Structure of Pseudomonas aeruginosa Populations Analyzed by Single Nucleotide Polymorphism and Pulsed-Field Gel Electrophoresis Genotyping

Abstract

Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.

Staphylococcus aureus Genotyping Using Novel Real-Time PCR Formats

“…This is consistent with other studies that have shown that, in clonal organisms, a SNP set defines about as many genotypes as there are SNPs; conversely, in nonclonal organisms, the number of genotypes can be much more than the number of SNPs (6,9,11,12,15). With S. aureus, the SNPs that discriminate clonal complex founders from single-locus variants are likely of recent origin, have not been reassorted by recombination, and in consequence, are polymorphic in a tiny fraction of the species' diversity and have little informative power when interrogated.…”

Impact of Pseudomonas aeruginosa Genomic Instability on the Application of Typing Methods for Chronic Cystic Fibrosis Infections

“…It has been reported that the SNP typing method is 99.97% accurate in discriminating between P. aeruginosa strains (27). Wiehlmann et al (39) also found that the results from the SNP genotyping method did not always correspond with PFGE due to the presence or absence of genomic islands (39).…”

Sequence diversity of the mucABD locus in Pseudomonas aeruginosa isolates from patients with cystic fibrosis

“…Boiled colonies of each strain were subjected to PCR with appropriate primers to amplify DNA fragments containing the SNP, as described by Morales et al (2004). Amplified DNA was digested with the restriction enzyme that discriminated each SNP (Table 1), and the fragments generated were analysed by agarose gel electrophoresis and ethidium bromide staining.…”

“…Typing of strain collections by single nucleotide polymorphisms (SNPs), DNA fragment length polymorphisms and phenotypic traits indicates that the current P. aeruginosa population is in linkage equilibrium, and consists of a network of equivalent genotypes (termed clones), whereby a subset of clones is overrepresented due to epidemic spread (Curran et al, 2004;Morales et al, 2004;Pirnay et al, 2002a, b).…”

“…This study reports on the sequence diversity of the mucABD operon in nine environmental and 37 CF P. aeruginosa isolates. The association between mucABD SNP haplotype and chromosomal genotype has been inferred from SpeI restriction fragment patterns (Römling et al, 1994) and multilocus SNP genotypes (Morales et al, 2004). The CF strains were isolated from 10 patients at onset and at a chronic late stage of airway colonization.…”