Surveillance of Clostridioides difficile in Canadian retail meat and genomic linkages to community-associated human clinical infections in Canada.

Abstract

Community-associated Clostridioides difficile infections (CA-CDI) remain a concern in Canada, comprising a quarter of cases previously reported through the Canadian Nosocomial Infection Surveillance Program. Previous Canadian studies have reported toxigenic C. difficile isolated from Canadian retail meat, suggesting that it may be a source of exposure for CA-CDI in Canada. In this study, 3/219 (1.4%) of retail pork and 0/99 (0%) of retail beef samples tested positive for toxigenic C. difficile, which were molecularly characterized by PCR ribotyping and whole-genome sequencing. All three isolates were obtained from pork and belonged to sequence types (STs)/ribotypes (RTs) that have previously been isolated from human clinical CA-CDI cases in Canada: ST1/RT027, ST8/RT002, and ST10/RT015. Retail meat isolates were susceptible to the antimicrobials tested, save one isolate with intermediate resistance to clindamycin. Genomic comparison to Canadian human clinical CA-CDI isolates with the same corresponding ST/RT types showed two of the three pork isolates clustered with CA-CDI isolates via core-genome multilocus sequencing typing, with single nucleotide variant (SNV) analysis showing further genomic relatedness of 2-11 SNVs. Retail meat may therefore be a low source of CA-CDI exposure in Canada, with the potential for foodborne transmission of select clones.