Pseudomonas aeruginosa population structure revisited

Abstract

At present there are strong indications that Pseudomonas aeruginosa exhibits an epidemic population structure; clinical isolates are indistinguishable from environmental isolates, and they do not exhibit a specific (disease) habitat selection. However, some important issues, such as the worldwide emergence of highly transmissible P. aeruginosa clones among cystic fibrosis (CF) patients and the spread and persistence of multidrug resistant (MDR) strains in hospital wards with high antibiotic pressure, remain contentious. To further investigate the population structure of P. aeruginosa, eight parameters were analyzed and combined for 328 unrelated isolates, collected over the last 125 years from 69 localities in 30 countries on five continents, from diverse clinical (human and animal) and environmental habitats. The analysed parameters were: i) O serotype, ii) Fluorescent Amplified-Fragment Length Polymorphism (FALFP) pattern, nucleotide sequences of outer membrane protein genes, iii) oprI, iv) oprL, v) oprD, vi) pyoverdine receptor gene profile (fpvA type and fpvB prevalence), and prevalence of vii) exoenzyme genes exoS and exoU and viii) group I pilin glycosyltransferase gene tfpO. These traits were combined and analysed using biological data analysis software and visualized in the form of a minimum spanning tree (MST). We revealed a network of relationships between all analyzed parameters and non-congruence between experiments. At the same time we observed several conserved clones, characterized by an almost identical data set. These observations confirm the nonclonal epidemic population structure of P. aeruginosa, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise. One of these clones is the renown and widespread MDR serotype O12 clone. On the other hand, we found no evidence for a widespread CF transmissible clone. All but one of the 43 analysed CF strains belonged to a ubiquitous P. aeruginosa "core lineage" and typically exhibited the exoS(+)/exoU(-) genotype and group B oprL and oprD alleles. This is to our knowledge the first report of an MST analysis conducted on a polyphasic data set.

Figure 1. Overview of the characteristics and test results of P. aeruginosa strains 1-82/328.

ABR: antibiotic resistance; ATCC: American Type Culture Collection; BWC: burn wound centre; CC: clonal complex; CF: cystic fibrosis; COPD: chronic obstructive pulmonary disease; CPHL: Central Public Health Laboratory, London; DOM: defective oprD mutation; ESP: Ecole de Santé Publique, Brussels; FAFLP: fluorescent amplified fragment length polymorphism; HPA: Health protection Agency, Colindale; HSV: high sequence variability; IDEXX: laboratory for veterinary, food and water testing; ICU: intensive care unit; IG: insufficient growth; LMG: Laboratorium voor Microbiologie Gent, public bacteria collection; NA: no amplification; NIMR: National Institute for Medical Research, London; NT: not typable; POS: positive; TRM: reaction terminated. * ABR: antibiotic resistance, expressed as the number of antibiotic classes to which resistance was observed. ** Detected using degenerate primers.

Figure 2. Overview of the characteristics and test results of P. aeruginosa strains 83-164/328.

Figure 3. Overview of the characteristics and test results of P. aeruginosa strains 165-246/328.

Figure 4. Overview of the characteristics and test results of P. aeruginosa strains 247-328/328.

Figure 5. Congruence between experiments, as calculated using the Pearson product-moment correlation coefficient.

Figure 6. UPGMA dendrograms, with assignment of allele codes, for the oprI (a), oprL (b), and oprD (c) alleles detected in 328 P. aeruginosa strains.

Figure 7. Minimum spanning tree of the similarity matrix of the composite data set consisting of the FAFLP pattern, serotype, oprI, oprL, and oprD gene sequences, pyoverdine receptor profile and prevalence of exoS/U for 328 P. aeruginosa strains.

Each circle corresponds to a polyphasic profile (PP). The circles are scaled with member count. Branch lengths are logarithmic. Coloured zones surround PPs that belong to the same clonal complex. These complexes are also indicated with a capital letter. The lines between PPs indicate inferred phylogenetic relationships and are represented as bold, plain, discontinuous and light discontinuous depending on the number of differences between profile types. Discontinuous links are only indicative. Two bold black indent lines delimit the P. aeruginosa “core lineage”; the MDR serotype O12 clone is encircled by a red dotted line.