LAUSR

Abstract Dogs are a potential source of zoonotic Salmonella transmission. We had previously estimated the prevalence of Salmonella shedding among shelter dogs throughout Texas using a repeated cross‐sectional study design. Our current objectives were to fully characterize the Salmonella isolates and to assess their relatedness, using whole‐genome sequencing. Antimicrobial resistance (AMR) genes were detected in 4/27 (15%) of the isolates. The fosfomycin resistance gene fosA7 was identified in two isolates; to our knowledge, there are no published reports of this gene in canine Salmonella isolates. The biocide resistance gene qacEdelta1, conferring resistance to quaternary ammonium compounds, was detected in an isolate that had four additional AMR genes. The most frequently identified serotypes were Newport (6/27, 22%) and Javiana (4/27, 15%), both of which were widespread among animal shelters. For these serotypes, there was evidence of both transmission of Salmonella within the shelter environment and separate introductions of Salmonella into a shelter. Several canine Salmonella isolates were closely related to human clinical isolates (four canine isolates within 10 SNPs and six more within 20 SNPs), suggesting a shared pathogen population. Educational outreach programmes targeting animal shelter workers would be useful for optimizing knowledge of Salmonella and other canine‐associated zoonotic pathogens.