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BMC Genomics

, 16:1032

Prokaryote microbial genomics


BackgroundWhile the taxonomy and genomics of environmental strains from the P. fluorescens species-complex has been reported, little is known about P. fluorescens strains from clinical samples. In this report, we provide the first genomic analysis of P. fluorescens strains in which human vs. environmental isolates are compared.

ResultsSeven P. fluorescens strains were isolated from respiratory samples from cystic fibrosis CF patients. The clinical strains could grow at a higher temperature >34 °C than has been reported for environmental strains. Draft genomes were generated for all of the clinical strains, and multi-locus sequence analysis placed them within subclade III of the P. fluorescens species-complex. All strains encoded type- II, −III, −IV, and -VI secretion systems, as well as the widespread colonization island WCI. This is the first description of a WCI in P. fluorescens strains. All strains also encoded a complete I2-PfiT locus and showed evidence of horizontal gene transfer. The clinical strains were found to differ from the environmental strains in the number of genes involved in metal resistance, which may be a possible adaptation to chronic antibiotic exposure in the CF lung.

ConclusionsThis is the largest comparative genomics analysis of P. fluorescens subclade III strains to date and includes the first clinical isolates. At a global level, the clinical P. fluorescens subclade III strains were largely indistinguishable from environmental P. fluorescens subclade III strains, supporting the idea that identifying strains as ‘environmental’ vs ‘clinical’ is not a phenotypic trait. Rather, strains within P. fluorescens subclade III will colonize and persist in any niche that provides the requirements necessary for growth.

KeywordsPseudomonas fluorescens Genomics Human Lung Metal Efflux pumps Cystic fibrosis AbbreviationsP. fluorescensPseudomonas fluorescens

CFCystic fibrosis

MLSAMulti-locus sequence analysis

T3SSType III secretion system

UVUltra violet

ANIAverage nucleotide identity

UPGMAUnweighted pair group method with arithmetic mean

COGSClusters of orthologoups groups

RNDResistance nodulation cell division

GCIGC Islands

T2SSType II secretion system

gspgeneral secretion pathway

Hrp1Hypersensitive response in plants

T4SSType IV secretion system

WCIWidespread colonization island

T6SSType VI secretion system

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-2261-2 contains supplementary material, which is available to authorized users.

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Autor: Brittan S. Scales - John R. Erb-Downward - Ian M. Huffnagle - John J. LiPuma - Gary B. Huffnagle


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