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

Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom.
Eurosurveillance: bulletin europeen sur les maladies transmissibles = European communicable disease bulletin (Impact Factor: 5.72). 10/2013; 18(42). DOI: 10.2807/1560-7917.ES2013.18.42.20611
Source: PubMed


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.

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    • "The advances of next-generation sequencing progressively turned genome sequence of bacteria and microbial eukaryotes somewhat feasible and inexpensive. In addition, it allows the analysis of several thousand of SNPs and may link epidemiology to pathogen biology, genome evolution, gene characterization in terms of resistance and virulence, gather information from noncoding and coding regions across the entire genome, give relevant evidence regarding linkage, recombination, chromosomal aberrations, and low frequency events such as horizontal gene transfer (Araujo 2014; Snyder et al. 2013). Microbial identification, SNP genotyping, resequencing, and analyses of difficult DNA secondary structures are some of the fields under exploitation by next-generation sequencing (Schuster 2008). "
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