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, among Campylobacter concisus strains from South Africa. A Polymerase Chain Reaction (PCR) assay described for identifying strains belonging to Genomospecies 1 and 2 was applied in 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

Novel <i>Campylobacter lari</i>-like bacteria from humans and molluscs: description of <i>Campylobacter peloridis</i> sp. nov., <i>Campylobacter lari</i> subsp. <i>concheus</i> subsp. nov. and <i>Campylobacter lari</i> subsp. <i>lari</i> subsp. nov.

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA–DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVAT (=LMG 23910T =CCUG 55787T) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897RT (=LMG 21009T =CCUG 55786T) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846T=NCTC 11352T)

Differential methods for rRNA superfamily VI

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