Genomic Characterization of Carbapenem-Resistant Bacteria from Beef Cattle Feedlots

Carbapenems are considered a last resort for the treatment of multi-drug-resistant bacterial infections in humans. In this study, we investigated the occurrence of carbapenem-resistant bacteria in feedlots in Alberta, Canada. The presumptive carbapenem-resistant isolates (n= 116) recovered after ertapenem enrichment were subjected to antimicrobial susceptibility testing against 12 different antibiotics, including four carbapenems. Of these, 72% of the isolates (n= 84) showed resistance to ertapenem, while 27% of the isolates (n= 31) were resistant to at least one other carbapenem, with all except one isolate being resistant to at least two other drug classes. Of these 31 isolates, 90% were carbapenemase positive, while a subset of 36 ertapenem-only resistant isolates were carbapenemase negative. The positive isolates belonged to three genera;Pseudomonas,Acinetobacter, andStenotrophomonas, with the majority beingPseudomonas aeruginosa(n= 20) as identified by 16S rRNA gene sequencing. Whole genome sequencing identified intrinsic carbapenem resistance genes, includingblaOXA-50and its variants (P. aeruginosa),blaOXA-265(A. haemolyticus),blaOXA-648(A. lwoffii),blaOXA-278(A. junii), andblaL1andblaL2(S. maltophilia). The acquired carbapenem resistance gene (blaPST-2) was identified inP. saudiphocaensisandP. stutzeri. In a comparative genomic analysis, clinicalP. aeruginosaclustered separately from those recovered from bovine feces. In conclusion, despite the use of selective enrichment methods, finding carbapenem-resistant bacteria within a feedlot environment was a rarity.Keywords:carbapenem-resistant bacteria;antimicrobial resistance;beef production system;whole genome sequencing