Multidrug-resistant Stenotrophomonas maltophilia: Description of new MLST profiles and resistance and virulence genes using whole-genome sequencing.

Abstract

Stenotrophomonas maltophilia is an opportunistic pathogen that has high intrinsic and acquired antimicrobial resistance, with great genetic diversity. The aim of this study was to characterise four S. maltophilia clinical isolates displaying different susceptibility profiles using whole-genome sequencing. The whole genomes of four clinical isolates of S. maltophilia from three patients were sequenced using Ion Torrent™ PGM technology. The isolates presented different susceptibilities to trimethoprim/sulfamethoxazole (SXT) and levofloxacin. Three new multilocus sequence typing (MLST) profiles were identified (ST144, ST172 and ST173), differing in virulence and resistance genes. The ST172 isolate had more genes related to toxins than related to motility or adhesion and had different types of efflux pumps than the other isolates. The SXT-resistant strains belonged to ST172 or ST144 and did not harbour the sul1, sul2 or dfrA resistance genes. Strains I and II, from the same patient and belonging to the same ST but differing in resistance to SXT, had all of the resistance genes searched for in common, except for the SmeABC efflux pump complex genes that were only found in the SXT-resistant strain. All strains, including the strain susceptible to levofloxacin, harboured the qnrB gene, which may question the importance of this gene in determining levofloxacin resistance in S. maltophilia. Here we describe three new MLST profiles. Resistance to SXT in these strains appears to be associated with efflux pumps.