Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing

Abstract

. Epidemiological investigation of Pseudomonas aeruginosa isolates from a six-year-long hospital outbreak using high-throughput whole genome sequencing. Euro Surveill. 2013;18(42) Although previous bacterial typing methods have been informative about potential relatedness of isolates collected during outbreaks, next-generation sequencing has emerged as a powerful tool to not only look at similarity between isolates, but also put differences into biological context. In this study, we have investigated the whole genome sequence of five Pseudomonas aeruginosa isolates collected during a persistent six-year outbreak at Nottingham University Hospitals National Health Service (NHS) Trust -City Campus, United Kingdom. Sequencing, using both Roche 454 and Illumina, reveals that most of these isolates are closely related. Some regions of difference are noted between this cluster of isolates and previously published genome sequences. These include regions containing prophages and prophage remnants such as the serotype-converting bacteriophage D3 and the cytotoxin-converting phage phi CTX. Additionally, single nucleotide polymorphisms (SNPs) between the genomic sequence data reveal key single base differences that have accumulated during the course of this outbreak, giving insight into the evolution of the outbreak strain. Differentiating SNPs were found within a wide variety of genes, including lasR, nrdG, tadZ, and algB. These have been generated at a rate estimated to be one SNP every four to five months. In conclusion, we demonstrate that the single base resolution of whole genome sequencing is a powerful tool in analysis of outbreak isolates that can not only show strain similarity, but also evolution over time and potential adaptation through gene sequence changes.

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

“…Using whole-genome sequencing and PCR screening, only one SNP was identified in multiple isolates, in pmrB, resulting in a missense mutation. Studies on the evolution of CF-associated lineages of P. aeruginosa have reported similar mutation rates, estimated at 2.1-2.6 SNPs per year 43,44 . Interestingly, a missense SNP in pmrB has also been identified as a fixed, adaptive mutation in the evolutionary history of the CF-associated DK2 lineage of P. aeruginosa 5 .…”

High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

“…Most of the isolates (74/87, 85%) produced VIM-2 carbapenemase, but some had IMP variants (5) (11,3,4,3,2,2,5,4,6/8); these were distributed among multiple hospitals and appeared to show no clear pattern, although all the IMP-only producers had a profile of 11,3,4,3,2,2,5,4,6. Ten isolates (from patients P42, P52, and P55 and environmental isolates E10 to E14) from a single laboratory (London_26) (one patient also attended London_28), that were related in time and space, shared a consistent profile of 11,3,4,3,2,2,6,4,7; these were the only isolates in the WGS set with this profile and clustered together by all methods tested.…”

“…Understanding these pathways will be critical for precise public health interventions to contain these highrisk clones effectively. Whole-genome sequencing (WGS) can provide this resolution and has been used to investigate outbreaks of Klebsiella pneumoniae ST-258 producing K. pneumoniae carbapenemase (KPC) enzymes (3), the Nottingham strain of P. aeruginosa (4), and many others (e.g., see reference 5).…”

Genomic Analysis of Bacterial Outbreaks

“…A single reaction occurs per well so that when a hydrogen atom is released after the incorporation of each nucleotide during amplification, the pH in the media changes in a nucleotide-specific manner, so that the system is able to translate chemical into digital information. Reads produced by the Ion Torrent were of relatively good quality and was punctually applied to the study of Escherichia coli outbreaks and Pseudomonas aeruginosa (Snyder et al, 2013;Witney et al, 2014).…”