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The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

Lisa C Crossman1, Virginia C Gould2, J Maxwell Dow3, Georgios S Vernikos1, Aki Okazaki2, Mohammed Sebaihia1, David Saunders1, Claire Arrowsmith1, Tim Carver1, Nicholas Peters1, Ellen Adlem1, Arnaud Kerhornou1, Angela Lord1, Lee Murphy1, Katharine Seeger1, Robert Squares1, Simon Rutter1, Michael A Quail1, Mari-Adele Rajandream1, David Harris1, Carol Churcher1, Stephen D Bentley1, Julian Parkhill1*, Nicholas R Thomson1 and Matthew B Avison2*

Author Affiliations

1 Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

2 Department of Cellular and Molecular Medicine, University of Bristol, School of Medical Sciences, University Walk, Bristol, BS8 1TD, UK

3 Biomerit Research Centre, Department of Microbiology, Biosciences Institute, National University of Ireland, Cork, Ireland

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Genome Biology 2008, 9:R74  doi:10.1186/gb-2008-9-4-r74

Published: 17 April 2008



Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of the Xanthomonadaceae. The organism has been isolated from both clinical and soil environments in addition to the sputum of cystic fibrosis patients and the immunocompromised. Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads.


The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance.


The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.