SEARCH · PubMed Health

Results for “Multilocus sequence typing”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources

PubMed2004

Predominant clonal evolution leads to a close parity between gene expression profiles and subspecific phylogeny in Trypanosoma cruzi.

We investigated the relationships between overall phylogenetic diversity in Trypanosoma cruzi evidenced by multilocus markers (MLEE and RAPD) on the one hand, and gene expression patterns, revealed by mRNA analysis on the other hand. Nineteen laboratory-cloned stocks representative of this parasite's overall phylogenetic diversity and ecogeographical range were analyzed using random amplified differentially expressed sequences (RADES). The bat trypanosome T. cruzi marinkellei was taken as outgroup. The profiles obtained showed that RADES polymorphism cannot be considered as a simple subsample of general RAPD polymorphism. Indeed, many RADES bands were not present in general RAPD profiles, and vice versa. Phylogenies obtained from RADES on the one hand, and MLEE/RAPD on the other hand, were very similar. This suggests that in spite of the recent observation of hybrid genotypes and mosaic genes in T. cruzi, clonal evolution in this parasite has been preponderant enough on an evolutionary scale to carve the polymorphism on all types of DNA sequences, including expressed genes, although these genes are assumed to undergo natural selection pressure contrary to noncoding sequences and neutral polymorphisms.

Animals↗

PubMed1987

Diallelic multilocus model of neutral genes.

The evolution of a completely linked diallelic multilocus system of neutral genes in a finite population is studied. A diffusion model incorporating random genetic drift and mutation is used. We neglect the recombination. To begin with, the spectral analysis of the Kolmogorov backward equation for this model is investigated. We apply this to two extreme situations when the number of sites approaches to infinity. One is a DeMoivre-Laplace type approximation and the other is a Poisson type approximation. The former is applied to the study of the simultaneous distribution and evolution of a large number of neutral genes. It is applicable to the distribution of a polygenic character controlled by clustered loci on a chromosome, and we show that it differs from the normal distribution on account of random genetic drift and linkage disequilibrium. The latter is applied to the distribution of the number of segregating sites in DNA nucleotide sequences, and the rate of evolution is obtained.

Alleles↗

PubMed2004

Genotyping of Cryptosporidium parvum with microsatellite markers.

Recent outbreaks of cryptosporidiosis caused by Cryptosporidium parvum in the United States and other countries, as well as the emergence of cryptosporidiosis as a frequent cause of morbidity and mortality in immunodeficient individuals, have raised the interest of the research community in this parasite. The genus Cryptosporidium, phylum Apicomplexa, comprises an undefined number of species, of which only C. parvum is of public health concern. Cryptosporidiosis is contracted through the ingestion of oocysts, the stage of the parasite produced in large numbers by infected hosts. Because the oocysts are small, typically about 5 microm in diameter, and lack species-specific morphological features, there is a need for molecular markers to distinguish between human-infectious C. parvum and other species that do not (or only infrequently) cause disease in humans. Genetic characterization of Cryptosporidium oocysts using restriction fragment length or sequence polymorphism has revealed host-associated genotypes, that are often referred to as species. In addition, C. parvum was found to include two genotypes, designated type 1 and type 2. Type 1 is almost exclusively found in humans, whereas type 2 infects humans and various mammalian hosts. The frequent occurrence of Cryptosporidium oocysts in untreated surface water and the potential for contamination of drinking water have emphasized the need for molecular markers to track the source of oocysts within a watershed or water distribution system, and to discriminate between oocysts infectious to humans and nonpathogenic species. Genetic markers are also needed to study the taxonomy of Cryptosporidium. Several laboratories have identified microsatellites in the genome of C. parvum and have investigated the level of polymorphism at these loci. For instance, 10 alleles of marker 5B12 have been found to date among C. parvum isolates from various geographical and host origins. Multilocus haplotypes based on such markers are suitable for discriminating individual isolates of C. parvum. In an attempt to develop rapid and cost-effective methods for typing isolates of C. parvum, we have pursued two methods, a traditional polymerase chain reaction (PCR) method followed by gel electrophoresis, and real-time PCR using SYBR Green I melting curve analysis for allele identification.

Animals↗

PubMed2001

Unusual abundance of atypical strains associated with human ocular toxoplasmosis.

To facilitate genotyping of Toxoplasma gondii in vitreous fluid of patients with severe or atypical ocular toxoplasmosis, polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) assays were developed for SAG3 (p43) and SAG4 (p18), 2 single-copy surface antigen genes. Together with strategies for SAG1, SAG2, and B1, multilocus RFLP analyses were performed on PCR-amplified parasite DNA present in 12 clinical specimens. Most samples (8/12) were not infected by type II or type III mouse-avirulent strains. Only 1 type III and 3 type II strains were identified, all from immunosuppressed patients. In 6 otherwise healthy adults and in 1 immunosuppressed patient, the SAG1 allele associated with mouse virulence was amplified. Of 12 samples, 3 possessed true type I strains; 5 of 12 had new recombinant genotypes with alleles typical of type I or III strains at all loci examined. The unusual bias toward type I and/or recombinant genotypes bearing the SAG1 type I allele associated with mouse virulence in immunocompetent adults has important implications for the epidemiology and efficacious treatment of ocular toxoplasmosis.

Animals↗

PubMed1999

Clonal relationship among invasive and non-invasive strains of enteroinvasive Escherichia coli serogroups.

The genetic relatedness among 96 invasive Escherichia coli belonging to several serogroups and 13 non-invasive of several serotypes that share the same O antigen was investigated by multilocus enzyme electrophoresis analysis. The invasive strains were isolated in different parts of the world and most of them recovered from dysentery. Twenty-nine electrophoretic types were distinguished and the most invasive strains were found to belong to two major lineages. These results suggested that the invasive ability in these strains has evolved in divergent chromosomal backgrounds, presumably through the horizontal spread of plasmid-borne invasion genes. The maintenance of invasive phenotypes in separate lineages suggests that this ability confers a selective advantage to invasive strains.

Dysentery↗

PubMed1995

A recombination event occurring within two complex 5q13.1 microsatellite repeat polymorphisms suggests a telomeric mapping of spinal muscular atrophy.

The gene for the childhood spinal muscular atrophies (SMAs) has been mapped to 5q13.1. The interval containing the SMA gene has been defined by linkage analysis as 5qcen-D5S629-SMA-D5S557-5qter. We have identified a recombination event within this interval on a type-I SMA chromosome. The recombination maps to a region of multilocus microsatellite repeat (MSR) markers, and occurs between different subloci of two such markers, CMS-1 and 7613. While the possibility of a novel mutation caused by the recombination cannot be discounted, we believe when viewed in the context of a similar recombination in a Dutch SMA family, a centromeric boundary at the recombination site for the critical SMA interval is likely. This new proximal boundary would reduce the minimal region harboring the SMA locus from approximately 1.1 Mb to approximately 600 kb.

Alleles↗

PubMed2000

Identification of two genetic groups in Bacteroides fragilis by multilocus enzyme electrophoresis: distribution of antibiotic resistance (cfiA, cepA) and enterotoxin (bft) encoding genes.

Ninety-three Bacteroides fragilis strains of different origin were analysed by multilocus enzyme electrophoresis (MLEE). Fourteen of the 15 genetic loci analysed were polymorphic, whilst nucleoside phosphorylase was monomorphic. There was a mean of six alleles per locus and a mean genetic diversity of 0.393. Cluster analysis identified 90 electrophoretic types (ETs) separated into two major phylogenetic divisions at a genetic distance of 0.70. Division I consisted of 81 ETs carrying the endogenous class A beta-lactamase gene cepA, whereas division II comprised 9 ETs carrying the class B beta-lactamase gene cfiA, but not cepA. The presence of these two genes was assessed by PCR and the expression of the cfiA gene was investigated by determining the level of resistance to the antibiotic imipenem. MLEE showed a smaller genetic distance among the genotypes of the imipenem-resistant than among the imipenem-susceptible strains. No other particular cluster was observed. The enterotoxin gene (bft) was detected by PCR: DNA sequencing of the products obtained showed that the different bft alleles (bft-1, bft-2 and bft-3) were scattered randomly troughout the phylogenetic tree. No association between distinct clones and clinical manifestations (sepsis, abscesses, diarrhoea), geographical origin or host origin (human or animal) could be found.

Alleles↗

PubMed2000

Molecular variation among type IV pilin (bfpA) genes from diverse enteropathogenic Escherichia coli strains.

Typical enteropathogenic Escherichia coli (EPEC) strains produce bundle-forming pili (BFP), type IVB fimbriae that have been implicated in EPEC virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells (LA). BFP are polymers of bundlin, a pilin protein that is encoded by the bfpA gene found on a large EPEC plasmid. Striking sequence variation has previously been observed among type IV pilin genes of other gram-negative bacterial pathogens (e.g., Pseudomonas and Neisseria spp.). In contrast, the established sequences of bfpA genes from two distantly related prototype EPEC strains vary by only a single base pair. To determine whether bundlin sequences vary more extensively, we used PCR to amplify the bfpA genes from 19 EPEC strains chosen for their various serotypes and sites and years of isolation. Eight different bfpA alleles were identified by sequencing of the PCR products. These alleles can be classified into two major groups. The alpha group contains three alleles derived from strains carrying O55, O86, O111, O119, O127, or O128 somatic antigens. The beta group contains five alleles derived from strains carrying O55, O110, O128ab, O142, or nontypeable antigens. Sequence comparisons show that bundlin has highly conserved and variable regions, with most of the variation occurring in the C-terminal two-thirds of the protein. The results of multilocus enzyme electrophoresis support the hypothesis that bfpA sequences have spread horizontally across distantly related clonal lineages. Strains with divergent bundlin sequences express bundlin protein, produce BFP, and carry out autoaggregation and LA. However, four strains lack most or all of these phenotypes despite having an intact bfpA gene. These results have important implications for our understanding of bundlin structure, transmission of the bfp gene cluster among EPEC strains, and the role of bundlin variation in the evasion of host immune system responses.

Alleles↗

PubMed1995

Induction of deletion mutations by methoxyacetaldehyde in Chinese hamster ovary (CHO)-AS52 cells.

We have reported previously that methoxyacetaldehyde (MALD), a metabolite of 2-methoxyethanol, induces gpt gene mutations in Chinese hamster ovary (CHO)-AS52 cells but not hprt gene mutations in the standard CHO-K1-BH4 cells. In addition, MALD induces chromosome aberrations in both CHO cell lines. The data presented suggest that MALD induces deletion-type mutations. In this study, we analyzed MALD-induced CHO-AS52 mutants for deletion-type mutations using the nested-polymerase chain reaction (nested-PCR) assay. Spontaneous CHO-AS52 mutants are used as untreated control. Ethylnitrosourea (ENU)-induced CHO-AS52 mutants are used as negative control for multilocus deletions since ENU is a potent inducer of point mutations. The results show that the frequency of MALD-induced mutants containing total deletion of the gpt gene is 42.4% which is 2.3-fold higher than that from spontaneous mutants (18.6%). The frequency of ENU-induced deletion mutation is 3%. The data substantiate our hypothesis that MALD induces major deletion mutations.

Acetaldehyde↗

PubMed1998

Characterisation of diarrhoeagenic Escherichia coli clones by ribotyping and ERIC-PCR.

The ability of ribotyping and enterobacterial repetitive intergenic concensus-polymerase chain reaction (ERIC-PCR) to discriminate diarrhoeagenic Escherichia coli clones of 122 strains belonging to 26 distinct serotypes was evaluated. The 26 serotypes corresponded to 24 ribotypes and 25 ERIC-types. Correlation between multilocus enzyme electrophoresis, ERIC-PCR and ribotyping was c. 90% for the dominant ribotypes. Related clones such as O55:H7 and O157:H7 presented similar ribotypes and clustered together in a dendrogram, and the two divergent clonal groups of enteropathogenic E. coli (EPEC) and enterohaemorrhagic E. coli (EHEC) were included in distinct branches. The results suggest the possibility of applying these two simpler techniques as tools to identify clones of diarrhoeagenic E. coli.

Bacterial Typing Techniques↗

PubMed1993

Clonal relationships among Escherichia coli strains that cause hemorrhagic colitis and infantile diarrhea.

The genetic relationships among 1,300 isolates of Escherichia coli representing 16 serotypes associated with enteric disease, including O157:H7 strains recovered from patients with hemorrhagic colitis and hemolytic uremic syndrome and O26:H11, O55:H6, O55:H7, O111:H2, and O128:H2 strains, many of which were isolated originally from infants with diarrhea, were estimated from allelic variation among 20 enzyme-encoding genes detected by multilocus enzyme electrophoresis. Multiple electrophoretic types were observed among isolates of each serotype, with isolates of the same O serogroup differing on average at 28% of the enzyme loci. Comparisons of the multilocus enzyme profiles revealed that 72% of the isolates belong to 15 major electrophoretic types, each of which corresponds to a bacterial clone with a wide geographic distribution. Genetically, the O157:H7 clone is most closely related to a clone of O55:H7 strains that has long been associated with worldwide outbreaks of infantile diarrhea. We propose that the new pathogen emerged when an O55:H7-like progenitor, already possessing a mechanism for adherence to intestinal cells, acquired secondary virulence factors (Shiga-like cytotoxins and plasmid-encoded adhesins) via horizontal transfer and recombination.

Alleles↗

PubMed2003

Short tandem repeat (STR) DNA markers are hypervariable and informative in Cannabis sativa: implications for forensic investigations.

Short tandem repeat (STR) markers are the DNA marker of choice in forensic analysis of human DNA. Here we extend the application of STR markers to Cannabis sativa and demonstrate their potential for forensic investigations. Ninety-three individual cannabis plants, representing drug and fibre accessions of widespread origin were profiled with five STR makers. A total of 79 alleles were detected across the five loci. All but four individuals from a single drug-type accession had a unique multilocus genotype. An analysis of molecular variance (AMOVA) revealed significant genetic variation among accessions, with an average of 25% genetic differentiation. By contrast, only 6% genetic difference was detected between drug and fibre crop accessions and it was not possible to unequivocally assign plants as either drug or fibre type. However, our results suggest that drug strains may typically possess lower genetic diversity than fibre strains, which may ultimately provide a means of genetic delineation. Our findings demonstrate the promise of cannabis STR markers to provide information on: (1) agronomic type, (2) the geographical origin of drug seizures, and (3) evidence of conspiracy in production of clonally propagated drug crops.

Alleles↗

PubMed2005

Development and amplification of multiple co-dominant genetic markers from single spores of arbuscular mycorrhizal fungi by nested multiplex PCR.

Multiple co-dominant genetic markers from single spores of the arbuscular mycorrhizal (AM) fungi Glomus mosseae, Glomus caledonium, and Glomus geosporum were amplified by nested multiplex PCR using a combination of primers for simultaneous amplification of five loci in one PCR. Subsequently, each marker was amplified separately in nested PCR using specific primers. Polymorphic loci within the three putative single copy genes GmFOX2, GmTOR2, and GmGIN1 were characterized by sequencing and single strand conformation polymorphisms (SSCP). Primers specific for the LSU rDNA D2 region were included in the multiplex PCR to ensure correct identification of the Glomus spp. spores. Single AM fungal spores were characterized as multilocus genotypes by combining alleles of each amplified locus. Only one copy of each putative single copy gene could be amplified from each spore, indicating that spores are homokaryotic. All isolates of G. mosseae had unique genotypes. The amplification of multiple co-dominant genetic markers from single spores by the nested multiplex PCR approach provides an important tool for future studies of AM fungi population genetics and evolution.

Alleles↗

PubMed2006

Application of multilocus variable-number tandem-repeat analysis for molecular typing of the agent of leptospirosis.

Leptospirosis is a worldwide-distributed zoonosis, endemic in tropical areas. Epidemiologic investigations of leptospirosis still rely on tedious serological identification tests. Recently, molecular typing systems based on variable-number tandem-repeat (VNTR) analysis have been described and have been used to identify Leptospira interrogans strains. Although L. interrogans is the most common Leptospira species encountered in human infections around the world, other pathogenic species, such as Leptospira kirschneri and Leptospira borgpetersenii, are also frequently associated with human leptospirosis. In this study, we aimed to extend multilocus VNTR analysis (MLVA) identification of strains to species other than L. interrogans. We designed primers for VNTR loci found in L. interrogans, L. kirschneri, and L. borgpetersenii. The discriminatory power of the redefined primers was evaluated on collection strains and then on clinical strains. We also carried out a retrospective study on 156 strains isolated from patients and animals from New Caledonia, an area of high endemicity in the South Pacific. Our results show that this simple PCR-based MLVA typing technique is a powerful methodology for the epidemiology of leptospirosis.

Animals↗

PubMed1991

DNA sequence analysis of X-ray induced Adh null mutations in Drosophila melanogaster.

The mutational spectrum for 28 X-ray induced mutations and 2 spontaneous mutations, previously determined by genetic and cytogenetic methods, consisted of 20 multilocus deficiencies (19 induced and 1 spontaneous) and 10 intragenic mutations (9 induced and 1 spontaneous). One of the X-ray induced intragenic mutations was lost, and another was determined to be a recombinant with the allele used in the recovery scheme. The DNA sequence of two X-ray induced intragenic mutations has been published. This paper reports the results of DNA sequence analysis of the remaining intragenic mutations and a summary of the X-ray induced mutational spectrum. Only one of the X-ray induced mutations is a single base change, a C to G transversion (AdhnLA80). Therefore, the mutational spectrum of X-ray induced mutations consists predominantly of deletions that are observed to range in size from two base pairs to deletions of a large number of loci as determined by genetic complementation analysis. The combination of DNA sequence analysis with genetic complementation analysis shows a continuous distribution in size of deletions rather than two different types of mutations consisting of deletions and "point mutations." Sequencing is shown to be essential for detecting intragenic deletions. Of particular importance for future studies is the observation that all of the intragenic deletions consist of a direct repeat adjacent to the break-point with one of the repeats deleted.

Alcohol Dehydrogenase↗

PubMed1986

Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism.

Restriction maps of 145 human mtDNAs representing samples from five geographic regions were used to construct multilocus genotypes for 28 genetic loci of the mitochondrial genome. Alleles were defined as distinct combinations of the presence or absence of polymorphic restriction sites within each locus. The 28 loci included 13 genes encoding proteins, 10 genes specifying tRNAs, 2 genes specifying rRNAs, and 3 noncoding regions consisting of the D loop, the light strand origin of replication, and the 5' noncoding sequence. In 35 comparisons of allele frequency distributions to expected distributions predicted by neutral mutation theory (assuming an infinite alleles model), the results revealed that most genetic diversity values (71%) fell within the range predicted by the neutral model; however, excesses in the frequencies of common alleles and in the number of singleton alleles within populations were observed at specific loci. Departures from the neutral mutation model are most readily explained by the effects of the recent expansion of the human population and the action of purifying selection. Coefficients of population differentiation suggest that gene flow of mtDNA types between certain geographic regions may be limited.

Alleles↗

PubMedDate not supplied

[Study on the polymorphism of the coagulase gene by the method of sequencing in methicillin-resistant Staphylococcus aureus strains, isolated in hospitals in different regions of Russia and Belarus].

This method was used for typing of 31 Staphylococcus aureus methicillin-resistant (MRSA) strains; of these, 27 were clinical isolates obtained in hospitals of different cities of Russia and Belarus and 4 were international epidemic strains EMRSA-1, -2, -3, -12. The sequencing of the variable area, located in the middle part of the coagulase gene between nucleotides 979-1355 and detected with the use of information technologies, was carried out. The results of this sequencing were compared with those of the earlier study on the polymorphism of the area of the same gene between nucleotides 1513-2188, carried out by the method of PCR-restrictive fragment length polymorphism. The sequencing of the part of the coagulase gene made it possible to confirm the presence of essential differences in the nucleotide sequences of the coagulase gene in international strains EMRSA-1, -3, -12, grounds for classifying clinical isolates of MRSA strains with two groups (4 and 5), as well as the genetic relationship of different phage types, isolated in different clinics. The study revealed considerable similarity in the nucleotide composition of strains EMRSA-2 and EMRSA-12 despite the fact that, according to the results of Cfol restriction of the 3'-end, they were classified with different groups; the study also revealed the identity of the nucleotide sequences of the coagulase gene in the cultures of group 5, isolated in hospitals of Moscow, St. Petersburg, Orenburg, and strain EMRSA-2, as well as methicillin-sensitive S. aureus strain 8325-4; in addition, in clinical isolates of group 4 and strain EMRSA-1 a considerable degree of homology was revealed. The study of two different loci made it possible to find out the strain with the recombinant form of the coagulase gene. The approach used in this study permitted the differentiation of the international epidemic strains EMRSA-1, -2, -3 and -12 into individual groups, which coincided with the results of Enright et al. (2002) who used multilocus sequencing.

Coagulase↗

PubMed1998

Structure and function of repetitive sequence elements associated with a highly polymorphic domain of the Neisseria meningitidis PilQ protein.

Secretins are a large family of proteins associated with membrane translocation of macromolecular complexes, and a subset of this family, termed PilQ proteins, is required for type IV pilus biogenesis. We analysed the status of PlIQ expression in Neisseria meningitidis (Mc) and found that PlIQ mutants were non-piliated and deficient in the expression of pilus-associated phenotypes. Sequence analysis of the 5' portion of the pilQ ORF of the serogroup B Mc strain 44/76 showed the presence of seven copies of a repetitive sequence element, in contrast to the situation in N. gonorrhoeae (Gc) strains, which carry either two or three copies of the repeat. The derived amino acid sequence of the consensus nucleotide repeat was an octapeptide PAKQQAAA, designated as the small basic repeat (SBR). This gene segment was studied in more detail in a collection of 52 Mc strains of diverse origin by screening for variability in the size of the PCR-generated DNA fragments spanning the SBRs. These strains were found to harbour from four to seven copies of the repetitive element. No association between the number of copies and the serogroup, geographic origin or multilocus genotype of the strains was evident. The presence of polymorphic repeat elements in Mc PilQ is unprecedented within the secretin family. To address the potential function of the repeat containing domain, Mc strains were constructed so as to express chimeric PilQ molecules in which the number of SBR repeats was increased or in which the repeat containing domain was replaced in toto by the corresponding region of the Pseudomonas aeruginosa (Pa) PilQ protein. Although the strain expressing PilQ with an increased number of SBRs was identical to the parent strain in pilus phenotypes, a strain expressing PilQ with the equivalent Pa domain had an eightfold reduction in pilus expression level. The findings suggest that the repeat containing domain of PilQ influences Mc pilus expression quantitatively but not qualitatively.

Amino Acid Sequence↗