| Summary: | <p>Abstract</p> <p>Background</p> <p>There is poor understanding of most aspects of <it>Clostridium perfringens</it> type A as a possible cause of neonatal diarrhea in piglets, and the prevalence and types of <it>C. perfringens</it> present on Ontario swine farms is unknown. To study the prevalence of fecal <it>C. perfringens</it> and selected toxin genes, 48 Ontario swine farms were visited between August 2010 and May 2011, and 354 fecal samples were collected from suckling pigs, lactating sows, weanling pigs, grower-finisher pigs, and gestating sows, as well as from manure pits. The fecal samples were cultured quantitatively, and toxin genes were detected by real-time multiplex polymerase chain reaction (PCR).</p> <p>Results</p> <p>In mixed multivariable linear analysis, log<sub>10</sub><it>C. perfringens</it> in fecal samples from suckling pigs were higher than that of weanling pigs, grower-finisher pigs, and manure pit samples (<it>P <</it>0.05). In mixed multivariable logistic analysis, the <it>C. perfringens</it> isolates recovered from lactating sows (OR = 0.069, P <0.001), gestating sows (OR = 0.020, P <0.001), grower-finishers (OR = 0.017, P <0.001), and manure pits (OR = 0.11, P <0.001) were less likely to be positive for the consensus beta2 toxin gene <it>cpb2</it> compared to the isolates from suckling pigs. The prevalence of <it>cpb2</it> in the isolates recovered from weanlings did not differ significantly from suckling pigs. <it>C. perfringens</it> isolates that were positive for <it>cpb2</it> were more likely to carry the atypical <it>cpb2</it> gene (<it>atyp-cpb2</it>) (OR = 19, <it>P <</it>0.001) compared to isolates that were negative for <it>cpb2</it>. Multivariable analysis did not identify farm factors affecting the presence of consensus <it>cpb2</it> and <it>atyp-cpb2</it> genes.</p> <p>Conclusions</p> <p>This study provides baseline data on the prevalence of <it>C. perfringens</it> and associated toxin genes in healthy pigs at different stages of production on Ontario swine farms. The study suggests that if <it>C. perfringens</it> type A are involved in neonatal enteritis, there may be strains with specific characteristics that cannot be identified by the existing genotyping system.</p>
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