SEARCH · Search PubMed

Results for “FINGERPRINTS”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

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

At least 1,027 records · Page 57Linked to original sources

PubMed1995

[Clinical utility of DNA fingerprinting by arbitrarily-primed polymerase chain reaction (AP-PCR) in nosocomial infection caused by methicillin-resistant Staphylococcus aureus].

Recently, nosocomial outbreaks of MRSA have become an serious social problem in Japan. To examine the routes of transmission of MRSA, the establishment of an accurate MRSA typing system is essential. Previously, we reported that the DNA fingerprinting by AP-PCR might be a useful method to differentiate MRSA strains. In this study, we tried to investigate the clinical usefulness of DNA fingerprinting by AP-PCR using clinically-isolated MRSA strains. Twenty-four MRSA strains (12 with coagulase type IV, and 12 with coagulase type II) isolated from patients in our department were used. Other typing methods (the sensitivity of antibiotics, pulsed-field gel electrophoresis, and plasmid analysis) were also performed. As a result, the typing pattern by AP-PCR correlated well with other typing methods. MRSA strains with coagulase type IV showed almost the same pattern, suggesting that these strains were nosocomially transmitted. On the other hand, MRSA strains with coagulase type II showed various patterns, suggesting these strains were not nosocomially transmitted. In conclusion, the typing by AP-PCR seemed to be a useful tool evaluate a nosocomial MRSA transmission.

Cross Infection↗

PubMed1995

[DNA fingerprinting by arbitrarily primed polymerase chain reaction (AP-PCR) for methicillin-resistant Staphylococcus aureus].

Recently, nosocomial outbreaks of MRSA have become an important social problem in Japan. To examine the routes of transmission of MRSA, the establishment of accurate MRSA typing system is essential. However, more recently, because MRSA strains with type II coagulase have been increasing, it is difficult to discriminate MRSA strains by the coagulase typing method. Under this background, our study was designed to evaluate the clinical significance of DNA fingerprinting by arbitrarily primed polymerase chain reaction (AP-PCR). Several MRSA strains isolated from patients in our department were used in this study. To optimize the condition of AP-PCR, the differences of amplified products by AP-PCR were evaluated according to the following conditions: extracting methods of DNA from MRSA strains, buffer conditions, the temperature of AP-PCR, cycles of AP-PCR, and several primers. As a result, the optimal conditions of AP-PCR were as follows: extracted DNA using the InstaGene kit, amplified DNA by two-step AP-PCR using a M13 reverse primer with a buffer condition of 3.5 mM of magnesium chloride, and a pH of 8.5. The results of AP-PCR correlated well with the results of pulsed-field gel electrophoresis. In conclusion, DNA fingerprinting by AP-PCR seems to be useful in examining the nosocomial MRSA outbreak.

Bacterial Typing Techniques↗

PubMed1996

Strain typing with IS200 fingerprints in Salmonella abortusovis.

A collection of Salmonella abortusovis isolates was examined for the presence of insertion element IS200. All proved to contain three or four copies of the element. One IS200 hybridization band of approximately 9 kb was found in all isolates, indicating that all S. abortusovis strains carry an IS200 element in similar or identical locations; this band can be potentially useful for serovar identification. S. abortusovis collection isolates from distinct geographic areas were highly polymorphic, suggesting that IS200 fingerprints might provide information on the geographic origin of S. abortusovis strains. Isolates obtained from the same geographic area (the island of Sardinia, Italy) were less polymorphic: all shared three constant IS200 hybridization bands, indicating that they derive from a single ancestor. Most strains analyzed contained an additional copy of IS200 in the variable region of the virulence plasmid. Certain Sardinian flocks proved to be infected by only one S. abortusovis strain, while others harbored two strains. Strain typing with IS200 fingerprints proved to be more reliable than plasmid analysis, because the latter yielded a high degree of polymorphism, even among isolates from the same flock.

Abortion, Veterinary↗

PubMed1997

Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints.

Most species of the diazotrophic Proteobacteria Azoarcus spp. occur in association with grass roots, while A. tolulyticus and A. evansii are soil bacteria not associated with a plant host. To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis. Commonly used primers targeted to REP (repetitive extragenic palindromic) and ERIC (enterobacterial repetitive intergenic consensus) sequence elements failed to amplify fragments from the two species tested. In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences. PCR profiles of an additional PCR assay using primers targeted to tRNA genes (tDNA-PCR, for tRNA(IIe)) were more discriminative, allowing differentiation at species-specific (for two species) or infraspecies-specific level. Our protocol of several consecutive PCR assays consisted of 16S ribosomal DNA (rDNA)-targeted, genus-specific PCR followed by BOX- and tDNA-PCR; it enabled us to assign new diazotrophic isolates originating from fungal resting stages (sclerotia) to known species of Azoarcus. The assignment was confirmed by phylogenetic analysis of 16S rDNA sequences. Additionally, the phylogenetic distances and the lack of monophyly suggested emendment of the genus Azoarcus: the unnamed species Azoarcus groups C and D and a new group (E) of Azoarcus, which was detected in association with fungi, are likely to have the taxonomic rank of three different genera. According to its small subunit rRNA, the sclerotium-forming basidiomycete was related to the Ustilagomycetes, facultatively biotrophic parasites of plants. Since they occurred in a field which was under cultivation with rice and wheat, these fungi might serve as a niche for survival for Azoarcus in the soil and as a source for reinfection of plants.

Bacteria↗

PubMed1999

Amplified fragment length polymorphism fingerprinting of Pseudomonas strains from a poultry processing plant.

Molecular typing has been used previously to identify and trace dissemination of pathogenic and spoilage bacteria associated with food processing. Amplified fragment length polymorphism (AFLP) is a novel DNA fingerprinting technique which is considered highly reproducible and has high discriminatory power. This technique was used to fingerprint 88 Pseudomonas fluorescens and Pseudomonas putida strains that were previously isolated from plate counts of carcasses at six processing stages and various equipment surfaces and environmental sources of a poultry abattoir. Clustering of the AFLP patterns revealed a high level of diversity among the strains. Six clusters (clusters I through VI) were delineated at an arbitrary Dice coefficient level of 0.65; clusters III (31 strains) and IV (28 strains) were the largest clusters. More than one-half (52.3%) of the strains obtained from carcass samples, which may have represented the resident carcass population, grouped together in cluster III. By contrast, 43.2% of the strains from most of the equipment surfaces and environmental sources grouped together in cluster IV. In most cases, the clusters in which carcass strains from processing stages grouped corresponded to the clusters in which strains from the associated equipment surfaces and/or environmental sources were found. This provided evidence that there was cross-contamination between carcasses and the abattoir environment at the DNA level. The AFLP data also showed that strains were being disseminated from the beginning to the end of the poultry processing operation, since many strains associated with carcasses at the packaging stage were members of the same clusters as strains obtained from carcasses after the defeathering stage.

Abattoirs↗

PubMed2000

Genetic diversity of Vibrio cholerae in Chesapeake Bay determined by amplified fragment length polymorphism fingerprinting.

Vibrio cholerae is indigenous to the aquatic environment, and serotype non-O1 strains are readily isolated from coastal waters. However, in comparison with intensive studies of the O1 group, relatively little effort has been made to analyze the population structure and molecular evolution of non-O1 V. cholerae. In this study, high-resolution genomic DNA fingerprinting, amplified fragment length polymorphism (AFLP), was used to characterize the temporal and spatial genetic diversity of 67 V. cholerae strains isolated from Chesapeake Bay during April through July 1998, at four different sampling sites. Isolation of V. cholerae during the winter months (January through March) was unsuccessful, as observed in earlier studies (J. H. L. Kaper, R. R. Colwell, and S. W. Joseph, Appl. Environ. Microbiol. 37:91-103, 1979). AFLP fingerprints subjected to similarity analysis yielded a grouping of isolates into three large clusters, reflecting time of the year when the strains were isolated. April and May isolates were closely related, while July isolates were genetically diverse and did not cluster with the isolates obtained earlier in the year. The results suggest that the population structure of V. cholerae undergoes a shift in genotype that is linked to changes in environmental conditions. From January to July, the water temperature increased from 3 degrees C to 27.5 degrees C, bacterial direct counts increased nearly an order of magnitude, and the chlorophyll a concentration tripled (or even quadrupled at some sites). No correlation was observed between genetic similarity among isolates and geographical source of isolation, since isolates found at a single sampling site were genetically diverse and genetically identical isolates were found at several of the sampling sites. Thus, V. cholerae populations may be transported by surface currents throughout the entire Bay, or, more likely, similar environmental conditions may be selected for a specific genotype. The dynamic nature of the population structure of this bacterial species in Chesapeake Bay provides new insight into the ecology and molecular evolution of V. cholerae in the natural environment.

DNA Fingerprinting↗

PubMed2000

Suitability of PCR fingerprinting, infrequent-restriction-site PCR, and pulsed-field gel electrophoresis, combined with computerized gel analysis, in library typing of Salmonella enterica serovar enteritidis.

Strains of Salmonella enterica (n = 212) of different serovars and phage types were used to establish a library typing computerized system for serovar Enteritidis on the basis of PCR fingerprinting, infrequent-restriction-site PCR (IRS-PCR), or pulsed-field gel electrophoresis (PFGE). The rate of PCR fingerprinting interassay and intercenter reproducibility was low and was only increased when DNA samples were extracted at the same time and amplified with the same reaction mixtures. Reproducibility of IRS-PCR technique reached 100%, but discrimination was low (D = 0.52). The PFGE procedure showed an intercenter reproducibility value of 93.3%. The high reproducibility of PFGE combined with the previously determined high discrimination directed its use for library typing. The use of PFGE with enzymes XbaI, BlnI, and SpeI for library typing of serovar Enteritidis was assessed with GelCompar 4.0 software. Three computer libraries of PFGE DNA profiles were constructed, and their ability to recognize new DNA profiles was analyzed. The results obtained pointed out that the combination of PFGE with computerized analysis could be suitable in long-term epidemiological comparison and surveillance of Salmonella serovar Enteritidis, specially if the prevalence of genetic events that could be responsible for changes in PFGE profiles in this serovar was low.

Animals↗

PubMed2000

Use of a single, triplicate arbitrarily primed-PCR procedure for molecular fingerprinting of lactic acid bacteria.

Arbitrarily primed (AP)-PCR can be used to generate characteristic DNA fingerprint patterns. However, small changes in reaction conditions can cause band irreproducibility. In this study, a single methodology encompassing triplicate reactions, which were intentionally exposed to three different annealing temperatures, enabled bands that were reproducibly generated to be recognized. A single triplicate AP-PCR (TAP-PCR) procedure, using an 18-mer primer, was developed and used to fingerprint representative isolates from the major genera of lactic acid bacteria and Bifidobacterium to the strain level.

Bacteria↗

PubMed2002

Application of amplified fragment length polymorphism fingerprinting for taxonomy and identification of the soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi.

The soft rot bacteria Erwinia carotovora and Erwinia chrysanthemi are important pathogens of potato and other crops. However, the taxonomy of these pathogens, particularly at subspecies level, is unclear. An investigation using amplified fragment length polymorphism (AFLP) fingerprinting was undertaken to determine the taxonomic relationships within this group based on their genetic relatedness. Following cluster analysis on the similarity matrices derived from the AFLP gels, four clusters (clusters 1 to 4) resulted. Cluster 1 contained Erwinia carotovora subsp. carotovora (subclusters 1a and 1b) and Erwinia carotovora subsp. odorifera (subcluster 1c) strains, while cluster 2 contained Erwinia carotovora subsp. atroseptica (subcluster 2a) and Erwinia carotovora subsp. betavasculorum (subcluster 2b) strains. Clusters 3 and 4 contained Erwinia carotovora subsp. wasabiae and E. chrysanthemi strains, respectively. While E. carotovora subsp. carotovora and E. chrysanthemi showed a high level of molecular diversity (23 to 38% mean similarity), E. carotovora subsp. odorifera, E. carotovora subsp. betavasculorum, E. carotovora subsp. atroseptica, and E. carotovora subsp. wasabiae showed considerably less (56 to 76% mean similarity), which may reflect their limited geographical distributions and/or host ranges. The species- and subspecies-specific banding profiles generated from the AFLPs allowed rapid identification of unknown isolates and the potential for future development of diagnostics. AFLP fingerprinting was also found to be more differentiating than other techniques for typing the soft rot erwinias and was applicable to all strain types, including different serogroups.

Bacterial Typing Techniques↗

PubMed2003

Fingerprinting microbial assemblages from the oxic/anoxic chemocline of the Black Sea.

Biomass samples from the Black Sea collected in 1988 were analyzed for SSU genes from Bacteria and Archaea after 10 years of storage at -80 degrees C. Both clonal libraries and direct fingerprinting by terminal restriction fragment length polymorphism (T-RFLP) analyses were used to assess the microbial community. Uniform and discrete depth distributions of different SSU phylotypes were observed. However, most recombinant clones were not restricted to a specific depth in the water column, and many of the major T-RFLP peaks remain uncharacterized. Of the clones obtained, an epsilon-Proteobacteria and a Pseudoalteromonas-like clone accounted for major peaks in the fingerprint, while deeply branching lineages of alpha- and gamma-Proteobacteria were associated with smaller peaks. Additionally, members were found among both the delta-Proteobacteria related to sulfate reducers and the Archaea related to phylotypes from the ANME groups that anaerobically oxidize methane.

Aerobiosis↗

PubMed2004

Detection and characterization of a dehalogenating microorganism by terminal restriction fragment length polymorphism fingerprinting of 16S rRNA in a sulfidogenic, 2-bromophenol-utilizing enrichment.

Terminal restriction fragment length polymorphism analysis of reverse-transcribed 16S rRNA during periods of community flux was used as a tool to delineate the roles of the members of a 2-bromophenol-degrading, sulfate-reducing consortium. Starved, washed cultures were amended with 2-bromophenol plus sulfate, 2-bromophenol plus hydrogen, phenol plus sulfate, or phenol with no electron acceptor and were monitored for substrate use. In the presence of sulfate, 2-bromophenol and phenol were completely degraded. In the absence of sulfate, 2-bromophenol was dehalogenated and phenol accumulated. Direct terminal restriction fragment length polymorphism fingerprinting of the 16S rRNA in the various subcultures indicated that phylotype 2BP-48 (a Desulfovibrio-like sequence) was responsible for the dehalogenation of 2-bromophenol. A stable coculture was established which contained predominantly 2BP-48 and a second Desulfovibrio-like bacterium (designated BP212 based on terminal restriction fragment length polymorphism fingerprinting) that was capable of dehalogenating 2-bromophenol to phenol. Strain 2BP-48 in the coculture could couple reductive dehalogenation to growth with 2-bromophenol, 2,6-dibromophenol, or 2-iodophenol and lactate or formate as the electron donor. In addition to halophenols, strain 2BP-48 appears to use sulfate, sulfite, and thiosulfate as electron acceptors and is capable of simultaneous sulfidogenesis and reductive dehalogenation in the presence of sulfate.

Bacteria↗

PubMed2004

Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray.

Investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on PCR amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifH. Recent work has suggested that DNA macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifH amplicons (G. F. Steward, B. D. Jenkins, B. B. Ward, and J. P. Zehr, Appl. Environ. Microbiol. 70:1455-1465, 2004). Here we report the application of macroarrays for a study in the Chesapeake Bay. Samples from different locations in the bay yielded distinct fingerprints. Analysis of replicates and samples from different locations by cluster analysis showed that replicates clustered together, whereas different samples formed distinct clusters. There was a correspondence between the hybridization pattern observed and that predicted from the distribution of sequence types in a corresponding clone library. Some discrepancies between the methods were observed which are likely a result of the high nifH sequence diversity in the Chesapeake Bay and the limited number of sequences represented on this version of the array. Analyses of sequences in the clone library indicate that the Chesapeake Bay harbors unique, phylogenetically diverse diazotrophs. The macroarray hybridization patterns suggest that there are spatially variable communities of diazotrophs, which have been confirmed by quantitative PCR methods (S. M. Short, B. D. Jenkins, and J. P. Zehr, Appl. Environ. Microbiol., in press). The results show that DNA macroarrays have great potential for mapping the spatial and temporal variability of functional gene diversity in the environment.

Base Sequence↗

PubMed2004

Characterization of Nocardia asteroides isolates from different ecological habitats on the basis of repetitive extragenic palindromic-PCR fingerprinting.

Thirteen isolates of Nocardia asteroides from both soils and aquatic samples (lake and moat sediments, as well as scum from activated sludge), together with a type strain and two known clinical isolates of this species, were characterized by repetitive extragenic palindromic-PCR fingerprinting with the BOX-A1R primer. The resulting DNA fingerprint patterns proved to be strain specific, and cluster analysis distinguished the soil isolates, the aquatic isolates, and the known strains as being in separate groups.

Bacterial Typing Techniques↗

PubMed2005

Fingerprinting of Bacillus thuringiensis type strains and isolates by using Bacillus cereus group-specific repetitive extragenic palindromic sequence-based PCR analysis.

A total of 119 Bacillus thuringiensis strains (83 type strains and 26 native isolates), as well as five B. cereus group species, were analyzed by repetitive extragenic palindromic sequence-based PCR analysis (Rep-PCR) fingerprinting. Primers Bc-REP-1 and Bc-REP-2 were specifically designed according to an extragenic 26-bp repeated sequence found in the six B. cereus group genomes reported. A total of 47 polymorphic bands were detected, and the patterns varied from 5 to 13 bands in number and from 0.2 to 3.8 kb in size. Virtually each type strain showed a distinctive B. cereus (Bc)-Rep-PCR pattern, except for B. thuringiensis serovars dakota (H serotype 15 [H15]) and sotto (H4a,4b), as well as serovars amagiensis (H29) and seoulensis (H35), which shared the same patterns. As expected, serovar entomocidus (H6) and its biovar subtoxicus showed an identical pattern; similarly, serovars sumiyoshiensis (H3a,3d) and fukuokaensis (H3a,3d,3e), which share two antigenic determinants, also showed identical Bc-Rep-PCR patterns. Interestingly, serovars israelensis (H14) and malaysiensis (H36), which share several phenotypic attributes, also showed identical Bc-Rep-PCR patterns. Native, coleopteran-active strains, including the self-agglutinated LBIT-74 strain, showed Bc-Rep-PCR patterns identical or very similar to that of the tenebrionis strain. Likewise, native mosquitocidal strains (including some self-agglutinated strains) also showed patterns identical or very similar to that of the serovar israelensis IPS-82 strain. Additionally, native beta-exotoxin-producing strains from serovar thuringiensis showed patterns identical to that of the B. thuringiensis type strain. The B. cereus group-specific Bc-Rep-PCR fingerprinting technique was shown to be highly discriminative, fast, easy, and able to identify B. thuringiensis serotypes, including nonflagellar and self-agglutinated strains.

Bacillus cereus↗

PubMed2005

Quantitative molecular assay for fingerprinting microbial communities of wastewater and estrogen-degrading consortia.

A quantitative fingerprinting method, called the real-time terminal restriction fragment length polymorphism (real-time-t-RFLP) assay, was developed for simultaneous determination of microbial diversity and abundance within a complex community. The real-time-t-RFLP assay was developed by incorporating the quantitative feature of real-time PCR and the fingerprinting feature of t-RFLP analysis. The assay was validated by using a model microbial community containing three pure strains, an Escherichia coli strain (gram negative), a Pseudomonas fluorescens strain (gram negative), and a Bacillus thuringiensis strain (gram positive). Subsequently, the real-time-t-RFLP assay was applied to and proven to be useful for environmental samples; the richness and abundance of species in microbial communities (expressed as the number of 16S rRNA gene copies of each ribotype per milliliter) of wastewater and estrogen-degrading consortia (enriched with 17alpha-estradiol, 17beta-estradiol, or estrone) were successfully characterized. The results of this study strongly suggested that the real-time-t-RFLP assay can be a powerful molecular tool for gaining insight into microbial communities in various engineered systems and natural habitats.

Bacillus thuringiensis↗

PubMed1994

DNA fingerprinting of medically important microorganisms by use of PCR.

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.

Animals↗

PubMed2006

IS1301 fingerprint analysis of Neisseria meningitidis strains belonging to the ET-15 clone.

Meningococci of the ET-15 clone frequently cause clusters of invasive meningococcal disease (IMD) and are associated with a high case-fatality ratio. Timely typing of strains from outbreaks of IMD caused by this clone is hampered by the low variability of its surface antigens. We present a new Southern blot-based typing method for ET-15 meningococci based on the insertion element IS1301, which was present in all 70 ET-15 strains tested. Fingerprints were stable in vitro over a period of 100 days of cultivation on agar plates. The discriminatory power of IS1301 fingerprinting exceeded that of typing by serogrouping and antigen sequencing of the outer membrane proteins PorA and FetA, as determined by the analysis of 52 epidemiologically unrelated strains. In addition, the method provided conclusive results with regard to the comparison of strains from clusters of IMD. The investigation of insertion sites of IS1301 revealed several new intragenic insertions, among others, into open reading frames homologous to mafB and tspB. A previously described insertion in nadA was present in more than two-thirds of the strains analyzed, suggesting that NadA is probably an unreliable vaccine candidate for the prevention of ET-15 disease.

Bacterial Proteins↗

PubMed1991

Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus.

In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections.

Biomarkers↗