{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T00:06:39Z","timestamp":1788998799598,"version":"build-2803163510"},"reference-count":67,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T00:00:00Z","timestamp":1754352000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,8,5]],"date-time":"2025-08-05T00:00:00Z","timestamp":1754352000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100000199","name":"U.S. Department of Agriculture","doi-asserted-by":"publisher","award":["CA-V-PHR-4142-H"],"award-info":[{"award-number":["CA-V-PHR-4142-H"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,8,5]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      <jats:italic toggle=\"yes\">Mannheimia haemolytica<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Pasteurella multocida<\/jats:italic>\n                      are two of the main bacterial pathogens associated with bovine respiratory disease (BRD). BRD represents one of the most significant health challenges in the cattle industry, causing substantial economic losses through animal morbidity and mortality while raising serious welfare concerns. The objectives of this project were to (i) characterize virulence factor (VF) and antimicrobial resistance (AMR) genes in\n                      <jats:italic toggle=\"yes\">M. haemolytica<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">P. multocida<\/jats:italic>\n                      isolates from dairy cattle of different ages with and without BRD using whole-genome sequencing (WGS); (ii) evaluate associations between microbial genetic elements and animal disease status; and (iii) assess the accuracy of genome-based predictions for the antimicrobial resistance phenotype. Using a case-control study, AMR and VF genes were characterized from 149\n                      <jats:italic toggle=\"yes\">P<\/jats:italic>\n                      .\n                      <jats:italic toggle=\"yes\">multocida<\/jats:italic>\n                      and 68\n                      <jats:italic toggle=\"yes\">M<\/jats:italic>\n                      .\n                      <jats:italic toggle=\"yes\">haemolytica<\/jats:italic>\n                      isolates from preweaned calves, weaned heifers, and cows with and without BRD. The large genetic diversity observed in both bacterial species prevented the identification of unique genetic markers associated with disease status or age group. AMR genes (22 genes) from 12 antimicrobial classes were identified in\n                      <jats:italic toggle=\"yes\">P. multocida<\/jats:italic>\n                      isolates, while 11 AMR genes for seven antimicrobial classes were identified in\n                      <jats:italic toggle=\"yes\">M. haemolytica<\/jats:italic>\n                      isolates. Additionally, 28 and 15 virulence genes were identified in\n                      <jats:italic toggle=\"yes\">P. multocida<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">M. haemolytica<\/jats:italic>\n                      , respectively. The ability of WGS-based predictions to predict phenotypic antimicrobial resistance showed variable accuracy across different antimicrobials, achieving moderate levels of agreement overall. Findings from this project demonstrate that identifying genomic markers based on gene presence\/absence lacks discriminatory power within this population for identifying unique genotypes associated with disease status in these genomically diverse organisms.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      This case-control study provides key microbial ecological advances by elucidating the role of bacteria in the bovine respiratory disease complex in dairy cattle. Previous research has identified specific virulence factors in both bacterial genomes that resulted in disease. Our results challenge this perception and are of high impact, revealing that the pan-genome of both bacteria did not differentiate among the clinical cases or age groups, and a specific pathogenic pathotype was not evident in the isolates from this study, and it did not emerge when including additional public whole-genome sequences to increase the analytical power of the analysis (the first study to use this approach to evaluate bovine respiratory disease in cattle). In addition to these novel discoveries, this study describes the first population-scale genomic comparison of both\n                      <jats:italic toggle=\"yes\">Mannheimia haemolytica<\/jats:italic>\n                      and\n                      <jats:italic toggle=\"yes\">Pasteurella multocida<\/jats:italic>\n                      genomes collected from affected and healthy dairy cattle from different age groups and from multiple farms.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01200-25","type":"journal-article","created":{"date-parts":[[2025,6,16]],"date-time":"2025-06-16T09:49:01Z","timestamp":1750067341000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":9,"title":["Comparison of virulence and resistance genes in\n                    <i>Mannheimia haemolytica<\/i>\n                    and\n                    <i>Pasteurella multocida<\/i>\n                    from dairy cattle with and without bovine respiratory disease"],"prefix":"10.1128","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3464-6670","authenticated-orcid":true,"given":"Adriana","family":"Garzon","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-6079-7576","authenticated-orcid":true,"given":"Craig","family":"Miramontes","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7471-1978","authenticated-orcid":true,"given":"Bart C.","family":"Weimer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]},{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"100K Pathogen Genome Project, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rodrigo","family":"Profeta","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]},{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"100K Pathogen Genome Project, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alejandro","family":"Hoyos-Jaramillo","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heather M.","family":"Fritz","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"California Animal Health and Food Safety Lab, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2028-8761","authenticated-orcid":true,"given":"Richard V.","family":"Pereira","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05rrcem69","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Population Health and Reproduction, School of Veterinary Medicine, University of California","place":["Davis, USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","unstructured":"USDA. 2014. 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