Phenotypic and DNA relatedness between nematode symbionts and clinical strains of the genus Photorhabdus (Enterobacteriaceae)

Bacterial strains isolated from wide ranges of nematode hosts and geographic sources and strains isolated from human clinical specimens were used to assess the taxonomic structure of the genus Photorhabdus. The following two methods were used: DNA relatedness and phenotypic characterization. Analysis of the DNA relatedness data revealed that all of the strains studied were congeneric and that the genus Photorhabdus is, on the basis of DNA relatedness data, more homogeneous than the other genus of nematode-symbiotic bacteria, the genus Xenorhabdus. In contrast to previous reports, only two DNA relatedness groups were identified in the genus Photorhabdus. These groups corresponded to the symbiotic strains and the clinical strains. There appeared to be some subgroups within the symbiotic strain group on the basis of the interactions of the strains with nematodes, which corresponded to some extent with the DNA relatedness data. However, there were significant ambiguities in the DNA relatedness data, and this group could not be subdivided on the basis of DNA relatedness data or phenotypic data. The distinct functional differences within and between the DNA relatedness groups of symbiotic Photorhabdus strains indicated that there are biologically significant sub-groups within the genus Photorhabdus that cannot be defined at this time. Further investigation of the taxonomy of Photorhabdus by using different approaches and a suitably wide range of strains is recommended. However, it is clear that the clinical strains form a recognizable subgroup within the genus even though no formal subtaxon can be defined at this time.     

Karyotyping of Saccharomyces strains with different temperature profiles

This study examined the karyotype, the fermentation performance and the optimum growth temperature (Topt) of 28 yeast strains all identified as species belonging to Saccharomyces sensu stricto. The strains were isolated from fermented musts, which had not been inoculated, at two temperature ranges: 20-40 degrees C and approximately 0-6 degrees C. The results demonstrated a correlation between the Topt and the chromosome organization. In particular, strains with Topt of less than 30 degrees C showed only two bands in the region between 365 and 225 kb, while those with a Topt greater than 30 degrees C had three bands in this size range. From a taxonomic viewpoint, the Topt is a better indicator for the Saccharomyces sp. than the ceiling temperature of 37 degrees C currently used to differentiate cryotolerant Saccharomyces bayanus and S. pastorianus from non-cryotolerant S. cerevisiae and S. paradoxus strains.     

Ineffective and non-nodulating mutant strains of Rhizobium japonicum

Mutant strains of Rhizobium japonicum that were unable to allow the Corsoy cultivar of soybean to reduce acetylene or fix N2 were isolated. These strains grow as well as the wild type in a variety of media. Mutant strains SM1 and SM2 did not form nodules on the host plant; however, they reduced acetylene in the nonsymbiotic assay. Strains SM3 and SM4 produced nodules that did not have the characteristic pink pigment caused by leghemoglobin. The nodules formed by these strains also were small. One mutant strain, SM5, produced large pink nodules. The lesion in this strain seems to be in the gene that specifies nitrogenase component II.     

Analysis of stable low-molecular-weight RNA profiles of members of the family Rhizobiaceae

Staircase electrophoresis in polyacrylamide gels was used to analyze the stable low-molecular-weight (LMW) RNA profiles of 24 type strains belonging to the family Rhizobiaceae. This new electrophoretic technique results in good separation of the molecules forming the LMW RNA profiles. Differences in the number and distribution of the RNA bands in these profiles allowed us to identify differences among the 24 strains assayed. Species assignments based on LMW RNAs proved to be consistent with the established taxonomic classification. Analysis of the data obtained and the corresponding dendrograms revealed relationships between genera and species; these relationships were essentially the same as those obtained with other techniques, such as DNA hybridization and 16S rRNA sequencing. Use of the technique described here, with which it is possible to analyze a large number of strains in a short time, permits rapid identification of species belonging to the family Rhizobiaceae and should in the future facilitate biodiversity studies and detection of new species.     

Neisseria weaveri sp. nov. (formerly CDC group M-5), from dog bite wounds of humans

The taxonomic relationships of strains belonging to Centers for Disease Control group M-5 were examined. Previous studies of rRNA cistron similarities placed this organism on the Neisseriaceae rRNA branch of rRNA superfamily III; the closest neighbors included the genus Neisseria and groups EF-4a and EF-4b. The group M-5 strains were characterized by a range of phenotypic tests, and their G + C contents and DNA-DNA relatedness levels were determined. In addition, a numerical taxonomic analysis of the whole-cell protein patterns (obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis) of group M-5 and related taxa was performed. The strains studied included 45 group M-5 strains, the type strains of six Neisseria species or subspecies, three group EF-4a reference strains, and three group EF-4b reference strains plus the type strain of the phenotypically similar organism Oligella urethralis. Our results showed that the group M-5 strains were members of a homogeneous taxon distinct from phylogenetically closely related taxa. The genomic divergence as revealed by levels of rRNA cistron similarity and phenotypic characteristics indicate that group M-5 can be considered a new species of the genus Neisseria. We therefore propose the new species Neisseria weaveri, with NCTC 12742 (= CCUG 4007 = ISL775/91 = LMG 5135) as the type strain. N. weaveri strains are strictly aerobic, gram-negative, nonmotile, rod-shaped organisms which are catalase and oxidase positive, nonsaccharolytic, and able to grow on MacConkey agar and do not reduce nitrate but generally reduce nitrite.(ABSTRACT TRUNCATED AT 250 WORDS)     

Genotypic relationships among strains classified under the (Pasteurella) haemolytica-complex as indicated by ribotyping and multilocus enzyme electrophoresis

Two-hundred and one strains classified under the (Pasteurella) haemolytica-complex isolated from cattle, sheep, deer, pigs, hares and rabbits were investigated by ribotyping. Fifty-nine of these strains were selected for further studies using multilocus enzyme electrophoresis (MEE). A correlation between the clusters identified by ribotyping and MEE was demonstrated and the results furthermore indicated that a genetic basis exists for most clusters previously outlined by the use of quantitative evaluation of phenotypic data. The taxonomic relevance of ornithine decarboxylase and fermentation of L-arabinose, D-sorbitol and glucosides for taxonomic delineation within the (P.) haemolytica-complex was supported. A taxonomic importance was further indicated for ONPG, ONPX, ONPF, meso-inositol, D-xylose, maltose, dextrine and NPG in relation to some of the taxa. Within the porcine taxon 15, however, differences in ornithine decarboxylase did not correspond to genetic clusters. Six lineages were revealed by MEE. Lineage A contained electrophoretic types (ETs) representing biogroups 1, 3A-3H, 8A and 9, indicating a genetic relationship between these groups--an observation which was supported by ribotyping. Lineage B included biogroup 8D, 3 strains from biogroup 10 and a single strain from biogroup 1 and taxon 18/biovar 1. Lineage C contained strains allocated to biogroup 6 from ruminants and the porcine taxon 15. The similarity between these two groups was accentuated by ribotyping. Lineage D and the single isolate in lineage E contained strains allocated to biogroups 7, 10, 8B and 8C, in addition to single strains from biogroups 6 and 9. The same strains were found in the heterogenous ribotype cluster 17. Lineage F contained strains representing the leprine taxon 20 and the ruminant (P.) granulomatis. Ribotyping indicated that the ruminant biogroup 3J was affiliated with both taxon 20 and (P.) granulomatis.     

Numerical analysis of the characteristics of Corynebacterium diphtheriae strains isolated in Victoria from 1962 to 1971

A study of the incidence of diphtheria in the State of Victoria, Australia, was carried out. Numerical analysis of the characteristics of 264 strains of Corynebacterium diphtheriae isolated between 1962 and 1971 placed them into 18 varieties plus six strains which were unique in their combination of reactions to the characteristics examined. During the 10-year period, some varieties appeared intermittently and were recognized by certain defining characteristics but exhibited a gradual change in their antigenic structure. In contrast, when the outbreaks were examined over shorter periods of time, a number of varieties and single strains were found which differed greatly from each other yet possessed the same major serotype antigen. These findings are discussed in terms of a 'one-parent' concept in which the varieties and single strains represent phases of a common ancestor. By inspection and analysis of the characteristics of the strains, certain associations were apparent. For instance, a correlation was found between the antigenic structure of the organism and the colonial appearance on tellurite blood agar. Similarly, correlation was observed between bacteriophage type, diphthericin type and biochemical activity in that a strain which was highly active in one of the properties was also very active in the other two.     

New Bradyrhizobium japonicum strains that possess high copy numbers of the repeated sequence RS alpha

In a survey of DNA fingerprints of indigenous Bradyrhizobium japonicum with the species-specific repeated sequences RS alpha and RS beta, 21 isolates from three field sites showed numerous RS-specific hybridization bands. The isolates were designated highly reiterated sequence-possessing (HRS) isolates, and their DNA hybridization profiles were easily distinguished from the normal patterns. Some HRS isolates from two field sites possessed extremely high numbers of RS alpha copies, ranging from 86 to 175 (average, 128), and showed shifts and duplications of nif- and hup-specific hybridization bands. The HRS isolates exhibited slower growth than normal isolates, although no difference in symbiotic properties was detected between the HRS and normal isolates. Nucleotide sequence analysis of 16S rRNA genes showed that HRS isolates were strains of B. japonicum. There was no difference in the spectra of serological and hydrogenase groupings of normal and HRS isolates. Some HRS isolates possessed a tandem repeat RS alpha dimer that is similar to the structure of (IS30)2, which was shown to cause a burst of transpositional rearrangements in Escherichia coli. The results suggest that HRS isolates are derived from normal isolates in individual fields by genome rearrangements that may be mediated by insertion sequences such as RS alpha.     

Characterization of Rickettsia tsutsugamushi strains newly isolated in Ehime Prefecture, Japan]

Five strains of Rickettsia tsutsugamushi were isolated in Ehime Prefecture during December 1987 to January 1990. Of these, two strains, the Yamazaki and Noma-3, were isolated at Noma area of Imabari city and three strains, the Kakiwara-10, -11, -12, at Kakiwara area of Uwajima city. The Yamazaki strain was isolated from a patient of tsutsugamushi disease and the other strains from wild rodents (Apodemus speciosus). These strains showed virulence in euthymic mice. The calculated LD50 of the Yamazaki and Kakiwara-10 strains showed 10(-3.0) and 10(-1.8), respectively. The immunofluorescent antibody test using thirty monoclonal antibodies to six representative strains, the Gilliam, Karp, Kato, Irie, Hirano and Shimokoshi, revealed that two strains isolated at Noma area, the Yamazaki and Noma-3, were identified as the Karp type and three strains at Kakiwara area, the Kakiwara-10, -11, -12, were identified as the Kato type. It was clarified that the serotypic differences were present among the strains isolated in Ehime Prefecture. Moreover, these five strains isolated in Ehime Prefecture did not react with the serotype-specific monoclonal antibodies to the Irie, Hirano and Shimokoshi strains known as the representative strains of so-called new type of tsutsugamushi disease, showing antigenic differences.     

Biotyping of Campylobacter strains isolated in Lagos, Nigeria using the modified Preston biotype

Fifty-eight Compylobacter strains were isolated from children with diarrhoea at various health centres in Lagos and from healthy chicken. Twenty-nine strains of Campylobacter were isolated from humans, while the same number were isolated from chicken. The strains were biotyped using the modified Preston biotype scheme. The Preston biotyping results have been compared with the results of Penner serotyping. Out of fifty-eight strains studied, the technique identified ten strains (17%) as C. coli, three (5%) as C. lari and fourty-five (78%) as C. jejuni, by the coding system. This technique identified twenty-eight Campylobacter species. This method highlights the usefulness of this technique in the biotyping of local strains, however, when the two schemes are used in combination they give excellent typing results suitable for epidemiological purposes.     

Determination of genotypes of Toxoplasma gondii strains isolated from patients with toxoplasmosis

To determine the genotypes of Toxoplasma gondii strains associated with human toxoplasmosis, we developed a sensitive approach for typing parasites grown from clinical samples by short-term in vitro culture. A newly described nested PCR assay was capable of amplifying genomic DNA from as few as five parasites in the presence of host tissues. Typing was based on DNA polymorphisms at the SAG2 locus, encoding tachyzoite surface antigen p22. Restriction fragment length polymorphisms in PCR-amplified SAG2 products were used to classify strains into one of the three major lineages of T. gondii. This approach was successfully used to determine the genotypes of 68 of 72 samples that had been previously isolated from patients with congenital, cerebral, and disseminated toxoplasmosis. Type II strains of T. gondii were found in a majority of the samples, accounting for 55 (81%) of the 68 toxoplasmosis cases. In contrast, type I and III strains were found in only 7 (10%) and 6 (9%) of the 68 cases, respectively. The results of this study support the previous finding that type II strains are most often associated with human toxoplasmosis. Nested PCR analysis at the SAG2 locus provides rapid assignment of T. gondii to a specific genotype that should be useful in analyzing a variety of clinical samples.     

Polynucleotide sequence divergence among strains of Salmonella sub-genus IV and closely related organisms

Polynucleotide sequence relatedness studies were carried out to determine the extent of divergence present in Salmonella sub-genus IV strains, related strains of Salmonella of other sub-genera and the Citrobacter genus. Salmonella sub-genus IV were 91-97% related. The Salmonella of sub-genus I, II and III showed lower binding (79-87%) to Salmonella sub-genus IV. The change in thermal elution midpoint closely followed the reassociation data. Relatedness of Salmonella sub-genus IV and C. freundii ranged between 44 and 57%, which confirms that these organisms belong to different genera. The taxonomic position of Salmonella sub-genus IV is discussed according to the actual classification of the family Enterobacteriaceae.     

Comparison of genomic methods for differentiating strains of Enterococcus faecium: assessment using clinical epidemiologic data

Genomic DNA extracted from 45 vancomycin-resistant Enterococcus faecium (VRE) isolates was cleaved with HindIII and HaeIII and subjected to agarose gel electrophoresis. The ability of this method (restriction endonuclease analysis [REA]) to distinguish strains at the subspecies level was compared with results previously determined by pulsed-field gel electrophoresis (PFGE). Chart reviews were performed to provide a clinical correlation of possible epidemiologic relatedness. A likely clinical association was found for 29 patients as part of two outbreaks. REA found 21 of 21 isolates were the same type in the first outbreak, with PFGE calling 19 strains the same type. In the second outbreak with eight patient isolates, HindIII found six were the same type and two were unique types. HaeIII found three strains were the same type, two strains were a separate type, and three more strains were unique types, while PFGE found three were the same type and five were unique types. No single "ideal" method can be used without clinical epidemiologic investigation, but any of these techniques is helpful in providing focus to infection control practitioners assessing possible outbreaks of nosocomial infection.     

Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of puget sound Cycloclasticus strains

Phenanthrene- and naphthalene-degrading bacteria were isolated from four offshore and nearshore locations in the Gulf of Mexico by using a modified most-probable-number technique. The concentrations of these bacteria ranged from 10(2) to 10(6) cells per ml of wet surficial sediment in mildly contaminated and noncontaminated sediments. A total of 23 strains of polycyclic aromatic hydrocarbon (PAH)-degrading bacteria were obtained. Based on partial 16S ribosomal DNA sequences and phenotypic characteristics, these 23 strains are members of the genus Cycloclasticus. Three representatives were chosen for a complete phylogenetic analysis, which confirmed the close relationship of these isolates to type strain Cycloclasticus pugetii PS-1, which was isolated from Puget Sound. PAH substrate utilization tests which included high-molecular-weight PAHs revealed that these isolates had similar, broad substrate ranges which included naphthalene, substituted naphthalenes, phenanthrene, biphenyl, anthracene, acenaphthene, and fluorene. Degradation of pyrene and fluoranthene occurred only when the strains were incubated with phenanthrene. Two distinct partial PAH dioxygenase iron sulfur protein (ISP) gene sequences were PCR amplified from Puget Sound and Gulf of Mexico Cycloclasticus strains. Phylogenetic analyses of these sequences revealed that one ISP type is related to the bph type of ISP sequences, while the other ISP type is related to the nah type of ISP sequences. The predicted ISP amino acid sequences for the Gulf of Mexico and Puget Sound strains are identical, which supports the hypothesis that these geographically separated isolates are closely related phylogentically. Cycloclasticus species appear to be numerically important and widespread PAH-degrading bacteria in both Puget Sound and the Gulf of Mexico.     

Human antibodies to the conserved region of the M protein: opsonization of heterologous strains of group A streptococci

A 20-mer peptide (p145) in the carboxyl-terminal region of the M protein of group A streptococci (GAS) has previously been defined as the target of bactericidal antibodies. Sequence analysis of seven field isolates from indigenous Australians living in an area highly endemic for GAS and five laboratory reference strains (encompassing nine unique serotypes plus three nontypeables) demonstrates that this region is highly conserved (sequence identity ranging from 65 to 95%) with six of the 12 sequences being identical to p145. Most of the sequence dissimilarity is contained within the last seven amino acids of p145. Competitive ELISA demonstrates that human antibodies specific for p145 cannot discriminate between p145 and synthetic peptides representing four from four of the variant sequences tested. Ig purified from endemic sera was able to opsonize each of the GAS isolates and free p145 as well as a peptide expressing a minimal conformational epitope within p145 (requiring amino acids between positions 2 and 13 of p145), but not an irrelevant peptide, were able to partially or completely inhibit opsonization of all isolates and reference strains. Thus adult endemic sera contain antibodies which are bactericidal for multiple GAS serotypes and which are specific for a sequence of 12 amino acids contained within the p145 region of the M protein.     

Differential patterns of T-cell receptor BV-specific activation of T cells by gp120 from different HIV strains

Studies by several groups have suggested that HIV infection in vivo results in a BV-specific alteration of the TCR repertoire and that this might play a role in the pathogenesis of AIDS. Our earlier studies demonstrated that both a crude extract of HIV451 as well as purified gp 160 from HIV451 could specifically activate, in vitro, T cells expressing a common set of TCRBV segments (TCRBV3, 12, 14, 15, and sometimes BV17 and 20) in individuals of disparate HLA type. Furthermore, purified gp120 from HIV451 was shown to have a similar ability to activate T cells, although with a slightly different TCRBV-specific pattern. In order to determine whether gp120 from other HIV strains could similarly activate T cells in a TCRBV-specific pattern, PBMC from HIV seronegative individuals of disparate HLA type were stimulated with gp120 from three strains of HIV (451, IIIB, and MN). The authors found that gp120 from all three strains activate T cells bearing TCRBV2 and BV3 in nearly every individual. T cells expressing other BV segments are also activated, but this is more variable and appears to be unique to each individual. Furthermore, gp120(451) and gp120 from HIVIIIB and HIVMN differ in their ability to activate T cells expressing these other TCRBV segments. These observations suggest that variation in the structure of gp120 and in the genetic and/or environmental background of the individual play an important role in determining which TCRBV segments are 'triggered' by gp120. Furthermore, these observations may have important implications for the rate of disease progression in HIV-infected individuals.     

Enteroaggregative Escherichia coli strains as a cause of traveler's diarrhea: a case-control study

To elucidate the importance of enteroaggregative Escherichia coli (EAggEC) strains as a cause of traveler's diarrhea in Spanish travelers, a prospective case-control 1:1 study was done in a university hospital clinic for travelers. EAggEC strains were isolated from 23 of 165 case-patients and from 4 of 165 controls (P = .0003). In 16 patients, this was the only isolate recovered. Six of the EAggEC-positive isolates from the case-patients and 2 from the controls were positive for the enteroaggregative stable toxin type 1 gene. Other enteropathogens were also isolated. Shigella and enterotoxigenic E. coli strains showed significant differences between cases and controls (P = .0023 and P < .0001, respectively). Geographic distribution of the EAggEC strains was homogeneous, and the clinical symptom, secretory diarrhea, did not differ statistically with that for the enterotoxigenic E. coli strains. EAggEC strains are a cause of secretory diarrhea in Spaniards traveling to developing countries.     

Molecular characterization of two Bordetella bronchiseptica strains isolated from children with coughs

During a surveillance program associated with the Italian clinical trial for the evaluation of new acellular pertussis vaccines, two bacterial isolates were obtained in cultures of samples from immunocompetent infants who had episodes of cough. Both clinical isolates were identified as Bordetella bronchiseptica by biochemical criteria, although both strains agglutinated with antisera specific for Bordetella parapertussis, suggesting that the strains exhibited some characteristics of both B. bronchiseptica and B. parapertussis. Both children from whom these strains were isolated exhibited an increase in serum antibody titer to pertussis toxin (PT), a protein that is produced by Bordetella pertussis but that is not thought to be produced by B. bronchiseptica. We therefore examined whether the clinical isolates were capable of producing PT. Neither strain produced PT under laboratory conditions, although both strains appeared to contain a portion of the ptx region that encodes the structural subunits of PT. In order to determine whether the ptx genes may encode functional proteins, we inserted an active promoter directly upstream of the ptx region of one of these strains. Biologically active PT was produced, suggesting that this strain contains the genetic information necessary to encode an active PT molecule. Sequence analysis of the ptx promoter region of both strains indicated that, while they shared homology with the B. bronchiseptica ATCC 4617 sequence, they contained certain sequence motifs that are characteristic of B. parapertussis and certain motifs that are characteristic of B. pertussis. Taken together, these findings suggest that variant strains of B. bronchiseptica exist and might be capable of causing significant illness in humans.     

Hemolytic activity reevaluation of putative nonpathogenic Listeria monocytogenes strains

Identification of 12 strains originally characterized as nonpathogenic Listeria monocytogenes was reassured following the evaluation of their hemolytic capability with a newly developed horse blood agar plate. Seven of the strains were observed consistently to be hemolytic and confirmed as L. monocytogenes with the use of two commercial systems: the Gene-Trak L. monocytogenes-specific colorimetric DNA hybridization assay and the API Listeria system. Except for one strain that formed typical smooth colonies, these hemolytic strains formed rough colonies on a selective medium, lithium chloride-ceftazidime agar. The rest of the strains were nonhemolytic and did not hybridize with the DNA probe; they were identified as Listeria innocua on the basis of their API Listeria system biochemical profile. All but one of these nonhemolytic strains formed smooth colonies on lithium chloride-ceftazidime agar.     

Production of A and C variants of staphylococcal beta-lactamase by methicillin-resistant strains of Staphylococcus aureus

Most methicillin-resistant Staphylococcus aureus (MRSA) strains produce beta-lactamase. To determine whether this enzyme(s) is identical to one or more of the four beta-lactamases produced by methicillin-susceptible strains, the beta-lactamases of 50 MRSA isolates were typed by using substrate profile analysis. Forty type A, no type B, ten type C, and no type D beta-lactamase-producing strains were identified. The beta-lactamase inhibitor sulbactam reduced the MICs of beta-lactamase-labile antibiotics, including ampicillin, penicillin G, and cefazolin, for type A and type C MRSA strains.