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Background   Stenotrophomonas maltophilia  is a ubiquitous Gram-negative bacterium previously named as  Xanthomonas maltophilia . This organism is an important nosocomial pathogen associated with infections in immunocompromised patients. Clinical isolates of  S. maltophilia  are mostly resistant to multiple antibiotics and treatment of its infections is becoming problematic. Several virulent bacteriophages, but not temperate phage, of  S. maltophilia  have been characterized.    Results  In this study, a temperate myophage of  S. maltophilia  (Smp131) was isolated and characterized. Sequence analysis showed that its genome is 33,525-bp long with 47 open reading frames (ORFs). Its similarity to P2-like phages and prophages in  S. maltophilia  and several  Xanthomonas  pathovars includes genomic organization, arrangement of several operons, and possession of a slippery sequence T 7 G for translational frameshifting in tail assembly genes. Smp131 encodes a tyrosine family integrase that shares low degrees of similarity with those of other phages and a lysin belonging to family 19 chitinase that is observed in plants and some bacteria, although not in phages. tRNA are the preferred sites for host integration of Smp131 and the related phages: tRNA-Thr for Smp131 and prophage of  S. maltophilia  K279a; tRNA-Lys for prophages of  X. campestris  pv. campestris ATCC33913,  X. oryzae  pv. oryzae strains MAFF311018, and KACC10331; and tRNA-Asn for prophage of  X. oryzae  pv. oryzae PXO99A and remnant of  X. axonopodis  pv. citri 306. Regions flanking the prophages are varied highly in nucleotide sequence and rich in transposase genes, suggesting that frequent insertion/excision had occurred.    Conclusions  Prevalence of closely related prophages in  Stenotrophomonas  and  Xanthomonads  may have contributed to the diversity of these closely related species owing to possible horizontal gene transfer mediated by the phages.

Genomic sequence of temperate phage Smp131 of Stenotrophomonas maltophilia that has similar prophages in xanthomonads