Similar ectopic gene conversion frequencies in the backbone genome of pathogenic and nonpathogenic Escherichia coli strains

We previously showed that gene conversions were more frequent in the genomes of three Escherichia coli pathogenic strains than in the genome of the nonpathogenic K-12 E. coli strain. However, that study did not address whether the more frequent conversions observed in the genes of pathogenic strains occurred between the backbone genes common to these four strains or in the numerous horizontally transferred genes found only in pathogenic strains. Here, we show that ectopic gene conversions are equally frequent in the backbone genes of pathogenic and nonpathogenic strains, that most of these conversions are short, and that the nucleotide changes they generate are probably selectively neutral. Backbone genes are therefore under similar selective constraints in both pathogenic and nonpathogenic E. coli strains. The higher frequency of gene conversions we previously observed in pathogenic strains is therefore due to higher conversion frequencies between the numerous horizontally transferred genes found only in pathogenic strains.     

Taxonomy of four marine bacterial strains that produce tetrodotoxin

Four strains of tetrodotoxin-producing bacteria isolated from a red alga and from pufferfish were characterized. Two of these strains are members of the genus Listonella MacDonell and Colwell. The phenotypic characteristics, guanine-plus-cytosine contents, and base sequences of the 16S rRNAs of these organisms indicated that they are members of Listonella pelagia (Vibrio pelagius) biovar II. The other two strains are members of the genus Alteromonas Baumann et al. and the genus Shewanella MacDonell and Colwell. These two strains are mutually distinct and distinct from the previously described Alteromonas and Shewanella species and therefore are placed in new species. The names Shewanella alga and Alteromonas tetraodonis are proposed for these organisms; the type strains are strains OK-1 and GFC, respectively.     

Isolation and characterization of an isogenic set of Salmonella typhimurium strains analogous to the "Ames" tester strains

The standard Ames tester strains of Salmonella typhimurium contain a number of genetic differences at loci other than his. The fact that these strains contain independently isolated uvrB-bio-gal deletions and rfa mutations implies that these are likely to vary from strain to strain. Since the strains were isolated from different parental stocks of S. typhimurium LT-2, they differ in their ability to metabolize arabinose. Other, unknown differences may exist because the isolation of some of the strains involved ultraviolet and chemical mutagenesis. We have isolated a set of isogenic S. typhimurium strains that contain the relevant genetic markers of the standard Ames tester strains. These strains all contain the same uvrB-bio-gal deletion and the same rfa mutation; they differ only in the nature of their his mutations and in the presence or absence of the plasmid pKM101. We have assessed the responsiveness of these strains to a number of mutagens and conclude that their mutagenic specificities are the same as those of the corresponding Ames strains: TA98, TA100, TA1535, TA1537 and TA1538. Therefore, the specificity of the standard Ames strains with respect to these mutagens is a result solely of the differences in the nature of their his mutations and the effects of pKM101.     

Characteristics of the MRSA clone with reduced susceptibility to vancomycin

The MIC of vancomycin was determined for all S. aureus strains isolated during 1997 in one hospital. MIC values for most isolates were in the range of 0.5-2 mg/l. In 18 strains, MIC was = 6 mg/L. All these strains were MRSA. Recently described VISA strains possessed MIC values for vancomycin equal or higher than 8 mg/l and such strains were not detected in the investigated group. Although strains with MIC = 6 mg/l are not VISA, but they are candidate for reduced vancomycin susceptibility, e.g. during therapy in compromised patients. Analysis of DNA of these strains by pulsed-field gel electrophoresis (PFGE) revealed that 15 of them shared a significant similarity, allowing to place them in the same group. The comparison data of phage patterns as well as antibiotic resistance patterns strongly suggest that all these strains were derivatives of a single clone.     

Genomic characterization of antibiotic resistance-encoding genes in clinical isolates of Vibrio cholerae non-O1/non-O139 strains from Kolkata,India: generation of novel types of genomic islands containing plural antibiotic resistance genes

Non-O1/non-O139 nontoxigenic Vibrio cholerae associated with cholera-like diarrhea has been reported in Kolkata, India. However, the property involved in the pathogenicity of these strains has remained unclear. The character of 25 non-O1/non-O139 nontoxigenic V. cholerae isolated during 8 years from 2007 to 2014 in Kolkata was examined. Determination of the serogroup showed that the serogroups O6, O10, O35, O36, O39, and O70 were represented by two strains in each serogroup, and the remaining isolates belonged to different serogroups. To clarify the character of antibiotic resistance of these isolates, an antibiotic resistance test and the gene analysis were performed. According to antimicrobial drug susceptibility testing, 13 strains were classified as drug resistant. Among them, 10 strains were quinolone resistant and 6 of the 13 strains were resistant to more than three antibiotics. To define the genetic background of the antibiotic character of these strains, whole-genome sequences of these strains were determined. From the analysis of these sequences, it becomes clear that all quinolone resistance isolates have mutations in quinolone resistance-determining regions. Further research on the genome sequence showed that four strains possess Class 1 integrons in their genomes, and that three of the four integrons are found to be located in their genomic islands. These genomic islands are novel types. This indicates that various integrons containing drug resistance genes are spreading among V. cholerae non-O1/non-O139 strains through the action of newly generated genomic islands.     

Genetic variations in the pgm locus among natural isolates of Yersinia pestis

A PCR-based screening method was used to study the genetic variations of the pgm locus among natural isolates of Yersinia pestis from China. Our results indicate that genetic variations in the pgm locus are well correlated with biovars of Y. pestis and plague foci, suggesting that the pgm locus plays a role in Y. pestis adaptation to its environment. The gene encoding two-component regulatory system sensor kinase became a pseudogene in all strains of biovar Orientalis due to a thymidine deletion, while it is intact in all the strains of the other biovars. Only strains from Foci H and L are the same as Yersinia pseudotuberculosis in that they have an intact transmembrane helix in the sensor kinase protein, which is lost in all the other strains because of the 18 bp in-frame deletion. The IS100 element that flanks the 39 terminus of the pgm locus was inserted into the chromosome during the within-species microevolution of Y. pestis, which is absent in strains from Foci G, H and L and also in Y. pseudotuberculosis. This fact indicates that the strains from these three foci are of an older lineage of Chinese Y. pestis. It is this IS100 element's absence that maintained high stability of the pgm locus in the Y. pestis strains from these three foci. The IS285 element insertion in the pigmentation segment and the IS100 element insertion in the downstream flanking region of the pgm locus are only present in strains from Foci H and L. The flanking region outside the 59 terminus of the upstream IS100 element is identical in the strains from these two foci, which is different in the other strains. All of these unique characteristics suggest that they are of a special lineage of Chinese Y. pestis.     

Host specificity of septicemic Escherichia coli: human and avian pathogens

Extraintestinal pathogenic Escherichia coli (ExPEC) strains are the cause of a diverse spectrum of invasive human and animal infections, often leading to septicemia. ExPEC strains contain virulence factors that enable them to survive in the host blood and tissues. Most of these virulence factors are distributed in ExPEC strains in a host-independent fashion. Genomic analyses of these strains provide evidence for numerous recombinational events and horizontal gene transfer, as well as for a high diversity of virulence factors. In studies of human and avian septicemic strains of serotypes O2 and O78 it appears that there is a positive correlation between virulence, invasiveness and clonal origin. Yet, it is clear that clonal division in these strains, as well as distribution of virulence factors, is independent of the host and closely related clones reside in different hosts. Although the possibility exists that ExPEC strains do have a certain degree of host specificity, which is not obvious from genomic studies, it is clear that the similarity of virulence factors presents a significant zoonotic risk.     

The Penicillium commune Thom and Penicillium clavigerum Demelius fungi--fumigaclavines A and B producers

The type strains Penicillium clavigerum VKM F-447 and P. commune VKM F-3233 are found to produce fumigaclavines A and B. Of the seven other strains of these species, only two strains, P. commune VKM F-3088 and F-3491, possess the ability to synthesize these alkaloids. It is suggested that the five other strains under study either lost such an ability or require very specific conditions for the synthesis of these alkaloids.     

Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.

We determined the nucleotide sequences of 16S rRNA gene segments from five Rhizobium strains that have been isolated from tropical legume species. All share the capacity to nodulate Phaseolus vulgaris L., the common bean. Phylogenetic analysis confirmed that these strains are of two different chromosomal lineages. We defined the host ranges of two strains of Rhizobium etli and three strains of R. tropici, comparing them with those of the two most divergently related new strains. Twenty-two of the 43 tested legume species were nodulated by three or more of these strains. All seven strains have broad host ranges that include woody species such as Albizia lebbeck, Gliricidia maculata, and Leucaena leucocephala.     

阿氏浮丝藻mcyT基因序列多样性研究

为研究我国浮丝藻（Planktothrix Anagnostidis et Komrek）的毒素相关基因,选取分离自我国不同省份水体的13株阿氏浮丝藻,通过PCR检测其微囊藻毒素合成酶基因mcyA、mcyE及mcyT研究其毒素基因特性。PCR结果表明除mcyT之外其他引物检测均无扩增产物,说明这13株浮丝藻不具备产微囊藻毒素的能力。通过克隆测序得到mcyT序列,并进行分子系统分析,构建了关于mcyT序列的Neighbor-Joining系统树,结果表明mcyT序列可以将产毒与不产毒浮丝藻分为两大独立的分支,两个分支之间的最低序列相似度分别为98.5%和99.1%。研究结果可为后续研究我国浮丝藻的微囊藻毒素合成相关基因的多样性以及分子监测提供参考。       

A role for Ca2+ in the effect of very low frequency electromagnetic field on the blastogenesis of human lymphocytes

Methicillin-resistant clinical isolates of Staphylococcus aureus are intrinsically resistant to beta-lactam antibiotics in that the resistance mechanism is unrelated to the possession of beta-lactamases. We have demonstrated that a new, high-molecular-mass penicillin-binding protein (PBP) is present in these strains with a low affinity for beta-lactams and that its amount is regulated by the growth conditions. The new PBP from all strains that have been examined has an identical mobility on SDS gel electrophoresis and is the only PBP still present in an uncomplexed state with beta-lactams (and therefore the only functional PBP when these strains are grown in media containing concentrations of beta-lactam antibiotics sufficient to kill sensitive strains.     

Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing

Many bacteria display substantial intra-specific genomic diversity that produces significant phenotypic variation between strains of the same species. Understanding the genetic basis of these strain-specific phenotypes is especially important for industrial microorganisms where these characters match individual strains to specific industrial processes. Oenococcus oeni, a bacterium used during winemaking, is one such industrial species where large numbers of strains show significant differences in commercially important industrial phenotypes. To ascertain the basis of these phenotypic differences, the genomic content of ten wine strains of O. oeni were mapped by array-based comparative genome hybridization (aCGH). These strains comprised a genomically diverse group in which large sections of the reference genome were often absent from individual strains. To place the aCGH results in context, whole genome sequence was obtained for one of these strains and compared with two previously sequenced, unrelated strains. While the three strains shared a core group of conserved ORFs, up to 10% of the coding potential of any one strain was specific to that isolate. The genome of O. oeni is therefore likely to be much larger than that present in any single strain and it is these strain-specific regions that are likely to be responsible for differences in industrial phenotypes.     

Multicopy Tn10 tet plasmids confer sensitivity to induction of tet gene expression.

We inserted the Tn10 tetracycline resistance determinant (tet) into the multicopy plasmid pACYC177, and we examined the phenotype of Escherichia coli K-12 strains harboring these plasmids. In agreement with others, we find that Tn10 tet exhibits a negative gene dosage effect. Strains carrying multicopy Tn10 tet plasmids are 4- to 12-fold less resistant to tetracycline than are strains with a single copy of Tn10 in the bacterial chromosome. In addition, we find that multicopy tet strains are 30- to 100-fold less resistant to the tetracycline derivative 5a,6-anhydrotetracycline than are single-copy tet strains. Multicopy tet strains are, in fact, 10- to 25-fold more sensitive to anhydrotetracycline than are strains that lack tet altogether. The hypersensitivity of multi-copy strains to anhydrotetracycline is correlated with the effectiveness of anhydrotetracycline as an inducer of tet gene expression, rather than its effectiveness as an inhibitor of protein synthesis. Anhydrotetracycline is 50- to 100-fold more effective than tetracycline as an inducer of tetracycline resistance and as an inducer of beta-galactosidase in strains that harbor tet-lac gene fusions. In contrast, anhydrotetracycline appears to be two- to fourfold less effective than tetracycline as an inhibitor of protein synthesis. Both anhydrotetracycline and tetracycline induce synthesis of tet polypeptides in minicells harboring multicopy tet plasmids. Differences between E. coli K-12 backgrounds influence the tetracycline and anhydrotetracycline sensitivity of multicopy strains; ZnCl2 enhances the tetracycline and anhydrotetracycline sensitivity of these strains two- to threefold. We propose that the overexpression of one or more Tn10 tet gene products inhibits the growth of multicopy tet strains and accounts for their relative sensitivity to inducers of tet gene expression.     

Erwinia aphidicola,a new species isolated from pea aphid,Acyrthosiphon pisum

Five strains of Gram-negative, oxidase-negative, facultatively anaerobic, fermentative, motile, rod-shaped bacterium with the general characteristics of the family Enterobacteriaceae were isolated from the gut of multiple specimens of the pea aphid. All the strains caused aphid mortality when ingested by insects via a synthetic diet. The results of biochemical tests showed that these strains are most related to Erwinia herbicola and Pantoea agglomerans. According to DNA-DNA hybridization, the five strains showed more than 96% relatedness to each other, indicating that these organisms are members of a single species. These strains were most closely related to Erwinia herbicola (22% DNA relatedness). Phenotypic differentiation of these strains from Erwinia herbicola, which was also detected from aphid gut, was based on negative reactions in tests of yellow pigment production, gelatin liquefaction, acid production from inulin, starch and dulcitol, and positive acid production from melibiose, inositol, cellobiose and glycerol. On the basis of these data, the name Erwinia aphidicola is proposed for the new organism. The type strain is strain X 001 (=IAM 14479).     

Phenotypic instability of Salmonella typhimurium tester strains: an example of a plasmid-enhanced genetic drift?

Strains derived from Salmonella typhimurium LT-2, which are used as tester strains in mutagenicity assays, show significant changes in biochemical phenotypes. The presence of plasmid pKM101 in these strains greatly increases both the frequency of these shifts as well as the spectrum of phenotypes involved. It is suggested that in plasmid-free strains these variations reflect the effects of endogeneously induced mutations which are amplified in the absence of a functional uvrB gene product. In plasmid-containing strains this genetic drift may be promoted further by the pKM101-coded error-prone DNA repair system. The observation of a plasmid-mediated genetic drift lends support to the suggestion that transposons may contribute to the carcinogenic process.     

Genetics and complementation of Haemophilus influenzae mutants deficient in adenosine 5''-triphosphate-dependent nuclease.

Eight different mutations in Haemophilus influenzae leading to deficiency in adenosine 5'-triphosphate (ATP)-dependent nuclease have been investigated in strains in which the mutations of the originally mutagenized strains have been transferred into the wild type. Sensitivity to mitomycin C and deoxycholate and complementation between extracts and deoxyribonucleic acid (DNA)-dependent ATPase activity have been measured. Genetic crosses have provided information on the relative position of the mutations on the genome. There are three complementation groups, corresponding to three genetic groups. The strains most sensitive to mitomycin and deoxycholate, derived from mutants originally selected on the basis of sensitivity to mitomycin C or methyl methanesulfonate, are in one group. Apparently all these sensitive strains lack DNA-dependent ATPase activity, as does a strain intermediate in sensitivity to deoxycholate, which is the sole representative of another group. There are four strains that are relatively resistant to deoxycholate and mitomycin C, and all of these contain the ATPase activity. Three of these are in the same genetic and complementation group, whereas the other incongruously belongs in the same group as the sensitive strains. It is postulated that there are three cistrons in H. influenzae that code for the three known subunits of the ATP-dependent nuclease.     

Variations in maxi-circle and mini-circle sequences in kinetoplast DNAs from different Trypanosoma brucei strains

We have compared a total of 30 recognition sites for eight restriction endonucleases on the 20-kilobase-pair maxi-circle of kinetoplast DNAs from five different Trypanosoma brucei strains. In addition to three polymorphic sites were have found a 5 kilobase-pair region that is not cleaved by any of the eight enzymes and that varies in size over 1 kilobase pair in the strains analysed. Mini-circles from these five strains, digested with endonuclease TaqI or MboII, yield very complex fragment patterns, showing that extensive mini-circle sequence heterogeneity is a common characteristic of these T. brucei strains. The size distribution of mini-circle fragments in these digests was identical for different clones of the 427 strain, but very different for mini-circles from different strains. These results show that maxi-circle sequence is conserved, whereas mini-circle sequence is not. Restriction digests of maxi-circles could be useful in determining how closely two Trypanosoma strains are related, whereas mini-circle digests can serve as sensitive tags for individual strains.     

Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally

Rickettsia are endosymbionts of arthropods, some of which are vectored to vertebrates where they cause disease. Recently, it has been found that some Rickettsia strains harbour conjugative plasmids and others encode some conjugative machinery within the bacterial genome. We investigated the distribution of these conjugation genes in a phylogenetically diverse collection of Rickettsia isolated from arthropods. We found that these genes are common throughout the genus and, in stark contrast to other genes in the genome, conjugation genes are frequently horizontally transmitted between strains. There is no evidence to suggest that these genes are preferentially transferred between phylogenetically related strains, which is surprising given that closely related strains infect similar host species. In addition to detecting patterns of horizontal transmission between diverse Rickettsia species, these findings have implications for the evolution of pathogenicity, the evolution of Rickettsia genomes and the genetic manipulation of intracellular bacteria.