,114,174,283],"detection":[107,175,202],"one":[110,118],"AMR":[113,173,201,246,282,317,342],"databases,":[115],"(iii)":[117],"minimum":[120,219],"inhibitory":[121],"concentration":[122],"(MIC)":[123],"prediction":[124],"tool.":[125],"For":[126,200],"isolates":[128],"sequenced":[129],"here,":[130],"methods":[134,165,176,203],"outperformed":[135],"traditional":[136,159],"resolved":[139],"all":[140,197],"un-typable":[141],"and/or":[142],"ambiguous":[143],"serotype":[144,160,252],"assignments.":[145],"Serotypes":[146],"assigned":[147],"showed":[150,166,178],"greater":[151],"congruency":[152],"with":[153,225,271],"phylogeny":[157],"than":[158],"assignments,":[161],"high":[167,180],"(99%":[169],"agreement).":[170],"In":[171,239],"additionally":[177],"degree":[181],"concordance,":[183],"regardless":[184],"pipeline":[187],"or":[188],"database":[189],"used":[190],"(\u226598%":[191],"agreement":[192],"between":[193],"susceptible/resistant":[194],"assignments":[195],"pipeline/database":[198,237],"combinations).":[199],"relied":[205],"exclusively":[206],"nucleotide":[208,220,229],"BLAST,":[209],"could":[211],"be":[212],"maximized":[213],"by":[214],"using":[215],"range":[217],"identity":[221,230],"coverage":[223,233],"thresholds,":[224],"thresholds":[226],"75%":[228],"50-60%":[232],"adequate":[234],"most":[236],"combinations.":[238],"characterization":[241],"dynamics":[247,315],"each":[249],"six":[251],"groups":[253],"S.":[255],"Anatum,":[256],"Cerro,":[257],"Kentucky,":[258],"Meleagridis,":[259],"Newport,":[260],"Typhimurium/Typhimurium":[261],"variant":[262],"Copenhagen)":[263],"revealed":[264],"some":[266],"lineages":[267],"were":[268,276,288],"strongly":[269],"farms,":[273],"while":[274],"others":[275],"distributed":[277],"across":[278],"farms.":[280],"Numerous":[281],"acquisition":[284,293],"loss":[286],"events":[287],"identified,":[289],"including":[290],"recent":[292],"cephalosporin":[295],"resistance-conferring":[296],"bla":[297,301],"CMY":[298],"-":[299],"CTX-M":[302],"-type":[303],"beta-lactamases.":[304],"The":[305],"results":[306],"presented":[307],"here":[308],"provide":[309],"high-resolution":[310],"insight":[311],"into":[312],"temporal":[314],"scale":[321],"highlight":[327],"both":[328],"strengths":[330],"limitations":[332],"WGS":[334],"tracking":[336],"pathogens":[338],"determinants":[343],"livestock-human":[346],"interface.":[347]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2021-10-25T00:00:00"}
