Genetic and physical characterization of trimethoprim resistance plasmids from Shigella sonnei and Shigella flexneri

Analysis of six Shigella flexneri and four S. sonnei isolates with trimethoprim (Tp) resistance from clinical cases in Ontario has shown that, in all isolates, the Tp resistance is mediated by gene(s) on conjugative, multiple antibiotic-resistance plasmids. The physical and genetic characterization of these plasmids revealed that there are three different Tp resistance plasmids. One group, composed of all six S. flexneri plasmids, consists of plasmids which are about 70 megadaltons (MDa) and inhibit the fertility of an Escherichia coli Hfr strain (Fi+). A representative member of this group, pPT4, demonstrates a weak incompatibility reaction with IncFl plasmid R455-2. Another group, three of the four S. sonnei plasmids, contains plasmids which are about 43 MDa, Fi-, and mediate propagation of phage PRD1. The third group, the remaining S. sonnei plasmid, is 53 MDa, fi+, mediates propagation of phages fd and MS2, and is incompatible with IncFII plasmid R100. These plasmids also have been differentiated by restriction endonuclease fragment profiles. Analysis of pPT4 has revealed that the Tp resistance of this plasmid is transposable. The transposon, Tn536, is different from previously described Tp resistance transposons; it is 16 MDa, and in addition to Tp, it encodes resistance to mercuric chloride ions, spectinomycin, streptomycin, and sulfonamides.     

Development and use of solid-phase test-systems for the detection of O-antigen of Shigella sonnei and Shigella flexneri

The possibility of the diagnosis of dysentery caused by S. sonnei and S. flexneri, as well as the determination of the dynamics of the distribution of specific O-antigen in the patient's body, by means of the enzyme-linked immunosorbent assay system developed on the basis of antibody preparations obtained by immunosorption has been studied. The study has shown that for better diagnosis the use of fecal extracts is preferable in assays; when used in combination with bacteriological analysis, these assays make it possible to increase the confirmation of the diagnosis of dysentery by several fold.     

Gene cloning and characterization of alanine racemases from Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Shigella sonnei.

Alanine racemase genes (alr) from Shigella dysenteriae, Shigella boydii, Shigella flexneri, and Shigella sonnei were cloned and expressed in Escherichia coli JM109. All genes encoded a polypeptide of 359 amino acids, and showed more than 99% sequence identities with each other. In particular, the S. dysenteriae alr was identical with the S. flexneri alr. Differences in the amino acid sequences between the four Shigella enzymes were only two residues: Gly138 in S. dysenteriae and S. flexneri (Glu138 in the other) and Ile225 in S. sonnei (Thr225 in the other). The S. boydii enzyme was identical with the E. coli K12 alr enzyme. Each Shigella alr enzyme purified to homogeneity has an apparent molecular mass about 43,000 by SDS-gel electrophoresis, and about 46,000 by gel filtration. However, all enzymes showed an apparent molecular mass about 60,000 by gel filtration in the presence of a substrate, 0.1 M l-alanine. These results suggest that the Shigella alr enzymes having an ordinary monomeric structure interact with other monomer in the presence of the substrate. The enzymes were almost identical in the enzymological properties, and showed lower catalytic activities (about 210 units/mg) than those of homodimeric alanine racemases reported.     

稳定、无抗药的痢疾福氏2a和宋内双价菌苗候选株的构建

通过体内外基因重组,将大肠杆菌粘附因子cs3基因定位整合到痢疾杆菌福氏2a疫苗株T32菌染色体的asd基因内,使asd基因灭活;将来内O抗原基因克隆至无抗药性表达载体pXL378,获得重组质粒pXL390,将其转化asd-的T32受体菌,构建成福氏2a和宋内双价苗苗株FS01。实验表明:重组质粒pXL390在不带任何抗菌素基因的情况下,在asd-的T32受体菌内是稳定的。FS01株遗传稳定,能表达两种痢疾菌的PLS-O抗原,无明显毒性作用。动物试验表明,以FS01株皮下免疫的小鼠对福氏2a和宋内有毒株的腹腔攻击有100％的保护。     

An AFLP-based database of Shigella flexneri and Shigella sonnei isolates and its use for the identification of untypable Shigella strains

Amplified fragment length polymorphism (AFLP) can be used to assess the genetic diversity of closely related microbial genomes. In this study, the first of its kind for identification of Shigella, the high discriminatory power of AFLP has been used to determine the genetic relatedness of 230 isolates of Shigella flexneri and Shigella sonnei strains. An AFLP database was generated to demonstrate its utility in the discrimination of closely related strains. Based on AFLP, S. flexneri strains could be grouped into separate clusters according to their serotypes. Within each serotype, strains demonstrated 80–100% similarity indicating that identical strains and closely related strains could be distinguished by this technique. S. flexneri 6 formed a distinct cluster with 55% similarity to the rest of the S. flexneri strains showing significant divergence from the rest of the S. flexneri strains. Significantly, S. sonnei isolates formed a distinct group and showed approximately the same level of genetic linkage to S. flexneri as Escherichia coli strains. Untypable isolates that showed conflicting agglutination reactions with conventional typing sera were identifiable by AFLP. Thus AFLP can be used for genetic fingerprinting of Shigella strains and aid in the identification of variant untypable isolates.     

An AFLP-based database of Shigella flexneri and Shigella sonnei isolates and its use for the identification of untypable Shigella strains

Amplified fragment length polymorphism (AFLP) can be used to assess the genetic diversity of closely related microbial genomes. In this study, the first of its kind for identification of Shigella, the high discriminatory power of AFLP has been used to determine the genetic relatedness of 230 isolates of Shigella flexneri and Shigella sonnei strains. An AFLP database was generated to demonstrate its utility in the discrimination of closely related strains. Based on AFLP, S. flexneri strains could be grouped into separate clusters according to their serotypes. Within each serotype, strains demonstrated 80-100% similarity indicating that identical strains and closely related strains could be distinguished by this technique. S. flexneri 6 formed a distinct cluster with 55% similarity to the rest of the S. flexneri strains showing significant divergence from the rest of the S. flexneri strains. Significantly, S. sonnei isolates formed a distinct group and showed approximately the same level of genetic linkage to S. flexneri as Escherichia coli strains. Untypable isolates that showed conflicting agglutination reactions with conventional typing sera were identifiable by AFLP. Thus AFLP can be used for genetic fingerprinting of Shigella strains and aid in the identification of variant untypable isolates.     

Lipopolysaccharides of Shigella sonnei

Immunobiological properties of native lipopolysaccharides (LPS) from virulent and avirulent strains of Shigella sonnei bacteria (LPS-V and LPS-A, respectively) were studied. In avirulent bacteria, LPS-V induced immunosuppressive activity specific of the virulent strain. LPS of the avirulent strain, whereas LPS-A lacked this property. Native LPS-V with immunosuppressive activity were isolated from the virulent strain by and immune affinity method. Treatment of LPS-V with phenol or TCA abolished its activity and converted it into the LPS-A form. The data showed that LPS-A can be converted back to the LPS-V form by redox treatment. This approach seems to be promising for activating LPS extracted from cells with TCA or a water-phenol mixture.     

Immune response and immune tolerance to the O-antigen of Shigella flexneri VI

The method for the determination of the number of cells synthetizing antibodies to S. flexneri VI O-antigen in the spleen of mice has been developed. Primary immune response to this antigen has been studied with the use of the new method. Immune response to the optimum immunogenic dose of O-antigen has a manifest variable character. The intensity of primary immune response has been shown to rise with the increase of the dose of O-antigen from 0.004 to 50 micrograms. The preliminary injection of 200 micrograms of O-antigen, followed by the injection of cyclophosphamide 2 days later, leads to the development of specific immunological tolerance to O-antigen in experimental animals.     

痢疾杆菌酸抗性系统相关基因缺失突变体的构建

依赖于谷氨酸脱羧酶的酸抗性系统对痢疾杆菌在宿主细胞内的生存和繁殖至关重要,hdeA、hdeB、yhiE和yhiF是其中几个重要的酸抗性基因。借助Red系统的重组功能,PCR扩增两翼与目的基因上下游同源的抗性基因片段,电击转化痢疾杆菌2457T,对筛选到的阳性转化子再导入编码FLP位点特异性重组酶的质粒pCP20以去除抗性基因。结果成功的敲除了hdeA、hdeB、yhiE和yhiF等4个酸抗性系统相关基因,为深入研究痢疾杆菌酸抗性基因的调控网络奠定了基础.     

Colicine Typing of Shigella sonnei

Colicine typing of Shigella sonnei using the methods of Naito et al. and Abbott and Shannon were performed in parallel on a large number of epidemic strains, the indicator strains used in both methods, and on stock strains used to test the accuracy of the indicators. The following results were obtained after typing 462 epidemic strains: by Naito's method, 18 strains were in A₁, 87 in A₂, 33 in B₁, 253 in B₂, 38 in C₁, 3 in C₂, 2 in D, and 3 in E, and 25 strains were unclassifiable; while by Abbott and Shannon's method, using the present authors' simplified designation, 189 strains were in type 6/11, 124 in type 4/14, 85 in type O, and 41 in type 8, and 23 strains were either in other types or found unclassifiable. Naito's type A was in large part, equivalent to Abbott and Shannon's type O, but included some type 6/11 and type 4/14 strains. Naito's type B consisted of types 6/11, 4/14, 3A and 13, and type E consisted of 1A, IB, 3, 5, 9, and 10. Type C coincided with type 8 and type D with type 12. In addition, there were strains determined to be Abbott and Shannon's types 6/11, 4/14, 2, 7 and 9. The Abbott and Shannon's method revealed the possibilities of these strains to be classified in further detail. This is considered to be attributable not merely to the lack of indicators in the Naito's method corresponding to those of Abbott and Shannon's, but also to insufficient production of certain colicines in the Naito's method. Because of the type distribution found in Japan at present, further investigation should be done so that types 6 and 11, and types 4 and 14 can be separated.     

Colicine Typing of Shigella sonnei

The colicine typing method of Shigella sonnei is described with experimental evidence supporting it as well as the manner of selection of eight indicator strains. The disparity of principle between this method and that of Abbott and Shannon's method is (1) selection of the indicators only from wild strains existing in this country, (2) employment of heart infusion broth for colicine production, (3) performance of the typing within 48 hours, and (4) determination of types and subtypes of test-strains by combining their colicinogenic activity against the indicators and their sensitivity to colicines produced by the indicators. A modification of the method is advocated which requires three days to extract colicine by cultivation and one day for sensitivity tests and which uses peptone as the sole nutriment in media. The efficiency of the technique of Abbott and Shannon, McGeachie and McCormick, and the authors' two methods was compared using the selected indicators. Only the technique of McGeachie and McCormick showed some discrepancies.     

Colicin Typing of Shigella sonnei

The relative amount of extracellular polymer which remains about Azotobacter vinelandii, Zoogloea ramigera, Klebsiella pneumoniae, and Diplococcus pneumoniae after critical-point drying was studied by electron microscopy. The results obtained with this technique are compared to those obtained with methods that illustrate extracellular polymer, such as freeze-etching and ruthenium red staining. Comparative results indicate critical-point drying to be a rapid, reliable method for the determination of capsule-like polymer surrounding bacterial cells. In addition, critical-point drying can be used to observe morphogenetic changes, such as vesicle production.     

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

Background

On most common microarray platforms many genes are represented by multiple probes. Although this is quite common no one has systematically explored the concordance between probes mapped to the same gene.

Results

Here we present an analysis of all the cases of multiple probe sets measuring the same gene on the Affymetrix U133a GeneChip and found that although in the majority of cases both measurements tend to agree there are a significant number of cases in which the two measurements differ from each other. In these cases the measurements can not be simply averaged but rather should be handled individually.

Conclusion

Our analysis allows us to provide a comprehensive list of the correlation between all pairs of probe sets that are mapped to the same gene and thus allows microarray users to sort out the cases that deserve further analysis. Comparison between the set of highly correlated pairs and the set of pairs that tend to differ from each other reveals potential factors that may affect it.