Characterization of extended-spectrum cephalosporin-resistant Klebsiella recovered from dairy manure in Southern Ontario, Canada

Abstract

Extended-spectrum cephalosporin (ESC)-resistant Klebsiella pneumoniae are a problem in human patients and have been studied extensively. However, there is a paucity of information regarding ESC-resistant K. pneumoniae from livestock in general, and in Canada in particular. This study characterized ESC-resistant K. pneumoniae recovered from dairy manure in Ontario, Canada, and their ESC-resistance plasmids. ESC-resistant K. pneumoniae ( n  = 73) and K. quasipneumoniae (n = 11) isolates were screened by PCR for bla CTX-M , bla CMY and bla SHV prior to undergoing antimicrobial susceptibility testing using disk diffusion. Isolates from dairy manure carrying bla CTX-M ( n  = 74), and additional isolates from turkeys ( n  = 8) and dogs ( n  = 2), underwent short-read whole genome sequencing (WGS) and a subset of these ( n  = 35) had additional long-read sequencing and hybrid assembly for confirmation. Isolates were characterized using multi-locus sequence typing (MLST) and antimicrobial resistance (AMR) gene profiles. Thirty known sequence types (STs) and four novel STs were identified for K. pneumoniae, and two STs among K. quasipneumoniae . The isolates were found at various treatment stages of the manure on one farm but were only sporadically found on any of the other farms investigated. The majority of isolates (86%) were multi-drug resistant. Variants of CTX-M were identified in diverse STs and included bla CTX-M-15 ( n  = 81), bla CTX-M-1 ( n  = 2) and bla CTX-M-32 ( n  = 1). The bla CTX-M-15 gene was located on diverse IncF, IncHI1 or IncY replicons as well as on the chromosome, whereas bla CTX-M-1 was harboured on the epidemic IncI1/ST3 plasmid, and bla CTX-M-32 on an IncN plasmid. Plasmids were characterized based on core gene SNPs, replicon types and AMR genes, and compared to plasmids from Escherichia coli from a parallel study. Transfer of bla CTX-M plasmids between bacterial species by conjugation was also assessed. Conjugation of IncI1 and IncFII plasmids occurred from K. pneumoniae to E. coli strains but not vice versa . Notably, IncY replicons were identified as conjugative plasmids and transfer was demonstrated between E. coli strains as well as from K. pneumoniae to E. coli . No strain overlap was observed between dairy manure isolates and those from turkey and dogs, however we did identify similarities between K. pneumoniae MLST and resistance profiles from publicly available human clinical isolates to our isolates found in dairy manure (ST37 and 405), turkeys (ST45) and dogs (ST711).