Characterisation of Campylobacter concisus strains from South Africa using Amplified Fragment Length Polymorphism (AFLP) profiling and a Genomospecies-specific Polymerase Chain Reaction (PCR) assay: Identification of novel genomospecies and correlation with clinical data

Amplified Fragment Length Polymorphism (AFLP) profiling was used to evaluate the distribution of phenotypically indistinguishable, but genetically distinct, amongCampylobacter concisus strains from South Africa. A Polymerase Chain Reaction (PCR) assay described for identifying strains belonging to Genomospecies 1 and 2 was appliedin this study. Forty-seven C. concisus strains were studied in total, of which 42 were of South African origin. Forty of the South African isolates were assigned to the major existing genomospecies typified by the type strain of oral origin (GS1), and reference strains from bloody diarrhoea (GS2). Eighteen South African isolates were distributed in the GS1 cluster including two oral strains. Twenty-two faecal South African isolates clustered with reference GS2 strains. Two novel genomospecies (GS 5 and 6) were inferred by their AFLP profile characteristics. Use of an existing PCR assay first described for identification of GS1 and GS2 strains generally indicated that the tool was accurate, although the novel genomospecies described here yielded an amplicon in the GS2 assay. No consistent clinical pattern among the diarrhoea South African strains could be discerned. The study extends the known genetic diversity among C. concisus, elucidates the presence of multiple genomospecies in South Africa, and confirms for the first time an association of GS1 with diarrhoea as well as the utility (with caveats) of a PCR assay for identifying GS1 and GS2 strains.   Key words: AFLP, Campylobacter concisus strains, bloody diarrhoea, genomospecies, PCR .