RAPD (arbitrary primer) PCR is more sensitive than multilocus enzyme electrophoresis for distinguishing related bacterial strains
TLDR
RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species, and should be used for studies of bacterial population genetic structure and evolution, as well as for epidemiology.Abstract:
The RAPD (random amplified polymorphic DNA) fingerprinting method, which utilizes low stringency PCR amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments, was calibrated relative to the widely used, protein-based multilocus enzyme electrophoretic (MLEE) typing method. RAPD fingerprinting was carried out on five isolates from each of 15 major groups of Escherichia coli strains that cause diarrheal disease worldwide (75 isolates in all). Each group consisted of isolates that were not distinguishable from one another by MLEE typing using 20 diagnostic enzyme markers. In our RAPD tests, three or more distinct subgroups in each MLEE group were distinguished with each of five primers, and 74 of the 75 isolates were distinguished when data obtained with five primers were combined. Thus, RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species. Despite their different sensitivities, the same general relationships among strains were inferred from MLEE and RAPD data. Thus, our results recommend use of the RAPD method for studies of bacterial population genetic structure and evolution, as well as for epidemiology.read more
Citations
More filters
Book ChapterDOI
Phenotypic Characterization and the Principles of Comparative Systematics
TL;DR: The methods described in this chapter are based primarily on methods developed for the characterization and identification of organisms which have usually been isolated on nutrient-rich media.
Journal ArticleDOI
Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloë dactyloides
TL;DR: Large regional differences among the diploid races will facilitate further study of polyploid evolution in buffalograss and multiple correlation Mantel techniques revealed that the correlations were low on an individual by individual basis.
Journal ArticleDOI
High Prevalence of Mucosa-Associated E. coli Producing Cyclomodulin and Genotoxin in Colon Cancer
Emmanuel Buc,Emmanuel Buc,Damien Dubois,Damien Dubois,Pierre Sauvanet,Pierre Sauvanet,Jennifer Raisch,Jennifer Raisch,Julien Delmas,Julien Delmas,Arlette Darfeuille-Michaud,Arlette Darfeuille-Michaud,Denis Pezet,Denis Pezet,Richard Bonnet,Richard Bonnet +15 more
TL;DR: Cyclomodulin-producing E. coli belonging mostly to B2 phylogroup colonize the colonic mucosa of patients with CRC and exhibited a non significant difference in the distribution of CRC and diverticulosis specimens.
Journal ArticleDOI
Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth
Mireia Lopez-Siles,Tanweer M. Khan,Sylvia H. Duncan,Hermie J. M. Harmsen,L. Jesús Garcia-Gil,Harry J. Flint +5 more
TL;DR: Many F. prausnitzii isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to Bacteroides spp.
Journal ArticleDOI
Molecular epidemiology of extraintestinal pathogenic (uropathogenic) Escherichia coli
James R. Johnson,Thomas A. Russo +1 more
TL;DR: O Ongoing discovery of new putative virulence factors (VFs), increasing awareness of the importance of VF expression and molecular variants of VFs, and growing appreciation of transmission as an important contributor to ExPEC infections provide abundant stimulus for future molecular epidemiological studies.
References
More filters
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
DNA polymorphisms amplified by arbitrary primers are useful as genetic markers
TL;DR: A new DNA polymorphism assay based on the amplification of random DNA segments with single primers of arbitrary nucleotide sequence is described, suggesting that these polymorphisms be called RAPD markers, after Random Amplified Polymorphic DNA.
Journal ArticleDOI
Fingerprinting genomes using PCR with arbitrary primers
John Welsh,Michael McClelland +1 more
TL;DR: The generality of the arbitrarily primed PCR method is demonstrated by application to twenty four strains from five species of Staphylococcus, eleven strains of Streptococcus pyogenes and three varieties of Oryza sativa.
Journal ArticleDOI
How clonal are bacteria
TL;DR: Data from multilocus enzyme electrophoresis of bacterial populations were analyzed using a statistical test designed to detect associations between genes at different loci, and found panmictic, epidemic, and clonal population structures.
Journal ArticleDOI
DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting
TL;DR: The RAPD (or AP-PCR) DNA fingerprinting method was used to distinguish among clinical isolates of Helicobacter pylori, a bacterium whose long term carriage is associated with gastritis, peptic ulcers and gastric carcinomas.