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

Gregory H. Tyson, Olgica Ceric, Jake Guag, Sarah Nemser, Stacey Borenstein, Durda Slavic, Sarah Lippert, Rebecca McDowell, Aparna Krishnamurthy, Shannon Korosec, Cheryl Friday, Neil Pople, Matthew E. Saab, Julie Hélène Fairbrother, Isabelle Janelle, Deanna McMillan, Yugendar R. Bommineni, David Simon, Shipra Mohan, Susan SanchezAshley Phillips, Paula Bartlett, Hemant Naikare, Cynthia Watson, Orhan Sahin, Chloe Stinman, Leyi Wang, Carol Maddox, Vanessa DeShambo, Kenitra Hendrix, Debra Lubelski, Amy Burklund, Brian Lubbers, Debbie Reed, Tracie Jenkins, Erdal Erol, Mukeshbhai Patel, Stephan Locke, Jordan Fortner, Laura Peak, Udeni Balasuriya, Rinosh Mani, Niesa Kettler, Karen Olsen, Shuping Zhang, Zhenyu Shen, Martha Pulido Landinez, Jay Kay Thornton, Anil Thachil, Melissa Byrd, Megan Jacob, Darlene Krogh, Brett Webb, Lynn Schaan, Amar Patil, Sarmila Dasgupta, Shannon Mann, Laura B. Goodman, Rebecca June Franklin-Guild, Renee R. Anderson, Patrick K. Mitchell, Brittany D. Cronk, Missy Aprea, Jing Cui, Dominika Jurkovic, Melanie Prarat, Yan Zhang, Katherine Shiplett, Dubra Diaz Campos, Joany Van Balen Rubio, Akhilesh Ramanchandran, Scott Talent, Deepanker Tewari, Nagaraja Thirumalapura, Donna Kelly, Denise Barnhart, Lacey Hall, Shelley Rankin, Jaclyn Dietrich, Stephen Cole, Joy Scaria, Linto Antony, Sara D. Lawhon, Jing Wu, Christine McCoy, Kelly Dietz, Rebecca Wolking, Trevor Alexander, Claire Burbick, Renate Reimschuessel

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number109006
JournalVeterinary Microbiology
Volume254
DOIs
StatePublished - Mar 2021
Externally publishedYes

Keywords

  • Antimicrobial resistance
  • Genomics
  • Staphylococcus pseudintermedius

ASJC Scopus subject areas

  • Microbiology
  • veterinary(all)

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