Genomic snapshot of Klebsiella spp. isolates from clinically ill animals reveal diverse lineages with limited relatedness to human isolates.

Abstract

Background: Klebsiella spp. is an important human and animal pathogen, and it is commonly found with resistance to clinically important antimicrobials worldwide. The main goals of this study were to determine the prevalence of antimicrobial resistance genes in our study population and to assess the relatedness between Klebsiella spp. isolated from humans and animals. Isolates were collected in 2019 and 2020 from various animal hosts that presented to veterinary hospitals in the U.S. that participate in the FDA's Center for Veterinary Medicine Veterinary Laboratory Investigation and Response Network's antimicrobial resistance monitoring program.

Results: We sequenced a total of 204 Klebsiella spp. isolates. A majority of isolates were identified as K. pneumoniae (149/204, 73.0%), followed by K. quasipneumoniae (30/204, 14.7%), K. variicola (15/204, 7.4%), K. aerogenes (5/204, 2.5%), K. oxytoca (4/204, 2.0%), and K. grimontii (1/204, 0.5%). Out of 204 isolates, 138 were recovered from dogs, 25 from horses, 17 from cats, 6 from avian species, 5 from cows and 3 from pigs. The remaining 10 isolates were recovered from a few other mammal species. Klebsiella spp. isolates were very diverse. In silico multilocus sequence typing (MLST), using WGS data, identified a total of 88 known sequence types across all isolates. Seventeen isolates were not assigned an MLST sequence type due to combinations of alleles not previously found in the PubMLST database. 45 of the 204 isolates were assigned to 20 different single nucleotide polymorphism (SNP) clusters in the National Center for Biotechnology Information (NCBI) Pathogen Detection browser, and out of those, four isolates were assigned SNP clusters that also contained human isolates, all from dogs. The closest human isolate was 29 SNPs from a dog isolate. A total of 36 resistance genes were identified. The three most common resistance genes were oqxAB, fosA, and bla_SHV. None of the isolates had carbapenem resistance genes, although one isolate from a goat had mcr-8.1, a colistin resistance gene.

Conclusions: To our knowledge, this is the largest collection of sequenced Klebsiella from sick animals ever assembled, and the results found limited relatedness between these isolates and those from humans, despite the diversity of sequenced isolates.