ABSTRACT
Bacterial isolates from respiratory and urinary tract infections in an Indian hospital setting were genotyped using FAFLP analysis. The 77 different isolates analyzed belonged to five genera namely Escherichia, Staphylococcus, Pseudomonas, Enterobacter and Pantoea. Before carrying out FAFLP analysis all the isolates were subjected to16S-23S ribosomal RNA-based species identification. Cluster analysis of FAFLP profiles of 77 isolates generated five groups corresponding to five bacterial genera that are used in the study. Further analyses of the dendrograms revealed efficient species and strain differentiation. Cluster analysis identified genetically distant clones among the clinical isolates of Staphylococcus aureus, two distinct genetic lineages among the Escherichia coli strains and a single cluster of closely related Pseudomonas aeruginosa isolates. Ribosomal spacer region amplification identified different species accurately but intraspecies discrimination could not be accomplished completely. Comparison of FAFLP profiles of our isolates, with a pilot database of validated strains, was very useful in identification and worked better in conjunction with dendrogram analysis.
Subject(s)
DNA, Bacterial/analysis , Molecular Epidemiology , Polymorphism, Restriction Fragment Length , Bacterial Typing Techniques , Cluster Analysis , Cross Infection , DNA, Bacterial/genetics , Fluorescence , Gram-Negative Bacteria/classification , Gram-Negative Bacteria/genetics , Gram-Negative Bacteria/isolation & purification , Gram-Negative Bacterial Infections/epidemiology , Gram-Negative Bacterial Infections/genetics , Gram-Negative Bacterial Infections/microbiology , Hospitals , Humans , India/epidemiology , Phylogeny , Polymerase Chain Reaction , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/genetics , Respiratory Tract Infections/microbiology , Species Specificity , Urinary Tract Infections/epidemiology , Urinary Tract Infections/genetics , Urinary Tract Infections/microbiologyABSTRACT
AmpliBASE MT is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT is based on a relational database management system that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs and large sequence polymorphisms along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT is expected to be a very helpful tool in strengthening the concept of 'geographic genomics' and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis.
