Geographically distinct isolates of Mycobacterium leprae exhibit no genotypic diversity by restriction fragment-length polymorphism analysis

Differentiation of microorganisms for taxonomic purposes is based primarily on phenotypic characteristics, which are the direct or cumulative result of gene expression. Since expression of phenotypic characteristics usually relies on in vitro growth of a microorganism, non-cultivable organisms, such as Mycobacterium leprae, present major problems for the identification of potential variants based on phenotypic similarities or differences between individual isolates. We have employed the use of restriction fragment-length polymorphism (RFLP) analysis of chromosomal DNA of M. leprae isolates, including human isolates from geographically distinct regions of the world and isolates from a Sooty Mangabey monkey and an armadillo, to assess the relatedness among these isolates. Restriction endonuclease (EcoRI, BstEII, PstI, and PvuI) digests of chromosomal DNA were analysed using DNA probes encoding all or part of the 12 kD, 18 kD, 28 kD, 65 kD and 70 kD proteins of M. leprae as well as a probe containing an M. leprae-specific sequence repeated up to 20 times in the M. leprae chromosome. Comparison of the resulting autoradiographs showed that the RFLP patterns were all identical, indicating that these isolates contained no polymorphism with respect to the restriction endonuclease sites analysed. In addition, RFLP patterns of two separate human M. leprae isolates remained unchanged after three cycles of experimental infection in the armadillo model. These results indicated that the M. leprae isolates tested in this study were indistinguishable at the genotypic level, strongly suggesting homogeneity among members of this species.     

Nucleotide sequence of the Mycobacterium leprae katG region.

Synthetic oligonucleotide primers based on the DNA sequence data of the Escherichia coli, Mycobacterium tuberculosis, and Mycobacterium intracellulare katG genes encoding the heme-containing enzyme catalase-peroxidase were used to amplify and analyze the Mycobacterium leprae katG region by PCR. A 1.6-kb DNA fragment, which hybridized to an M. tuberculosis katG probe, was obtained from an M. leprae DNA template. Southern hybridization analysis with a probe derived from the PCR-amplified fragment showed that the M. leprae chromosome contains only one copy of the putative katG sequence in a 3.4-kb EcoRI-BamHI DNA segment. Although the nucleotide sequence of the katG region of M. leprae was approximately 70% identical to that of the M. tuberculosis katG gene, no open reading frame encoding a catalase-peroxidase was detectable in the whole sequence. Moreover, two DNA deletions of approximately 100 and 110 bp were found in the M. leprae katG region, and they seemed to be present in all seven M. leprae isolates tested. These results strongly suggest that M. leprae lacks a functional katG gene and catalase-peroxidase activity.     

Genetic characterization of Legionella pneumophila serogroup 1 associated with respiratory disease in Australia.

Techniques were developed for genetic characterization of Legionella pneumophila serogroup 1 by using restriction fragment length polymorphism analysis. Allozyme analysis provided an index of the discrimination achieved by restriction fragment length polymorphism. Isolates from human cases of legionellosis were examined by both methods, and their profiles were compared with reference strains of L. pneumophila serogroup 1 obtained from the American Type Culture Collection. Eighteen distinct clones were evident among the isolates examined. Both methods could be used to trace the source of an outbreak of legionellosis caused by L. pneumophila serogroup 1.     

Genetic characterization of Legionella pneumophila serogroup 1 associated with respiratory disease in Australia.

Techniques were developed for genetic characterization of Legionella pneumophila serogroup 1 by using restriction fragment length polymorphism analysis. Allozyme analysis provided an index of the discrimination achieved by restriction fragment length polymorphism. Isolates from human cases of legionellosis were examined by both methods, and their profiles were compared with reference strains of L. pneumophila serogroup 1 obtained from the American Type Culture Collection. Eighteen distinct clones were evident among the isolates examined. Both methods could be used to trace the source of an outbreak of legionellosis caused by L. pneumophila serogroup 1.     

Biochemical and biological characterization of four isolates of Spodoptera exigua nuclear polyhedrosis virus

Biological and biochemical properties of four nuclear polyhedrosis virus isolates from beet armyworm, Spodoptera exigua, were investigated. The isolates originated from the United States (SeNPV‐US), Thailand (SeNPV‐TH) and from two locations in Spain (SeNPV‐SP1 and SeNPV‐SP2). Restriction endonuclease analysis of the viral genomes revealed limited restriction fragment length polymorphism and indicated that these viruses contained distinct, but closely related, genotypes (variants). One BglII fragment from each isolate can serve as a restriction fragment length polymorphism marker for the identification of each isolate. The estimated genome size of the SeNPVs is approximately 134 kilobase pairs. The mobility profiles of the occluded virion polypeptides and polyhedrins of the four SeNPV isolates were very similar. Staphylococcus aureus V8 digestion of polyhedrin suggested that the polyhedrin from SeNPV‐US is distinct from the polyhedrins of the other isolates. Bioassays of the isolates in second‐instar S. exigua larvae showed that the SeNPV‐TH was the most potent SeNPV for beet armyworm with an LD₅₀ value of only 1.5 polyhedra per second‐instar larva.     

Detection of gene mutations related with drug resistance in Mycobacterium leprae from leprosy patients using Touch-Down (TD) PCR

The lack of methods to identify Mycobacterium leprae with the resistance against multi-drugs quickly and specifically has hindered effective chemotherapy against M. leprae infection. To screen M. leprae with resistance against multi-drugs, the Touch-Down (TD)-PCR has been used in this study. Sequences of the folP, rpoA, B, and gyrA, B genes were analyzed for isolates of M. leprae from leprosy patients in Korea. We amplified designated region of several genes in M. leprae involved in drug resistance and could obtain the PCR products of each gene. The mutations in the particular region of folP, rpoB, and gyrB gene were certified by TD-PCR single-stranded conformational polymorphism and DNA sequencing, respectively.     

Genomic features of intertypic recombinant sabin poliovirus strains excreted by primary vaccinees

The trivalent oral poliomyelitis vaccine (OPV) contains three different poliovirus serotypes. It use therefore creates particularly favorable conditions for mixed infection of gut cells, and indeed intertypic vaccine-derived recombinants (VdRec) have been frequently found in patients with vaccine-associated paralytic poliomyelitis. Nevertheless, there have not been extensive searches for VdRec in healthy vaccinees following immunization with OPV. To determine the incidence of VdRec and their excretion kinetics in primary vaccinees, and to establish the general genomic features of the corresponding recombinant genomes, we characterized poliovirus isolates excreted by vaccinees following primary immunization with OPV. Isolates were collected from 67 children 2 to 60 days following vaccination. Recombinant strains were identified by multiple restriction fragment length polymorphism assays. The localization of junction sites in recombinant genomes was also determined. VdRec excreted by vaccinees were first detected 2 to 4 days after vaccination. The highest rate of recombinants was on day 14. The frequency of VdRec depends strongly on the serotype of the analyzed isolates (2, 53, and 79% of recombinant strains in the last-excreted type 1, 2, and 3 isolates, respectively). Particular associations of genomic segments were preferred in the recombinant genomes, and recombination junctions were found in the genomic region encoding the nonstructural proteins. Recombination junctions generally clustered in particular subgenomic regions that were dependent on the serotype of the isolate and/or on the associations of genomic segments in recombinants. Thus, VdRec are frequently excreted by vaccinees, and the poliovirus replication machinery requirements or selection factors appear to act in vivo to shape the features of the recombinant genomes.     

Characterization and taxonomic implications of the rRNA genes of Mycobacterium leprae.

The number of rRNA genes of Mycobacterium leprae was determined by restriction analysis of M. leprae total chromosomal DNA. A single set of rRNA genes was found. This set was subcloned from a cosmid library of M. leprae DNA into pUC13 and was characterized by restriction analysis and hybridization with Escherichia coli rRNA genes. The 16S, 23S, and 5S genes of M. leprae were clustered on a 5.3-kilobase DNA fragment. On one hand, restriction analysis of the set of rRNA genes showed the uniqueness of M. leprae among mycobacteria, but on the other hand, it suggested that M. leprae strains of several origins are very much alike. Quantitative hybridization studies between M. leprae rDNA and total DNA of various bacteria demonstrated a close relatedness between M. leprae and corynebacteria, nocardia, and mycobacteria, especially Mycobacterium tuberculosis.     

用AFLP技术和16S rDNA PCR-RFLP分析毛苜蓿根瘤菌的遗传多样性

采用选择主增片断长度多态性（简称ＡＦＬＰ）ＤＮＡ指纹技术对采自我国云南省与西藏交界的高山地区的野生型豆科植物毛苜蓿根际土样分离的２９１株毛苜蓿（Ｍｅｄｉｃａｇｏ ｅｄｇｅｗｏｒｔｈｉｉ）根瘤菌进行遗传多样性的研究。从ＡＦＬＰ图谱中,揭示出毛苜蓿根瘤菌有较显著的遗传多样性,从２９１株中选择出９０年代表株用计算机进行树状图的分析。结果表明,所分析的菌株在７９％的相似性水平上聚类成３个群。对这９０年代表     

我国17株绵羊肺炎支原体分子分型及其菌体蛋白免疫印迹

【目的】分别从基因和蛋白水平研究我国部分地区绵羊肺炎支原体(Mycoplasma ovipneumoniae)分离株的分子特征,并了解其免疫原性蛋白的差异。【方法】对分离自8个地区的17株绵羊肺炎支原体进行扩增片段长度多态性(Amplified Fragment Length Polymorphism,AFLP)和十二烷基磺酸钠-聚丙烯酰胺凝胶电泳(Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis,SDS-PAGE)分析,采用NTsys-2.10e软件对AFLP和SDS-PAGE结果进行聚类,并用绵羊肺炎支原体模式株Y98高免血清对部分分离株进行免疫印迹分析。【结果】当相似系数分别为0.78和0.85时,绵羊肺炎支原体分离株可根据8个来源地区分成8个AFLP群和8个SDS-PAGE群;用8株分离株进行免疫印迹共出现6条蛋白条带,分子质量分别为105 kDa、83 kDa、65 kDa、42 kDa、40 kDa或26 kDa,其中83 kDa和40 kDa蛋白为8个菌株保守的免疫原性蛋白。【结论】我国部分地区绵羊肺炎支原体分离株之间存在遗传差异,不同分离株的主要免疫原性蛋白也存在一定差异,但83 kDa和40 kDa蛋白为其保守的免疫原性蛋白。本研究首次对我国部分地区绵羊肺炎支原体分离株进行了分子分型与免疫印迹分析,结果将为绵羊肺炎支原体病的新型诊断技术开发和疫苗研制奠定理论基础。     

Intraspecific variation in Radopholus similis isolates assessed with restriction fragment length polymorphism and DNA sequencing of the internal transcribed spacer region of the ribosomal RNA cistron.

Restriction fragment length polymorphism and direct sequencing of the internal transcribed spacer rDNA region of 19 isolates of Radopholus similis yielded significant diversity, both among isolates and within some individuals. Restriction fragment length polymorphism with HaeIII, AluI and Tru9I yielded two sets of patterns. Digestion with RsaI revealed one or two supernumerary bands in single nematodes from five isolates, and sequencing confirmed microheterogeneity in four of these. Phylogenetic analysis grouped most isolates closely together, except for the five isolates with additional bands for RsaI. Our data reveal more population structure than previously found and lend further support to the synonymy of R. similis and 'Radopholus citrophilus'.     

Polymorphic repetitive DNA sequences in Mycobacterium tuberculosis detected with a gene probe from a Mycobacterium fortuitum plasmid

Clinical isolates of Mycobacterium tuberculosis were shown by Southern blotting to contain DNA sequences hybridizing to a probe derived from a Mycobacterium fortuitum plasmid. Two such M. tuberculosis DNA fragments, isolated from a gene library, were used as probes to show restriction fragment length polymorphism in M. tuberculosis strains by detecting a repetitive sequence apparently located at different points on the chromosome. This could indicate the presence of a transposable element in M. tuberculosis which is partly homologous to a region of the M. fortuitum plasmid. The probes described can be used to fingerprint M. tuberculosis isolates, and in addition are capable of distinguishing M. tuberculosis from Mycobacterium bovis and BCG.     

Mycobacterium avium restriction fragment length polymorphism-IS IS1245 and the simple double repetitive element polymerase chain reaction typing method to screen genetic diversity in Brazilian strains

Simple double repetitive element polymerase chain reaction (MaDRE-PCR) and Pvu II-IS1245 restriction fragment length polymorphism (RFLP) typing methods were used to type 41 Mycobacterium avium isolates obtained from 14 AIDS inpatients and 10 environment and animals specimens identified among 53 mycobacteria isolated from 237 food, chicken, and pig. All environmental and animals strains showed orphan patterns by both methods. By MaDRE-PCR four patients, with multiple isolates, showed different patterns, suggesting polyclonal infection that was confirmed by RFLP in two of them. This first evaluation of MaDRE-PCR on Brazilian M. avium strains demonstrated that the method seems to be useful as simple and less expensive typing method for screening genetic diversity in M. avium strains on selected epidemiological studies, although with limitation on analysis identical patterns except for one band.     

Host-mediated modification of PvuII restriction in Mycobacterium tuberculosis.

Restriction endonuclease PvuII plays a central role in restriction fragment length polymorphism analysis of Mycobacterium tuberculosis complex isolates with IS6110 as a genetic marker. We have investigated the basis for an apparent dichotomy in PvuII restriction fragment pattersn observed among strains of the M. tuberculosis complex. The chromosomal regions of two modified PvuII restriction sites, located upstream of the katG gene and downstream of an IS1081 insertion sequence, were studied in more detail. An identical 10-bp DNA sequence (CAGCTGGAGC) containing a PvuII site was found in both regions, and site-directed mutagenesis analysis revealed that this sequence was a target for modification. Strain-specific modification of PvuII sites was identified in DNA from over 80% of the nearly 800 isolates examined. Furthermore, the proportion of modifying and nonmodifying strains differs significantly from country to country.     

Sequence and immunogenicity of the 70-kDa heat shock protein of Mycobacterium leprae

The gene encoding the Mycobacterium leprae 70-kDa heat shock protein has been isolated from a cosmid library using a fragment of the clone JKL2. Southern blot analysis of a positive clone identified a 4.4-kb fragment containing the entire coding region of the gene plus 2.4 kb upstream. Sequencing revealed the gene to encode a 621-amino acid protein, bearing 56% identity with the Escherichia coli dnaK gene product and 47% and 46% identity with the human and Caenorhabditis elegans hsp70, respectively. Comparison with the C-terminal 203 amino acids of the Mycobacterium tuberculosis 71-kDa Ag yielded 70% identity. Recombinant M. leprae p70 was produced in E. coli as a fusion protein (rp70f) with a portion of the schistosomal glutathione-S-transferase, using the expression vector, pGEX-2T. Cleavage with thrombin resulted in the release of a 70.0-kDa protein (rp70c) from the glutathione-S-transferase. Examination of the proteins by immunoblotting demonstrated that anti-M. leprae mAb, L7, and sera from lepromatous leprosy patients bound to both the cleaved and fusion proteins. We compared the T cell reactivity of the M. leprae recombinant proteins with that of mAb affinity-purified bacille Calmette-Guerin (BCG) 70-kDa Ag using proliferation assays. PBMC of BCG vaccinees responded to both M. leprae cleaved and fusion p70, though more subjects responded to the rp70c (18 of 20) than to rp70f (13 of 20). Responses were generally higher to rp70c than to rp70f, however all responses to the M. leprae recombinant proteins were lower than to mAb affinity-purified BCG p70. Thus, the M. leprae 70-kDa heat shock protein elicits T and B cell responses in subjects exposed to mycobacteria, despite its homology with the human hsp70.     

Comparison of 23S polymerase chain reaction-restriction fragment length polymorphism and amplified fragment length polymorphism techniques as typing systems for thermophilic campylobacters

In this study, we evaluated the combination of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplified fragment length polymorphism (AFLP) molecular typing techniques for the analysis of thermophilic campylobacter species isolated from clinical and poultry samples. 23S PCR-RFLP analysis performed to fingerprint 69 strains exhibited an excellent level of typability. Eleven different types were defined at 100% linkage level following numerical analysis of band patterns. Differentiation of Campylobacter jejuni and Campylobacter coli at species level was achieved although no significant relationship could be observed between the profiles and the origin of the strains. Simplified AFLP analysis of the isolates disclosed the presence of 66 different banding patterns. The resulting dendrogram showed a high diversity among the strains studied. All the isolates were grouped within eight main types with a 69% homology degree among them. Differentiation at subspecies level was possible but no significant relationship could be observed between the AFLP profiles and the origin of the strains. When used in combination, 23S PCR-RFLP and single-enzyme AFLP methods can be applied to determine taxonomic and epidemiological relationships among thermophilic campylobacters.     

Characterization of IS999, an unstable genetic element in Mycobacterium avium

An IS3-family insertion element, IS999, was identified in the opportunistic pathogen Mycobacterium avium. The 1347 bp element has 29 bp inverted repeats and two overlapping open reading frames coding for putative transposases. It was detected in the genomes of ten of 12 M. avium isolates examined. Copy numbers ranged from four to 16. IS999 is less stable than IS1245, the most commonly-used marker for typing M. avium isolates. Among 60 colonies picked from a single patient isolate, there were two distinct IS1245 restriction fragment length polymorphism banding patterns compared to eight distinct IS999 patterns (five in one IS1245 group and three in the other). In view of its instability, we asked whether transposition of IS999 might have phenotypic consequences. Nucleotide sequence analysis of insertion sites in four isolates revealed 16 putative structural genes that were variably disrupted by IS999. Insertions into hdhA, a gene that codes for a putative short chain alcohol dehydrogenase, were distributed non-randomly between colony type variants, consistent with phenotypic consequences that exert selective pressure. These observations illustrate the genetic heterogeneity that can exist within populations of M. avium that appear to be homogeneous by IS1245 analysis. IS999 may be a useful marker for tracking, at the sub-strain level, the rapid genetic drift that M. avium isolates undergo in nature and in the laboratory.     

Genetic variation in Armillaria mellea subsp. nipponica estimated using IGS-RFLP and AFLP analyses

In this study, genetic variation of Armillaria mellea subsp. nipponica was estimated using intergenic spacer-restriction fragment length polymorphism (IGS-RFLP) and amplified fragment length polymorphism (AFLP) analyses. Four IGS-RFLP phenotypes were produced, of which two have never been reported. AFLP analysis suggested that the 11 isolates used could be divided into five subgroups, and the isolates within the same subgroup were distributed throughout a relatively large area in Japan. A parental isolate and its offspring (single-spore isolates) showed an almost identical AFLP profile to each other. These results suggest that the large distribution of the isolates within the same subgroup were established via the basidiospore from a common parental strain. Contribution no. 378 of The Tottori Mycological Institute     

Concordant evolution of mitochondrial and nuclear genomes in the wheat pathogen Phaeosphaeria nodorum

We compared patterns of mitochondrial restriction fragment length polymorphism (RFLP) diversity with patterns of nuclear RFLP diversity to investigate the effects of selection, gene flow, and sexual reproduction on the population genetic structure and evolutionary history of the wheat pathogen Phaeosphaeria nodorum. A total of 315 fungal isolates from Texas, Oregon, and Switzerland were analyzed using seven nuclear RFLP probes that hybridized to discrete loci and purified mitochondrial DNA that hybridized to the entire mtDNA genome. Forty-two different mitochondrial haplotypes and 298 different nuclear haplotypes were detected. The two most frequent mtDNA haplotypes were present in every population and represented 32% of all isolates. High levels of gene flow, low levels of population subdivision, no evidence for either host specificity or cyto-nuclear disequilibrium were inferred from the analysis of both genomes. The concordance in estimates of these population genetic parameters from both genomes suggests that the two genomes experienced similar degrees of migration, genetic drift and selection.