scholarly journals Genetic Diversity of Clinical and Environmental Isolates of Vibrio cholerae Determined by Amplified Fragment Length Polymorphism Fingerprinting

2000 ◽  
Vol 66 (1) ◽  
pp. 148-153 ◽  
Author(s):  
Sunny C. Jiang ◽  
Maria Matte ◽  
Glavur Matte ◽  
Anwar Huq ◽  
Rita R. Colwell
Keyword(s):  
Vibrio Cholerae ◽  
Restriction Enzyme ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Genomic Dna ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Clinical Isolates ◽  
Environmental Isolates ◽  
El Tor

ABSTRACT Vibrio cholerae, the causative agent of major epidemics of diarrheal disease in Bangladesh, South America, Southeastern Asia, and Africa, was isolated from clinical samples and from aquatic environments during and between epidemics over the past 20 years. To determine the evolutionary relationships and molecular diversity of these strains, in order to understand sources, origin, and epidemiology, a novel DNA fingerprinting technique, amplified fragment length polymorphism (AFLP), was employed. Two sets of restriction enzyme-primer combinations were tested for fingerprinting of V. cholerae serogroup O1, O139, and non-O1, O139 isolates. Amplification of HindIII- and TaqI-digested genomic DNA produced 30 to 50 bands for each strain. However, this combination, although capable of separating environmental isolates of O1 and non-O1 strains, was unable to distinguish between O1 and O139 clinical strains. This result confirmed that clinical O1 and O139 strains are genetically closely related. On the other hand, AFLP analyses of restriction enzyme ApaI- andTaqI-digested genomic DNA yielded 20 to 30 bands for each strain, but were able to separate O1 from O139 strains. Of the 74 strains examined with the latter combination, 26 serogroup O1 strains showed identical banding patterns and were represented by the O1 El Tor strain of the seventh pandemic. A second group, represented by O139 Bengal, included 12 strains of O139 clinical isolates, with 7 from Thailand, 3 from Bangladesh, and 2 from India. Interestingly, an O1 clinical isolate from Africa also grouped with the O139 clinical isolates. Eight clinical O1 isolates from Mexico grouped separately from the O1 El Tor of the seventh pandemic, suggesting an independent origin of these isolates. Identical fingerprints were observed between an O1 environmental isolate from a river in Chile and an O1 clinical strain from Kenya, both isolated more than 10 years apart. Both strains were distinct from the O1 seventh pandemic strain. Two O139 clinical isolates from Africa clustered with environmental non-O1 isolates, independent of other O139 strains included in the study. These results suggest that although a single clone of pathogenic V. cholerae appears responsible for many cases of cholera in Asia, Africa, and Latin America during the seventh pandemic, other cases of clinical cholera were caused by toxigenic V. choleraestrains that appear to have been derived locally from environmental O1 or non-O1 strains.

scholarly journals Amplified fragment length polymorphism analysis of Mycobacterium avium complex isolates recovered from southern California

2007 ◽  
Vol 56 (9) ◽  
pp. 1152-1160 ◽  
Author(s):  
Stacy L. Pfaller ◽  
Timothy W. Aronson ◽  
Alan E. Holtzman ◽  
Terry C. Covert
Keyword(s):  
Mycobacterium Avium ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Southern California ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Polymorphism Analysis ◽  
Environmental Isolates

Fine-scale genotyping methods are necessary in order to identify possible sources of human exposure to opportunistic pathogens belonging to the Mycobacterium avium complex (MAC). In this study, amplified fragment length polymorphism (AFLP) analysis was evaluated for fingerprinting 159 patient and environmental MAC isolates from southern California. AFLP analysis accurately identified strains belonging to M. avium and Mycobacterium intracellulare and differentiated between strains within each species. The method was also able to differentiate strains that were presumed to be genetically identical in two previous studies using large RFLP analysis with PFGE, or PCR-amplification of DNA segments located between insertion sequences IS1245 and IS1311. For M. avium, drinking-water isolates clustered more closely with each other than with patient or food isolates. Patient isolates were more genetically diverse. None of the environmental isolates shared identical AFLP patterns with patient isolates for either species. There were, however, environmental isolates that shared identical patterns, and patient isolates that shared identical patterns. A subset of the isolates, which are referred to as MX isolates due to their ambiguous identification with the Gen-Probe system, produced AFLP patterns similar to those obtained from M. intracellulare isolates. Sequence analysis of 16S rDNA obtained from the MX isolates suggests that they are strains of M. intracellulare that were not correctly identified by the M. intracellulare AccuProbe from Gen-Probe.

scholarly journals Analysis of Genetic Heterogeneity in Chlamydia trachomatis Clinical Isolates of Serovars D, E, and F by Amplified Fragment Length Polymorphism

2000 ◽  
Vol 38 (9) ◽  
pp. 3463-3466 ◽  
Author(s):  
Servaas A. Morré ◽  
Jacobus M. Ossewaarde ◽  
Paul H. M. Savelkoul ◽  
Jeroen Stoof ◽  
Chris J. L. M. Meijer ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Length Polymorphism ◽  
Genetic Heterogeneity ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Clinical Isolates ◽  
Insight Into

Amplified fragment length polymorphism (AFLP) fingerprinting of clinical isolates of Chlamydia trachomatis serovars D, E, and F showed a low percentage of genetic heterogeneity, but clear differences were found. Isolates from index patients and partners had identical AFLP patterns and AFLP markers. Characterization of these AFLP markers could give more insight into the differences in virulence and clinical course of C. trachomatis infections.

scholarly journals Emergence of Vibrio cholerae O1 Biotype El Tor Serotype Inaba from the Prevailing O1 Ogawa Serotype Strains in India

2000 ◽  
Vol 38 (11) ◽  
pp. 4249-4253 ◽  
Author(s):  
Pallavi Garg ◽  
Ranjan K. Nandy ◽  
Papiya Chaudhury ◽  
Nandini Roy Chowdhury ◽  
Keya De ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Vibrio Cholerae ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Gel Electrophoresis ◽  
Fragment Length Polymorphism ◽  
Pulsed Field Gel Electrophoresis ◽  
Vibrio Cholerae O1 ◽  
El Tor ◽  
Restriction Fragment Length

The toxigenic Inaba serotype of Vibrio cholerae O1 biotype El Tor reappeared in India in 1998 and 1999, almost 10 years after its last dominance in Calcutta in 1989. Extensive molecular characterization by ribotyping, restriction fragment length polymorphism, and pulsed-field gel electrophoresis indicated that recent Inaba strains are remarkably different from the earlier Inaba strains but are very similar to the prevailing V. choleraeO1 Ogawa El Tor biotype strains. The antibiograms of the Inaba strains were also similar to those of the recent V. cholerae Ogawa strains. These V. cholerae O1 Inaba strains appear to have evolved from the currently prevailing Ogawa strains and are likely to dominate in the coming years.

scholarly journals Genome-Sequence-Based Fluorescent Amplified-Fragment Length Polymorphism Analysis ofMycobacterium tuberculosis

2000 ◽  
Vol 38 (3) ◽  
pp. 1121-1126 ◽  
Author(s):  
Jonathan N. Goulding ◽  
John Stanley ◽  
Nick Saunders ◽  
Catherine Arnold
Keyword(s):  
Genome Sequence ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Clinical Isolates ◽  
Resolving Power ◽  
Base Substitution ◽  
Polymorphism Analysis

The whole-genome fingerprinting technique, fluorescent amplified-fragment length polymorphism (FAFLP) analysis, was applied toMycobacterium tuberculosis. Sixty-five clinical isolates were analyzed to determine the value of FAFLP as a stand-alone genotyping technique and to compare it with the well-established IS6110 typing system. The genome sequence of M. tuberculosis strain H37Rv (S. T. Cole et al., Nature 393:537–544, 1998) was used to model computer-generated informative primer combination(s), and the precision and reproducibility of FAFLP were evaluated by comparing the results of in vitro and computer-generated experiments. Multiplex FAFLP was used to increase resolving power in a predictable and systematic fashion. FAFLP analysis was broadly congruent with IS6110 typing for those strains with multiple IS6110 copies. It was also able to resolve an epidemiologically unlinked group of strains with only one copy of IS6110; up to 10% of clinical isolates may fall into this category. For certain epidemiological investigations, it was concluded that a combination of FAFLP and IS6110 typing would give higher resolution than would either alone. FAFLP data were digital, precise, reproducible, and suitable for rapid electronic dissemination, manipulation, interlaboratory comparison, and storage in national or international epidemiological databases. Because FAFLP samples and analyzes base substitution across the genome as a whole, FAFLP could generate new information about the microevolution of the M. tuberculosis complex.

scholarly journals Genetic Diversity of Vibrio cholerae in Chesapeake Bay Determined by Amplified Fragment Length Polymorphism Fingerprinting

2000 ◽  
Vol 66 (1) ◽  
pp. 140-147 ◽  
Author(s):  
Sunny C. Jiang ◽  
Valerie Louis ◽  
Nipa Choopun ◽  
Anjana Sharma ◽  
Anwar Huq ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Evolution ◽  
Chesapeake Bay ◽  
Vibrio Cholerae ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Environmental Conditions ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism

ABSTRACT Vibrio cholerae is indigenous to the aquatic environment, and serotype non-O1 strains are readily isolated from coastal waters. However, in comparison with intensive studies of the O1 group, relatively little effort has been made to analyze the population structure and molecular evolution of non-O1 V. cholerae. In this study, high-resolution genomic DNA fingerprinting, amplified fragment length polymorphism (AFLP), was used to characterize the temporal and spatial genetic diversity of 67 V. choleraestrains isolated from Chesapeake Bay during April through July 1998, at four different sampling sites. Isolation of V. choleraeduring the winter months (January through March) was unsuccessful, as observed in earlier studies (J. H. L. Kaper, R. R. Colwell, and S. W. Joseph, Appl. Environ. Microbiol. 37:91–103, 1979). AFLP fingerprints subjected to similarity analysis yielded a grouping of isolates into three large clusters, reflecting time of the year when the strains were isolated. April and May isolates were closely related, while July isolates were genetically diverse and did not cluster with the isolates obtained earlier in the year. The results suggest that the population structure of V. choleraeundergoes a shift in genotype that is linked to changes in environmental conditions. From January to July, the water temperature increased from 3°C to 27.5°C, bacterial direct counts increased nearly an order of magnitude, and the chlorophyll aconcentration tripled (or even quadrupled at some sites). No correlation was observed between genetic similarity among isolates and geographical source of isolation, since isolates found at a single sampling site were genetically diverse and genetically identical isolates were found at several of the sampling sites. Thus, V. cholerae populations may be transported by surface currents throughout the entire Bay, or, more likely, similar environmental conditions may be selected for a specific genotype. The dynamic nature of the population structure of this bacterial species in Chesapeake Bay provides new insight into the ecology and molecular evolution ofV. cholerae in the natural environment.

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