Genetic relationships among the oral streptococci.

Genetic relationships and species limits among the oral streptococci were determined by an analysis of electrophoretically demonstrable variation in 16 metabolic enzymes. Fifty isolates represented 40 electrophoretic types, among which the mean genetic diversity per locus was 0.857. Mannitol-1-phosphate dehydrogenase was not detected in isolates of the sanguis species complex, and glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase were absent in species of the mutans complex. Clustering from a matrix of Gower's coefficient of genetic similarity placed the 40 electrophoretic types in 10 well-defined groups corresponding to the Streptococcus species S. mutans, S. sobrinus, S. cricetus, S. rattus, S. ferus, S. oralis (mitior), two distinct assemblages of S. sanguis strains, and two subdivisions of "S. milleri." The assignments of isolates to these groups were the same as those indicated by DNA hybridization experiments, and the coefficient of correlation between genetic distance estimated by multilocus enzyme electrophoresis and genetic similarity indexed by DNA hybridization was -0.897 (P less than 0.001) for 50 pairwise combinations of isolates. S. ferus, which is widely believed to be a member of the mutans complex, was shown to be phylogenetically closer to species of the sanguis complex.     

Genetic variability of the emm-related genes of the large vir regulon of group A streptococci: potential intra- and intergenomic recombination events

One of the most prevalent genetic lineages of group A streptococci (GAS) harbors a genomic locus termed the large vir regulon, which contains an emm gene encoding the antiphagocytic M protein, and structurally related fcrA and enn (emm-related) genes encoding immunoglobulin-binding proteins. In the present study more than 100 large vir regulons from 42 different GAS serotypes were analyzed by PCR and partial DNA sequencing. On comparing these data to published sequences, sites of mutational and putative recombinational events were identified and ordered with respect to their intra/intergenic or intra/intergenomic nature. The emm-related genes were found to display small intragenic deletions or insertions, were completely deleted from, or newly inserted into the genome, or were fused to adjacent genes. Intergenomic exchanges of complete emm-related genes, or segments thereof, between different vir regulons were detected. Most of these processes seem to involve short flanking direct repeats. Occasionally, the structural changes could be correlated with changes in the functions of the encoded proteins.     

Genetic diversity among Plantagos

Summary In the progenies of the crosses between disomics and trisomies, two plants were isolated which carried an extra chromosome that was unlike any in the standard complement. The plants were not alike; while one carried a metacentric, the other had a telocentric extra chromosome. Their detailed structure and possible modes of origin are discussed.     

Genetic diversity among the Newars of Nepal

Genetic diversity among the Newars of Nepal has been studied using Wright's FST and the ratio of observed variance to theoretical variance following Lewontin and Krakauer's 1973 method, based on six genetic characteristics. The gene differentiation among the Newars is only 1.7%. These observations are further corroborated by the results obtained through genetic distance analysis. The average heterozygosity per locus is high (ranging from 35 to 42%) for all the groups. About 95% of total gene diversity exists within the Newar groups, the intergroup components being only about 5%.     

Genetic diversity among Enterococcus faecalis

Enterococcus faecalis, a ubiquitous member of mammalian gastrointestinal flora, is a leading cause of nosocomial infections and a growing public health concern. The enterococci responsible for these infections are often resistant to multiple antibiotics and have become notorious for their ability to acquire and disseminate antibiotic resistances. In the current study, we examined genetic relationships among 106 strains of E. faecalis isolated over the past 100 years, including strains identified for their diversity and used historically for serotyping, strains that have been adapted for laboratory use, and isolates from previously described E. faecalis infection outbreaks. This collection also includes isolates first characterized as having novel plasmids, virulence traits, antibiotic resistances, and pathogenicity island (PAI) components. We evaluated variation in factors contributing to pathogenicity, including toxin production, antibiotic resistance, polymorphism in the capsule (cps) operon, pathogenicity island (PAI) gene content, and other accessory factors. This information was correlated with multi-locus sequence typing (MLST) data, which was used to define genetic lineages. Our findings show that virulence and antibiotic resistance traits can be found within many diverse lineages of E. faecalis. However, lineages have emerged that have caused infection outbreaks globally, in which several new antibiotic resistances have entered the species, and in which virulence traits have converged. Comparing genomic hybridization profiles, using a microarray, of strains identified by MLST as spanning the diversity of the species, allowed us to identify the core E. faecalis genome as consisting of an estimated 2057 unique genes.     

Genetic diversity of the Campylobacter genes coding immunodominant proteins

Three Campylobacter jejuni 72Dz/92 genes (cjaA (ompH1), cjaC (hisJ) and cjaD (omp18)) encoding immunodominant proteins are considered to be potential chicken vaccine candidates. The presence and conservation of cjaA, cjaC and cjaD genes among different Campylobacter clinical isolates were determined. The genes were detected in thirty Campylobacter strains using hybridization as well as Western blot analysis. However, PCR products of the predicted size were amplified only from ten out of thirty examined strains regardless of the employed primer pair. The nucleotide sequence of the C. jejuni 72Dz/92 genes was compared with the nucleotide sequences of their homologs cloned from other Campylobacter strains as well as with the whole genome sequence of C. jejuni NCTC 11168. The examined sequences revealed 0 to 16% divergence. Strain-dependent levels of divergence were observed. The polymorphism detected in cjaC was mainly within the 5' region of the gene, while the nucleotide substitutions in cjaA and cjaD are distributed uniformly along the whole genes. Most of the observed nucleotide substitutions occurred at the third base of the codons. This observation is consistent with the results of Western blot experiments.     

Genetic heterogeneity of the pathogenic potentials of human and bovine group B streptococci

One-hundred seventy-two B-streptococcal strains of human and bovine origin were analyzed for the presence of 9 genes potentially involved in virulence. Some of genes (glnA, cyl, hylB, scaA andcfb) were revealed in all the strains. However, the presence of others (bca, bac, scpB, lmb) varied from strain to strain. Taken together, 3 and 5 different types of pathogenic potential were found among human and bovine group B streptococci (GBS) strains, respectively, and only one type (bca ⁺ bac scpB⁺ glnA⁺ cyl⁺ hylB⁺ lmb⁺ scaA⁺ cfb⁺) was common for both kinds of strains. We propose that different virulence genes can be involved in the development of infectious processes in humans and animals. A reliable PCR protocol with 3 pairs of primers (for the genesbca, bac andscpB) in the same reaction mixture was developed for the fast identification of the pathogenic potential of GBS. In comparison with the classical immunological methods this procedure displayed higher specificity and sensitivity as well as a shorter time of analysis. It can be recommended for use in the clinical and veterinary practice for studying the epidemiological relationship between the isolates and the ready identification of the clone causing the infection.     

Genetic variability of the emm-related genes of the large vir regulon of group A streptococci: potential intra- and intergenomic recombination events

One of the most prevalent genetic lineages of group A streptococci (GAS) harbors a genomic locus termed the large vir regulon, which contains an emm gene encoding the antiphagocytic M protein, and structurally related fcrA and enn (emm-related) genes encoding immunoglobulin-binding proteins. In the present study more than 100 large vir regulons from 42 different GAS serotypes were analyzed by PCR and partial DNA sequencing. On comparing these data to published sequences, sites of mutational and putative recombinational events were identified and ordered with respect to their intra/intergenic or intra/intergenomic nature. The emm-related genes were found to display small intragenic deletions or insertions, were completely deleted from, or newly inserted into the genome, or were fused to adjacent genes. Intergenomic exchanges of complete emm-related genes, or segments thereof, between different vir regulons were detected. Most of these processes seem to involve short flanking direct repeats. Occasionally, the structural changes could be correlated with changes in the functions of the encoded proteins.     

Transformation of group A streptococci by electroporation

Abstract The introduction, via electroporation, of free plasmid DNA into three strains of Streptococcus pyogenes is described. The method is very simple and rapid and efficiencies vary from 1 × 10³ to 4 × 10⁴ per μg of DNA. The method was also used to introduce an integrative plasmid and transformants were obtained, albeit at a somewhat lower frequency (2 × 10²). Some of the plasmids used in this study are derivatives of the Lactococcus lactis subsp. cremoris Wg2 plasmid pWV01. These broad host range vectors replicate in Gram-positives as well as Gram-negatives (viz. Escherichia coli ). Here we show that they also replicate in S. pyogenes and S. sanguis .     

Genetic diversity among Lassa virus strains

The arenavirus Lassa virus causes Lassa fever, a viral hemorrhagic fever that is endemic in the countries of Nigeria, Sierra Leone, Liberia, and Guinea and perhaps elsewhere in West Africa. To determine the degree of genetic diversity among Lassa virus strains, partial nucleoprotein (NP) gene sequences were obtained from 54 strains and analyzed. Phylogenetic analyses showed that Lassa viruses comprise four lineages, three of which are found in Nigeria and the fourth in Guinea, Liberia, and Sierra Leone. Overall strain variation in the partial NP gene sequence was found to be as high as 27% at the nucleotide level and 15% at the amino acid level. Genetic distance among Lassa strains was found to correlate with geographic distance rather than time, and no evidence of a "molecular clock" was found. A method for amplifying and cloning full-length arenavirus S RNAs was developed and used to obtain the complete NP and glycoprotein gene (GP1 and GP2) sequences for two representative Nigerian strains of Lassa virus. Comparison of full-length gene sequences for four Lassa virus strains representing the four lineages showed that the NP gene (up to 23.8% nucleotide difference and 12.0% amino acid difference) is more variable than the glycoprotein genes. Although the evolutionary order of descent within Lassa virus strains was not completely resolved, the phylogenetic analyses of full-length NP, GP1, and GP2 gene sequences suggested that Nigerian strains of Lassa virus were ancestral to strains from Guinea, Liberia, and Sierra Leone. Compared to the New World arenaviruses, Lassa and the other Old World arenaviruses have either undergone a shorter period of diverisification or are evolving at a slower rate. This study represents the first large-scale examination of Lassa virus genetic variation.     

Genetic diversity among Norwegian Vibrio parahaemolyticus

Aims: To examine the variability among environmental Vibrio parahaemolyticus (including trh+ isolates) from Norway, and to compare these to clinical isolates and isolates from imported foods. Methods and Results: A total of 246 V. parahaemolyticus were successfully digested with NotI, and the fragments were separated by pulsed field gel electrophoresis (PFGE). The isolates could be divided into 72 clusters and 103 pulsotypes. Eleven clusters contained 4–31 environmental isolates, and the isolates within these clusters greatly varied with respect to origin. None of the trh+ and /or tdh+ isolates clustered with trh?/tdh? isolates. The trh+ environmental isolates included in the study belonged to two separate clusters. A subset of isolates was serotyped, and great serotype diversity was observed among the environmental V. parahaemolyticus. The clinical isolates included O3:K6 and O3:KUT, and these were identical or related to a pandemic reference strain by PFGE. Conclusions: Environmental V. parahaemolyticus (including trh+) were genetically diverse, but certain variants occurred throughout the coastal environment, and some were persistent over time. Significance and Impact of the Study: Although trh+ V. parahaemolyticus persisted in the Norwegian environment, no evidence indicated that indigenous isolates have caused disease.     

Superantigen gene profile diversity among clinical group A streptococcal isolates

This study examines the diversity of superantigen gene profiles between and within emm-genotypes of 92 clinical group A streptococcal isolates (30 STSS, 24 sepsis, 25 erysipelas, and 12 tonsillitis) collected in Sweden between 1986 and 2001. The emm-genotype and the distribution of smeZ, speG, speJ, speA, speC, speH, speI, speK/L, speL/M, speM, and ssa genes, and the smeZ allelic variant were determined using PCR and DNA sequencing. Forty-five emm1 isolates revealed 10 superantigen gene profiles. One profile dominated and was identified in 22 isolates collected over 14 years. The results indicate that a selective advantage maintained this genotype in circulation. The superantigen content among the emm1 isolates ranged from three to seven, with smeZ-1, speG, and speA present in all but one profile. The 47 isolates of 27 other emm-genotypes exhibited 29 superantigen gene profiles. Thus, the distribution of superantigen genes was highly variable within isolates regardless of emm-genotype. Two novel emm1 subtypes and 14 novel smeZ allelic variants were identified. The 22 smeZ alleles were generally linked to the emm-genotype. The results of the investigation show that superantigen gene profiling is useful for tracking spread of clones in the community.     

Survey of the plasmid content of group A streptococci

Abstract Examination of 70 M-prototype group A streptococci showed small plasmids (2.0–2.5 MDa) to be present in strains representative of M-types 28, 57, 61, 63, 64 and 69. Identical results were obtained from M _r and restriction endonuclease analyses of a 2.2-MDa plasmid (pDN691) found in the M-type 69 strain and similar plasmids in the M57 prototype and two other independently isolated M-type 57 strains. In all four strains the presence of plasmid correlated with the production of bacteriocin-like inhibitory activity identifiable as P type 614. Similar analysis revealed a possible relationship between a 2.5-MDa plasmid in the prototype M61 and M64 strains and the production of P-type 216 inhibitory activity. A survey of 56 group A streptococci recovered in association with either rheumatic fever or nephritis failed to demonstrate plasmid DNA with the exception of 2.2-MDa plasmids in four nephritis-associated M-type 57 isolates.