A comparative and phylogenetic analysis of the genome of Pseudomonas aeruginosa

Pseudomonas aeruginosa remains a constant threat both in the community and nosocomially, accounting for approximately 10% of hospital acquired infections (Davies, 2002). In particular, this free living, extremely virulent pathogen is a worry to clinicians involved in the care of patients suffering from cystic fibrosis, the genetically acquired, multi-system disease. Within the CF lung, P. aeruginosa is known to undergo genomic changes resulting in the progression to chronic infection and a worsening prognosis. The most notable example of this phenomenon is the switch to the mucoid phenotype resulting from frame-shift mutations in the mucA gene leading to overproduction of alginate. In this work, we have identified this switch in phenotype as a marker for host adaptation by the bacterium to the CF lung environment and therefore have sequenced three mucoid strains and their non-mucoid progenitors. Using a variety of comparative genomics software, we have identified that two of these pairings are true, isogenic, host adapted counterparts. Each mucoid strain demonstrates evidence associated with such host adaption including genome shrinkage as a result of genomic island and phage loss, as well as decreased virulence and motility. In order to determine the contribution of each genomic anomaly to the change in phenotypes observed, we have utilised a variety of phenotypic analyses including a LC-MS metabolomics analysis of the CF isolates grown in artificial sputum media to mimic chronic lung infection. Further to this, in an attempt at mapping the core genome of P. aeruginosa and providing the community with a greater understanding of the genomic basis of this pathogen, we have also sequenced four well known environmental isolates as well as a further clinical isolate and its rugose small colony variant. With this new data we have developed a new typing method that we believe is superior and more thorough to MLST analysis, noting that P. aeruginosa exists in three distinct groupings.

Name dc:type.qualificationname

phd

Level dc:type.qualificationlevel

doctoral-pg

Grantor dc:publisher.institution

University of Strathclyde

Year dc:date.issued

2015

Author dc:creator

• Stewart, Lewis James

DOI

10.48730/kfdw-m396

Identifier

T14043

Author Identifier

201059191

OAI identifier oai:identifier

oai:strathclyde:cr56n1010