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PubMed1995

Fluorescence-based DNA fingerprinting elucidates nosocomial transmission of phenotypically variable Pseudomonas aeruginosa in intensive care units.

DNA fingerprinting based on automated laser fluorescence analysis of randomly amplified polymorphic DNA (RAPD-ALFA) is a rapid and convenient technique for detecting clonal relatedness of bacterial isolates of nosocomial concern. During an outbreak of Pseudomonas aeruginosa among five patients in a medical intensive care unit, transmission was not suspected because of the phenotypic variability of the initial isolates. However, DNA fingerprinting by RAPD-ALFA and macrorestriction analysis identified a single genotype (strain A) for isolates from three patients and another genotype (strain B) for isolates from the remaining two patients. Strain A isolates displayed three phenotypes defined by different antibiotypes and distinct colony appearance. Retrospective analysis of DNA fingerprints demonstrated that strain A had been transmitted to the index patient one year previously in a different intensive care unit. The study demonstrates that genetic typing approaches are warranted should epidemiological relatedness be identified between phenotypically variant pathogens. Automated laser fluorescence analysis of PCR fingerprints may facilitate routine screening of bacterial isolates for in-house epidemiological surveillance. Antibiograms are an unsuitable approach for the typing of Pseudomonas aeruginosa.

Adult↗
PubMed2003

DNA fingerprinting of Lactobacillus crispatus strain CTV-05 by repetitive element sequence-based PCR analysis in a pilot study of vaginal colonization.

Lactobacillus crispatus is one of the predominant hydrogen peroxide (H(2)O(2))-producing species found in the vagina and is under development as a probiotic for the treatment of bacterial vaginosis. In this study, we assessed whether DNA fingerprinting by repetitive element sequence-based PCR (rep-PCR) can be used to distinguish the capsule strain of L. crispatus (CTV-05) from other endogenous strains as well as other species of vaginal lactobacilli. Vaginal and rectal lactobacilli were identified to the species level by using whole-chromosome probe DNA hybridization. The DNAs from L. crispatus, L. jensenii, L. gasseri, and an as-yet-unnamed H(2)O(2)-negative Lactobacillus species designated 1086V were subjected to rep-PCR. The results of gel electrophoresis and ethidium bromide staining of the DNA fingerprints obtained were compared. L. crispatus CTV-05 had a unique DNA fingerprint compared to all other lactobacilli. DNA fingerprints for 27 production lots of L. crispatus sampled from 1994 through 2001 were identical to that of the original strain isolated in 1993, suggesting strain stability. In a pilot study of nine women, this DNA fingerprinting method distinguished CTV-05 from other endogenous vaginal lactobacilli prior to and after vaginal capsule use. rep-PCR DNA fingerprinting is useful for strain typing and for evaluating longitudinal loss or acquisition of vaginal lactobacilli used as probiotics.

Bacterial Typing Techniques↗
PubMed1996

[The study of DNA fingerprint of hydatidiform moles and the clinical outcome].

OBJECTIVE: To study the genetic origin of hydatidiform moles (HM) and the clinical outcome. METHODS: 41 cases of hydatidiform mole were collected mainly from Beijing area and studied for genetic components by DNA fingerprints. The diagnosis of persistent gestational trophoblastic disease (PTD) was made if blood hCG remained higher than normal 8 weeks after mole evacuation. RESULTS: Among 41 HM samples, 32 produced identifiable DNA fingerprints. DNA from only paternal origin was found in 21, in which 6 were PTD, DNA from both parents in 11, none of which developed PTD. CONCLUSIONS: DNA from only paternal origin was more frequently found than from both parents in HM, and there was a higher risk of PTD in the former group than in the latter.

DNA Fingerprinting↗
PubMed1991

[The application of alpha-globin-3'HVR probe for DNA fingerprinting in forensic science].

Using alpha-globin-3'HVR as the molecular hybridization probe, A clear and readable DNA fingerprint has been obtained. Based on the DNA fingerprint analysis of 200 unrelated individuals living in Beijing area, the probability of chance association of two random individuals was 4.0 x 10(-12). The study of 32 related individuals of 6 families showed that the inheritance of DNA fingerprint bands conformed to the Mendelian law. The method is reliable for the individual identification and paternity test. It provides a scientific basis for solving cases such as rape, homicide etc. and it has been used in our actual case work.

DNA Fingerprinting↗
PubMed2001

Helicobacter pylori detection in Chinese subjects: a comparison of two common DNA fingerprinting methods.

This study aims to demonstrate DNA diversity in Helicobacter pylori strains obtained from patients with peptic ulcer disease and compare the results from two DNA fingerprinting techniques. H. pylori strains (n = 42), collected from June 1996 to August 1999, were cultured from storage at -80 degrees C. DNA diversity was determined by the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis, and random amplified polymorphic DNA (RAPD)-PCR. Isolates showed a significant DNA sequence diversity by both methods. RAPD-PCR demonstrated 33 distinct strain-specific band patterns, whereas PCR-RFLP demonstrated six distinct restriction patterns. PCR-RFLP identified four of the 42 strains as mixed growth, compared with RAPD-PCR which did not reveal any co-colonisation. Diversity among H. pylori clinical isolates was demonstrated distinctly by both methods; however, RAPD-PCR showed greater discriminatory power in distinguishing between isolates.

Bacterial Typing Techniques↗
PubMed2002

DNA fingerprinting of Mycobacterium tuberculosis isolates from epidemiologically linked case pairs.

DNA fingerprinting was used to evaluate epidemiologically linked case pairs found during routine tuberculosis (TB) contact investigations in seven sentinel sites from 1996 to 2000. Transmission was confirmed when the DNA fingerprints of source and secondary cases matched. Of 538 case pairs identified, 156 (29%) did not have matching fingerprints. Case pairs from the same household were no more likely to have confirmed transmission than those linked elsewhere. Case pairs with unconfirmed transmission were more likely to include a smear-negative source case (odds ratio [OR] 2.0) or a foreign-born secondary case (OR 3.4) and less likely to include a secondary case <15 years old (OR 0.3). Our study suggests that contact investigations should focus not only on the household but also on all settings frequented by an index case. Foreign-born persons with TB may have been infected previously in high-prevalence countries; screening and preventive measures recommended by the Institute of Medicine could prevent TB reactivation in these cases.

Adolescent↗
PubMed1995

DNA fingerprint analysis in acute leukemias.

Restriction fragment length polymorphism (RFLP) analysis by Southern blotting or direct in-gel hybridization is a routine procedure in any genetic laboratory. Minisatellites and simple repeat probes for RFLP analysis have proved to be highly informative genetic markers, depending on their degree of homology and index of heterozygosity. Several of these probes have considerable individualization potential, thus yielding 'fingerprint' pattern. In the setting of acute leukemia DNA fingerprint (DNA-F) analysis is able to provide considerable information concerning the genetic instability of the leukemic clone. DNA-F is capable of detecting randomly occurring genetic alterations of unknown localization and to identify new hotspots of malignant transformation. As DNA-F analysis is not likely to be hampered by the effects of chemotherapy or DNA methylation, altered fingerprints may be regarded as characteristic of the leukemic clone. With the introduction of polymerase chain reaction (PCR) and increasing sensitivity, DNA-F analysis is likely to be of significant importance in monitoring minimal residual disease in human leukemia.

DNA Fingerprinting↗
PubMed1991

Increased band sharing in DNA fingerprints of an inbred human population.

We have compared band sharing between the DNA fingerprints of members of an inbred human population with band sharing between members of an outbred population. It had not previously been determined whether the high rate of mutation at minisatellite loci is sufficient to prevent an increase in band sharing in moderately inbred populations. We have found that there is an increase in band sharing in the 2-kb to 9-kb size range, but not in the greater than 9-kb size range, in the inbred population. The difference was consistently observed using four different multi-locus probes, viz. 33.6, 33.15, (CAC)5 and M13. Thus, we have demonstrated that moderate but prolonged inbreeding can lead to increased similarity in human DNA fingerprints. This should be considered when analysing DNA fingerprints in forensic or paternity cases involving members of an inbred community.

Base Sequence↗
PubMed1995

Identification and minisatellite linkage analysis of SMXA recombinant inbred strains of mice by DNA fingerprinting.

SMXA recombinant inbred (RI) strains of mice were produced by systematic inbreeding from the F2 generation of a cross between two progenitor inbred strains, A/J and SM/J, which differ considerably with respect to many characteristics, and consists of 28 inbred strains. In this study, we investigated the applicability of DNA fingerprinting with M13 phage DNA to the identification of these closely related strains. DNA fingerprints of the SMXA RI strains and their progenitors, SM/J and A/J, showed strain-specific patterns, with the same banding patterns within each strain. Linkage analysis by using strain distribution patterns of minisatellite loci with 108 genetic markers containing microsatellites, biochemical and immunological marker genes allowed 23 minisatellite loci to be assigned to 11 chromosomes. The results suggested that DNA fingerprinting with M13 phage DNA is applicable not only for strain identification but also for genetic monitoring of RI strains on almost all chromosomes.

Animals↗
PubMed1993

[Paternity test by DNA fingerprinting in a sexual assault].

We have applied the method of DNA fingerprinting to resolve a paternity case. DNA samples were extracted from the blood of mother, child (4 months old fetus) and alleged father, digested with the restriction endonuclease Hinf I and Hae III, size separated by agarose gel electrophoresis, and hybridized with the multi-locus minisatellite probe B.E.S.T.-MZ1.3 digoxigenin. DNA fingerprinting patterns in the child and alleged father indicated possibly paternity. Following extraction of DNA from cord blood (infant of 26 to 39 week's gestation), the quantity of DNA isolated was determined on a spectrophotometer at 260 nm and its integrity by electrophoresis in agarose gels. We found that high-molecular-weight DNA could be recovered in large quantities from cord blood as well as from adult blood.

DNA↗
PubMed1996

DNA fingerprinting data and the problem of non-independence among pairwise comparisons.

Multilocus DNA fingerprinting is commonly used to assess genetic similarity within and between geographically disjunct populations. Typically, the proportion of DNA fingerprinting bands shared between two individuals (SXY) is calculated for all possible pairwise comparisons and the resulting data analysed parametrically to test differences in mean band-sharing among groups. The degree to which covariation among interdependent SXY values (S(ab)-Sbc) biases the analyses is often unknown. Here, we assess the extent of covariation in four DNA fingerprinting studies and evaluate the effectiveness of two corrective procedures, a permutation test and a subsampling routine using only independent pairwise comparisons drawn without replacement from the overall data. Covariation among interdependent SXY values was significantly greater than zero in every data set examined, including those from a bee, a rodent, and two passerine birds. Permutation tests did not correct for interdependence and yielded significance values nearly identical to those derived from uncorrected parametric procedures. In contrast, the subsampling procedure yielded corrected estimates of the standard error that were two to four times larger than those derived parametrically. As a result, comparisons that were significant using parametric tests were either non-significant or only marginally significant with the subsampling routine. We conclude that interdependence among SXY values poses a substantial obstacle to hypothesis testing that must be addressed in future studies.

Analysis of Variance↗
PubMed1992

Somatic mutation during metastasis of a mouse fibrosarcoma line detected by DNA fingerprint analysis.

Metastatic nodules were examined by DNA fingerprint analysis. The probes used, Pc-1 and Pc-2, detect mutations as shifts in bands of the minisatellite loci which are dispersed among chromosomes. Four clonal lines of a fibrosarcoma from an F1 mouse (C57BL/Ka x C3H/He) were selected for various metastatic potentials upon inoculation into syngeneic mice. These four lines exhibited many extra bands resulting from recombination and/or DNA slippage, indicating accumulation of mutations during the successive passages in mice. One of the four, a 505 cell line which had been passaged extensively in vitro and consisted of a heterogenous population, was inoculated into thirteen syngeneic mice, and gave rise to six lung metastatic nodules in two mice. All the nodules showed band-patterns distinct from one another, although nodules within a given mouse tended to show similar patterns. When a genetically tagged 505-05-01 clone was analyzed, three of nine metastatic nodules obtained also revealed new bands. These results strongly suggest that somatic mutations occur at a high frequency during metastasis, providing direct evidence of genetic instability of the tumor cells.

Animals↗
PubMed2001

Identification of genomic imbalances in gastric MALT lymphoma using arbitrarily primed PCR DNA fingerprinting.

Arbitrarily primed PCR (AP-PCR) is a unique method to identify the cancer cell specific losses and gains of chromosomal regions by targeting specific genes or chromosomal segments. In the present study, introducing the AP-PCR technique with a single primer, we have ascertained the gains and losses of DNA fingerprints in 15 MALT lymphoma samples. Out of 15 prominent DNA fingerprints, the signal intensity of two fingerprints, labeled bands G and I, were significantly lower in 40 and 50% of tumors as compared to adjacent normal DNA fingerprints, respectively. Similarly, gains of signal intensity of DNA fingerprints (bands A and C) were detected in 13% of tumor samples studied. Variations in signal intensities were also found in other bands within a few samples. Although, the functional importance of these bands is unknown, this study indicates that the AP-PCR generated under or over amplified DNA fingerprints may participate during the progression of MALT lymphoma in human stomach. Moreover, these studies also suggest that the AP-PCR technique, with different primers, can be utilized for the determination of new chromosomal segments in MALT lymphoma samples that can be used for the identification of these diseases.

Biopsy↗
PubMed1994

Use of DNA fingerprinting for accurate typing of Actinobacillus pleuropneumoniae.

DNA fingerprinting was tested as a method for detailed differentiation of 23 strains of the causal agent of porcine pleuropneumonia--Actinobacillus pleuropneumoniae. The set consisted of twelve reference strains, each representing one serotype, and eleven field strains belonging to serotype 9 which occurs most frequently in the Czech Republic. Nine of the reference strains could be differentiated from each other and from serotypes 1, 9 and 11, but a very close relatedness was demonstrated among the latter three by repeated examination. Four DNA types were identified among the twelve serotype 9 strains. The findings are discussed within the context of the production and efficiency of industrial and autogenous vaccines.

Actinobacillus pleuropneumoniae↗
PubMed1993

[Application of DNA fingerprinting to investigation of genetic relationships between laboratory rabbit strains].

It is well known that laboratory rabbits are not controlled genetically like laboratory mice and rats. In order to test the usefulness of DNA fingerprinting in investigation of genetic uniformity of the laboratory rabbits strains and their relationships, we applied DNA fingerprinting using bacteriophage M13 probe to five strains (2 inbreds (JWY-NIBS and DuY-NIBS) and 3 outbreds (JW-NIBS, Icl:JW and WHHL)). DNA fingerprints of 2 inbred strains showed the same banding patterns within each strain but the strain-specific patterns. Although there were no rabbits showing the same banding patterns in 3 outbred strains, average percent differences (APD) were 13.7 to 18.6. A dendrogram based on APD of DNA fingerprints was constructed by 2 large clusters, JW group and DuY. The dendrogram was essentially similar to that based on rabbit mandible measurements. These results suggest that DNA fingerprinting is available not only for the genetic monitoring of the laboratory rabbit strains but also for the investigation of their genetic relationships.

Animals↗
PubMed1995

Leishmania (Viannia) braziliensis: genetic relationships between strains isolated from different areas of Brazil as revealed by DNA fingerprinting and RAPD.

Leishmania (Viannia) braziliensis isolates from two different geographic areas in Brazil were studied by DNA fingerprinting with the 33.15 multilocal probe and PCR with arbitrary primers (random amplification of polymorphic DNA-RAPD). The genetic distance of strains was measured by band sharing. The results showed that the strains isolated in Minas Gerais, southeastern Brazil, are very different from those isolated in Pará, northern Brazil. Strains from Minas Gerais constituted a relatively homogeneous group, presenting DNA fingerprint patterns with 76% of shared bands and RAPD profiles with 93% of shared bands. In contrast, strains from Pará showed higher genetic variability, with only 17 and 45% of shared bands in DNA fingerprint and RAPD patterns, respectively. This study suggests that genetic differences between L. braziliensis from both areas might have an epidemiological significance.

Animals↗
PubMed2000

Increase of genetic variation over time in a recently founded population of great reed warblers (Acrocephalus arundinaceus) revealed by microsatellites and DNA fingerprinting.

Genetic similarity within pairs of individuals was examined using both 10 polymorphic microsatellite loci and multi-locus DNA fingerprinting profiles in a semi-isolated population of great reed warblers at Lake Kvismaren, south Central Sweden, in 1987-1993. The population was founded by a few individuals in 1978, followed by a gradual increase in numbers until 1988, since when the population has remained relatively stable with about 60 breeding birds. We have previously found that high genetic similarity between pair-mates in the population during the early part of the study period reduced egg hatching success, and hence reproductive success. The measures of pairwise genetic similarity, microsatellite allele sharing and DNA fingerprinting band sharing, were highly correlated with pedigree-based relatedness. Both microsatellite and DNA fingerprinting similarities between pair-mates declined significantly over the study period, and the pattern was most pronounced in the DNA fingerprinting data. Analyses restricted to the microsatellite data showed that the average annual microsatellite similarity between pairwise combinations of individuals, as well as individual homozygosity in males, declined significantly over the study period, and that several immigrants carrying novel alleles entered the population during the study. Hence, the temporal decline in genetic similarity of mates in the population is probably a consequence of increased immigration, facilitated by the recent expansion of the species in the region. These results suggest that the population has now recovered genetically, or is in the process of recovering, from a recent founder event.

Animals↗