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

Gracia Morales,¹ Lutz Wiehlmann,² Peter Gudowius,^2, Christian van Delden,³ Burkhard Tümmler,² José Luis Martínez,¹ and Fernando Rojo^1*

Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus U.A.M., Cantoblanco, E-28049 Madrid, Spain,¹ Klinische Forschergruppe, Pediatric Pneumology, Medizinische Hochschule Hannover, D-30625 Hannover, Germany,² Department of Genetics and Microbiology, University of Geneva, CMU, CH-1211 Geneva 4, Switzerland³

Received 11 December 2003/ Accepted 24 March 2004

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.

Present address: Universitätskinderklinik, Universität Düsseldorf, D-40225 Düsseldorf, Germany.

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