Evaluation of the Polymorphisms Associated with Tandem Repeats for Pseudomonas aeruginosa Strain Typing

Abstract

We report on the development of a scheme for the typing of Pseudomonas aeruginosa, multiple-locus variable number of tandem repeat (VNTR) analysis (MLVA). We first evaluated the polymorphisms of 201 tandem repeat loci selected from more than 3,000 such sequences present in strain PAO1 with a test collection of 12 genotypically distinct clinical strains. Seven VNTR loci which can be easily scored with the technology used here were identified and used to genotype a collection of 89 clinical isolates that had previously been classified into 46 ribotypes, including 2 widespread ribotypes. Seventy-one different MLVA genotypes could be distinguished. With only two exceptions, strains with identical ribotypes were grouped together upon cluster analysis of the MLVA data. The 27 isolates with the most frequent ribotype were divided into 14 MLVA types, and the 18 isolates with the second most frequent ribotype were divided into 15 MLVA types. Analysis of a subset of 17 strains belonging to the major ribotype by pulsed-field gel electrophoresis with the enzyme SpeI distinguished seven types, identical to the number of MLVA types in this subset. Our data show that MLVA typing of P. aeruginosa based on the first set of loci has a high discriminatory power. Because MLVA is highly reproducible and easily portable among laboratories, it represents a very promising tool for the molecular surveillance of P. aeruginosa. A free, online strain identification service based on the genotyping data produced herein has been developed.

Distribution and characterization of staphylococcal interspersed repeat units (SIRUs) and potential use for strain differentiation

“…These loci have a characteristic structure consisting of a variable number of near-identical repeated DNA sequences arranged consecutively. A general term for these repeats is variable-number tandem repeats (VNTRs), and true VNTRs have now been reported in Bacillus anthracis, Legionella pneumophila, Pseudomonas aeruginosa, Salmonella enterica and Escherichia coli O157 (Keim et al, 2000;Liu et al, 2003;Noller et al, 2003;Onteniente et al, 2003;Pourcel et al, 2003). With the exception of M. tuberculosis, these studies have been confined to comparisons of molecular strain differentiation techniques.…”

Subtyping of ST22-MRSA-IV (Barnim epidemic MRSA strain) at a university clinic in Germany from 2002 to 2005

“…Variable-number tandem repeats (VNTRs) have been used as markers for the strain typing of various bacteria (Francois et al, 2005;Hawkey et al, 2003;Onteniente et al, 2003;van Belkum, 1999). Determination of the number of repeats at each locus produces a digital profile, providing a highly portable typing method allowing comparisons between laboratories.…”

Characterization of a tandem repeat polymorphism in Rickettsia strains

“…The MLVA approach has been proven to present high discriminatory power, reproducibility and portability, making it a strong candidate for the increased development of reference databases that allow online strain identification services (Supply et al, 2001;Onteniente et al, 2003).…”