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PubMed2002

DNA fingerprinting analysis of coagulase negative staphylococci implicated in catheter related bloodstream infections.

AIMS: The epidemiological assessment of cases of coagulase negative staphylococcal catheter related bloodstream infection. METHODS: Two hundred and thirty patients with suspected catheter related bloodstream infection were evaluated over a two year period. Central venous catheters were cultured both endoluminally and extraluminally. Peripheral blood, catheter hubs, skin entry, and skin control sites were also cultured. Pulsed field gel electrophoresis (PFGE) was used to DNA fingerprint coagulase negative staphylococci isolated from patients with presumptive catheter related bloodstream infection. RESULTS: Sixty cases of catheter related bloodstream infection were identified, 21 of which were attributed to coagulase negative staphylococci. Two hundred and ninety four separate isolates of coagulase negative staphylococci from the 21 cases of catheter related bloodstream infection were subjected to PFGE (mean of 14 for each case). Catheter related bloodstream infection was only confirmed by PFGE analysis in 16 of the 21 cases because in the remaining five cases peripheral blood and central venous catheter coagulase negative staphylococci isolates were different. Skin entry, control skin, and central venous catheter hub isolates matched peripheral blood isolates in six, four, and seven cases, respectively. Coagulase negative staphylococci isolates could not be cultured from the patients' own skin in seven cases of catheter related bloodstream infection. Central venous catheter lumens were colonised in all cases of catheter related bloodstream infection compared with 44-81% of cases that had positive external surface catheter tip cultures, depending on the threshold used to define significant growth. CONCLUSIONS: Catheter related bloodstream infection as a result of coagulase negative staphylococci may be over stated in about a quarter of cases, unless a discriminatory technique is used to fingerprint isolates. No single, simplistic route of bacterial contamination of central venous catheters was identified, but endoluminal catheter colonisation is invariably present in cases of catheter related bloodstream infection.

Bacteremia↗
PubMed1992

Genomic fingerprinting of penicillinase-producing strains of Neisseria gonorrhoeae in Valencia, Spain.

OBJECTIVE: To compare the value of different markers and their combinations with the restriction enzyme technique in the differentiations of penicillinase-producing N. gonorrhoeae (PPNG) strains. MATERIALS AND METHODS: 17 PPNG strains isolated from symptomatic, untreated male patients with urethritis were characterised by antibiotic sensitivity testing, auxotyping, serotyping, plasmid profile, and restriction endonuclease fingerprinting (Hind III digestion). Cluster analysis with the method of unweighted pair-group average (UPGMA) linkage was used to calculate similarity or dissimilarity for PPNG strains. MAIN RESULTS: Either auxotyping or plasmid profile alone differentiated three groups of PPNG strains, whereas the combination auxotyping/serotyping identified 10. Although the combination auxotyping/serotyping/plasmid profile and the restriction enzyme technique showed a similar discrimination ability (differentiation of 11 PPNG strains), genomic fingerprinting gave highly specific restriction patterns on individual gonococcal isolates. CONCLUSIONS: The combination of different markers gave more epidemiological information than the use of only one. The sequence of discriminating ability for PPNG strains was: auxotyping/serotyping less than auxotyping/serotyping/plasmid profile less than restriction patterns of genomic DNA.

DNA Fingerprinting↗
PubMed1991

DNA fingerprinting in reptiles: Bkm hybridization patterns in Crocodilia and Chelonia.

The simple tetranucleotide repeat GATA (GACA) occurs in all eukaryotes so far studied. In many species, the arrangement of these sequences varies considerably among individuals. Thus GATA (GACA) type probes produce DNA fingerprints when hybridized with restricted DNA from different individuals within a species. Banded krait minor (Bkm) satellite DNA (related to sequences originally recovered from the W chromosome of the banded krait and consisting essentially of a series of GATA repeats) is found in a wide spectrum of vertebrates and invertebrates. We used the Bkm 2(8) clone to evaluate the occurrence of this satellite in DNA from five species of Crocodilia and six species of Chelonia, including the sea turtles Chelonia mydas and Lepidochelys kempi. Well-resolved DNA fingerprints were obtained. Among the crocodilians, fewer restriction fragments were generated and fewer of the fragments were polymorphic, than among the chelonians, consistent with the view that the crocodilians are less divergent within species. The Bkm 2(8) clone can accordingly be used to advantage in individual, familial, and population studies, and perhaps in the evaluation of taxonomic relationships in these animals. This is of potential value in endangered species such as C. mydas and L. kempi.

Alligators and Crocodiles↗
PubMed1995

Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting.

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.

Base Sequence↗
PubMed1998

Comparative genome analysis of Bacillus sphaericus by ribotyping, M13 hybridization, and M13 polymerase chain reaction fingerprinting.

A comparative genome analysis of 15 strains representing the five homology groups of the highly heterogeneous species Bacillus sphaericus was performed by M13 hybridization fingerprinting, M13 polymerase chain reaction fingerprinting, and ribotyping with the whole rrn operon. The computer cluster analyses of the polymorphic patterns, presented in dendrograms, showed that these methods allow the differentiation of the individual strains and some homology groups. Our results confirm the close genetic relatedness of the mosquito pathogenic strains of group IIA and support the idea for differentiation of a separate species. At the same time, we present additional proof of the significant genetic heterogeneity of B. sphaericus and the necessity of reconsideration of its present classification.

Bacillus↗
PubMed1990

Application of DNA fingerprinting to parentage and extended family relationship testing.

For the purpose of applying DNA fingerprinting to parentage or other extended blood relationship testing, we have developed a general system for estimating blood relationship between a set of individuals. This system can be used for any blood relationship testing, even if critical family members are unavailable. A general formula for calculating the probability of such relationships based on Bayes' theorem has been devised and the ability of DNA fingerprinting produced by Jeffrey's polycore probe to determine the relationships has been evaluated.

Bayes Theorem↗
PubMed1994

A multilocus DNA fingerprint with built-in security devices.

An unusual case of paternity testing is reported in which determination of paternity was an essential part of a genetic diagnosis. A Y-chromosomal abnormality, observed in a 33-year-old male whose wife had experienced a series of spontaneous abortions, was not found in his alleged father. DNA fingerprinting with the oligonucleotide multilocus probe (CAC)5 yielded two aberrant bands for the proband, i.e. bands exhibited by neither parent. This finding resulted in a comparatively low paternity probability of 0.02934 which is suggestive of, but does not unequivocally prove, false paternity. Subsequent analysis with other multi- and single-locus systems, however, failed to confirm this preliminary result. The paternity probability computed on the basis of the single-locus systems was 0.99997, providing compelling evidence in favour of true paternity. The present case thus demonstrates that even when two mutations turn up in a DNA fingerprint, these may be readily recognized as such.

Abortion, Spontaneous↗
PubMed1994

Recombinant thyroid peroxidase autoantibodies can be used for epitopic "fingerprinting" of thyroid peroxidase autoantibodies in the sera of individual patients.

Four human monoclonal antibodies (SP1.4, WR1.7, TR1.8, and TR1.9) map the immunodominant region on thyroid peroxidase (TPO) recognized by autoantibodies in patients' sera. We used a pool of these monoclonal antibodies, expressed in bacteria as antigen-binding fragments [F(ab)], to compete for TPO autoantibody binding to radiolabeled TPO. The F(ab) inhibited TPO binding by 32 patients' sera by 82 +/- 14% (mean +/- SD), with a range from 51-100%. When each F(ab) was tested individually for its ability to compete for autoantibody binding to TPO, F(ab) TR1.8 was the most potent among the 32 sera. However, there was a wide spectrum of TPO binding inhibition when each serum was considered individually, thereby allowing an epitopic "fingerprint" to be drawn for the TPO autoantibodies in a patient's serum. There was a close association between the proportions of TPO autoantibodies to the TR1.8 and TR1.9 epitopes as well as between those to the SP1.4 and WR1.7 epitopes. These associations correspond to the previously described A and B epitopic domains in the TPO immunodominant region. No TPO epitope was observed to be associated with clinically apparent ophthalmopathy of Graves' disease, nor was there an association between TPO epitopes and patient age or sex. In summary, the present study on a large sample of sera with TPO autoantibodies indicates that by using TPO-specific F(ab) selected to cover all regions of the TPO immunodominant region, it is possible to obtain a TPO epitopic fingerprint for each serum. These data open the way to future studies directed at testing the hypothesis of disease-associated TPO epitope(s).

Autoantibodies↗
PubMed2006

Intersimple sequence repeats (ISSR) molecular fingerprinting markers for authenticating populations of Dendrobium officinale Kimura et Migo.

Intersimple sequence repeats (ISSR) molecular fingerprinting markers have been employed to authenticate eight populations of Dendrobium officinale using 10 primers selected from 76 ISSR primers. A total of 127 DNA fragments were amplified, of which 115 were polymorphic (90.5% of all bands). Sixteen specific authentication markers have been found. To enhance the efficiency of authentication, ISSR fingerprinting codes have been constructed using six polymorphic bands for authenticating D. officinale populations. Eight wild populations of D. officinale have been authenticated accurately using ISSR.

DNA Fingerprinting↗
PubMed1998

Evidence of genetic heterogeneity in a BALB/c mouse colony as determined by DNA fingerprinting.

A genetic monitoring of the BALB/c mouse foundation colony in our animal facility was carried out. The techniques of choice were skin grafting, coat colour test, flow cytometric analysis for H2 antigens (loci H2-D and H2-A), electrophoretic analysis of isoenzymes (loci Idh1, Pep3, Es3 and Mod1), PCR-amplified microsatellites (loci Igh-V, Ngfg, Plau, Crp, Igh, D16Mit5, D3Mit49 and D17Mit16) and DNA fingerprinting (multilocus probes 33.6, 33.15 and (CAC)5). No evidence of genetic contamination was found, ruling out the possibility of an outcross with AKR, the other albino strain maintained at the facility. Nevertheless, DNA fingerprint patterns revealed evidence of genetic heterogeneity in four out of nine lines of the nucleus colony, interpreted as minisatellite mutations favoured for a single line system with more than 40 generations of separation from the ancestral pair. These mice are mainly used in cancer and immunological research within the institute.

Animals↗
PubMed1995

DNA fingerprinting study on the intraspecific variation and the origin of Prunus yedoensis (Someiyoshino).

In order to investigate the intraspecific variation of Prunus yedoensis (Someiyoshino) and interspecific relationship among P. yedoensis, P. lannesiana (Oshimazakura) and P. pendula (Edohigan), DNA fingerprinting study was conducted by using two different kinds of probes, M13 repeat sequence and (GACA)4 synthetic oligonucleotide. In this study, 68 plants of P. yedoensis grown in 46 prefectures in Japan were investigated. All the P. yedoensis individuals investigated showed the completely same banding pattern, indicating their clonal origin from a single plant. On the other hand, each of P. lannesiana and P. pendula individuals investigated showed a unique banding pattern, suggesting a considerable amount of genetic variation in these two species. About 90% of bands in DNA fingerprints of P. yedoensis were detected in either P. lannesiana or P. pendula. This result supports the hypothesis that P. yedoensis is an interspecific hybrid between P. lannesiana and P. pendula. From those results, it is concluded that P. yedoensis was produced only once through hybridization between P. lannesiana and P. pendula, and that this particular hybrid plant has been spread vegetatively all over Japan.

Base Sequence↗
PubMed1995

DNA fingerprinting of animal genomes by CA-repeat primed polymerase chain reaction.

CA-repeat primed polymerase chain reaction (CAP-PCR), using degenerate primers which anneal at the ends of (CA)n sequences in eukaryotic genomes, was attempted to assess its potential to monitor the genomic polymorphisms in various animals. Three mammalian, three avian, one fish and one insect species were examined and all showed primer-specific DNA fingerprints by CAP-PCR. Polymorphic bands observed in a laboratory-bred vole family were segregated in Mendelian manner. The present CAP-PCR DNA fingerprinting therefore is a simple and useful method for examining genomic variations in most animals without prerequisite knowledge of DNA sequences.

Animals↗
PubMed1993

Clefts of the lip and palate in twins: use of DNA fingerprinting for zygosity determination.

The study of twins is a well-established method for evaluating the relative roles of heredity and environmental factors in the etiology of diseases. Conclusions depend on zygosity determination and on the classification of minor forms of diseases. This paper reports on ten (5 mono- and 5 dizygotic) out of thirteen twin pairs among 1039 patients with cleft lip and palate (n = 677) or cleft palate (n = 362). Zygosity was determined using "DNA fingerprinting" on blood samples in all 10 pairs and on cleft-associated tissue in one pair. Including minor forms of clefting, two of five pairs of monozygotic and two of five pairs of dizygotic twins of the same sex showed concordance. "DNA fingerprinting" should be established as a definitive method for zygosity determination, and the calculation of concordance rates should always include minor forms of diseases.

Adolescent↗
PubMed2000

DNA fingerprinting of Cryptosporidium parvum isolates using amplified fragment length polymorphism (AFLP).

The genetic variability of 10 Cryptosporidium parvum isolates of human and animal origin was investigated using amplified fragment length polymorphism (AFLP). Analysis of fluorescent dye-labeled amplified products was carried out using an ABI PRISMS 377 DNA sequencer and ABI PRISMS GeneScan software. One-hundred and twelve primer combinations were evaluated using a single C. parvum isolate. The patterns generated were highly reproducible. For subsequent study, a subset of 9 primer pairs that yielded 30-90 DNA fragments after the polymerase chain reaction, within the size range of 50-500 bp, was used to screen the 10 C. parvum isolates, including 7 bovine, 1 equine, and 2 of human origin. The animal isolates produced identical fingerprint patterns with every primer combination tested. Of the 2 human isolates tested, 1 of the isolates, passaged in calves, generated the same AFLP DNA banding patterns as the animal isolates, whereas the other isolate, obtained directly from human feces, produced unique patterns. Polymorphism, detected by comparison of the fingerprint patterns of the latter human isolate with the common pattern shared by all other isolates, ranged from 17 to 35% for the 9 primer pairs. The results show that AFLP is a useful method for differentiating C. parvum isolates into 2 distinct genotypes.

Animals↗
PubMed2002

A cryptic clonal line of the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) evidenced by induced gynogenesis, interspecific hybridization, microsatellite genotyping and multilocus DNA fingerprinting.

In Memanbetsu town, Hokkaido island, Japan, a high frequency of natural triploid loaches Misgurnus anguillicaudatus (7.4% on average) was detected by flow cytometry for relative DNA content. Among sympatric diploid females (n=6) from a single population, we found two unique females that laid unreduced diploid eggs. They gave normal diploid progeny even after induction of gynogenesis with genetically inert UV-irradiated sperm. When fertilized with normal loach sperm, some unreduced eggs developed into triploids, but the rest into diploids. Hybridization using goldfish Carassius auratus sperm gave both normal diploid loaches and inviable allotriploid hybrids possessing the diploid loach genome and the haploid goldfish genome. Microsatellite genotyping and DNA fingerprinting demonstrated that the diploid progeny developing from the unreduced eggs were genetically identical to the mother, while the triploids had some of the paternal DNA. These results indicate that the diploid eggs reproduced unisexually as a diploid clone and in other cases developed into triploids after accidental incorporation of sperm nucleus. The presence of at least one clonal line in this area was shown by the identical DNA fingerprint detected in five out of 17 diploid loaches examined.

Animals↗
PubMed2003

Subtracted restriction fingerprinting--a tool for bacterial genome typing.

Reproducible, discriminative, high-throughput methods are required for the identification of bacterial strains and isolates in a clinical environment. A new molecular typing method for bacteria was developed and tested on Salmonella and E. coli species. The technique is called subtracted restriction fingerprinting and is based on double restriction enzyme digestion of genomic DNA followed by end labeling. The "detection" enzyme produces TTAA overhangs that are filled in with digoxigenated nucleotides for subsequent detection, while the "subtraction" enzyme produces GCGC overhangs that are filled in with biotinylated nucleotides that permit the removal of this subset of fragments with either streptavidin-coated magnetic particles or AffiniTip streptavidin columns. The two restriction enzymes are selected to produce a fragment size profile suitable for a specific analytical system. In this demonstration of the principle of subtracted restriction fingerprinting, analysis of Salmonella enterica subsp. enterica serovar Dublin and E. coli on a 30-cm 1.2% agarose gel revealed up to 50 sharp evenly spaced bands, which were sufficient for the discrimination between various isolates and substrains. The restriction enzyme combinations suitable for the analysis of Salmonella and E. coli are presented. The method requires fewer enzymatic steps than amplified fragment length polymorphism, does not need the specialized DNA preparation essential for pulsed field gel electrophoresis, and has a higher reproducibility than PCR-based methods.

DNA Fingerprinting↗
PubMed2002

Assessment of genetic variability and relatedness among atypical Aeromonas salmonicida from marine fishes, using AFLP-fingerprinting.

Atypical strains of Aeromonas salmonicida are the causal agent of atypical furunculosis or ulcer disease in various fish species, including spotted wolffish Anarhichas minor, which is a promising species in the Norwegian fish-farming industry. Isolates of atypical A. salmonicida comprise a very heterogenous group showing large variety in biochemical, molecular and virulence characteristics. The genetic variability among atypical isolates from wolffish was characterised using amplified fragment length polymorphism analysis: AFLP-fingerprinting. Additional isolates from halibut Hippoglossus hippoglossus, turbot Scophthalmus maximus, cod Gadus morhua and several salmonid fishes were included for assessment of variability and relatedness among a total of 56 atypical isolates of A. salmonicida. They were compared to reference strains of A. salmonicida subspecies and to other Aeromonas species pathogenic in fishes. AFLP-fingerprints subjected to similarity analysis yielded a grouping of the isolates into several clusters, revealing genetic heterogeneity among the isolates. There seems to be a correlation between genetic similarity among isolates and the fish host. The Icelandic isolates, mainly from cod, formed a very homogeneous subcluster, which was closely related to the wolffish isolates. All atypical isolates from spotted and common wolffish grouped together in a large cluster and appear to be very homogeneous, even though they had been isolated over a period of 8 yr at different locations in Norway. On the other hand, most of the isolates from turbot and halibut grouped together into 2 different clusters, while the 9 atypical isolates from salmonids appeared in 4 different clusters. Thus, the atypical isolates of A. salmonicida from halibut, turbot and salmonid fishes seem to be more genetically diverse than those from wolffish and cod.

Aeromonas↗
PubMed1994

Genetic diversity among commercial chicken populations estimated from DNA fingerprints.

Blood samples were obtained from parental pure lines representing a large majority of commercial meat-type (broiler) and white egg layer lines presently available in the USA. From blood mixes of each line, DNA was extracted and a DNA fingerprint pattern characteristic of that line was produced. Additionally, DNA fingerprints representing wild jungle fowl and two randombred control populations were produced. Three analyses were conducted: 1) among broiler sire lines, jungle fowl, and one control line; 2) among broiler dam lines, jungle fowl, and one control line; and 3) among parental lines of white egg layers, jungle fowl, and the second control line. Bandsharing levels were calculated, providing an estimate of genetic diversity among lines. Conclusions were that, at present, broiler sire lines, broiler dam lines, and parental lines of white egg layers that make up the majority of commercial breeding populations available in the USA contain a considerable reservoir of genetic diversity.

Animals↗