A rapid PCR-enzyme-linked immunosorbent assay for identification of 10 important emm gene types of Streptococcus pyogenes was developed. The emm genotypes of a coded panel of strains of known M serotype were determined, and in 144 of 149 cases (97%) the results were congruous. Strains of types that were not included in the panel of capture probes were emm genotyped by sequencing.

Seven laboratories participated in a WHO-sponsored international collaborative study, to evaluate methods for subtyping Listeria monocytogenes, by performing restriction fragment length polymorphism (RFLP) analysis-based subtyping of an international study set of 80 strains of L. monocytogenes that included 22 epidemiologically related groups. The RFLP analysis was done by Southern hybridization with one of two types of probes found in multiple copies on the chromosome of L. monocytogenes. Six laboratories performed ribotyping. These laboratories used EcoRI enzyme to restrict the L. monocytogenes DNA and ribosomal RNA or DNA as the probe for Southern hybridizations. The seventh laboratory used NciI to restrict the DNA. and two probes, one randomly cloned and the other containing repeat sequences cloned from L. monocytogenes DNA. The overall discriminating power of ribotyping, as estimated by calculation of Simpson's index of diversity, ranged from 0.83 to 0.88 for the six laboratories. The discriminating power of the combination of two probes used by Laboratory 7 was 0.91. Ribotyping and the cloned probes used by Laboratory 7 discriminated poorly between serotype 4b strains. Neither method identified three atypical strains (identified by other subtyping methods) included in three apparently epidemiologically related groups. Ribotyping did not discriminate between strains of serotypes 4b and 4b(X) in one epidemiologically related group of strains; one cloned probe used by Laboratory 7 discriminated between these strains. Intra-laboratory reproducibilities for the seven laboratories ranged from 80.0 to 100%, as determined by their abilities to correctly identify 11 pairs of duplicate strains included in the study set. Inter-laboratory reproducibilities were generally very good considering that no attempt was made to standardize protocols used by the participants.

A method based on long PCR amplification and restriction endonuclease analysis of the virulence regulon was developed for a rapid (2 days), simple differentiation of group A streptococci. The PCR product size varied from 12.3 kb for serotypes M1 (NCTC 8198) and M12 (NCTC 10085) to 7.8 kb for serotype M6 (NCTC 8302). The fragment patterns formed on HaeIII digestion of the products were unique and this allowed the differentiation of each of the M-type strains (M1, M3, M4, M5, M6, M11, M12, M28, M76 and M78) studied. Contemporary M1 isolates all gave the same fragment pattern but differed from the prototype strain (NCTC 8198) in not having a 1.25-kb fragment. Isolates of serotypes M1 and M3 each had similar patterns, an indication of their clonality and global dispersion. In contrast, more than one restriction fragment length polymorphism (RFLP) pattern was detected among clinical isolates of serotypes M5, M6, M12, M4, M(R)28 and M78. Two strains that were M-protein non-typable by serological means were provisionally classified as M6 by comparisons of HaeIII long PCR fragment patterns.

The 16S rRNA-encoding gene sequences from strains of the family Legionellaceae, Sarcobium lyticum, and Coxiella burnetii were determined. Phylogenetic relationships revealed that all Legionella spp. were members of a coherent monophyletic family. The blue-white autofluorescent species formed a defined cluster bounded by Legionella bozemanii and Legionella tucsonensis. The strains of Legionella pneumophila subsp. pneumophila and Legionella pneumophila subsp. fraseri shared 99.2% sequence identity. A legionella-like amoebal pathogen (LLAP-3) showed 99.4% sequence identity to the obligate intracellular bacterial parasite Sarcobium lyticum. A proposal is made for the transfer of Sarcobium lyticum from the genus Sarcobium to the genus Legionella as Legionella lytica comb. nov. On the basis of serology and phenetic and phylogenetic comparisons, the taxa Legionella erythra and Legionella rubrilucens may be regarded as subspecies.

Polyphasic methods were used to examine the taxonomic positions of three newly identified Grahamella species. A comparison of the 16S rRNA gene sequences of these organisms with the sequences available for other bacteria revealed that these three species form a tight monophyletic cluster with members of the genus Bartonella. This cluster is only remotely related to other members of the order Rickettsiales. Determinations of the levels of DNA relatedness between Grahamella species and Bartonella species (by using a modified hydroxyapatite method) revealed that all of the species belonging to these two genera are distinct but closely related. On the basis of these data and the results of guanine-plus-cytosine content and phenotypic characterization studies, we propose that the genera Grahamella and Bartonella should be unified and that the latter name should be retained. Bartonella talpae and Bartonella peromysci, new combinations for former Grahamella species, are created, and the following three new Bartonella species are described: Bartonella grahamii, Bartonella taylorii, and Bartonella doshiae. A taxonomic analysis of Grahamella species complete the study of all members of the family Bartonellaceae, and the results of this study support the proposal that the family should be transferred out of the order Rickettsiales.

A method based on PCR amplification of the 16S rRNA gene (rDNA)-23S rDNA intergenic regions was developed for the identification of species within the family Legionellaceae. The sizes of the PCR products varied from 1,353 to 350 bp. Strains of Legionella pneumophila were characterized as having products of approximately 900 and 530 bp, and L. birminghamensis had products of 1,390, 960, and 380 bp. Of the 38 species of legionellae examined, only 7 were indistinguishable (L. erythra from L. rubrilucens, L. anisa or L. cherrii from L. tucsonensis, and L. quateirensis from L. shakespearei). Two environmental isolates were identified as L. pneumophila. Strain LLAP-3, which was a symbiont of amoebae, could not be associated with any Legionella sp. studied.

The family Legionellaceae and genus Legionella were defined in 1979 for a single species Legionella pneumophila. Since then 38 other species of Legionella have been identified. Species in the family form a coherent phenotypic taxon, being easily identified by in-vitro growth requirements and cell-wall components. Phylogenetic analysis of the 16S rRNA gene sequences also support this view. Classification at the genus level has been controversial; most workers supporting a single genus, Legionella, but others have proposed division into three genera: Legionella, Tatlockia and Fluoribacter. Phylogenetic studies demonstrate that the species of the family Legionellaceae are monophyletic, showing no discrete divisions, and if the family were to be divided many genera with only one or two species would be created. The phenotypic data do not support this view because, although identification of members of the genus is relatively simple, distinguishing between species is difficult and usually requires the application of molecular techniques. A wide range of immunological, biochemical and molecular techniques have been used to fingerprint or type legionellae and these have undoubtedly been of considerable value in elucidating the epidemiology of legionellosis. However, the limitations of available methods must be appreciated, particularly when undertaking environmental studies.

DNA coding for the 16S rRNA of six strains of the obligate intracellular bacterium Coxiella burnetti was directly amplified from lysed host cells using the polymerase chain reaction. The amplification product was sequenced using a linear-PCR procedure and compared with other published 16S rRNA sequences. The results of this analysis confirm the position of C. burnetii in the gamma subgroup of the proteobacteria. The data show that all of the C. burnetii strains are highly related (> 99%) on the basis of 16S rRNA sequences although they had different geographic origins and phenotypic characteristics. The data support a phylogenetic homogeneity of the genus Coxiella with only one species which is C. burnetii.

DNA coding for the 16S rRNA of six strains of the obligate intracellular bacterium Coxiella burnetii was directly amplified from lysed host cells using the polymerase chain reaction. The amplification product was sequenced using a linear-PCR procedure and compared with other published 16S rRNA sequences. The results of this analysis confirm the position of C. burnetii in the gamma subgroup of the proteobacteria. The data show that all of the C. burnetii strains are highly related (> 99%) on the basis of 16S rRNA sequences although they had different geographic origins and phenotypic characteristics. The data support a phylogenetic homogeneity of the genus Coxiella with only one species which is C. burnetii.

Twenty-two red-autofluorescent Legionella strains were identified serologically as either Legionella rubrilucens or L. erythra. A rRNA probe was used for restriction fragment length polymorphism (RFLP) analysis of the strains and the patterns generated were used as an additional method of identifying the strains to species level. In two instances strains which were identified as L. rubrilucens by serology appeared to belong to the species L. erythra by RFLP analysis. This apparent contradiction was resolved by measurements of DNA/DNA homology which confirmed the existence of a second serogroup of L. erythra serologically indistinguishable from L. rubrilucens.

The relationship between serogroup and genotype of Legionella pneumophila strains was investigated by restriction fragment length polymorphism (RFLP) typing with a previously standardised method. Of the 51 RFLP types identified, 19 comprised strains of more than one serogroup. Several RFLP types included strains of five or more serogroups. To determine if sharing the same RFLP type indicates that strains are genotypically indistinguishable or merely that they are superficially similar, 31 strains were selected for further analysis with an extended range of restriction endonucleases and nucleic acid probes. In some cases, strains of a particular RFLP type were indistinguishable, while in others the restriction fragment patterns showed minor differences. It is possible that in the latter case the strains are diverging representatives of a parent clone. We conclude that analysis of restriction fragment patterns, either probed or unprobed, provides a more accurate measure of the ancestral relationship between strains than can be obtained with serological methods.

The 16S-rRNA gene of Bartonella bacilliformis was amplified using the polymerase-chain reaction (PCR). The amplification product was sequenced using a linear-PCR procedure and compared with other published 16S-rRNA sequences. The results of this analysis placed B. bacilliformis in the alpha subgroup of the proteobacteria, and more specifically demonstrated its close phylogenetic relationship to Rochalimaea quintana. This relationship is supported by similarities in the size and mean base composition of the genomes of the two species, and by shared phenotypic characteristics.

DNA coding for the 16S rRNA of an intracellular bacterium was directly amplified from lysed cells of a host amoebae using the polymerase chain reaction and primers specific for eubacteria. The amoebae had been used to recover an uncultured bacterium observed in the sputum of a patient with pneumonia. The amplified DNA was sequenced directly and compared with published 16S rRNA sequences. The analysis revealed that the intracellular bacterium is a member of the genus Legionella and that it is different from species, including L. pneumophila, for which 16S ribosomal RNA sequence data are available.

The use of probes derived from rRNA sequences to detect restriction fragment length polymorphisms (RFLPs) associated with the ribosomal RNA genes for epidemiological typing (ribotyping) is a powerful and readily applicable tool. Different probes and enzymes for ribotyping were compared for a series of 73 unrelated Legionella pneumophila serogroup 1 strains. The probes compared were cDNAs, transcribed from L. pneumophila or Escherichia coli rRNA subunits, and a cloned L. pneumophila rRNA gene. The cloned rRNA gene probe gave the best discrimination and this probe was further compared with cloned probes comprised of randomly selected (non-rRNA) parts of the L. pneumophila chromosome. In this instance the greatest discrimination was achieved when one of the non-ribosomal RNA gene probes was employed. The overall discrimination of RFLP typing was enhanced by combining the data obtained with both rRNA and non-rRNA probes.

The 16S ribosomal RNA sequences of Legionella pneumophila, L. erythra, L. hackeliae, L. spiritensis, L. longbeachae, L. bozemanii (Fluoribacter bozemanae) and L. micdadei (Tatlockia micdadei) were determined using reverse transcriptase. The sequences were compared with published sequences for Gram-negative bacteria and phylogenetic trees were constructed. The data confirm previous work which showed that the family Legionellaceae forms a monophyletic subgroup within the gamma subdivision of the Proteobacteria. The data show that all of the legionellae studied are highly related (greater than 95%) on the basis of 16S rRNA sequences and do not support the division of the family Legionellaceae into three genera.

A series of strains, presumptively identified as legionellas on the basis of their nutritional requirements and biochemical reactivity, were isolated from two unrelated environmental sources in the UK. Representatives of each of these series had a restriction endonuclease digest pattern indistinguishable from that of the Legionella quinlivanii type strain (1442-AUS-E) and the identity of these strains was confirmed by DNA homology studies. Serological examination of the two strains showed that they were distinct from the type strain 1442-AUS-E but indistinguishable from each other. A second serogroup, L. quinlivanii serogroup 2 (type strain LC870; NCTC 12434), is proposed to accommodate these strains.

Summary. A restriction fragment length polymorphism (RFLP) typing method for Legionella pneumophila serogroup 1 was developed. The method depended upon the use of cloned EcoRl fragments from L. pneumophila (Knoxville-1) probing Neil restriction fragments of chromosomal DNA. Examination of strains of L. pneumophila which were apparently unrelated showed that inter-strain RFLPs were common, and these formed the basis of the typing scheme. The technique was found to be highly reproducible and discriminatory. When the RFLP data were compared to that obtained by monoclonal antibody (MAb) subgrouping both methods of strain differentiation gave consistent results. The isolates examined by either method were also sub-divided by the alternative technique. The analysis of RFLPs by cloned probes should be of considerable epidemiological value.

A restriction fragment length polymorphism (RFLP) typing method for Legionella pneumophila serogroup 1 was developed. The method depended upon the use of cloned EcoR1 fragments from L. pneumophila (Knoxville-1) probing Nci1 restriction fragments of chromosomal DNA. Examination of strains of L. pneumophila which were apparently unrelated showed that inter-strain RFLPs were common, and these formed the basis of the typing scheme. The technique was found to be highly reproducible and discriminatory. When the RFLP data were compared to that obtained by monoclonal antibody (MAb) subgrouping both methods of strain differentiation gave consistent results. The isolates examined by either method were also sub-divided by the alternative technique. The analysis of RFLPs by cloned probes should be of considerable epidemiological value.

One hundred and seventy-nine isolates of Legionella pneumophila serogroup 1, obtained from a site associated with an outbreak of Legionnaires' disease, were examined by monoclonal antibody subgrouping, restriction fragment length polymorphism typing, restriction endonuclease analysis and plasmid content. Nine distinct phenotypes were detected but at the genotypic level all strains were closely related. The data presented indicate that phenotypic variation of a single parent strain can occur within an environmental site. The implications of these findings are discussed in relation to the investigation of outbreaks of Legionnaires' disease.

A typing method based on analysis of restriction fragment length polymorphisms has previously been developed for Legionella pneumophila serogroup 1. Here data are presented demonstrating the utility of this method for typing strains of all other L. pneumophila serogroups described to date. The method, which is highly discriminatory, should be of considerable value in epidemiological investigations of legionella infections.