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PubMed1995

Evaluation of DNA fingerprinting by PFGE as an epidemiologic tool for Salmonella infections.

To evaluate DNA fingerprinting as an epidemiologic tool, pulsed-field gel electrophoresis (PFGE) was performed on isolates of Salmonella, including S. typhimurium, S. thompson, and S. enteritidis. Chromosomal DNA was digested with the restriction endonucleases Bln I and Xba I. The patterns of S. thompson and S. typhimurium isolates from various sources were different from one another. There was no correlation between the phage type and the digestion pattern of S. enteritidis isolates. Some strains belonging to one phage type were distinguished by their PFGE pattern in this study. These results suggest that the Bln I and Xba I digestion patterns of chromosomal DNA are useful for epidemiological analysis of an outbreak of Salmonella infection or food poisoning.

DNA Fingerprinting↗
PubMed1992

Differences in DNA fingerprints of continuous leukemia-lymphoma cell lines from different sources.

The genetic stability of human cell lines in long-term culture has been tested by DNA fingerprinting a panel of 31 different continuous cell lines from patients with leukemias or lymphomas. Duplicates of the same cell line obtained from different sources, subclones of cell lines, and samples of cell lines at different passage levels were studied. In most cases the fingerprints of duplicates of the same cell line remained perfectly preserved even after long-time passaging. However, in five cases there were notable differences between individual fragments of corresponding fingerprints. We have found four cases of mislabeled and/or cross-contaminated cell lines so far. Taken together, our results indicate that DNA fingerprinting qualifies as a very reliable means of cell line identification which allows the detection of mislabelling or contamination and of genetic variation among subclones.

Base Sequence↗
PubMed1989

Probe walking: development of novel probes for DNA fingerprinting.

The tandem repeat of a 28-base-pair (bp) sequence downstream of the human c-Ha-ras-1 oncogene was studied as a probe for DNA fingerprinting. Multiple hypervariable patterns were observed by Southern hybridization at low stringency. The patterns were specific to individuals, indicating the availability of the 28-bp repeat as a probe for DNA fingerprinting. Moreover, we cloned the tandem repeat of a 33-bp sequence, which cross-hybridized with the 28-bp repeat. This 33-bp repeat detected another set of hypervariable restriction fragments by Southern hybridization at the same stringency. These results suggests that 'probe walking' can be employed to develop novel probes that provide different DNA fingerprints.

Blotting, Southern↗
PubMed2002

Contact tracing using DNA fingerprinting in an asylum seeker with pulmonary tuberculosis.

BACKGROUND: The diagnosis of tuberculosis in asylum seekers is followed by contact tracing, which is routinely performed by the Municipal Health Service (MHS). We investigated cases of tuberculosis whose symptoms became apparent after closure of regular contact tracing. METHODS: Analysis of data from the DNA Fingerprinting Surveillance Project on all Mycobacterium tuberculosis isolates and contact tracing instances. RESULTS: Four additional cases of tuberculosis were detected, caused by bacteria of identical DNA fingerprints. No further contacts with a bacteriologically confirmed form of tuberculosis were found around these four new patients. CONCLUSION: DNA fingerprinting contributed to tracing instances of late manifestations of tuberculosis transmission.

Contact Tracing↗
PubMed1994

DNA fingerprinting in Falconidae.

This paper describes the use of the oligonucleotide probe (GTG)5 to reveal high polymorphic DNA regions in falcons (Falco peregrinus, F. rusticolus, F. cherrug and their interspecies hybrids). Ten microliters of the blood samples were immobilized, lysed and digested in low-melting point agarose. Oligonucleotide probe (GTG)5 gave rise to the great number of different fragments. Some of them were genus specific, another female specific and approx. 5-10% of the fragments were individual specific. Restriction endonucleases with 4 bp recognition sequences were preferred (Hinf I, Hae III and Msp I). After the use of such enzymes the DNA fingerprints were individual specific and allowed us to confirm known relations among individual birds. The results indicate, that DNA fingerprinting with oligonucleotide (GTG)5 as a probe could be a powerful method for differentiating among closely related falcon birds.

Animals↗
PubMedDate not supplied

Spatial heterogeneity of Escherichia coli DNA fingerprints isolated from cellulitis lesions in chickens.

Avian cellulitis in broiler chickens is characterized by subcutaneous lesions that result in economic losses because of the partial or complete condemnation of the carcasses at processing. Escherichia coli is the primary causative agent of this condition. Previous research with a biotyping system found that the E. coli of cellulitis origin were unique to each ranch, suggesting that these E. coli were endemic within the ranch environment. The objective of our study was to analyze the genetic variability of E. coli isolates associated with cellulitis. We analyzed the genetic relatedness of the isolates in relation to the houses, ranches, and complexes in which the broilers were grown. This analysis enabled us to assess the spatial heterogeneity, or genetic diversity on a spatial scale, of the isolates. Forty-nine broilers with cellulitis lesions were necropsied. These broilers came from six houses on four ranches on three complexes that had been placed with chicks from the same hatchery within a 2-wk period. Isolates of E. coli from the lesions were DNA fingerprinted by pulsed-field gel electrophoresis. Relatedness among isolates was determined with the Dice coefficient and an unweighted pair group method with average linkages cluster analysis. The complexes possessed isolates with a variety of DNA fingerprints, yet each complex appeared to have isolates with a unique set of DNA fingerprints. Isolates from the same complex tended to form clusters with similarity coefficients greater than 90%. Isolates from different complexes were genetically distinct. This heterogeneity at the level of the complex suggests that isolates were not disseminated from a source common to the complexes. The spatial heterogeneity of the E. coli isolates in this study implies an endemic population of cellulitis-associated E. coli exists in the broiler house environment.

Animals↗
PubMed2006

Use of short tandem repeats for DNA fingerprinting to rapidly diagnose graft-versus-host disease in solid organ transplant patients.

BACKGROUND: Graft-versus-host disease (GVHD) is a rare complication following liver transplantation and carries a poor prognosis with mortality approaching 90-95%. Diagnosis of GVHD is often delayed due to early symptoms mimicking more common, entities such as drug reactions and viral syndromes. To date, definitive diagnosis has been difficult and has relied on a constellation of clinical and histopathologic variables. We present the use of short tandem repeat DNA "fingerprinting" technology as a method of early, definitive diagnosis of GVHD in patients after liver transplantation. METHODS: A patient status-postorthotopic cadaveric-liver transplant, with an uncomplicated immediate posttransplant course, presented 4 weeks after transplant with fever, diarrhea, and maculopapular rash on her palms, soles, and back. The patient's condition worsened despite empiric treatment for an infectious etiology. Skin and rectal biopsies were suspicious for GVHD. RESULTS: DNA was isolated from the skin and rectal biopsies as well as from a donor lymph node. PCR amplification was done for nine highly polymorphic short tandem repeats for each specimen and a unique DNA "fingerprint" was obtained from each. DNA from skin and rectum demonstrated mixed chimerism with both donor and recipient alleles detected. Thorough analysis confirmed GVHD. CONCLUSION: Short tandem repeats for DNA fingerprinting represents an efficient and reproducible method for the definitive diagnosis of GVHD after liver transplantation. Rapid detection of GVHD using this technology, coupled with early initiation of therapy, may lead to improved survival for patients with GVHD after solid organ transplant.

DNA Fingerprinting↗
PubMed1987

DNA fingerprinting of Streptococcus zooepidemicus (Lancefield group C) as an aid to epidemiological study.

A collection of Streptococcus zooepidemicus strains from human and animal infections was examined for DNA banding patterns after nuclease digestion and agarose gel electrophoresis. The large variety of DNA fingerprints found revealed the complexity of the species but showed that isolates from clusters of outbreaks had identical prints. The results confirmed the specificity of bacteriocin and bacteriophage typing of S. zooepidemicus; the technique also gave useful profiles on untypable strains. Strains with common bacteriocin and biotyping patterns from sporadic infections could be differentiated by their DNA fingerprints. In several outbreaks and incidents, more than one strain of S. zooepidemicus were encountered, and the importance of carefully interpreting typing data is stressed. Chromosomal DNA fingerprinting is a very efficient technique for demonstrating differences between strains of S. zooepidemicus, and its use is recommended for future epidemiological studies of this infectious agent.

Animals↗
PubMed2004

Multilocus sequence typing is a reliable alternative method to DNA fingerprinting for discriminating among strains of Candida albicans.

Multilocus sequence typing (MLST) has emerged as a powerful new DNA-typing tool for the evaluation of intraspecies genetic relatedness. This method relies on DNA sequence analysis of nucleotide polymorphisms in housekeeping genes and has shown a high degree of intraspecies discriminatory power for bacterial and fungal pathogens. However, the results of the MLST scheme for Candida albicans have heretofore never been formally compared to those of other established typing techniques. To assess the value of MLST relative to those of other DNA fingerprinting tools for discriminating among strains of C. albicans, we applied it to a previously well-characterized set of 29 C. albicans isolates evaluated by the random amplified polymorphic DNA (RAPD), multilocus enzyme electrophoresis (MLEE), and Ca3 Southern hybridization probe techniques. MLST identified three clusters of genetically related isolates, with 82.3% direct concordance with MLEE, 82.7% with RAPD analysis, and 86.2% with the Ca3 Southern hybridization technique. When MLST was applied to a subset of 22 isolates of unrelated origins, it identified 21 independent diploid sequence types (DSTs), resulting in a discriminatory power of 99.6%. These DSTs were 96.9, 99.6, and 99.6% concordant with the genotypes identified by RAPD analysis, MLEE, and Ca3 Southern hybridization, respectively. These results demonstrate that MLST is a highly effective technique that performs at least comparably to other established DNA fingerprinting techniques.

Candida albicans↗
PubMed1991

Identification of markers associated with quantitative trait loci in chickens by DNA fingerprinting.

Three approaches for identifying VNTR alleles associated with quantitative traits in chickens are described. One approach is based on the comparison of well-defined selected and non-selected control strains. The second approach is based on analyzing chickens within a breeding population ranked according to specific traits and the third approach involves segregation analysis. In this latter approach a large number of offspring of a single male segregating for a quantitative trait are produced and tested for trait association of the male DNA fingerprinting bands. In all cases pooled DNA samples of birds, rather than individual samples, are analyzed and band intensity is assumed to reflect the relative frequency of an allele. Examples from the literature and from our laboratory indicate that these methods permit the identification of DNA fingerprinting bands associated with quantitative traits. After developing locus-specific probes for these bands it should ultimately be possible to detect and map quantitative trait loci.

Animals↗
PubMed1990

Use of deoxyribonucleic acid (DNA) fingerprints for identity determination: comparison with traditional paternity testing methods--Part I.

A study involving comparison of the deoxyribonucleic acid (DNA) finger-printing test with traditional methods used for paternity testing is presented. Samples from 191 cases were tested for a series of blood group and polymorphic protein markers. DNA "fingerprints" were then obtained for all samples using the multilocus probes 33.6 and 33.15. The results of DNA fingerprinting correlated well with those of traditional methods and proved to be informative in cases where traditional methods yielded inconclusive or insufficient results.

Autoradiography↗
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↗
PubMed1986

DNA "fingerprints" and segregation analysis of multiple markers in human pedigrees.

Tandem-repetitive DNA hybridization probes based on a putative human recombination signal detect multiple polymorphic minisatellite fragments in human DNA. The genetic complexity of the resulting individual-specific DNA "fingerprints" was investigated by studying a large sibship affected by neurofibromatosis and a more extensive pedigree segregating for two different hemoglobinopathies. The segregation of up to 41 different heterozygous DNA fragments from each parent could be analyzed in a single sibship, using two different repeat probes. Most of these variable DNA fragments could not be paired as alleles, to an extent which suggests that the DNA fingerprints are together derived from approximately 60 heterozygous loci (approximately 120 variable fragments), only a proportion of which can be scored in a given individual. Two or three of the DNA fragments detected by one probe showed tight linkage and may be derived from long minisatellite(s) that are cleaved to produce more than one polymorphic DNA fragment. Excluding allelic and linked DNA fragments, almost all remaining scorable fragments segregated independently, allowing up to 34 unlinked loci to be examined simultaneously. These loci are scattered over most or all of the human autosomes. Minisatellite probes are therefore suitable for rapid marker generation and can be applied to linkage analysis in human pedigrees.

Alleles↗
PubMed1991

Routine applications of DNA fingerprinting with the oligonucleotide probe (CAC)5/(GTG)5.

The use of DNA fingerprinting with synthetic oligonucleotides is illustrated for practical applications familiar in clinical diagnostics: pre- and postnatal zygosity determination and the monitoring of bone marrow transplantation. A simple method for non-radioactive detection is described which may be interesting for many diagnostic laboratories.

Bone Marrow Transplantation↗
PubMed1994

Forensic applications of DNA fingerprinting.

In many ways, DNA profiling technology is very similar to the conventional techniques used for forensic identification. As with, for example, blood grouping techniques, the molecular characteristics of the scene of crime sample may be determined and compared with those of the scene of reference samples from suspects and victim. If the molecular characteristics of the crime sample and the suspect are different, then they cannot be from the same person, whereas if they match, then the possibility remains that they may be from a single source. Similar material, such as blood or semen stains, may be used for both biochemical and genetic tests, and the main applications of identification and relationship testing are shared by both techniques. At this point, the similarity ends; DNA profiling has the following characteristics: 1. It is more sensitive, being able to generate sound data from only a tiny amount of even partially degraded biological material. 2. It is capable of resolving mixtures of semen or tissue from up to several individuals. 3. It has a far greater power of discrimination between individuals--sometimes up to 1 millionfold higher than conventional techniques. 4. It provides considerably more information on the nature of relationships, particularly in cases of incest. As such, the technique represents a quantum leap in forensic identification and relationship testing.

Accidents↗
PubMed1990

DNA fingerprinting of the intestinal parasite Giardia duodenalis with the M13 phage genome.

A DNA fingerprint procedure has been established for the intestinal parasite, Giardia duodenalis. This permits the identification of individual strains from both human and animal sources. Analysis of strain movement, resurgence and variation is now possible. The fingerprint probe is based on the tandem repetitive sequence found in bacteriophage M13 which hybridizes to a set of hypervariable polymorphic minisatellite sequences found in higher eukaryotes. This probe recognizes a weakly homologous set of hypervariable regions in the Giardia genome to provide a DNA fingerprint comparable to those seen in higher eukaryotes.

Animals↗
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↗
PubMed2004

DNA fingerprints provide a patient-specific breast cancer marker.

BACKGROUND: Detection of systemic breast cancer recurrence is limited by lack of universally expressed tumor cell markers. We hypothesized that a test that detects genetic alterations specific to breast cancer cells of an individual patient would provide a superior cancer marker. METHODS: DNA was extracted from blood, primary tumor, and axillary lymph nodes of 33 breast cancer patients and normal breast tissue of 12 control patients. A patient's genome was scanned by PCR amplification between Alu sequences. A DNA fingerprint of approximately 17-40 bands was produced for comparison between normal blood and sampled tissues. RESULTS: There were 7 stage I, 18 stage II, 7 stage III, and 1 stage IV breast cancer cases; 33 of 33 cancer cases showed DNA fingerprint differences between blood and primary tumor (P <.0001). This test predicted 100% of positive nodes. No false-negatives occurred, and in two cases malignancy was detected in histologically negative nodes. Three of the 12 controls showed a single similar band change. CONCLUSIONS: DNA fingerprinting is a method for detecting and characterizing genetic alterations specific to an individual patient's primary tumor in 100% of cases tested. These specific changes were also identified in 100% of positive nodes, proving the capacity of the test to detect metastases.

Alu Elements↗