Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring

Authors

Gregory H. Tyson, U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States. Electronic address: Gregory.Tyson@fda.hhs.gov.
Olgica Ceric, U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
Jake Guag, U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
Sarah Nemser, U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
Stacey Borenstein, U.S. Food and Drug Administration, Center for Veterinary Medicine, Office of Research, United States.
Durda Slavic, University of Guelph - Animal Health Laboratory, Canada.
Sarah Lippert, University of Guelph - Animal Health Laboratory, Canada.
Rebecca McDowell, University of Guelph - Animal Health Laboratory, Canada.
Aparna Krishnamurthy, University of Guelph - Animal Health Laboratory, Canada.
Shannon Korosec, Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada.
Cheryl Friday, Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada.
Neil Pople, Manitoba Agriculture and Resource Development - Veterinary Diagnostic Services, Canada.
Matthew E. Saab, Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Canada.
Julie-Hélène Fairbrother, Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec, Canada.
Isabelle Janelle, Complexe de diagnostic et d'épidémiosurveillance vétérinaires du Québec, Canada.
Deanna McMillan, University of Saskatchewan - Prairie Diagnostic Services Inc, Canada.
Yugendar R. Bommineni, Bronson Animal Disease Diagnostic Laboratory, United States.
David Simon, Bronson Animal Disease Diagnostic Laboratory, United States.
Shipra Mohan, Bronson Animal Disease Diagnostic Laboratory, United States.
Susan Sanchez, Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States.
Ashley Phillips, Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States.
Paula Bartlett, Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, The University of Georgia, United States.
Hemant Naikare, University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States.
Cynthia Watson, University of Georgia - Tifton Veterinary Diagnostic & Investigational Laboratory, United States.
Orhan Sahin, Iowa State University, United States.
Chloe Stinman, Iowa State University, United States.
Leyi Wang, University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States.
Carol Maddox, University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States.
Vanessa DeShambo, University of Illinois Veterinary Diagnostic Laboratory - College of Veterinary Medicine, United States.
Kenitra Hendrix, Indiana Animal Disease Diagnostic Laboratory, United States.
Debra Lubelski, Indiana Animal Disease Diagnostic Laboratory, United States.
Amy Burklund, Kansas State University, United States.
Brian Lubbers, Kansas State University, United States.

Document Type

Article

Publication Date

3-1-2021

Abstract

Whole-genome sequencing (WGS) has changed our understanding of bacterial pathogens, aiding outbreak investigations and advancing our knowledge of their genetic features. However, there has been limited use of genomics to understand antimicrobial resistance of veterinary pathogens, which would help identify emerging resistance mechanisms and track their spread. The objectives of this study were to evaluate the correlation between resistance genotypes and phenotypes for Staphylococcus pseudintermedius, a major pathogen of companion animals, by comparing broth microdilution antimicrobial susceptibility testing and WGS. From 2017-2019, we conducted antimicrobial susceptibility testing and WGS on S. pseudintermedius isolates collected from dogs in the United States as a part of the Veterinary Laboratory Investigation and Response Network (Vet-LIRN) antimicrobial resistance monitoring program. Across thirteen antimicrobials in nine classes, resistance genotypes correlated with clinical resistance phenotypes 98.4 % of the time among a collection of 592 isolates. Our findings represent isolates from diverse lineages based on phylogenetic analyses, and these strong correlations are comparable to those from studies of several human pathogens such as Staphylococcus aureus and Salmonella enterica. We uncovered some important findings, including that 32.3 % of isolates had the mecA gene, which correlated with oxacillin resistance 97.0 % of the time. We also identified a novel rpoB mutation likely encoding rifampin resistance. These results show the value in using WGS to assess antimicrobial resistance in veterinary pathogens and to reveal putative new mechanisms of resistance.

Publication Source (Journal or Book title)

Veterinary microbiology

First Page

109006

Recommended Citation

Tyson, G. H., Ceric, O., Guag, J., Nemser, S., Borenstein, S., Slavic, D., Lippert, S., McDowell, R., Krishnamurthy, A., Korosec, S., Friday, C., Pople, N., Saab, M. E., Fairbrother, J., Janelle, I., McMillan, D., Bommineni, Y. R., Simon, D., Mohan, S., Sanchez, S., Phillips, A., Bartlett, P., Naikare, H., Watson, C., Sahin, O., Stinman, C., Wang, L., Maddox, C., DeShambo, V., Hendrix, K., Lubelski, D., Burklund, A., & Lubbers, B. (2021). Genomics accurately predicts antimicrobial resistance in Staphylococcus pseudintermedius collected as part of Vet-LIRN resistance monitoring. Veterinary microbiology, 254, 109006. https://doi.org/10.1016/j.vetmic.2021.109006