Analysis of the microbiota of raw commercial feline diets to prioritize food safety investigations

Microbiota sharing between people and their companion animals is a concern for development of antimicrobial resistance. To assess the risks associated with feeding raw products to cats, with an emphasis on previously understudied freeze-dried products, a collection of 112 conventional and raw products was purchased and investigated using a combination of cultivation and high-throughput sequencing techniques. Here we show that bacterial cultures were exclusively isolated from raw foods. A total of 19 genera were cultured including Salmonella, Clostridium, Escherichia, Klebsiella, Enterobacter, and Cronobacter. Carbapenem-resistant Pseudomonas aeruginosa and Pseudomonas fulva, and Stenotrophomonas lactitubi were isolated from frozen raw products, and 6 Bacillus strains harbored carbapenemase gene bla₂. Multidrug efflux pumps were highly abundant in frozen raw isolates. Clostridium sensu stricto I genus detection predicted a raw, freeze-dried product with 95% sensitivity and 78% specificity. Genera Pseudomonas, Paraclostridium and Peptostreptococcus were associated with frozen raw food products while the Bacillus genus was associated with conventional processing. Parasite genes were exclusively detected in raw foods. The presence of pathogenic species and high load of resistance genes in raw commercial food products, particularly those sold on shelves at room temperature, suggests a considerable health risk to cats and the families who care for them.