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Background   Clostridium perfringens  is a widespread pathogen, but the precise quantification of this subdominant gut microbe remains difficult due to its low fecal count (particularly in asymptomatic subjects) and also due to the presence of abundant polymerase-inhibitory substances in human feces. Also, information on the intestinal carriage of toxigenic  C. perfringens  strains in healthy subjects is sparse. Therefore, we developed a sensitive quantitative real-time PCR assays for quantification of  C. perfringens  in human feces by targeting its α-toxin and enterotoxin genes. To validate the assays, we finally observed the occurrence of α-toxigenic and enterotoxigenic  C. perfringens  in the fecal microbiota of healthy Japanese infants and young adults.    Methods  The  plc -specific qPCR assay was newly validated, while primers for 16S rRNA and cpe genes were retrieved from literature. The assays were validated for specificity and sensitivity in pre-inoculated fecal samples, and were finally applied to quantify  C. perfringens  in stool samples from apparently healthy infants (n 124) and young adults (n 221).    Results  The qPCR assays were highly specific and sensitive, with a minimum detection limit of 10 3  bacterial cells/g feces. Alpha-toxigenic  C. perfringens  was detected in 36 % infants and 33 % adults, with counts ranging widely (10 3 -10 7  bacterial cells/g). Intriguingly, the mean count of α-toxigenic  C. perfringens  was significantly higher in infants (6.0 ± 1.5 log 10  bacterial cells/g), as compared to that in adults (4.8 ± 1.2). Moreover, the prevalence of enterotoxigenic  C. perfringens  was also found to be significantly higher in infants, as compared to that in adults. The mean enterotoxigenic  C. perfringens  count was 5.9 ± 1.9 and 4.8 ± 0.8 log 10  bacterial cells/g in infants and adults, respectively.    Conclusions  These data indicate that some healthy infants and young adults carry α-toxigenic and enterotoxigenic  C. perfringens  at significant levels, and may be predisposed to related diseases. Thus, high fecal carriage of toxigenic  C. perfringens  in healthy children warrants further investigation on its potential sources and clinical significance in these subjects. In summary, we present a novel qPCR assay for sensitive and accurate quantification of α-toxigenic and enterotoxigenic  C. perfringens  in human feces, which should facilitate prospective studies of the gut microbiota.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-015-0561-y) contains supplementary material, which is available to authorized users.

Sensitive quantification of Clostridium perfringens in human feces by quantitative real-time PCR targeting alpha-toxin and enterotoxin genes