Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites

Abstract The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients...

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Autores principales:	Dinesh Subedi, Ajay Kumar Vijay, Gurjeet Singh Kohli, Scott A. Rice, Mark Willcox
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Accessory Genome Pangenome Multi-locus Sequence Typing (MLST) Pseudomonas Genome Database (PGDB) Ocular Isolates Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d8c7d9e7db8140259cacc138ec40c026
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spelling	oai:doaj.org-article:d8c7d9e7db8140259cacc138ec40c0262021-12-02T15:08:29ZComparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites10.1038/s41598-018-34020-72045-2322https://doaj.org/article/d8c7d9e7db8140259cacc138ec40c0262018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-34020-7https://doaj.org/toc/2045-2322Abstract The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.Dinesh SubediAjay Kumar VijayGurjeet Singh KohliScott A. RiceMark WillcoxNature PortfolioarticleAccessory GenomePangenomeMulti-locus Sequence Typing (MLST)Pseudomonas Genome Database (PGDB)Ocular IsolatesMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-14 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Accessory Genome Pangenome Multi-locus Sequence Typing (MLST) Pseudomonas Genome Database (PGDB) Ocular Isolates Medicine R Science Q
spellingShingle	Accessory Genome Pangenome Multi-locus Sequence Typing (MLST) Pseudomonas Genome Database (PGDB) Ocular Isolates Medicine R Science Q Dinesh Subedi Ajay Kumar Vijay Gurjeet Singh Kohli Scott A. Rice Mark Willcox Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
description	Abstract The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.
format	article
author	Dinesh Subedi Ajay Kumar Vijay Gurjeet Singh Kohli Scott A. Rice Mark Willcox
author_facet	Dinesh Subedi Ajay Kumar Vijay Gurjeet Singh Kohli Scott A. Rice Mark Willcox
author_sort	Dinesh Subedi
title	Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
title_short	Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
title_full	Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
title_fullStr	Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
title_full_unstemmed	Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites
title_sort	comparative genomics of clinical strains of pseudomonas aeruginosa strains isolated from different geographic sites
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/d8c7d9e7db8140259cacc138ec40c026
work_keys_str_mv	AT dineshsubedi comparativegenomicsofclinicalstrainsofpseudomonasaeruginosastrainsisolatedfromdifferentgeographicsites AT ajaykumarvijay comparativegenomicsofclinicalstrainsofpseudomonasaeruginosastrainsisolatedfromdifferentgeographicsites AT gurjeetsinghkohli comparativegenomicsofclinicalstrainsofpseudomonasaeruginosastrainsisolatedfromdifferentgeographicsites AT scottarice comparativegenomicsofclinicalstrainsofpseudomonasaeruginosastrainsisolatedfromdifferentgeographicsites AT markwillcox comparativegenomicsofclinicalstrainsofpseudomonasaeruginosastrainsisolatedfromdifferentgeographicsites
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Comparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites

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