Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain

Abstract

Stenotrophomonas maltophilia is an opportunistic pathogen with an environmental origin, and it is an increasingly relevant cause of nosocomial infections. Here we present the whole-genome sequence of S. maltophilia strain D457, a clinical isolate that is being used as a model for studying antibiotic resistance in this bacterial species.

GENOME ANNOUNCEMENT

Stenotrophomonas maltophilia is a free-living bacterial species with biotechnological relevance for different applications, including the production of molecules of economic value, the biodegradation of pollutants, and use of the organism for the biological control of plant infections (12). In addition, S. maltophilia is an increasingly relevant human opportunistic pathogen that is involved in infections at hospitals and in patients with cystic fibrosis (5, 21). One of the most worrisome properties of S. maltophilia consists of its low susceptibility to most antibiotics currently in use for the treatment of infections (13). This lack of susceptibility is due at least in part to the presence in its genome of genes encoding antibiotic-inactivating enzymes, efflux pumps (1, 2, 6), and other proteins that contribute to the intrinsic resistance, such as SmQnr (15, 18). The strain D457 (3) is a clinical isolate that has been used for studying the presence of elements contributing to resistance in S. maltophilia and the regulation of these elements (2, 8, 9, 14–17).

In this article, we present the full sequence and the annotation of the genome of S. maltophilia D457. The genome was sequenced using the 454 GS FLX system with single ends and 3-kb paired ends (64 and 147 Mb, with 370,000 and 700,000 reads before assembly, respectively). All reads were assembled de novo by using the MIRA software (http://chevreux.org/projects_mira.html). Assembly was revised using the Gap4 software from the Staden package (20). The genome of S. maltophilia K279a (6) and information for paired ends were used as references to design PCR amplifications that, after Sanger sequencing, served to close the genome gaps and to solve the repeat regions. Coding sequences were initially annotated in the RAST server (4) followed by a manual curation. Pseudogenes were confirmed by assembly inspection. Hypothetical coding genes smaller than 250 nucleotides without similarity with other S. maltophilia strains were removed. Noncoding RNA genes were annotated by using several methods (7, 10, 19). Repeat sequences were analyzed to identify transposable elements and for mapping the inverted repeats at the end of the IS elements.

The chromosome comprises 4,769,156 bp, with a G+C content of 66.8%. It contains 4,209 genes, of which 4,101 are coding genes and 108 are noncoding RNA genes (13 rRNA, 71 tRNA, and 24 other RNAs). In addition, 30 pseudogenes (29 protein-coding genes and 1 tRNA) were identified. Six types of transposable elements were identified that comprised 19 complete and 3 defective forms. Only two of them were detected in other sequenced S. maltophilia strains (ISSmaD4 and Tn5044). Among the predicted coding sequences of D457, we found that more than 200 genes were not shared with the other strains of S. maltophilia with completely sequenced genomes (6, 11, 22). Notably, most of them encoded hypothetical proteins and transposases, which indicates that the core genome of S. maltophilia is large. No chromosomal rearrangements were detected when we compared the sequence to those of other published strains, except for the insertion of phages or other horizontally transferred genes.

Nucleotide sequence accession number.

The results of this whole-genome shotgun project have been deposited at the European Nucleotide Archive (ENA) under accession number HE798556.