Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa

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Genome sequencing and characterization of an extensively drug-resistant sequence type 111 serotype O12 hospital outbreak strain of Pseudomonas aeruginosa A.A. Witney, K.A. Gould, C.F. Pope, F. Bolt, N.G. Stoker, M.D. Cubbon, C.R. Bradley, A. Fraise, A.S. Breathnach, P.D. Butcher, T.D. Planche, J. Hinds Clinical Microbiology and Infection Volume 20, Issue 10, Pages O609-O618 (October 2014) DOI: 10.1111/1469-0691.12528 Copyright © 2014 European Society of Clinical Infectious Diseases Terms and Conditions

FIG. 1 (a) Phylogenetic relationship between Pseudomonas aeruginosa isolates sequenced in this study in the context of 35 genome sequences from public databases (see Table S2 for accessions), based on core genome alignments. Sequence-derived MLST type is included in square brackets. PA7 was excluded as an outlier. (1) Outbreak 1 strains. (2) Outbreak 2 strains. (3) Unrelated strain from hospital 1. (b) Phylogenetic reconstruction from 24 ST111-specific variant sites identified by comparing isolate read data with the reference genome LESB58 (RefSeq: NC_011770). The tree is rooted to NC_011770. Asterisks mark branches with 100% bootstrap support values. Ancestral site reconstruction was used to estimate the number of single-nucleotide polymorphism (SNP) changes on branches; branches with significant support values are labelled with the estimated number of SNPs out of the total number of SNP sites identified when mapped against LESB58, PAO1, and UCBPP-PA14 (RefSeq: NC_011770, NC_002516, and NC_008463), respectively. The scale bar indicates estimated mutations per site. ± refers to presence/absence of putative phage (see Fig. 2). See section Isolate phenotyping for isolate descriptions. Clinical Microbiology and Infection 2014 20, O609-O618DOI: (10.1111/1469-0691.12528) Copyright © 2014 European Society of Clinical Infectious Diseases Terms and Conditions

FIG. 2 Read coverage across differential phage regions within ST111 isolates. (a) Predicted genes; putative phage genes are coloured red. (b) PA128572. (c) PA48922. (d)PA46218. (e) PA38182. (f) PASwab. Clinical Microbiology and Infection 2014 20, O609-O618DOI: (10.1111/1469-0691.12528) Copyright © 2014 European Society of Clinical Infectious Diseases Terms and Conditions