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PubMed1998

Restriction fragment length polymorphism and spacer oligonucleotide typing: a comparative analysis of fingerprinting strategies for Mycobacterium bovis.

The combination of conventional investigation and DNA fingerprinting is yielding important insights into the epidemiology of Mycobacterium bovis infections. Various genetic markers used in restriction fragment length polymorphism (RFLP) have recently been exploited for fingerprinting of M. bovis isolates. The newly developed spacer oligonucleotide typing aimed to investigate the polymorphism of M. tuberculosis in the DR locus, has also been applied to the molecular typing of M. bovis isolates. This work compared the performance of the insertion sequence (IS) IS6110, IS1081 and the genetic elements polymorphic G + C-rich repeat (PGRS) and direct repeat (DR) used in RFLP analysis with spoligotyping using a group of 128 Spanish M. bovis isolates. In this study, the most sensitive technique for identifying polymorphism in M. bovis was PGRS-RFLP, closely followed by IS6110-RFLP. We propose several schemes for fingerprinting of these isolates, however, the clear geographical variations found by different authors makes the study of each local situation indispensable. An international consensus in the methods used would be desirable for efficient interlaboratory comparison of strains.

Animals↗
PubMed1999

Molecular fingerprinting of Riemerella anatipestifer by repetitive sequence PCR.

Riemerella anatipestifer is a gram-negative rod-shaped bacterium associated with epizootic infections in poultry. A total of 35 R. anatipestifer isolates including the type strain ATCC11845T, reference and field strains for 18 different serotypes were characterized by repetitive sequence based-PCR (rep-PCR) with outwardly-directed primers based on the repetitive extragenic palindromic (REP) consensus sequence. This technique was applied by using either extracted genomic DNA or preparation of whole bacterial cells harvested directly from plate cultures. Rep-PCR discriminated the R. anatipestifer isolates into 19 electrophoretic types. DNA fingerprints obtained from rep-PCR of extracted genomic DNA or from preparations of whole cells yielded comparable patterns. Substantial variation was seen among the rep-PCR fingerprints of different serotypes. Moreover, different polymorphisms of the rep-PCR fingerprints were evident among epidemiologically unrelated isolates of the same serotype. These results suggest the presence of repetitive extragenic palindromic-like elements within the genome of R. anatipestifer that can be used in some isolates to discriminate between different strains belonging to the same serotype. Rep-PCR may serve as a useful molecular tool for subtyping R. anatipestifer isolates for epidemiologic investigations. The whole cell procedure offers the advantage of ease of performance requiring only small quantities of cells.

Animals↗
PubMed2000

Genomic fingerprints, ARDRA profiles and quinone systems for classification of Pasteurella sensu stricto.

In order to investigate the relationships between species of the genus Pasteurella sensu stricto such as Pasteurella multocida, Pasteurella canis, Pasteurella stomatis, Pasteurella dagmatis, Pasteurella avium, Pasteurella volantium, Pasteurella gallinarum, Pasteurella species A, Pasteurella species B and "Pasteurella leonis" MCCM 00659 their genomic fingerprints and ARDRA profiles were compared and their quinone systems were analysed. Visual comparison of band patterns from rep-PCR (ERIC-, REP- and BOX-PCR) and the analyses of the combined band patterns by UPGMA (unweighted pair group method with averages) dendrogram derived from the combined fingerprint profiles demonstrated that each strain displays a distinct genomic fingerprint. In members of the same species several similarities in the band patterns were observed. Combined ARDRA profiles, obtained after digestion of amplified 23S rRNA coding genes with the enzymes DdeI, MseI and RsaI, revealed a dissection of the members of the genus Pasteurella sensu stricto into two groups which was in agreement with the two groups obtained from our analyses of the quinone systems. These two groups corresponded with the two phylogenetically determined subclusters 3A and 3B described previously. The species of subcluster 3A displayed a quinone system with ubiquinone Q-7 (32-56%) and ubiquinone Q-8 (44-63%) as major compounds. Members of subcluster 3B had a quinone system with ubiquinone Q-8 (86-97%) as the major compound. Based on these results it can be suggested that the genus Pasteurella sensu stricto should be restricted to the species of subcluster 3B including the species Pasteurella multocida, Pasteurella canis, Pasteurella stomatis, Pasteurella dagmatis and Pasteurella species B. In addition, evidence was found which would indicate that: 1) Pasteurella canis MCCM 00927 is misnamed and should be reclassified with Pasteurella multocida; 2) Pasteurella multocida subsp. septica may be classified as a separate species; and 3) "Pasteurella leonis" MCCM 00659 represents a separate species within subcluster 3B and thus could be described as a species of Pasteurella sensu stricto (also in a redefined genus) when more strains become available.

Bacterial Typing Techniques↗
PubMed1997

Use of different PCR-based DNA fingerprinting techniques and pulsed-field gel electrophoresis to investigate the epidemiology of Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

Acinetobacter calcoaceticus-Acinetobacter baumannii complex is an important nosocomial pathogen for which optimal typing methods in epidemiologic investigations have not been defined. We compared DNA macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) with different PCR-based DNA fingerprinting techniques, including enterobacterial repetitive intergenic consensus (ERIC) polymerase chain reaction (PCR), repetitive extragenic palindromic (REP) PCR, arbitrary-primed PCR with primer M13, and multiplex PCR with primers REP-1, REP-2 and M13, for characterization of 98 clinical isolates (including 10 apparent outbreak-related isolates and 68 presumed epidemiologically unrelated isolates) in a tertiary-care hospital over a 4-year period. The PFGE patterns after Smal restriction of the bacterial DNA were analyzed by computer software (Gelcompar) using the unweighted pair group method with arithmetic averages clustering and the Dice coefficient. A cluster of 48 isolates (cluster A), including 9 outbreak isolates, linked at a level of 83.4% similarity was observed. This epidemic strain and its variants were also found among the 68 presumed epidemiologically unrelated isolates, and this may represent ongoing endemic infection in this institution. The discrimination index for the PCR-based DNA fingerprinting techniques was 0.75 for enterobacterial repetitive intergenic consensus 1, 0.71 for M13, 0.77 for REP-1, 0.77 for REP-2, and 0.87 for multiplex PCR. The discriminatory power of PFGE was found to be higher than those of PCR-based techniques. It was concluded that both PFGE and PCR-based fingerprinting are useful for typing of A. calcoaceticus-A. baumannii complex. However, PFGE can detect minor mutations among outbreak strains, and this is important for epidemiological study of this species in a complex endemic setting.

Acinetobacter↗
PubMed1999

Molecular characterization by PCR-fingerprinting of Candida dubliniensis strains isolated from two HIV-positive patients in Spain.

Six Candida dubliniensis isolates were recovered from two HIV-infected individuals in the course of a prospective study of recurrent oral candidosis among HIV-positive patients in Spain. Candida albicans strains as well as non-albicans strains were also obtained from these two patients. C. dubliniensis strains were germ-tube-positive and produced abundant chlamydospores. Fingerprinting the genomic DNAs of these six C. dubliniensis with the C. albicans-specific probe 27A as well as karyotyping was performed to confirm the identification of these isolates. Further analysis of their genomic DNAs was performed by PCR-fingerprinting with the core sequence of phage M13, and they exhibited species-specific multilocus band patterns, clearly distinct from those of C. albicans isolates analyzed in this study and in a previous one (Diaz-Guerra 1997). Intraspecies variation was also seen among PCR patterns yielded by C. dubliniensis isolates from different patients. Although few strains have been analyzed, the use of this PCR-fingerprinting procedure is a promising tool for further epidemiologic studies with C. dubliniensis. The isolation of C. dubliniensis from Spanish HIV-infected patients contributes to the idea of widespread geographic distribution of this species.

Candida↗
PubMed1999

Analysis of genomic damage in the mutagen-sensitive mus-201 mutant of Drosophila melanogaster by arbitrarily primed PCR (AP-PCR) fingerprinting.

DNA repair mechanisms are important to maintain the stability of the genome. In Drosophila melanogaster, the mus-201 gene is required in the excision repair process. To study the contribution of the mus-201 gene in the stability of the Drosophila genome, we have used the arbitrarily primed PCR fingerprinting method (AP-PCR). We have analysed the changes in the genomic DNA fingerprints from the progeny of wild-type males crossed with mus-201 repair-deficient or repair-proficient females. After induction of DNA damage with 2-acetylaminofluorene (2-AAF) in the wild-type parental males, quantitative and qualitative differences in the AP-PCR fingerprints were detected between the two crosses, and the estimate of the genomic damage detected by AP-PCR has clearly shown that the mus-201 repair deficiency is associated with an increase of genomic damage. The predominant type of alterations detected by AP-PCR under the mus-201 repair-deficient conditions agree with the results obtained in microsatellite PCR analysis, suggesting that the role of the mus-201 gene, necessary in excision repair, is not associated to the mismatch repair process. The work reported here demonstrates that the AP-PCR is a suitable technique to analyse genetic alterations in D. melanogaster and, consequently, can be used to compare the susceptibility to genomic damage of different DNA repair mutants.

2-Acetylaminofluorene↗
PubMed2000

Usefulness of IS6110-restriction fragment length polymorphism typing of Brazilian strains of Mycobacterium tuberculosis and comparison with an international fingerprint database.

Strains of Mycobacterium tuberculosis isolated from 219 different tuberculosis patients, 115 from patients residing in Rio de Janeiro, 79 from Rio Grande do Sul and the remaining from other regions of the country, were analyzed by IS6110-restriction fragment length polymorphism fingerprinting. The IS6110-DNA patterns from these strains were highly polymorphic: 174 different patterns were observed and 25 patterns were shared by 70 isolates (32%). Most strains (93.4%) had multicopy patterns and only 17% of clustered strains had less than six IS6110 copies. Strain clustering was significantly higher for isolates from Rio Grande do Sul (36.7%) in comparison with strains from Rio de Janeiro (22.6%), but only when using high stringency during cluster analysis. Upon screening of an international database containing 3,970 fingerprints of M. tuberculosis strains, 15% of the patterns of Brazilian strains (21% of the strains) were identical to a fingerprint of an isolate from another country and one particular eight-band pattern forming the largest Brazilian cluster was detected in seven additional countries, suggesting that international transmission of tuberculosis from and to Brazil could be occurring frequently. Alternatively,preferential use of certain IS6110 integration sites could also be important in high-copy number strains, having important consequences for the use of databases for epidemiological studies on a large scale.

Bacterial Typing Techniques↗
PubMed1994

Insertion sequence IS200 fingerprinting of Salmonella typhi: an assessment of epidemiological applicability.

When Pst I-generated digests of genomic DNA from each of the type strains of 49 of the Vi phage types of Salmonella typhi were probed with a PCR-amplified IS200 gene probe, all strains were found to possess at least 11 IS200 elements carried on fragments in the range 24.2-1.2 kb. Fourteen fingerprints were identified but two patterns designated IS200Sty1 and IS200Sty2 predominated. In one strain, a plasmid-mediated IS200 element was identified. When IS200 fingerprinting was applied to epidemiologically-unrelated strains of S. typhi isolated in Ecuador, 3 patterns were identified in 10 strains belonging to 9 different phage types. It is concluded that Vi phage typing remains the method of choice for the primary differentiation of S. typhi but that IS200 fingerprinting may be of limited use in laboratories which do not have access to phage typing.

Bacteriophage Typing↗
PubMed2005

Microbicides for HIV/AIDS. 1. Electrophoretic fingerprinting the H9 cell model system.

An electrophoretic fingerprint of a CD4+ T-cell (H9) has been produced for the first time. Samples were taken from three separate cultures prepared at different times to obtain a general characterization of the cells. The availability of commercial instrumentation equipped with an auto-titrator has made possible the application of both the 2-dimensional and 3-dimensional representation of electrophoretic fingerprinting. The 2-dimensional treatment has been used to assess the reliability of the data and has detected hysteresis as a possible second-order effect. The 3-dimensional representation has been used to explore the data needed for a reliable overall pattern that characterizes the conditions of pH and conductivity required for an effective microbicide. The dome negative maximum in the electrophoretic fingerprint at high pH, along with the line of zero mobility (LZM) and a dome positive maximum at low pH, are interpreted as evidence for surface carboxyl groups prominent in the alkaline regime and surface amino groups prominent in the acid regime, suggesting that the H9 cell surface is zwitterionic. This has important implications as to the choice and design of microbicide actives.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Multiple paternity in wild common shrews (Sorex araneus) is confirmed by DNA-fingerprinting.

We have tested for the occurrence of multiple paternity in wild common shrews by karyotypic analysis and DNA-fingerprinting of five wild-caught females and their litters. Karyotypic data suggest that some litters were sired by more than one male, but provide no definitive evidence. By using DNA-fingerprinting, it was possible to establish that two males sired the litter of two females. The present report shows that multiple paternity is not a rare phenomenon in the common shrew and by using DNA-fingerprinting it is possible to assign individual offspring to different male parents even when none of the putative fathers are available for inspection.

Animals↗
PubMed1992

Analysis of mating systems in the schistosome-vector hermaphrodite snail Bulinus globosus by DNA fingerprinting.

Bulinus globosus, one of the intermediate hosts for Schistosoma, is a hermaphrodite freshwater snail. Multilocus DNA fingerprinting was applied in order to investigate the mating system of this facultatively self-fertilizing species. By analysing DNA fingerprints of eight broods, we have shown that selfed and outcrossed individuals could be unambiguously distinguished by comparison with their parent fingerprints. First, selfed offspring patterns shared a higher number of bands with their mother than did outcrossed ones. Secondly, at least three paternal bands could be detected per outcrossed offspring pattern.

Animals↗
PubMed1996

SINE sequences detect DNA fingerprints in salmonid fishes.

DNA probes homologous to two previously described salmonid short interspersed nuclear elements (SINEs) detected DNA fingerprint patterns in 14 species of salmonid fishes. The probes showed more homology to some species than to others and little homology to three nonsalmonid fishes. The DNA fingerprint patterns derived from the SINE probes are individual-specific and inherited in a Mendelian manner. Probes derived from different regions of the same SINE detect only partially overlapping banding patterns, reflecting a more complex SINE structure than has been previously reported. Like the human Alu sequence, the SINEs found in salmonids could provide useful genetic markers and primer sites for PCR-based techniques. These elements may be more desirable for some applications than traditional DNA fingerprinting probes that detect tandemly repeated arrays.

Animals↗
PubMed1996

The use of IgH fingerprinting and ASO-dependent PCR for the investigation of residual disease (MRD) in ALL.

In acute lymphoblastic leukaemia (ALL), investigation of minimal residual disease by conventional morphology and immunology fails to detect levels of residual disease of < 1 leukaemic in 10-100 normal cells. The use of polymerase chain reaction (PCR) to exploit the diversity of the complementarity determining region (CDR) and immunoglobulin variable heavy chain (VH) family specific usage has greatly improved the sensitivity up to one leukaemic cell in 10(5)-10(6) normal bone marrow cells. Here we report on a prospective study of 14 patients with ALL of B-cell lineage by using a combined PCR approach which estimates levels of disease between 1:10(3) and 1:10(5). The sequential use of allele-specific oligoprimer (ASO) independent tests (using framework 1. FR1 and 3, FR3 primers with a JH consensus primer, sensitivity up to 1:5 x 10(3)) and ASO-dependent PCR (sensitivity up to 1:10(5)) assays were applied to 64 bone marrow (BM) follow-up samples in a sequential array of tests. Results presented in this study indicate high concordance of MRD among different tests for samples with level of residual disease > 1:5 x 10(3). Consequently, samples positive by the FR1 and FR3 fingerprinting tests were confirmed by the more sensitive ASO-dependent tests, as expected. However, the ASO-dependent assays revealed levels of disease undetected by the FR1 and FR3 test. Although a higher level of sensitivity is provided by the ASO-dependent tests, the FR1 and FR3 fingerprinting tests allow MRD investigation in patients with oligoclonal B cell proliferations, CDR3 region of size < 15 bp or with ASO primers unsuitable for PCR investigation on technical grounds (i.e. background signal). If a sequential order of investigation from less (e.g. FR1 and FR3 fingerprinting) to more sensitive tests (ASO-dependent) is applied, an indirect estimate of MRD is obtained for patients with level of disease < 1:10(3).

Adolescent↗
PubMed1999

Molecular fingerprinting of Salmonella serotype Glostrup.

Thirteen isolates of Salmonella serotype Glostrup (antigenic formula, 6.8:z10:e,n,z15) from various sources and countries were analysed by ribotyping and IS200 fingerprinting. Both methods provided a high index of strain discrimination by allowing detection of three ribotypes and eight IS200 fingerprints which, though generally related, were readily distinguishable. The findings of this analysis confirm the usefulness of ribotyping and IS200 fingerprinting for studying the epidemiology of rarely isolated salmonellae of serogroup C.

Animals↗
PubMed2000

Clonal structure in a dwarf bamboo (Sasa senanensis) population inferred from amplified fragment length polymorphism (AFLP) fingerprints.

Amplified fragment length polymorphism (AFLP) fingerprints were used to reveal clonal structure of a dense population of dwarf bamboo, Sasa senanensis, in a 10-ha study plot at Sugadaira Montane Research Center, University of Tsukuba, Nagano, Japan. We generated AFLP fingerprints for 51 leaf samples, collected at 50 m intervals, using three selective primer pairs. A total of 135-166 fragments were detected per sample, and 22 different fingerprints were identified based on 24-83 differing fragments. Our results demonstrate that the S. senanensis population in our plot consists of at least 22 clones and that the largest single clone occurs over a distance of about 300 m. Furthermore, the clone distribution pattern implies a relationship between site quality and clonal structure.

Clone Cells↗
PubMed1999

Molecular epidemiology of Candida albicans isolates from AIDS and cancer patients using a novel standardized CARE-2 DNA fingerprinting technique.

A total of 277 Candida isolates from various body sites of 149 AIDS and cancer patients treated in four different university clinics in Würzburg, Germany were collected over a period of 27 months and phenotypically and genotypically characterized. The fingerprinting patterns of 194 Candida albicans isolates obtained with the moderately repetitive, C. albicans-specific DNA fragment CARE-2 were digitized and retrospectively compared with a highly accurate computer-assisted standardization method. A total of 168 different genotypic patterns (< 100% identity) could be differentiated using this technique. Although comparative analysis of C. albicans subsets revealed a pronounced tendency of C. albicans isolates from HIV patients to form clusters, the mean genetic variability in HIV and cancer patient isolates was virtually identical. Patients with a specific disease condition or in a certain age group were not found to harbour C. albicans isolates displaying a characteristic "signature genotype". Micro-evolutionary changes were detected by CARE-2 fingerprinting in temporal successive isolates of one patient, but nosocomial transmission of identical isolates between unrelated patients was never seen. Genotyping showed that patient isolates can replace one another; occasionally also species switches were observed. Secreted aspartic protease (SAP) production was not correlated with a specific C. albicans banding pattern; isolates obtained from HIV patients and from an internal control group secreted comparable amounts of SAP. Candida dubliniensis isolates in this study showed an elevated level of SAP production. When used under standardized conditions, CARE-2 fingerprinting is an efficient, reproducible and sensitive technique to characterize C. albicans isolates.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern.

Microbial communities inhabiting a multipond solar saltern were analysed and compared using SSU rRNA polymerase chain reaction (PCR)-based fingerprintings carried out in parallel by four laboratories. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied for Bacteria, Archaea and Eukarya, and laboratories applied their own techniques and protocols on the same set of samples. Members of all three domains were retrieved from all salt concentrations. Three fingerprinting techniques were used: denaturing gradient gel electrophoresis (DGGE), ribosomal internal spacer analysis (RISA), and terminal-restriction fragments length polymorphism (T-RFLP). In addition, each laboratory used its own biomass collection method and DNA extraction protocols. Prokaryotes were addressed using DGGE and RISA with different 'domain-specific' primers sets. Eukaryotes were analysed by one laboratory using DGGE and T-RFLP, but targeting the same 18S rDNA site. Fingerprints were compared through cluster analysis and non-metric multidimensional scaling plots. This exercise allowed fast comparison of microbial assemblages and determined to what extent the picture provided by each laboratory was similar to those of others. Formation of two main, salinity-based groups of samples in prokaryotes (4-15% and 22-37% salinity) was consistent for all the laboratories. When other clusters appeared, this was a result of the particular technique and the protocol used in each case, but more affected by the primers set used. Eukaryotic microorganisms changed more from pond to pond; 4-5% and 8-37% salinity were but the two main groups detected. Archaea showed the lowest number of bands whereas Eukarya showed the highest number of operational taxonomic units (OTUs) in the initial ponds. Artefacts appeared in the DGGE from ponds with extremely low microbial richness. On the other hand, different 16S rDNA fragments with the same restriction or internal transcribed spacer (ITS) length were the main limitations for T-RFLP and RISA analyses, respectively, in ponds with the highest OTUs richness. However, although the particular taxonomic composition could vary among protocols, the general structure of the microbial assemblages was maintained.

Archaea↗
PubMed1998

High-resolution genotyping of Salmonella strains by AFLP-fingerprinting.

High resolution AFLP fingerprinting, in which subsets of genomic restriction fragments are amplified by means of PCR, was used for the identification of different. Salmonella serotypes to investigate whether this technique is applicable in epidemiological studies. Seventy-eight different Salmonella strains comprising 62 serotypes were genetically identified by AFLP. Primer combination M00 (MseI primer without additional 3' nucleotides) and E11 (EcoRI primer with two additional 3' nucleotides) resulted in reproducible profiles containing approximately 50 bands. All serotypes were characterized by a unique profile. In addition, AFLP fingerprinting enabled phage type identification. Different strains previously identified as identical, using typing methods with lower resolution, could be distinguished, showing that AFLP fingerprinting is well suited for bacterial epidemiology and identification.

Bacterial Typing Techniques↗