Real-time TaqMan polymerase chain reaction-based genus-identification and pyrosequencing-based species identification of Campylobacter jejuni, C. coli, C. lari, C. upsaliensis, and C. fetus directly on stool samples

A new method was developed for Campylobacter identification and applied directly on 599 stool samples from diarrhoeagenic patients. Here, the gyrase B gene of Campylobacter was targeted in a 2-step process: first, TaqMan polymerase chain reaction (PCR)-based identification of C. jejuni, C. coli, C. upsaliensis, C. lari, and C. fetus at the genus level, and, second, pyrosequencing-based identification at the species level. The TaqMan PCR method was compared to culturing and identified 87 Campylobacter-positive samples of which 64 were culture positive. Among the discrepant 23 samples, 18 were confirmed positive by conventional PCR, underlining a significant increase in diagnostic yield by use of this molecular and culture-independent method. For species identification, the pyrosequencing method was compared to conventional PCR and among the 87 TaqMan PCR-positive samples, 74 Campylobacter species were identified by both methods, 10 samples gave discrepant results, and 3 samples were negative by both methods.