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PubMed2000

RAPD library fingerprinting of bacterial and human DNA: applications in mutation detection.

Random amplified polymorphic DNA (RAPD) fingerprinting is a modification of the polymerase chain reaction (PCR), which utilises a single, arbitrarily-chosen primer to amplify a number of fragments from a given template DNA to generate a discrete "fingerprint" when resolved by gel electrophoresis. Alterations by as little as a single base in the primer sequence lead to marked alterations in the fingerprints generated with a given template under optimised conditions. By inference, single base alterations in the genomic template DNA may also lead to changes in the RAPD fingerprints. We have examined this potential application to detect mutations in bacteria and cultured human cells. We have utilised Escherichia coli and human lymphoblastoid cell lines exposed to UV radiation, selected for by cellular mutation assays, and compared RAPD fingerprints of mutant and non-mutant samples. Polymorphisms became evident as the presence and/or absence of DNA fragments between the two samples. A dose-dependent increase in the number of polymorphic bands was seen with UV irradiation of E. coli. To a lesser degree, polymorphisms were also evident for human lymphoblastoid DNA. The possible underlying mechanisms for these alterations in fingerprints as a result of mutation(s) in the primer binding site(s) are discussed. The ability of RAPD fingerprinting to detect a mutant in a population of non-mutants is evaluated, and whilst the lack of sensitivity inherent in the technique precludes its use as a mutation screening assay, its potential for generation of mutant and non-mutant DNA probes for other mutation detection techniques may prove to be of great merit. Teratogenesis Carcinog. Mutagen. 20:49-63, 2000.

Cells, Cultured↗
PubMed1996

Chromosomal assignment of human DNA fingerprint sequences by simultaneous hybridization to arbitrarily primed PCR products from human/rodent monochromosome cell hybrids.

We have developed a technique for the simultaneous chromosomal assignment of multiple human DNA sequences from DNA fingerprints obtained by the arbitrarily primed polymerase chain reaction (AP-PCR). Radioactively labeled human AP-PCR products are hybridized to DNA fingerprints generated with the same arbitrary primer from human/rodent monochromosome cell hybrids after electroblotting to a nylon membrane. Human-specific hybridization bands in the human/rodent fingerprints unambiguously determine their chromosome of origin. We named this method simultaneous hybridization of arbitrarily primed PCR DNA fingerprinting products (SHARP). Using this approach, we determined the chromosomal origins of most major bands of human AP-PCR fingerprints obtained with two arbitrary primers. Altogether, the chromosomal localization of near 50 DNA fragments, comprehensive of all human chromosomes except chromosomes 21 and Y, was achieved in this simple manner. Chromosome assignment of fingerprint bands is essential for molecular karyotyping of cancer by AP-PCR DNA fingerprinting. The SHARP method provides a convenient and powerful tool for this purpose.

Animals↗
PubMed1995

Nucleic acid fingerprinting by PCR-based methods: applications to problems in aging and mutagenesis.

There are many methods of inference in common use in biology that are based on population sampling, including such diverse areas as sampling organisms to determine the population structure of an ecosystem, sampling a set of DNA sequences to infer evolutionary history, sampling genetic loci to build a genetic map, sampling differentially expressed genes to find phenotypic markers, and many others. Recently developed PCR-based methods for nucleic acid fingerprinting can be used as sampling tools with general applicability in molecular biology, evolution and genetics. These methods include arbitrarily primed PCR (AP-PCR; Welsh and McClelland, 1990) and random amplified polymorphic DNA (RAPD; Williams et al., 1990) for the fingerprinting of DNA, and RNA arbitrarily primed PCR (RAP-PCR; Welsh et al., 1992a) and differential display (DD; Liang and Pardee, 1992) for the fingerprinting of RNA. Novel ways of looking at genetic control are facilitated by the high data-acquisition capabilities of the fingerprinting methods. In this article, we review some of the applications of DNA fingerprinting to the study of mutagenesis, and of RNA fingerprinting to the study of normal and abnormal signal transduction. We propose that these fingerprinting approaches may also have applications in the study of senescence and aging.

Aging↗
PubMed1994

Population dynamics of DNA fingerprint patterns within and between populations.

DNA fingerprint is a pattern of a variable number of bands (DNA fragments) with different sizes on a Southern gel for each individual, generated by one or many VNTR loci. Genetic divergence between individuals within and between populations can be studied in terms of number of shared bands between individuals. Using a population genetic model we show that the expectations of measures of genetic distance between populations based on band sharing data from DNA fingerprint patterns are functions of composite parameters M = 4Nv, and time of divergence (t) between populations, where N is the effective size of the populations, and v, the mutation rate. The expected genetic distance remains linear with time of divergence at least up to N generations as long as the average heterozygosity at the DNA fingerprint loci remains at or below 90%. Neither incomplete knowledge of the allele frequencies at each locus, nor the unknown number of loci underlying DNA fingerprint pattern, compromise these evolutionary dynamics of DNA fingerprint patterns. Applications of this theory to data on three human populations, and review of literature indicate that co-migration of alleles, and the presence of syntenic loci underlying the fingerprint pattern have little impact of the reliability of evolutionary conclusions from DNA fingerprint studies.

DNA Fingerprinting↗
PubMed2001

Choice of methodology for assessing genetic impacts of environmental stressors: polymorphism and reproducibility of RAPD and AFLP fingerprints.

PCR-based multi-locus DNA fingerprints represent one of the most informative and cost-effective measures of genetic diversity and are useful population-level biomarkers of toxicologic and other anthropogenic impacts. However, concerns about reproducibility of DNA fingerprints have limited their wider use in environmental biology. We assessed polymorphism and reproducibility of two common fingerprinting techniques, RAPD (randomly amplified polymorphic DNA) and AFLP (amplified fragment length polymorphism), in pedigreed populations of rainbow trout (Oncorhynchus mykiss) to derive general rules for selective removal of problematic fingerprint bands. We found that by excluding bands that comprised less than 1% of total intensity, and by excluding the largest and smallest 10% of the bands, we could achieve nearly 100% reproducibility of AFLP fingerprints. Similar application of band exclusion criteria to RAPD fingerprints did not significantly enhance their reproducibility, and at least 15% of RAPD bands were not fully repeatable, heritable, or transmittable. The RAPD technique produced more polymorphic fingerprints than AFLP; however, considering that a substantial proportion of RAPD markers did not demonstrate Mendelian inheritance patterns, the AFLP methodology is to be preferred for future research.

Animals↗
PubMed1991

Genomic fingerprinting using arbitrarily primed PCR and a matrix of pairwise combinations of primers.

Polymorphisms in genomic fingerprints generated by arbitrarily primed PCR (AP-PCR) can distinguish between slightly divergent strains of any organism. Single oligodeoxyribonucleotide (oligo) primers have been used to generate such fingerprints, with the same primer being present at the 5' end of both strands for every PCR product. We used three arbitrary oligos, individually and in pairs, to generate six different genomic fingerprints of the same mouse genomic DNAs. Fewer than half of the products in genomic fingerprints generated using the oligos in pairs were the same as those produced by AP-PCR using one of the three oligos alone. Thus, a few oligos could be used in a very large number of single and pairwise combinations, each producing a distinct AP-PCR fingerprint with the potential to identify new polymorphisms. For example, 50 oligos can be used in a matrix of pairwise combinations to produce 2,500 fingerprints, in which at least half the data can be expected to be unique to each pair. We demonstrate this principle by using two oligos, alone and together, to generate three sets of fingerprints and map thirteen polymorphisms in the C57BL/6J x DBA/2J set of recombinant inbred mice.

Animals↗
PubMed1994

Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data.

DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the locus affiliation of alleles is directly observable. Yet DNA fingerprinting has been proved to be a cost-effective method of detecting hypervariable polymorphisms in several organisms, where the traditional loci fail to detect enough variation for microevolutionary studies. In the present paper we demonstrate that the above-mentioned features of DNA fingerprinting data do not cause any serious problem when they are used in evolutionary studies. Bias-corrected estimators of Nei's standard and minimum genetic distances are derived, and, by an application of this theory to data on seven short tandem repeat loci in three major human populations, it is shown that these modified measures of genetic distances based on DNA fingerprint patterns are quite close to Nei's distances based on locus-specific allele frequencies. Empirical as well as theoretical support of the adequacy of such genetic distances from DNA fingerprinting data is also discussed, and it indicates that the technical limitations of DNA fingerprinting should not deter the use of the method for short-term evolutionary studies.

Alleles↗
PubMed1994

Genomic DNA fingerprinting of clinical Haemophilus influenzae isolates by polymerase chain reaction amplification: comparison with major outer-membrane protein and restriction fragment length polymorphism analysis.

Non-capsulate strains of Haemophilus influenzae were genotyped by analysis of variable DNA segments obtained by amplification of genomic DNA with the polymerase chain reaction (PCR fingerprinting). Discrete fragments of 100-2000 bp were obtained. The reproducibility of the procedure was assessed by comparing: (i) the fingerprints of 16 colonies of a single H. influenzae strain; (ii) isolates obtained from individual sputum samples (a total of 57 H. influenzae isolates from three cystic fibrosis patients); and (iii) 17 isolates collected during an outbreak of H. influenzae infection in a local pulmonary rehabilitation centre. The discriminatory power of the method was demonstrated by showing that the PCR fingerprints of eight unrelated H. influenzae strains from sputum samples of patients with chronic obstructive pulmonary disease (COPD) and 32 strains from cystic fibrosis patients were all different. These 40 isolates also differed with respect to their restriction fragment length polymorphisms (RFLP) and major outer-membrane protein (MOMP) composition. Twelve MOMP antigenic strain variants from sputum samples of five COPD patients had identical PCR fingerprints and RFLPs. It was concluded that PCR fingerprinting is a reliable and reproducible method for genotyping non-capsulate strains of H. influenzae. The discriminatory power of PCR fingerprinting was similar to that of RFLP analysis, but the results of PCR fingerprinting were easier to interpret.

Bacterial Outer Membrane Proteins↗
PubMed1991

Use of DNA fingerprints for the detection of major genes for quantitative traits in domestic species.

The detection of marker loci linked to major genes or quantitative trait loci (QTL) of large effect in farm animal populations is of great potential value, both because it allows the easy manipulation of the major genes and because it provides a possible route to their ultimate isolation. At present the number of markers available is limited in farm animals. DNA fingerprints provide a promising source of informative marker loci and have the advantage that several loci can be detected on a single Southern hybridization. The disadvantage of DNA fingerprints is the difficulty in determining allelism of DNA fingerprint bands in different pedigrees and the fact that not all potentially resolvable loci can be resolved in a single pedigree. With probes capable of detecting 50 randomly distributed loci, about 50% of the genome of a typical domestic mammal might be expected to be closely linked to a marker (at a distance of 0.2 Morgans or less). If a proportion of DNA fingerprint loci prove to be clustered near chromosomal telomeres or elsewhere in the genome, coverage will be less. In order to detect linkage to a major gene, sires known or suspected to be heterozygous are used to produce large half-sibships, all animals in the pedigree are DNA fingerprinted and the phenotypes of the offspring are recorded. Where several heterozygous sires are available, sires can be selected in an attempt to maximize the number of marker loci resolved. The optimum number of sires needed to produce pedigrees will depend upon the size of the major gene, the number of DNA fingerprint probes available and the characteristics of the DNA fingerprints produced, but often one or two pedigrees will be optimum. Monte Carlo simulation was used to explore the power of detection of linkage between a major gene and a marker locus in a backcross. Maximum likelihood and analysis of variance of mean differences between marker genotypes were of similar power, but maximum likelihood provided reasonable estimates of the major gene effect and its linkage to the marker under some circumstances. One hundred offspring informative for the segregation of a marker would provide reasonable power for the detection of a gene causing a difference between the heterozygote and the homozygote of at least one within-sire, within-genotype standard deviation when linkage was very close (0.05 or less).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1998

Arbitrarily primed polymerase chain reaction fingerprinting for the genotypic identification of mutans streptococci from humans.

Determining whether two strains of bacteria are unique, identical or clonally related depends upon comparisons of phenotypic and/or genotypic traits. Individual isolates can then be grouped according to differences or similarities among those traits. One method of genotyping strains of bacteria is commonly referred to as chromosomal DNA fingerprinting. Previously, we generated chromosomal DNA fingerprints of mutans streptococci to study the transmission of this organism within families. Here, we developed and evaluated an arbitrarily primed polymerase chain reaction (AP-PCR) method for the genotypic characterization of mutans streptococci. Results were compared to those derived from the more conventional chromosomal DNA fingerprinting method. First, we showed that randomly selected clinical isolates displayed a unique banding profile by both methods; the mean similarity indices between DNA fragment patterns were 0.69 for chromosomal DNA fingerprinting and 0.74 for AP-PCR. This indicated that AP-PCR demonstrated less diversity than chromosomal DNA fingerprinting. Subsequently, we tested the agreement between chromosomal DNA fingerprinting and AP-PCR in determining genotypic similarities among 21 mutans streptococci strains obtained from 10 mother-child pairs, and 5 mutans streptococci strains from 5 fathers. The Kappa value for agreement was 0.88. We conclude that AP-PCR, which generates patterns of 8 to 12 amplicons, is capable of distinguishing strains of mutans streptococci among non-related individuals. Moreover, AP-PCR can discern both homogeneity and heterogeneity of mutans streptococci genotypes among mother and child pairs. Overall, we found that AP-PCR gave results comparable to those of chromosomal DNA fingerprinting.

Chromosomes, Bacterial↗
PubMed1998

Subtyping of Streptococcus dysgalactiae and Streptococcus uberis isolated from bovine mammary secretions by DNA fingerprinting.

Streptococcus dysgalactiae and Streptococcus uberis isolated from mammary secretions of cows from Tennessee and New Zealand were subtyped using polymerase chain reaction-based DNA fingerprinting. Such DNA fingerprinting using primer 8.6d (5'-GTAACGCC3') resulted in categorizing 116 S. dysgalactiae isolates into 25 different subtypes, with 17 subtypes observed in isolates from Tennessee and eight in isolates from New Zealand. All S. dysgalactiae DNA fingerprint profiles, regardless of origin, contained 700- and 330-base pair fragments. The majority of S. dysgalactiae isolates (73%) from Tennessee belonged to two subtypes. The remaining 23 isolates belonged to 15 different DNA fingerprint subtypes. Streptococcus dysgalactiae isolates from New Zealand (n = 32) were grouped into eight different subtypes; 66% belonged to two subtypes. A characteristic feature of S. dysgalactiae isolates from New Zealand was the presence of a 270-base pair DNA fragment seen infrequently in S. dysgalactiae isolates from Tennessee. When primer OPE-4 (5'-GTGACATGCC-3') was used, DNA fingerprinting differentiated S. uberis from Tennessee (n = 28) and New Zealand (n = 30) into 20 subtypes; 14 subtypes were observed in isolates from Tennessee, and six in isolates from New Zealand. All S. uberis DNA fingerprint profiles, regardless of origin, contained 1100-, 640-, and 450-base pair fragments. A characteristic feature of S. uberis isolates from New Zealand was the presence of a 300-base pair DNA fragment seen infrequently in S. uberis isolates from Tennessee. The most common subtypes of S. dysgalactiae and S. uberis from Tennessee herds were isolated in milk from lactating cows during monthly herd surveys, in milk from cows with clinical mastitis, and in mammary secretions from cows during the periparturient period, and thus were not confined to one particular stage of lactation. These data suggest that S. dysgalactiae and S. uberis from New Zealand are distinct from those isolated from the USA, and that DNA fingerprinting can be used as an epidemiological tool to differentiate streptococci and identify important sources of these mastitis pathogens on dairy farms.

Animals↗
PubMed1995

Discrepancy between Penner serotyping and polymerase chain reaction fingerprinting of Campylobacter isolated from poultry and other animal sources.

Thirty-four Campylobacter jejuni or coli strains, isolated from various livestock and darkling beetles from two Dutch poultry farms during different broiler production cycles, were subjected to Penner serotyping and polymerase chain reaction (PCR) fingerprint analysis. Ten different Penner serotypes were determined in the isolates. Visual scoring of the PCR fingerprints resulted in 14 clearly different profiles. Some strains with identical Penner serotypes exhibited different PCR fingerprints and conversely strains with different serotypes produced identical PCR fingerprints. Discrepancies between Penner serotyping and PCR fingerprinting were most obvious between isolates from different animal sources. Indications for the occurrence of genomic rearrangements were found. The inconsistency between serotyping and fingerprinting of Campylobacter strains suggests that conventional typing methods should be used in combination with fingerprinting if the epidemiological factors that contribute to Campylobacter colonization of live chickens are to be assessed reliably.

Animals↗
PubMed1994

Characterization of the formae speciales of Fusarium oxysporum causing wilts of cucurbits by DNA fingerprinting with nuclear repetitive DNA sequences.

The genetic relatedness of five formae speciales of Fusarium oxysporum causing wilts of cucurbit plants was determined by DNA fingerprinting with the moderately repetitive DNA sequences FOLR1 to FOLR4. The four FOLR clones were chosen from a genomic library made from F. oxysporum f. sp. lagenariae 03-05118. Total DNAs from 50 strains representing five cucurbit-infecting formae speciales, cucumerinum, melonis, lagenariae, niveum, and momordicae, and 6 strains of formae speciales pathogenic to other plants were digested with EcoRV and hybridized with 32P-labeled FOLR probes. The strains were clearly distinguishable at the formae specialis level on the basis of FOLR DNA fingerprints. Fifty-two fingerprint types were detected among the 56 strains by using all FOLR probes. These probes were used to infer phylogenetic relationships among the DNA fingerprint types by the unweighted pair group method using averages and parsimony analysis. The fingerprint types detected in each of the formae speciales cucumerinum, lagenariae, niveum, and momordicae were grouped into a single cluster. However, two different genetic groups occurred in the formae specialis melonis. The two groups also differed in pathogenicity: one group caused wilts of muskmelon and oriental melon, while the second was pathogenic only to muskmelon. The fingerprint types of different formae speciales pathogenic to plants other than cucurbits were distinguishable from one another and from the fingerprints of the cucurbit-infecting strains. These results suggest that the cucurbit-infecting formae speciales are intraspecific variants distinguishable at the DNA level and in their host range.

Cloning, Molecular↗
PubMed1993

Hybridization probes for conventional DNA fingerprinting used as single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans.

In conventional DNA fingerprinting, hypervariable and repetitive sequences (minisatellite or microsatellite DNA) are detected with hybridization probes. As demonstrated here, these probes can be used as single primers in the polymerase chain reaction (PCR) to generate individual fingerprints. Several conventional DNA fingerprinting probes were used to prime the PCR, yielding distinctive, hypervariable multifragment profiles for different strains of Cryptococcus neoformans. PCR fingerprinting with the oligonucleotide primers (GTG)5, (GACA)4, and the phage M13 core sequence (GAGGGTGGXGGXTCT), but not with (CA)8 or (CT)8, generated DNA polymorphisms with all 42 strains of C. neoformans investigated. PCR fingerprints produced by priming with (GTG)5, (GACA)4, or the M13 core sequence differentiated the two varieties of C. neoformans, C. neoformans var. neoformans (serotypes A and D) and C. neoformans var. gattii (serotypes B and C). Furthermore, strains of serotypes A, D, and B or C could be distinguished from each other by specific PCR fingerprint patterns. These primers, which also successfully amplified hypervariable DNA segments from other species, provide a convenient method of identification at the species or individual level. Amplification of polymorphic DNA patterns by PCR with these primers offers several advantages over classical DNA fingerprinting techniques, appears to be more reliable than other PCR-based methods for detecting polymorphic DNA, such as analysis of random-amplified polymorphic DNA, and should be applicable to many other organisms.

Base Sequence↗
PubMed1996

Usefulness of the secondary probe pTBN12 in DNA fingerprinting of Mycobacterium tuberculosis.

A comparison was made between DNA fingerprints of Mycobacterium tuberculosis produced with the insertion sequence IS6110 and those produced with the polymorphic GC-rich repetitive sequence contained in the plasmid pTBN12. A total of 302 M. tuberculosis isolates from the prison system in Madrid, Spain, and the Denver Public Health Department (Denver, Colo.) were analyzed with the two probes. Both probes identified the same isolates in the same clusters when the fingerprints had six or more copies of IS6110. Analysis of isolates with unique IS6110 fingerprints demonstrated that they were unique with pTBN12. The pTBN12 probe had greater discriminating power in isolates having five or fewer copies of IS6110. Forty-seven isolates from Denver having fewer than five copies of IS6110 which were grouped in 11 clusters with identical fingerprint patterns were subdivided into 35 different patterns by pTBN12. Isolates with IS6110 fingerprints with more than six copies of IS6110 that differed from one another by only one or two hybridizing bands were analyzed with pTBN12. Most of these sets of isolates demonstrated identical patterns with pTBN12. However, some exceptions were observed, suggesting that those having nearly identical IS6110 patterns should not necessarily be included in the same cluster. Since IS6110 provides more polymorphism in the fingerprint, it is most useful in identifying isolates with unique fingerprint patterns and those in clusters in which the isolates contain six or more copies of the insertion. However, it is necessary to employ a secondary probe, such as pTBN12, to discriminate isolates with five or fewer copies of IS6110 and those with similar but not identical IS6110 patterns.

DNA Fingerprinting↗
PubMed1997

Comparison of DNA fingerprint patterns of isolates of Mycobacterium africanum from east and west Africa.

Mycobacterium africanum is a pathogen found in tuberculosis patients in certain parts of Africa and is a member of the Mycobacterium tuberculosis complex. Biochemically, strains of M. africanum exhibit a high degree of variability, with some tendency to cluster according to their geographical origin. To investigate whether this phenotypic variability is reflected at the genetic level, we performed DNA fingerprint analysis of strains isolated from patients with pulmonary tuberculosis in Uganda and Sierra Leone. IS6110 DNA fingerprinting was carried out by the mixed-linker PCR method. A total of 138 strains of M. africanum were analyzed: 42 isolates from Uganda and 96 isolates from Sierra Leone. With few exceptions, the resulting DNA fingerprint patterns grouped together according to their country of origin. A striking lack of variability of DNA fingerprints was found for strains from Sierra Leone, where 70 of 96 isolates (61.5%) fell into clusters. The two largest clusters accounted for 41.7% of all isolates and differed by only one band, as confirmed by standard DNA fingerprinting. In contrast, only two clusters (7.1%) with two and three isolates, respectively, were found for M. africanum isolates collected in Uganda, and three of the DNA fingerprints contained fewer than seven bands. Strains of M. tuberculosis collected and processed during the same time period were highly variable in both countries. Our results support the concept of geographically defined subtypes of M. africanum. In addition, they demonstrate that natural geographic differences in the variability of IS6110 DNA fingerprints within the M. tuberculosis complex must be considered if this technique is used for epidemiologic studies.

Africa, Eastern↗
PubMed2000

Spoligotyping and polymorphic GC-rich repetitive sequence fingerprinting of mycobacterium tuberculosis strains having few copies of IS6110.

Several genetic loci have been utilized to genotype isolates of Mycobacterium tuberculosis. A shortcoming of the most commonly used method, IS6110 fingerprinting, is that it does not adequately discriminate between isolates having few copies of IS6110. This study was undertaken to compare pTBN12 fingerprinting of polymorphic GC-rich repetitive sequence genes and spoligotyping of the direct repeat locus as secondary typing procedures for M. tuberculosis isolates having fewer than six copies of IS6110. A total of 88 isolates (100% of the isolates with fewer than six copies of IS6110 isolated in Arkansas during 1996 and 1997) were included in this study. Among the 88 isolates, 34 different IS6110 patterns were observed, 10 of which were shared by more than 1 isolate, involving a total of 64 isolates. The 64 isolates were subdivided into 13 clusters (containing 37 isolates) and 27 unique isolates based on a combination of IS6110 and pTBN12 fingerprinting and into 11 clusters (containing 51 isolates) and 13 unique isolates based on a combination of IS6110 fingerprinting and spoligotyping. Identical spoligotypes were found among isolates having different IS6110 patterns, as well as among isolates showing different pTBN12 patterns. In contrast, all isolates that had different IS6110 patterns were found to be unique by pTBN12 typing. The clustering rate was 73, 58, and 42%, respectively, for IS6110 fingerprinting alone, IS6110 fingerprinting and spoligotyping combined, and IS6110 and pTBN12 combined fingerprinting. The data indicate that the pTBN12 method has greater discriminating power among low-copy-number isolates than does spoligotyping.

Arkansas↗
PubMed1998

Use of DNA fingerprinting to assess tuberculosis infection control.

BACKGROUND: DNA fingerprinting establishes the genetic relatedness of Mycobacterium tuberculosis isolates and has become a powerful tool in tuberculosis epidemiology. OBJECTIVE: To use DNA fingerprinting to assess the efficacy of current tuberculosis infection-control practices. DESIGN: Retrospective molecular and descriptive epidemiologic study. SETTING: A 700-bed urban public hospital that follows the Centers for Disease Control and Prevention (CDC) guidelines for tuberculosis infection control. PATIENTS: 183 patients who had positive cultures for M. tuberculosis from 1 April 1995 to 31 March 1996. RESULTS: 173 of 183 M. tuberculosis isolates from the study period underwent DNA fingerprinting. Fingerprinting revealed that five isolates represented false-positive cultures and that 91 (54%) of the remaining 168 isolates were in 15 DNA fingerprinting clusters, which ranged in size from 2 to 29 isolates. Risk factors for clustering were birth in the United States, African-American ethnicity, homelessness, substance abuse, and male sex. Retrospective epidemiologic analysis of inpatient and outpatient visits by the 91 patients who had clustered isolates revealed only one possible instance of patient-to-patient transmission. CONCLUSIONS: The DNA fingerprinting of all M. tuberculosis isolates from a 1-year period revealed one possible instance of nosocomial transmission and five false-positive M. tuberculosis cultures. However, these results did not lead to changes in infection-control practices or in clinical care. The study findings do not support the use of DNA fingerprinting for nosocomial tuberculosis surveillance, but they suggest that compliance with the CDC tuberculosis infection-control guidelines may control patient-to-patient transmission in high-risk urban hospitals.

Chicago↗