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PubMed1998

DNA fingerprinting of Mycobacterium tuberculosis complex culture isolates collected in Brazil and spotted onto filter paper.

The usefulness of filter paper for preservation of bacterial cells was shown by mixed-linker DNA fingerprint analysis of Mycobacterium tuberculosis isolates from 77 Brazilian patients. DNA fingerprints of samples spotted onto filter paper and conventional culture material were identical. Thus, filter paper specimens analyzed by an amplification-based typing method provide a new resource for epidemiological studies of infectious diseases.

Brazil↗
PubMed1999

Analyses of lipopolysaccharides, outer membrane proteins and DNA fingerprints reveal intraspecies diversity in Moraxella bovis isolated in Argentina.

Intra-specific diversity within Moraxella bovis was investigated analysing DNA fingerprints, outer membrane proteins (OMP) and lipopolysaccharides (LPS) profiles. Three collection strains and 57 isolates of M. bovis, collected during 3 years from cattle with infectious bovine keratoconjunctivitis (IBK) symptoms, from diverse geographical locations of Argentina, were examined. The LPS and OMP profiles were studied through SDS-PAGE analysis and genotype was determined by PCR-DNA fingerprinting. Genotyping identified five DNA types while analysis of LPS and OMP profiles identified three rough LPS types and three OMP types among the 60 isolates of M. bovis including the three collection strains. None of the three methods employed to assess diversity was discriminating when used alone because the degree of heterogeneity in each group of surface structures was limited, but when data of each typing method were combined, 15 distinct subgroups were determined. This subgrouping was clearly able to differentiate isolates of the same genotype. These typing methods appear to be useful to assess different aspects of the disease such as the diversity within a population of M. bovis associated to epidemic conditions, track the causal agent in an outbreak of the disease, monitoring vaccination programs and studies on virulence.

Animals↗
PubMed2000

Cluster analysis of AP-PCR generated DNA fingerprints of Vibrio vulnificus isolates from patients fatally infected after consumption of raw oysters.

Arbitrarily-primed-polymerase chain reaction (AP-PCR) DNA fingerprints were generated for 10 Vibrio vulnificus strains isolated from patients who became infected and died between 1993 and 1996 as a result of consuming raw oysters. Analysis of the DNA fingerprints with gel imaging and cluster analysis software revealed significant genetic heterogeneity among these strains, suggesting that V. vulnificus has a high degree of variation in its genomic organization, and that multiple pathogenic strains with greatly diverse genomic arrangements, rather than a single type of infective strain or serogroup, caused these infections.

Animals↗
PubMed1998

Follow up of Mycobacterium tuberculosis transmission in the French West Indies by IS6110-DNA fingerprinting and DR-based spoligotyping.

A total of 115 Mycobacterium tuberculosis isolates from 80 patients were typed using IS6110-DNA fingerprinting and DR-based spoligotyping to describe the active transmission of tuberculosis in a Caribbean setting over a 2-year period. A total of 61 different pattern types were observed by IS6110-RFLP and 10 clusters containing between two and 15 patients could be defined. By spoligotyping, 45 different pattern types were observed with 12 clusters containing two to 11 patients. Thirty-two patients could be included in eight spoligotype-defined clusters and in nine RFLP-defined clusters when strictly concordant matching results were put together. In conclusion, about 40% of the patient isolates were clustered by DNA fingerprinting suggesting recent transmission of tuberculosis in our region. This study confirmed the increased accuracy and discriminatory power of the association of IS6110-RFLP and spoligotyping for studies on the molecular epidemiology of M. tuberculosis, and suggests that despite good implementation of tuberculosis control programs in Guadeloupe, active transmission of tuberculosis may be far more important than suspected.

Bacterial Typing Techniques↗
PubMedDate not supplied

Similarity of DNA fingerprints due to chance and relatedness.

Given the DNA fingerprints of two individuals with some bands being shared by both individuals, we define a new measure of the degree of similarity between the DNA profiles of two individuals. We use this measure to calculate the expected DNA similarity of two unrelated individuals of a randomly mating population; this similarity is due to chance only. Then, the expected similarity between two related individuals is obtained; this similarity is due to chance and relatedness. From these results, the degree of similarity due to relatedness alone may be calculated.

Alleles↗
PubMed1999

DNA fingerprint analysis reveals differences in mutational patterns in experimentally induced rat peritoneal tumors, depending on the type of environmental mutagen.

We performed tumor DNA fingerprint analysis using the synthetic minisatellite probe S3315x2 based on the 33.15-repeat unit. The aim of the study was to investigate fingerprinting patterns of peritoneal tumors induced experimentally in Wistar rats by two carcinogens with unknown mechanism of action (crocidolite asbestos and nickel powder) and, as a positive control, benzo[a]pyrene. The carcinogens were administered intraperitoneally into rats. The banding patterns obtained with DNA from 71 peritoneal tumors were compared to the corresponding normal tissues. DNA derived from peritoneal tumors induced by the three carcinogens differed with respect to mutation frequencies and mutation patterns. The mutation frequencies in these tumors, revealed by DNA fingerprinting, were 18.2% for benzo[a]pyrene, 14.8% for crocidolite asbestos, and 40.9% for nickel powder. The alterations detected in the banding pattern of benzo[a]pyrene-induced peritoneal tumors were exclusively additional bands. On the contrary, in the DNA from asbestos-induced peritoneal tumors, only deletions of bands were observed on the autoradiographs. In the DNA from nickel-induced peritoneal tumors, both types of mutations occurred. The different mutation frequencies and mutation patterns appear to discriminate between benzo[a]pyrene, crocidolite asbestos, and nickel powder, and may be related to the mechanisms of action of these compounds.

Animals↗
PubMed2004

Evaluation of different primers for DNA fingerprinting of Legionella pneumophila serogroup 1 strains by polymerase chain reaction.

A DNA fingerprinting method for the characterization of Legionella pneumophila serogroup 1 strains was established. This method was based on the DNA extraction using Chelex 100 and subsequent PCR analysis using primers under conditions of low stringency. Sixteen single primers were tested for the typing of the 10 epidemiologically unrelated reference strains of L. pneumophila serogroup 1 as well as patient isolates and environmental strains isolated from the water system of a hospital where patients with legionellosis were treated. In addition, a combination of two primers (Lpm-1 and Lpm-2) originally established for the specific detection of Legionella strains was tested. The PCR results were compared with two further subtyping methods, i.e. monoclonal antibody analysis and pulsed-field gel electrophoresis. The type strains Philadelphia 1, Knoxville 1, Allentown 1, Benidorm 0303E, Bellingham 1, and France 5811 could be distinguished clearly in experiments using all of the primers. Depending on the primer used, Heysham 1 and Oxford 4032E showed different DNA profiles. The strains Olda and Camperdown 1 were nearly indistinguishable. In contrast, the analysis by PFGE and MAb subtyping revealed distinct types for all 10 reference strains. The discrimination of the patient isolates from two suspected cases of nosocomial legionellosis and environmental isolates was not possible with the 16 single primers used in the study. However, the PCR assay with the combination of Lpm-1 and Lpm-2 as well as the PFGE and MAb analysis were able to differentiate distinct types. The use of the sequence-specific primers under low-stringency annealing conditions allowed both simultaneous gene detection as well as epidemiological typing of Legionella strains.

Bacterial Typing Techniques↗
PubMed2003

[Study on DNA fingerprinting of Mycobacterium tuberculosis strains isolated in Southern Chinese army by IS6110-restriction fragment length polymorphism].

OBJECTIVE: To study the correlation between DNA fingerprinting of Mycobacterium tuberculosis (MTB) stains isolated from the Chinese army in the south and from local residents, and to investigate the molecular epidemiological characteristics of tuberculosis (TB) in the army, for the sake of TB prevention in the army. METHODS: MTB DNA was digested with restriction endonuclease PvuII and electrophoresed in agarose gel, after Southern Blotting, the membrane was hybridized with a 245 bp fragment of IS6110 which labeled [alpha(32)P]-dCTP as probe. Finally, a restriction fragment length polymorphism (RFLP) patterns was shown, and analyzed logestic with epidemiological data from the patients. RESULTS: A total number of 185 TB strains were detected and the IS6110 copy numbers ranged from 1 - 22. No significant difference was found in the IS6110 copy numbers between patients from army and local patients. IS6110 copy numbers of TB strains in army patients were centered in 6 - 20, however, with 7 - 20 copies in local TB patients. The TB strains were dispersed into 8 groups and the majority of TB strains in both army and local patients was centered in groups I, II, III. The distribution of DNA fingerprint for drug resistance TB strains was significantly different from those for sensitive strains. No different distribution of among groups was found regarding BCG history. CONCLUSIONS: The genetics of TB stains were roughly the same between the army patients and local ones, but there was a strong correlation in the gene levels. Data suggested that a close connection should be considered on TB prevention and treatment for TB patients in the army and local residents.

China↗
PubMed1996

DNA fingerprinting techniques for microorganisms. A proposal for classification and nomenclature.

A whole array of DNA-fingerprinting techniques, which provide indirect access to DNA sequence polymorphism in order to assess species or clonal identity of bacterial organisms or in order to study bacterial genome composition, have been described during past decades. Nomenclature has been sometimes erroneous and/or confusing, also because of hybrid techniques that combine different approaches. It can be shown that most techniques study the sequence polymorphism of only the chromosome, or only the plasmid(s) or only a gene or gene fragment and that the sequence polymorphism is revealed by AFLP (amplified fragment length polymorphism) or by RFLP (restriction fragment length polymorphism) or by special electrophoresis techniques. Starting from these considerations, some taxonomy of techniques, which enables more appropriate nomenclature, can be developed.

Bacteria↗
PubMed1989

[DNA fingerprinting of Rattus norvegicus: a new approach in genetic analysis].

Recent finding in highly effective DNA probes for RFLP testing (of hypervariable minisatellite DNA type) has led to the invention of DNA fingerprinting--the new technique of great value for identification of individuals, establishing biological kinship and studies in population genetics. We anticipate that DNA fingerprinting procedure with M13 phage DNA as a probe which we have developed earlier, makes it possible to apply new approach in genetic analysis--establishing, whether or not a particular locus is associated with the inheritance of genetic disease, by comparing the whole restriction fragment data from affected and unaffected animals. In this work, using the method described we characterized the Kroushynsky-Molodkina rat strain with hereditary disposition for epileptic attacks and performed comparative fingerprint analysis of these defective and normal rat genomes. The data obtained may hold some promises for further seeking the particular defective gene.

Animals↗
PubMed1999

Evolution of genetic abnormalities in hepatocellular carcinomas demonstrated by DNA fingerprinting.

Hepatocellular carcinomas (HCC) often contain subpopulations of cells showing heterogeneous differentiation within each tumour. The majority of HCCs first appear as well-differentiated lesions and proliferate with gradual dedifferentiation. The present study was designed to investigate the clonal diversity which is seen with progression in neoplasms. The degree of genomic heterogeneity of HCC nodules was assessed using the arbitrarily primed-polymerase chain reaction technique. Two or more sectors of 31 HCC nodules were needle-microdissected and amplified with two different arbitrary primers in appropriate conditions. In every HCC less than 6 mm in diameter (n=18, range 3-6 mm, mean diameter 4.7 mm), all sectors of each of these lesions had the same DNA fingerprint. All HCC nodules greater than 6 mm diameter (n=13, range 7-30 mm, mean diameter 15.4 mm) showed distinct DNA fingerprints in each sector sampled (p< 0. 05, compared with size less than 6 mm in diameter). When synchronous HCCs were present, no two tumour nodules had the same DNA fingerprint. These results suggest that a process of clonal evolution occurs in expanding HCC, with neoplasms more than 6 mm in diameter developing as multiple clones. The advent of laser capture microdissection technology makes such analysis much more rapid and easily applied. Studies of clonality in HCCs, including borderline cases, are made possible by the combination of these novel techniques.

Carcinoma, Hepatocellular↗
PubMed1995

Recrudescence of Helicobacter pylori after apparently successful eradication: novel application of randomly amplified polymorphic DNA fingerprinting.

The aim of this study was to find out if reinfection or recrudescence accounted for the recurrence of Helicobacter pylori infections after apparent eradication of the bacterium. Three hundred and twenty patients were treated with colloidal bismuth subcitrate (120 mg four times daily for four weeks), metronidazole and tetracycline (400 mg and 500 mg, respectively, thrice daily for the first week). H pylori was eradicated four weeks after the end of treatment as assessed by the rapid urease test, histological examination, Gram staining, and culture. However, the infection recurred in 29 (9.1%) of the patients one year after apparent eradication. Pre and posteradication isolates from five patients were available. DNA was extracted and used for restriction endonuclease analysis with Hind III and Hae III, and for polymerase chain reaction (PCR) based randomly amplified polymorphic DNA fingerprinting with a combination of two 10 nucleotide primers. Sodium dodecyl sulphate polyacrylamide gel electrophoretic analysis was performed also. Randomly amplified polymorphic DNA fingerprinting was unique in that it yielded highly discriminatory fingerprints, which showed that the pretreatment and recurrent isolates obtained from each of the five patients were indistinguishable from one another. This shows that recurrence of H pylori infection is probably caused by recrudescence and that the discriminatory power of randomly amplified polymorphic DNA fingerprinting is a practicable and discriminatory typing scheme for H pylori.

Adult↗
PubMed1997

Studies of polymorphic DNA fingerprinting and lipid pattern of Mycobacterium tuberculosis patient isolates in Japan.

Strain differentiation by DNA restriction fragment length polymorphism (RFLP) has been used mainly for the epidemiological purpose of Mycobacterium tuberculosis infection. In this study, we tried to connect the molecular and phenotypic characteristics of M. tuberculosis patient isolates by comparing the DNA fingerprints obtained by RFLP using IS6110 and lipid patterns using two-dimensional thin-layer chromatography (2-D TLC) with silica gel, since M. tuberculosis has a lipid-rich cell envelope which contributes to the virulence and immunomodulatory properties. We found that 66 isolates of M. tuberculosis from tuberculosis patients showed that the occurrence of IS6110 varied from 1 to 24 copies. The IS6110 patterns were highly variable among isolates. Fifty different RFLP patterns were observed, and 12 RFLP patterns were shared by two or more strains. By computerized analysis of the RFLP patterns of M. tuberculosis patient isolates, we found that 95% of the isolates fell into seven clusters, from A to G, with at least two isolates in each (> 30% similarity). Among the cellular lipids, the phospholipid composition did not differ by strain, whereas the glycolipid pattern differed markedly. Especially, the relative concentration of cord factor and sulfolipid, both of which were known as virulent factors, varied by strain. The fingerprints of some strains showed an association between the DNA and glycolipid patterns, even though some of the same DNA fingerprint strains showed differences in lipid patterns. Among the patient isolates, M. tuberculosis strain 249 possessed a specific glycolipid with 2-O-methyl-L-rhamnose and L-rhamnose, which is rarely found in other strains. This glycolipid showed serological activity against the sera of tuberculosis patients, even if the reactivity was not as strong as trehalose dimycolate. It also showed the inhibition of phagosome-lysosome fusion in macrophages, suggesting involvement with virulence. These results suggest that RFLP analysis using IS6110 is useful for clustering the human isolates of M. tuberculosis, however, for further strain differentiation on virulence, a lipid analysis provides more information.

Antibodies, Bacterial↗
PubMed1995

Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs.

Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands. The multilocus DNA fingerprinting technique showed very low levels of variation both within and between populations of the harbour seals. For one probe a significant difference in variation between populations was demonstrated. The estimated average heterozygosity, however, diverged more strongly between the two harbour seal populations because of more frequent occurrence of rare alleles in the Scottish population. Low levels of genetic variation seem to be characteristic for the subspecies Phoca vitulina vitulina, but not for all marine mammals in the North Sea, as the grey seal population showed significantly higher variation.

Animals↗
PubMedDate not supplied

DNA fingerprint analysis of standard, intermediate, and variant antigenic types of Salmonella enterica subspecies enterica serovar Gallinarum biovar pullorum.

DNA fingerprint profiles and antigenic types of 150 Salmonella enterica serovar Gallinarum biovar pullorum field isolates and seven reference strains were evaluated. Field isolates were submitted to the National Veterinary Services Laboratories (NVSL), Ames, Iowa, between Oct. 1, 1990, and Aug. 20, 1991. Three antigenic types (standard [n = 96], intermediate [n = 50], and variant [n = 4]) were identified among the field isolates. The NciI fingerprint profiles of all field isolates were identical. Differentiation of field isolates was observed by digestion of DNA with HpaII; three profiles were recognized. One HpaII profile (designated SP HpaII 001) was common among 144 isolates (standard, n = 90; intermediate, n = 50; and variant, n = 4); the remaining six pullorum standard type isolates were equally dispersed between two HpaII profiles (designated SP HpaII 002 and 003). Three antigenic types were identified among the seven reference strains (reference strains 11, 17, 19, and 20 [standard]; reference strain 4 [intermediate]; reference strains 79 and 296 [variant]). One NciI profile was recognized; two HpaII profiles were observed. Six reference strains (11, 17, 19, 20, 79, and 296) had profile SP HpaII 001, and reference strain 4 had profile SP HpaII 002. No correlations were established between DNA fingerprints and antigenic types.

Animals↗
PubMed1993

DNA fingerprinting reveals relationships between strains of Trypanosoma rangeli and Trypanosoma cruzi.

Very little is known about the structure and sequence of the genomic DNA and kDNA of T. rangeli and no highly polymorphic markers are known. In this paper, we show that the Jeffreys' multilocal probe 33.15 produces characteristic DNA fingerprints with these trypanosomes. The multiband patterns can be used to differentiate T. cruzi from T. rangeli and for recognizing relationships between strains of the latter from widely different geographic areas and different hosts. The topology of a UPGMA phenetic tree constructed from band-sharing data suggests the existence of two groups of T. rangeli: one encompassing parasites from Central America and the northern part of South America and another with the parasites from southern Brazil. This splitting was confirmed by the use of both nuclear and kinetoplast unique sequence probes. Among strains of T. rangeli, band sharing was generally negatively correlated with geographical distance. This work confirms the usefulness of DNA fingerprints as a potent technique for the analysis of relationships in trypanosomatid populations.

Animals↗
PubMed1995

DNA fingerprinting of pathogenic bacteria by fluorophore-enhanced repetitive sequence-based polymerase chain reaction.

Fluorophore-labeled oligonucleotide primers complementary to defined interspersed repetitive sequences conserved in diverse bacteria were used in the polymerase chain reaction to generate DNA fingerprint patterns from selected pathogenic bacteria. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction allowed discrimination between unrelated isolates of penicillin-resistant Streptococcus pneumoniae recovered from pediatric patients and Mycobacterium avium cultured from patients with acquired immunodeficiency syndrome. Combinations of oligonucleotide primers labeled with distinct fluorescent dyes enabled simultaneous DNA fingerprinting and Shiga-like toxin gene detection in enterohemorrhagic Escherichia coli isolates. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction was performed with either purified DNA or intact cells that were lysed during the polymerase chain reaction. Fluorophore-enhanced, repetitive sequence-based polymerase chain reaction successfully combines polymerase chain reaction amplification and fluorescent label detection for DNA fingerprinting of cultured bacterial pathogens.

Base Sequence↗
PubMed1993

DNA fingerprint bands applied to linkage analysis with quantitative trait loci in chickens.

An efficient approach to detect association between quantitative traits and bands of DNA fingerprint patterns uses intra-family tail analysis, which compares fingerprints of DNA mixes from individuals at the two tails of a phenotypic distribution. In analysis of 67 paternal half-sibs of a meat-type chicken family, of 57 sire bands generated by two probes, one sire-specific band (S6.6) was associated with abdominal fat deposition. The band effect was estimated by a linear model analysis to be 0.88 standard deviations, or about 30% of the family mean. The association between band S6.6 and abdominal fat was further examined by testing progeny of paternal half-sibs of the chickens which were used in the tail analysis, establishing genetic linkage between the DNA marker and a genetic locus affecting abdominal fat deposition.

Adipose Tissue↗