Keeping our cherished pets safe and healthy: using genomics to study bacterial pathogens of dogs and cats

A population genomics analysis of Staphylococcus pseudintermedius

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Sharing our lives with dogs and cats goes back tens of thousands of years. We love them, we cherish them, we care for them. They are beloved members of every family and thus we want to make sure that they are healthy and free from disease.

Co-author Colin McGonagle with Walter

Staphylococcus pseudintermedius is a common bacterial inhabitant of the skin and mucosa of dogs and cats. It is also a major opportunistic pathogen, often causing canine skin and ear infections. Understanding the diversity and evolution of this increasingly important pathogen is critical to advancing the health of man’s favorite companion and oldest domestic animal.

My lab in collaboration with the New Hampshire Veterinary Diagnostic Laboratory carried out a genomics study of 130 clinical S. pseudintermedius isolates from mostly dogs and a few cats in the New England region of the United States. Our samples came from New Hampshire, Connecticut, Maine, Massachusetts and Vermont located in the northeast region of the country.

Our results revealed the co-circulation of genetically diverse lineages that have access to a large pool of accessory genes. Accessory genes are genes found in one or few strains and may consist of genes necessary to adapt to unique environments, associated with pathogenicity or those that confer drug resistance. We identified methicillin-resistant and multidrug-resistant S. pseudintermedius clones. These have emerged through multiple independent, horizontal acquisition of resistance determinants and frequent genetic exchange that disseminate DNA to the broader population. When compared to previously published genomes from Texas (located in the southern part of the United States), we found evidence of clonal expansion of drug resistant lineages that have disseminated over large geographical distances. Overall, we found that the S. pseudintermedius within a local region (New England) and across the country is remarkably diverse in terms of their evolutionary relationships, virulence and drug resistant characteristics.

Our study highlights the application of population-level genomics approaches in microbes that infect animals. Microbial population genomics involves sequencing the genomes of hundreds and even thousands of closely related strains from different eukaryotic hosts or different environments. It has been instrumental in revolutionizing the epidemiology, surveillance and control strategies of infectious diseases that threaten human health, such as Staphylococcus aureus and Streptococcus pneumoniae. However, the application of population genomics in veterinary medicine remains limited.

Senior author Cheryl P. Andam with Thumper

Our study provides a general framework to integrating high throughput genome sequencing methods in veterinary medicine that will advance our ability to identify targets for strain differentiation, diagnostics and therapeutic options for infections caused by S. pseudintermedius. Our methods will be valuable in the study of other bacterial species that cause disease in many other companion and domestic animals. We hope that our study will inform other opportunities for fruitful cross-disciplinary research at the boundary of veterinary disease epidemiology, genomics and evolutionary biology.

Our paper can be found here: https://www.nature.com/articles/s42003-020-1009-y

 

Cheryl P. Andam

Assistant Professor, Univ at Albany, State Univ of New York

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