tRNA gene clusters at the 3' end of rRNA operons are specific to virulent subgroups of Streptococcus agalactiae strains, as demonstrated by molecular differential analysis at the population level.

The aim of this work was to characterize a 2.4 kb randomly amplified polymorphic DNA (RAPD) fragment described as a marker for a phylogenetic group of Streptococcus agalactiae strains significantly associated with neonatal meningitis. This fragment was analysed by cloning and sequencing, and showed that two types of tRNA gene cluster flank the 3' end of the rRNA operons in S. agalactiae strains. Both types of tRNA gene cluster act as markers for phylogenetic subgroups of strains within the species. One type could be used to distinguish two of the three virulent intraspecies subgroups to which most of the S. agalactiae strains able to invade the central nervous system of neonates belong. This raises the possibility that there is a link between these tRNA genes and the virulence of the bacterium. Based on this analysis, PCR primers were designed to determine whether S. agalactiae strains are likely to belong to lineages of organisms in which most of the highly virulent strains isolated from cerebrospinal fluid cluster. In addition, this work demonstrated that RAPD can be used to detect novel particularities within intraspecies variants of pathogens.

Shigella and enteroinvasive Escherichia coli strains are derived from distinct ancestral strains of E. coli.

The differentiation between Shigella subspecies, and the phylogenetic position of Shigella clones within Escherichia coli clones was determined by analysis of restriction fragment length polymorphisms of rDNA (ribotyping). Seventy-five Shigella strains belonging to the four subspecies and 13 enteroinvasive E. coli (EIEC) strains were compared with the 72 E. coli strains of the ECOR collection, which have been classified into four phylogenetic groups (A, B1, B2 and D). Seventeen Shigella dysenteriae ribotypes, 12 Shigella flexneri ribotypes, 23 Shiegella boydii ribotypes, 12 Shigella sonnei ribotypes and 13 EIEC ribotypes were identified following digestion with HindIII and EcoRI. Correspondence analysis of the data showed that S. boydii serotype 13 strains were distantly related to the other Shigella strains, and that S. sonnei and S. flexneri were distinct from S. boydii and S. dysenteriae. The ribotypes of Shigella and ECOR strains were indistinguishable, and S. sonnei, S. flexneri and most S. dysenteriae strains were closely related to phylogenetic group D, whereas S. dysenteriae serotype 1 strains belonged to phylogenetic group B1, and S. boydii strains were evenly distributed between the two groups. The Shigella strains were distantly related to group B2, which contains E. coli strains frequently implicated in extra-intestinal infections in humans. In contrast, the 13 EIEC strains were more widely distributed between phylogenetic groups B1, A and B2. Thus, there was no primordial Shigella species and Shigella and EIEC strains are derived from different ancestral strains.