Data regarding the epidemiology of Clostridium difficile infection (CDI) in South East Asian countries is limited, as is information on possible animal reservoirs of C. difficile in the region. This study aimed to investigate the prevalence of C. difficile in piglets and the piggery environment in Thailand and Malaysia, and determine the molecular epidemiology of C. difficile isolated.
Piglet rectal swabs (n=224) and piggery environmental specimens (n=23) were collected between 2015 and 2016 from 11 farms located in Thailand and Malaysia. All specimens were tested for the presence of C. difficile with toxigenic culture. PCR assays were performed on isolates to determine the ribotype (RT), and the presence of toxins A, B and binary toxin genes. Whole genome sequencing was used to determine the evolutionary relatedness of isolates of RT QX083 (the most prevalent RT identified) common to pigs and humans from Thailand and Indonesia.
C. difficile was recovered from 35% (58/165) and 92% (54/59) of the piglets, and 89% (8/9) and 93% (13/14) of the environmental specimens from Thailand and Malaysia, respectively. PCR assays performed on all strains from Thailand, and 30 strains from Malaysia (23 piglet and 7 environmental isolates) revealed all strains to be non-toxigenic. The most common strain belonged to a novel RT QX083, which accounted for 88% (51/58) of the piglet and 78% (7/9) of the environmental isolates from Thailand, and all of the isolates from Malaysia. Core-genome single nucleotide variant (SNV) analysis showed that piglet RT QX083 isolates from Thailand and Malaysia differed by only 18 SNVs. Moreover, these strains were, on average, 30 SNVs different from the human strains from Thailand and Indonesia, indicating that piglet and human C. difficile RT QX083 likely shared a common ancestor in the last two decades.