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At least 1,009 records · Page 56Linked to original sources
PubMed1993

Monitoring of relapse and remission in acute leukaemias by DNA-fingerprint analysis.

DNA-fingerprint (DNA-F) analysis was successfully performed with DNA from 22 adult patients with acute leukaemia, including 13 patients with acute myeloid leukaemia (AML) and nine patients with acute lymphoblastic leukaemia (ALL). The purpose of this study was to detect differences between the leukaemic phase (at diagnosis or relapse) and remission-phase DNA. We applied one simple repeat probe (GTG)5 and one minisatellite (M13) after DNA-digestion with different restriction endonucleases (HinfI and HaeIII) and agarose gel electrophoresis. In 7/13 patients with AML and 5/9 patients with ALL it was possible to detect loss of bands, additional bands or band shift with at least one of the probes. Together the probes M13 and (GTG)5 unveiled deviating fingerprint patterns in 54.6% of patients between leukaemic cells and remission-phase leucocytes. Allogeneic bone marrow transplantation was performed on six patients. In each case the DNA-F pattern of the donor was different from the relapse and the remission-phase pattern. We conclude from our studies that the probes M13 and (GTG)5 are useful in the detection of relapse and remission in acute leukaemias after chemotherapy and bone marrow transplantation.

Acute Disease↗
PubMed1995

Strain-specific fingerprints of Rhizobium galegae generated by PCR with arbitrary and repetitive primers.

Strain-specific genomic patterns of Rhizobium galegae were generated by PCR using both arbitrary and repetitive (BOX, ERIC and REP) primers. The identification of the strains was achieved also by RFLP analysis. However, the PCR genomic fingerprinting has significant advantages: it is not only simpler and faster, but it is also much more discriminative because it deals with the full bacterial genome and not only with parts of it as is the case with RFLP. In addition, both kinds of PCR fingerprinting (using arbitrary or repetitive primers) generated highly specific and reproducible patterns when parallel reactions with total bacterial DNA, extracted from independent liquid cultures were performed. The latter shows that AP- and rep-PCR are convenient for controlling the production and application of Rhizobium inoculants.

Base Sequence↗
PubMed1995

Salmonella typhimurium DT 193: differentiation of an epidemic phage type by antibiogram, plasmid profile, plasmid fingerprint and salmonella plasmid virulence (spv) gene probe.

Of over 2000 isolates of Salmonella typhimurium DT 193 from humans examined in the 2 year period 1991-92, 93% were antibiotic-resistant with the most common R-types being ASSuT (38%) and T (29%). Fourteen plasmid profiles were identified in DT 193 R-type ASSuT with the majority of isolates being characterized by a single plasmid of 80 MDa (pDEP 34) which in addition to coding for ASSuT, also hybridized with a spv gene probe prepared from the 50 MDa Salm. dublin serovar-specific plasmid. On the basis of restriction fragment length polymorphisms, two variant lines of pDEP 34-like plasmids were identified and a third line which had lost the genes coding for resistance to ampicillin, streptomycin and sulphonamides, was recognized. Although 18 plasmid profile types were identified in DT 193 R-type T, all isolates carried a high mol. wt plasmid which coded for tetracycline resistance only. Further discrimination was achieved on the basis of hybridization of tetracycline resistance plasmids with the spv gene probe and restriction enzyme fingerprinting. These results demonstrate that Salm. typhimurium DT 193 can be rapidly subdivided by antibiogram and that further subdivision can be achieved on the basis of plasmid profile, plasmid fingerprint and hybridization with a spv gene probe.

Animals↗
PubMed2005

PCR-fingerprinting and RAPD approaches for tracing the source of yeast contamination in a carbonated orange juice production chain.

AIMS: To investigate the sort and the origin of the contamination of a packed fruit juice. METHODS AND RESULTS: Fifty-eight yeast isolates were collected in a survey of two different visits to a carbonated orange juice factory. In each visit, samples were collected, six times, from seven points in the production chain. For each visit, no significant differences were observed among the yeast average values obtained in the control points considered. The random amplified polymorphic DNA (RAPD) with primer P24 and the PCR-fingerprinting with the microsatellites primers (GTG)5 and (GAC)5 were used, in order to discriminate the isolates, rendering 29 composite profiles; the most frequent one (24/58) was profile c, which included the yeast isolates from the final product and strains isolated before and after the pasteurization of the juice. These contaminant strains were identified as Pichia galeiformis by sequence analysis of D1/D2 26S rRNA gene. CONCLUSIONS: The results obtained point to an inefficient pasteurization of the juice related to the fouling of the heat-transfer surfaces of the plate-type exchanger. SIGNIFICANCE AND IMPACT OF THE STUDY: The combination of PCR-fingerprinting and RAPD assays showed to be very useful in tracking the route of contamination in a carbonated juice production chain.

Beverages↗
PubMed1993

Determination of paternity in dragonflies by Random Amplified Polymorphic DNA fingerprinting.

We used Random Amplified Polymorphic DNA (RAPD) fingerprinting to address issues of paternity in two odonate species. Amplification artifacts of RAPD markers were controlled by assessing paternity patterns relative to the banding patterns generated by quantitative mixtures of DNA from putative parents ('synthetic offspring'). In the aeshnid dragonfly Anax parthenope, for which the mating histories of both males and females were unknown, we found strong evidence for complete paternity success for the contact guarding male. In the highly polygamous libellulid dragonfly Orthetrum coerulescens, we detected and quantified mixed paternity in sequentially produced offspring clutches and demonstrated that fertilization success is correlated with the duration of copulation. Our results suggest that RAPD fingerprinting is suitable to address issues of paternity in systems which are genetically uncharacterized and produce large offspring clutches.

Animals↗
PubMed2004

Measuring the efficacy of insecticide treated bednets: the use of DNA fingerprinting to increase the accuracy of personal protection estimates in Tanzania.

Summary Insecticide-treated nets have proved successful in the prevention of malaria as a result of both the personal protection with which they provide the sleeper and also the 'mass effect' on the local mosquito population when they are used on a community-wide basis. Personal protection estimates are normally based on comparisons of the numbers of bloodfed mosquitoes found in rooms with and without nets, however it seemed possible that a number of those mosquitoes may not have fed on the occupants of the rooms in which they were found but had entered after feeding elsewhere. To address this possible source of error, we used an 8-locus microsatellite system to identify the source of bloodmeals of Anopheles gambiaes.l. and A. funestus mosquitoes collected in rooms and window traps in Tanzanian villages with and without nets treated with alphacypermethrin. DNA fingerprints were produced from blood samples taken from people who had slept in these rooms and were matched to fingerprints obtained from the mosquito bloodmeals. We were able to type successfully over 90% of the bloodmeals collected and found that proportions of bloodfed mosquitoes that had fed on occupants of the rooms in which they were found were high and only slightly greater in villages without treated nets than those with them (95% and 88%, respectively). When these percentages were used to adjust estimates of personal protection, it was found that the error due to mosquitoes not feeding in the rooms in which they were collected is negligible.

Adult↗
PubMed1990

Probe-specific DNA fingerprinting applied to the epidemiology of localized juvenile periodontitis.

Although Actinobacillus actinomycetemcomitans has been recognized as a primary etiological agent in localized juvenile periodontitis, questions remain concerning the source of infection, mode of transmission, and relative virulence of strains. DNA fingerprinting analysis, using a randomly cloned chromosomal DNA fragment as a probe, revealed that previously characterized strains of A. actinomycetemcomitans displayed significant restriction site heterogeneity which could be applied to the typing of clinical isolates of this bacterium such that individual strains or variants could be traced within subjects from localized juvenile periodontitis families. Hybridization data derived from an analysis of bacterial isolates obtained from families participating in an ongoing longitudinal study of the disease showed that a single individual could be infected with more than one strain or variant of A. actinomycetemcomitans and that various members of the same family could harbor different strains or variants of the bacterium. In several cases the clinical isolates were matched to characterized laboratory strains by comparing hybridization patterns generated by digestion of the DNA with several restriction enzymes in independent reactions. Thus, probe-specific DNA fingerprinting of A. actinomycetemcomitans will permit us to determine if particular strains or variants are frequently associated with sites of periodontal destruction. Attention could then be focused on determining the virulence properties of those strains or variants that have in vivo significance.

Actinobacillus↗
PubMed1997

Arbitrarily primed polymerase chain reaction fingerprinting and clonal analysis of oral Fusobacterium nucleatum isolates.

F. nucleatum is the most commonly isolated microorganism from subgingival plaque, but the role of this microorganism in periodontal diseases remains undefined. Arbitrarily primed polymerase chain reaction (AP-PCR) was evaluated as a method for fingerprinting F. nucleatum isolates and for use in clonal analysis. Pulsed field gel electrophoresis was used to further differentiate F. nucleatum isolates, with identical AP-PCR patterns. Extremely heterogeneous AP-PCR fingerprints were observed among the 98 F. nucleatum isolates, with 36 different genotypes observed with primer C1 and 30 different genotype detected with primer C2. Combining the results of the AP-PCR genotype analysis from C1 and C2 primer amplifications revealed that up to 7 different genotypes could be distinguished from isolates from the same oral cavity and that up to 4 different genotypes were observed within a single site. An intense amplicon at approximately 450 bp generated in AP-PCR amplification with primer C2 was associated with F. nucleatum subsp. nucleatum (ATCC 25586) and with 15 F. nucleatum isolates from diseased sites and 2 isolates from healthy sites. Pulsed field gel electrophoresis confirmed the AP-PCR genotypes and demonstrated increased discriminatory power over AP-PCR. The results indicated that AP-PCR and pulsed field gel electrophoresis provide a simple and sensitive means for differentiating oral F. nucleatum isolates and further demonstrate the heterogeneity of this species. These techniques may serve as useful tools in the clonal and epidemiological analysis of F. nucleatum isolates, which may help define the role of these microorganisms in periodontal diseases.

Bacterial Typing Techniques↗
PubMed2006

Analysis of the strain relatedness of oral Candida albicans in patients with diabetes mellitus using polymerase chain reaction-fingerprinting.

To increase our understanding of Candida pathogenicity, the identification of those strains most frequently associated with infections is of paramount importance. Polymerase chain reaction (PCR)-based methods are extremely effective in differentiating and determining reproducibility, they require minimum starting material and are rapid and simple to perform. In this study, the genetic relatedness of Candida albicans was assessed for two geographically different patient groups (London, UK and Parma, Italy) affected by diabetes mellitus. C. albicans samples from the oral cavities of non-diabetic healthy subjects were also examined by PCR fingerprinting to evaluate the possible genetic differences among endogenous strains in individuals with and without diabetes mellitus. PCR fingerprinting, with subsequent phylogenetic analysis of C. albicans isolates from the diabetic patients from London and Italy and from the non-diabetic subjects, revealed that there were significant differences (P < 0.0001) between C. albicans isolates indicative of the distinct ecological niches that occur in the oral cavities of these patient cohorts. The most diverse group comprised the isolates from the diabetic patients in the UK, possibly reflecting the antifungal treatment that these patients had received. Further studies that include isolates from patient cohorts with systemic diseases other than diabetes mellitus, and from more diverse geographic localities are required to explain the relatedness of C. albicans isolates in the mouth.

Candida albicans↗
PubMed1996

Analysis of production brewing strains of yeast by DNA fingerprinting.

Production brewing strains of the yeast Saccharomyces cerevisiae were analysed by DNA fingerprinting, using a Southern blotting and hybridization procedure and employing the Ty1-15 transposon as a probe. The ability to differentiate readily between strains was very dependent on the restriction enzyme used to digest the DNA prior to Southern blotting and hybridization; the enzymes EcoRI, PstI and SalI were found to be particularly useful in this respect. The method was applicable to the differentiation of both ale and lager yeasts, and was sufficiently sensitive to distinguish between very closely related strains. DNA fingerprinting by this approach confirmed, for example, that a flocculent strain isolated during a production-scale fermentation with a lager yeast was genotypically different from the parent.

Base Sequence↗
PubMedDate not supplied

DNA fingerprinting of Trypanosoma vivax isolates rapidly identifies intraspecific relationships.

Using the polymerase chain reaction and arbitrarily selected oligonucleotide primers of 10 or 11 bases, we have amplified DNA sequences from Trypanosoma vivax parasites isolated from South America and Africa. On the basis of polymorphisms in the DNA fingerprints generated by three of the primers, the parasites could be separated into two major groups, one comprising T. vivax isolates from Kenya and the second including all the other T. vivax parasites (from Colombia, The Gambia, Nigeria and Uganda). One of these three primers (ILo 525) also gave isolate-specific DNA fingerprints for the parasites tested, which will allow the use of this technique both in the species identification and discrimination of T. vivax parasites.

Animals↗
PubMed1994

Molecular epidemiology of Legionella pneumophila serogroup 1 by ribotyping with a non-radioactive probe and PCR fingerprinting.

Hybridization with acetylaminofluorene-labelled 16 + 23 S rRNA from Escherichia coli was used to detect DNA polymorphism among Legionella pneumophila serogroup 1 isolates. Isolates from unrelated patients showed at least four different rRNA restriction patterns, whereas those from related patients showed a single pattern. Amplification of genomic regions with an arbitrary primer by polymerase chain reaction was used to further analyze the isolates. Related isolates showed closely related patterns while unrelated isolates displayed six distinct patterns. We could differentiate the majority of unrelated isolates with the combination of the patterns obtained with the ribotyping and the PCR fingerprinting, while strains from the same outbreak remained highly related. The ribotyping and the PCR fingerprinting are proposed as useful and easy to perform epidemiological markers of L. pneumophila serogroup 1 infection.

Base Sequence↗
PubMed1996

Repetitive and arbitrary primer DNA sequences in PCR-mediated fingerprinting of outbreak and sporadic isolates of Campylobacter jejuni.

PCR-mediated fingerprinting with combined repetitive and arbitrary DNA primers (ERIC-2 and 1026) was used to type Campylobacter jejuni from a milk-associated outbreak, and from sporadic cases of the same and allied HS serotypes. The 14 outbreak strains had identical or similar DNA band profiles whereas the 25 strains from sporadic infections were more heterogeneous with 18 different DNA profiles. Although PCR-based DNA fingerprints lacked serotype specificity, the method was fast, simple to perform and reproducible, provided defined technical protocols were adhered to precisely. Profiles were highly discriminatory but did not consistently match types based on other molecular methods. We conclude that AP-PCR has demonstrable potential for initial rapid investigation of outbreaks, and when used in conjunction with PFGE analysis of DNA restriction profiles, provides a high resolution strategy for accurately defining subtypes of C. jejuni.

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↗
PubMed1994

Study of the influence of plasmids on the arbitrary primer polymerase chain reaction fingerprint of Escherichia coli strains.

To study the effect of plasmids on the arbitrary primer-polymerase chain reaction fingerprint of bacterial strains, the Escherichia coli strains DH5, Top10, and W3110 were transformed with plasmids of different sizes: respectively, pUC19, pCEP and two clinically important plasmids carrying resistance to several antibiotics. Total DNA, i.e. both chromosomal and plasmid DNA, was prepared from transformed cells by boiling the cell suspensions and by phenol-chloroform extraction; chromosomal DNA was prepared by the same methods from the non-transformed, plasmid-free strains; plasmid DNA of pUC19 was purchased; plasmid DNA of pCEP was purified from the transformed strains by caesium chloride density gradient centrifugation. Arbitrarily primed polymerase chain reaction was carried out for all of these preparations. Amplification carried out independently with three different primers resulted in similar patterns for the chromosomal preparations whether or not plasmid was present. Amplification of plasmid DNA gave different patterns, characterized by fragments larger than those obtained when total or chromosomal DNA were used as the target. These data illustrate that the plasmids studied here do not influence the chromosomal arbitrarily primed PCR fingerprint, although plasmids alone are amplified in the absence of chromosomal DNA. Experiments comparing different relative concentrations of plasmid and chromosomal DNA indicate that under natural conditions the amount of chromosomal DNA per cell is sufficient to inhibit observable amplification of the plasmid(s) present.

Base Sequence↗
PubMed1998

Detection of new and persistent Streptococcus uberis and Streptococcus dysgalactiae intramammary infections by polymerase chain reaction-based DNA fingerprinting.

Polymerase chain reaction-based DNA fingerprinting was used as a tool to differentiate new and persistent Streptococcus uberis and Streptococcus dysgalactiae intramammary infections (IMI) in dairy cows. The same subtype of S. uberis or S. dysgalactiae was detected from some infected mammary glands from one lactation to the next documenting the persistence of these infections. Conversely, some streptococci isolated from mammary glands during a lactation or from one lactation to the next were different subtypes suggesting that a new IMI occurred. These new streptococcal IMI would never have been detected using phenotypic methods of streptococcal identification. Results of this study indicate that PCR-based DNA fingerprinting can be used as an effective procedure to differentiate new and persistent S. uberis and S. dysgalactiae IMI in dairy cows. This technique will be useful in epidemiological investigations, and drug and vaccine efficacy studies when attempting to delineate new and persistent IMI.

Animals↗
PubMed1998

A PCR fingerprinting technique to distinguish isolates of Lactococcus lactis.

A fingerprinting technique similar to repetitive extragenic palindromic PCR was developed to identify strains of Lactococcus lactis. The method distinguishes closely related strains and discriminates among some with identical ldh sequences. The fingerprinting primer LL-Rep1 complements a moderately repeated sequence found in low G + C Gram-positive bacteria and may therefore prove useful for discriminating among strains of other low G + C Gram-positive species.

Base Composition↗
PubMed2002

Genetic relationships of Bacillus anthracis and closely related species based on variable-number tandem repeat analysis and BOX-PCR genomic fingerprinting.

Variable-number tandem repeats (VNTR) analysis and BOX-repeat-based PCR (BOX-PCR) genomic fingerprinting were performed on 25 Bacillus strains to investigate the genetic relatedness of Bacillus anthracis to the closely related species. Based on VNTR analysis, all B. anthracis strains could be assigned to (VNTR)(4), which is the most commonly found type in the world. Interestingly, a (VNTR)(2) was also observed in Bacillus cereus KCTC 1661 and with an exact match to the tandem repeats found in B. anthracis. This finding has never been reported before in the closely related species. According to the BOX-PCR, B. anthracis strains clustered together and separated reliably from the closely related species. However, B. cereus KCTC 1661 was linked to the B. anthracis cluster and showed close relationships with B. anthracis strains. These results indicated that there was a strong correlation between VNTR analysis and BOX-PCR genomic fingerprinting.

Bacillus↗