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PubMedDate not supplied

Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives.

The epidemiologic typing of bacterial pathogens can be applied to answer a number of different questions: in case of outbreak, what is the extent and mode of transmission of epidemic clone(s)? In case of long-term surveillance, what is the prevalence over time and the geographic spread of epidemic and endemic clones in the population? A number of molecular typing methods can be used to classify bacteria based on genomic diversity into groups of closely-related isolates (presumed to arise from a common ancestor in the same chain of transmission) and divergent, epidemiologically-unrelated isolates (arising from independent sources of infection). Ribotyping, IS-RFLP fingerprinting, macrorestriction analysis of chromosomal DNA and PCR-fingerprinting using arbitrary sequence or repeat element primers are useful methods for outbreak investigations and regional surveillance. Library typing systems based on multilocus sequence-based analysis and strain-specific probe hybridization schemes are in development for the international surveillance of major pathogens like Mycobacterium tuberculosis. Accurate epidemiological interpretation of data obtained with molecular typing systems still requires additional research on the evolution rate of polymorphic loci in bacterial pathogens.

Bacterial Typing Techniques↗

PubMedDate not supplied

[Determination of species belonging to the Lactobacillus genus with the use of RAPD-typing].

The numeric analysis of 14 strains of lactobacilli investigated by 57 phenotypical characteristics, has resulted in formation of three clusters: group L. delbrueckii, L. plantarum and the modular group formed by strains of various species. The API-testing, 16S rRNA sequencing and RAPD-typing with primers 5'-AGCAGCGTGG-3' and LP3-ST 5'-TGGTCCGAGC-3' have been carried out for several strains which position in a dendrogram did not correspond to their species diagnosis. The obtained data have allowed the reclassification of the strain L. delbrueckii subsp. bulgaricus B-1923T as L. plantarum B-1923T, L. agilis B-2603 as L. fermentum B-2603, L. amylophilus 30/4/(2) as L. plantarum 30/4/(2). Strain L. confusus 39T, identified by the phenotypical characteristics and data of API-testing as L. fermenturm, was reclassified on the basis of the phylogenetic analysis and RAPD-typing, as L. pentosus 39T.

Bacterial Typing Techniques↗

PubMed1998

Clonal nature of enterotoxigenic Escherichia coli serotype O6:H16 revealed by randomly amplified polymorphic DNA analysis.

The genetic relatedness among 29 enterotoxigenic Escherichia coli strains of serotype O6:H16 was investigated by randomly amplified polymorphic DNA (RAPD) analysis. The strains were isolated in different parts of the world, displayed CS1-CS3 or CS2-CS3 profiles, and expressed heat-labile toxin (LT) and heat-stable toxin; a single strain expressed only LT. Ten RAPD types were distinguished and showed significant similarity, having on average 82% of the amplified bands in common. These results indicated that, irrespective of the different geographical origin or virulence factors, these strains belonged to a widespread clonal group.

Bacterial Toxins↗

PubMed2004

Visceral leishmaniasis caused by Leishmania infantum in a Spanish patient in Argentina: What is the origin of the infection? Case report.

BACKGROUND: The question "Where have you been?" is a common one asked by doctors in Northern Europe and America when faced with clinical symptoms not typical of their country. This question must also arise in the clinics of developing countries in which non-autochthonous cases such as the one described here can appear. Important outbreaks of Leishmania infantum have been recorded in the last decade in several Latin American countries but its presence has not yet been recorded in Argentina. We report the first case of visceral leishmaniasis owing to L. infantum in this country. CASE PRESENTATION: A 71-year-old Spanish woman who has been living in Mendoza, Argentina, during the last 40 years presented with a history of high fever and shivering, anemia, leukopenia and splenomegaly over two years. Argentinian doctors did not suspect visceral leishmaniasis even when the histological analysis revealed the presence of "intracytoplasmatic spheroid particles compatible with fungal or parasitic infection". After a serious deterioration in her health, she was taken to Spain where she was evaluated and visceral leishmaniasis was established. Specific identification of the parasite was done by PCR-ELISA, isoenzyme electrophoresis and RAPD-PCR. CONCLUSION: We would like to point out that: i) cases such as the one described here, which appear in non-endemic areas, can pass unnoticed by the clinical physician. ii) in countries in which these introduced cases reside, in-depth parasitological studies are required into vectors and possible reservoirs to rule out the rare case of local infection and, once infection has taken place, to ensure that this does not spread by anthroponotic transmission or a competent reservoir.

Aged↗

PubMed2001

Random amplification of polymorphic DNA typing of Listeria monocytogenes isolated from meat.

To investigate the epidemiological characteristics of Listeria monocytogenes isolated from imported or domestic meats, L. monocytogenes was isolated and identified through biochemical and serological tests, and epidemiological analysis of the isolates was carried out through the random amplification of polymorphic DNA (RAPD) method. Fifty-four isolates were identified as L. monocytogenes through biochemical tests, of which 36 (67%) were confirmed as serotype 1, and 18 (33%) were serotype 4, through the microagglutination test. In the molecular epidemiological analysis using RAPD method, the isolates could be classified into 10, 6 and 6 types using three random primers, PB1, PB4, and HLWL74, respectively. Forty composite profiles were identified by a combination of the three primers. RAPD analysis demonstrated the relationships between the isolates from beef from Korea and the USA, pork from Korea and Denmark. These results suggested that RAPD could be a useful typing tool for the epidemiological study of L. monocytogenes and other bacteria.

Agglutination Tests↗

PubMed2001

Clustering of South African Helicobacter pylori isolates from peptic ulcer disease patients is demonstrated by repetitive extragenic palindromic-PCR fingerprinting.

The present report assesses the association between clonal groupings, disease, and the virulence fingerprint of 76 South African Helicobacter pylori cagA(+) strains isolated from 57 Cape-colored subjects. Two methods, repetitive extragenic palindromic (REP)-PCR and random amplified polymorphic DNA (RAPD)-PCR, were used to generate DNA fingerprints, and computer-assisted analysis was used to derive clusters. The two PCR techniques were only partially complementary (48%). REP-PCR fingerprints identified a distinct pathological cluster consisting of strains from 63% of the patients and was strongly associated with both disease (P < 0.00001) and the vacuolating cytotoxin A (vacA) signal sequence type (P < 0.003). RAPD-PCR fingerprinting was not associated with disease and was less strongly associated with vacA (P < 0.05) than REP-PCR was. Hierarchical analysis indicated that isolates from patients with peptic ulcer disease tended to cluster differently than isolates from patients with gastritis alone or gastric adenocarcinoma. These relationships are consistent with a loosely clonal population structure associated with disease for H. pylori in the Cape-colored population in South Africa.

Adolescent↗

PubMed2005

Phenotypic and genotypic characteristics of Streptococcus porcinus isolated from human sources.

The phenotypic and genotypic characteristics of 25 Streptococcus porcinus isolates recovered from human sources were investigated and compared to the characteristics of 17 reference strains obtained from nonhuman sources. All of the S. porcinus isolates were beta-hemolytic (wide zones), susceptible to vancomycin, gave positive results for the leucine aminopeptidase and l-pyrrolidonylarylamidase tests, and produced acids from mannitol and sorbitol. Most of them were positive for the CAMP test and resistant to bacitracin. The isolates were susceptible to most of the 14 antimicrobials tested, except for tetracycline, for which 80% of the human isolates and 35.2% of the nonhuman strains were resistant. The tet(M) and the tet(O) genes were detected in 23 (88.5%) and 8 (30.8%) of the 26 tetracycline-resistant isolates, respectively. Analysis of whole-cell protein profiles obtained after sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a high similarity among the profiles. Chromosomal DNA was analyzed by pulsed-field gel electrophoresis (PFGE) after digestion with SmaI and by random(ly) amplified polymorphic DNA (RAPD)-PCR using primer 1254. Analysis of SmaI-restricted genomic DNA revealed the substantial genetic diversity among S. porcinus isolates from nonhuman sources, which were also serologically more diverse. Most of the human isolates belonged to serogroup NG1 and shared highly related PFGE profiles that were distinct from profiles of isolates from nonhuman sources. These results were in agreement with those obtained by analysis of amplicons after RAPD-PCR, indicating the potential ability of these techniques for typing S. porcinus and suggesting the occurrence of a few clonal groups of S. porcinus strains adapted to the human host.

Adolescent↗

PubMed1998

[RAPD typing of Campylobacter jejuni and comparison with Lior's or Penner's serotyping system].

Campylobacter jejuni were isolated from 7 epidemic outbreaks (121 isolates), 15 patients with gastroenteritis, chicken meats (47 isolates) and chicken cecal contents (70 isolates). The isolates and one standard strain of C. jejuni JCM2013 were analysed by randomly amplified polymorphic DNA method (RAPD). Total of 254 C. jejuni isolates were divided 68 different RAPD types which included strains that did not to divided by Lior's or Penner's serotyping system. To compare the similarities of RAPD patterns among the isolates, the amplification patterns of DNA were estimated by means of the Dice coefficient, and clustering of strains was based on the unweighted average pair group method (UPGMA) to facilitate the plotting of a dendrogram. It suggests that amplification band patterns of human isolates were different from those of chicken ones. Thus additional information given from RAPD profiles serves for epidemiological investigation and RAPD analysis is recommended as rapid and effective typing method.

Animals↗

PubMed2001

Phase variation among major surface antigens of Mycoplasma penetrans.

The pathogenicity and prevalence of Mycoplasma penetrans, a Mycoplasma species recently isolated from humans, are still debated. A major P35 antigen, which is used as target epitope in serological assays, was shown to be a phase-variable lipid-associated membrane protein (LAMP). In this study, we performed a comparative analysis of the LAMP patterns from five M. penetrans clinical isolates and from the type strain. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles and immunoblots with sera serially collected from an M. penetrans-infected patient indicated that these strains expressed different LAMP repertoires. Furthermore, the intraclonal variation in the expression of LAMPs (P34A, P34B, P35, and P38) was monitored by immunoblot analysis with three specific monoclonal antibodies (MAbs) developed in this study and MAb 7 to P35. The phase variation of these LAMPs occurs in an independent manner, with frequencies of variation ranging from 10(-2) to 10(-4) per cell per generation. Consistent with their amphipathic nature, the P34B and P38 antigens were found exposed at the cell surface. The DNA sequence encoding the P38 antigen was defined and found to be related to those of the P35 gene and other putative LAMP-encoding genes, suggesting that these variable antigens are encoded by a family of related genes. Finally, the serum samples from an M. penetrans-infected patient contained antibodies that reacted with a P36 antigen expressed in different M. penetrans strains but not in the isolate recovered from this patient. This result suggested that in vivo phase variation of P36 occurred, which would support a role for these LAMP variations in avoiding the host's immune vigilance.

Amino Acid Sequence↗

PubMed2005

Streptomyces koyangensis sp. nov., a novel actinomycete that produces 4-phenyl-3-butenoic acid.

A 4-phenyl-3-butenoic acid-producing actinomycete, designated strain VK-A60T, was isolated from a soil sample collected from Koyang, Korea. Morphological and chemical characteristics of the strain were consistent with those of the genus Streptomyces. The cell wall of the strain contains LL-diaminopimelic acid. The predominant fatty acids are anteiso-C(15 : 0), iso-C(16 : 0) and C(16 : 0). The strain formed a distinct monophyletic line within the 16S rRNA gene sequence phylogenetic tree. Analyses of its morphological, physiological and biochemical characteristics, together with random amplified polymorphic DNA and DNA-DNA relatedness data, confirmed that strain VK-A60T represents a novel Streptomyces taxon that is distinguishable from closely related reference strains. Strain VK-A60T (=KCCM 10555T=NBRC 100598T) is proposed as the type strain of a novel species, for which the name Streptomyces koyangensis sp. nov. is proposed.

Bacterial Typing Techniques↗

PubMed2006

Clonal relationship among Vibrio cholerae O1 El Tor strains causing the largest cholera epidemic in Kenya in the late 1990s.

Eighty Vibrio cholerae O1 strains selected to represent the 1998-to-1999 history of the largest cholera epidemic in Kenya were characterized by ribotyping, antimicrobial susceptibility, and random amplified polymorphic DNA patterns. Except for 19 strains from 4 local outbreaks in North Eastern Province along the Somalia border, the other 61 strains from 25 outbreaks occurring in districts scattered around the country were all ribotype B27 and resistant to chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim. The 61 strains showed similar and specific amplified DNA patterns. These findings indicate that the predominant strains that caused the Kenyan epidemic had a clonal origin and suggest that ribotype B27 strains, which first appeared in West Africa in 1994, have had a rapid spread to eastern Africa.

Anti-Bacterial Agents↗

PubMed2005

Rosmarinic acid content and RAPD analysis of in vitro regenerated basil (Ocimum americanum) plants.

Various in vitro cultures were established from shoot tips of Ocimum americanum seedlings. Rosmarinic acid content of the in vitro produced plants as well as parent plant were determined by HPLC analysis and subjected to RAPD analysis. MS medium with BA at a concentration of 1 mg/l and 0.25 mg/l IAA supports maximum rosmarinic acid production in plants produced from cultures grown on that medium. RAPD analysis revealed 64 scorable bands from four primers, including six polymorphic bands. The band pattern revealed differences between the parent plant and the in vitro regenerated plants. Certain band changes were found in O. americanum plants regenerated in vitro, suggesting the existence of genetic variation that might affect the biochemical synthesis of plants derived from tissue culture.

Cell Culture Techniques↗

PubMed1997

Identification of Aeromonas clinical isolates by restriction fragment length polymorphism of PCR-amplified 16S rRNA genes.

Identification of Aeromonas species, emergent pathogens for humans, has long been controversial due to their phenotypic and genomic heterogeneities. Computer analysis of the published 16S rRNA gene sequences revealed that restriction fragment length polymorphism of the PCR-amplified 16S rRNA gene is a good and rapid way of assessing the identities of all known species of Aeromonas. The method was evaluated with the reference strains of all species (or DNA homology groups) and 76 clinical isolates of diverse origin. Most results from the two approaches were in agreement, but some discrepancies were discerned. Advantages over previous phenotypic and genetic methods are discussed.

Aeromonas↗

PubMed2005

Use of nodulation pattern, stress tolerance, nodC gene amplification, RAPD-PCR and RFLP-16S rDNA analysis to discriminate genotypes of Rhizobium leguminosarum biovar viciae.

Twenty-seven new Rhizobium isolates were obtained from root nodules of wild and crop legumes belonging to the genera Vicia, Lathyrus and Pisum from different agroecological areas in central and southern Italy. A polyphasic approach including phenotypic and genotypic techniques was used to study their diversity and their relationships with other biovars and species of rhizobia. Analysis of symbiotic properties and stress tolerance tests revealed that wild isolates showed a wide spectrum of nodulation and a marked variation in stress tolerance compared with reference strains tested in this study. All rhizobial isolates (except for the isolate CG4 from Galega officinalis) were presumptively identified as Rhizobium leguminosarum biovar viciae both by their symbiotic properties and the specific amplification of the nodC gene. In particular, we found that the nodC gene could be used as a diagnostic molecular marker for strains belonging to the bv. viciae. RFLP-PCR 16S rDNA analysis confirms these results, with the exception of two strains that showed different RFLP-genotypes from those of the reference strains of R. leguminosarum bv. viciae. Analysis of intraspecies relationship among strains by using the RAPD-PCR technique showed a high level of genetic polymorphism, grouping our isolates and reference strains into six different major clusters with a similarity level of 20%. Data from seven parameters of phenotypic and genotypic analyses were evaluated by using principal component analysis which indicated the differences among strains and allowed them to be divided into seven different groups.

Bacterial Proteins↗

PubMedDate not supplied

[Methods for the study of microbial communities in fermented foods].

The importance of ecological concepts to understand the presence and growth of microorganisms in foods is presently recognized. The production of fermented foods under controlled conditions and its safety assurance depend on the knowledge and control of their microbiota. Traditional fermented foods are obtained by natural fermentations (in which no inoculum is added) and contain complex microbiotas, which are difficult to describe through the use of traditional microbiological methods. The microbial structure of these foods can be studied with different approaches. One of them consists on the typification of isolated microorganisms with methods based on DNA as RFLP, ribotyping, AFLP, ARDRA and RAPD. In order to detect non-culturable or not yet cultured microorganisms, nucleic acids are directly extracted from foods and the microbial diversity is determined from them. Examples of these techniques are the construction of 16S rDNA clone libraries and fingerprinting techniques, such as DGGE and TGGE. Recent advances on the application of these techniques on the study of fermented foods are presented.

Bacteria↗

PubMed2001

Characterization of non-starter lactic acid bacteria from Italian ewe cheeses based on phenotypic, genotypic, and cell wall protein analyses.

Non-starter lactic acid bacteria (NSLAB) were isolated from 12 Italian ewe cheeses representing six different types of cheese, which in several cases were produced by different manufacturers. A total of 400 presumptive Lactobacillus isolates were obtained, and 123 isolates and 10 type strains were subjected to phenotypic, genetic, and cell wall protein characterization analyses. Phenotypically, the cheese isolates included 32% Lactobacillus plantarum isolates, 15% L. brevis isolates, 12% L. paracasei subsp. paracasei isolates, 9% L. curvatus isolates, 6% L. fermentum isolates, 6% L. casei subsp. casei isolates, 5% L. pentosus isolates, 3% L. casei subsp. pseudoplantarum isolates, and 1% L. rhamnosus isolates. Eleven percent of the isolates were not phenotypically identified. Although a randomly amplified polymorphic DNA (RAPD) analysis based on three primers and clustering by the unweighted pair group method with arithmetic average (UPGMA) was useful for partially differentiating the 10 type strains, it did not provide a species-specific DNA band or a combination of bands which permitted complete separation of all the species considered. In contrast, sodium dodecyl sulfate-polyacrylamide gel electrophoresis cell wall protein profiles clustered by UPGMA were species specific and resolved the NSLAB. The only exceptions were isolates phenotypically identified as L. plantarum and L. pentosus or as L. casei subsp. casei and L. paracasei subsp. paracasei, which were grouped together. Based on protein profiles, Italian ewe cheeses frequently contained four different species and 3 to 16 strains. In general, the cheeses produced from raw ewe milk contained a larger number of more diverse strains than the cheeses produced from pasteurized milk. The same cheese produced in different factories contained different species, as well as strains that belonged to the same species but grouped in different RAPD clusters.

Animals↗

PubMed2000

Genomic polymorphism in Uruguayan Creole cattle using RAPD and microsatellite markers.

Uruguayan Creole cattle inhabit areas that cannot sustain conventional farming. They have adapted to fragile environments and are influenced only by natural selection. In this study, random amplified polymorphic DNA (RAPD) and microsatellite (MS) markers were used to analyse Creole cattle genome polymorphism. A comparative analysis using the RAPD technique was performed in pooled DNA of three cattle breeds (Holstein Friesian, Creole and Hereford) in order to evaluate their amplification patterns. A primary screening of RAPD primers allowed us to select and use those with higher percentage of GC base composition. A total of 215 loci ranging between 300 and 2500 bp were amplified. Bandsharing frequency (BSF) among breeds showed that less related fingerprints were observed between Creole and Hereford cattle (0.77), while the highest similarity frequency corresponded to Holstein Friesian compared to Hereford (0.81). Specific RAPD bands were identified in the three DNA pools and they were tested in every individual of each breed. It may be possible to isolate and sequence these bands to create breed-specific molecular markers. The identification of multiple alleles of the MSCYP 21 in Creole cattle with an heterozygosity of He = 0.846 supported the variability of this genetic resource. The use of molecular markers such as RAPD s and microsatellites is proposed to establish genetic distance among American Creole cattle and possibly related ancestral Iberian breeds.

Alleles↗

PubMed1999

Use of molecular subtyping to document long-term persistence of Corynebacterium diphtheriae in South Dakota.

Enhanced surveillance of patients with upper respiratory symptoms in a Northern Plains community revealed that approximately 4% of them were infected by toxigenic Corynebacterium diphtheriae of both mitis and gravis biotypes, showing that the organism is still circulating in the United States. Toxigenic C. diphtheriae was isolated from five members of four households. Four molecular subtyping methods-ribotyping, multilocus enzyme electrophoresis (MEE), random amplified polymorphic DNA (RAPD), and single-strand conformation polymorphism-were used to molecularly characterize these strains and compare them to 17 archival South Dakota strains dating back to 1973 through 1983 and to 5 isolates collected from residents of diverse regions of the United States. Ribotyping and RAPD clearly demonstrated the household transmission of isolates and provided precise information on the circulation of several distinct strains within three households. By MEE, most recent and archival South Dakota strains were identified as closely related and clustered within the newly identified ET (electrophoretic type) 215 complex. Furthermore, three recent South Dakota isolates and eight archival South Dakota isolates were indistinguishable by both ribotyping and RAPD. All of these molecular methods showed that recent South Dakota isolates and archival South Dakota isolates were more closely related to each other than to the C. diphtheriae strains isolated in other parts of the United States or worldwide. The data also supported the improbability of importation of C. diphtheriae into this area and rather strongly suggest the long-term persistence of the organism in this region.

Bacterial Typing Techniques↗