Trimethoprim-sulfamethoxazole (co-trimoxazole) is one of the antimicrobials of choice for the treatment of Stenotrophomonas maltophilia infections. The analysis of mutants either lacking or overexpressing the efflux pump SmeDEF shows that this efflux pump contributes to intrinsic and acquired co-trimoxazole resistance in S. maltophilia. Since SmeDEF can extrude a variety of antibiotics, selection with such antimicrobials, including quinolones, might also select for S. maltophilia co-trimoxazole resistance.T he treatment of Stenotrophomonas maltophilia, an opportunistic pathogen involved in different nosocomial infections, is difficult, owing to its low level of susceptibility to several antibiotics and its capability to acquire further resistance during clinical treatment. The intrinsic resistance of this pathogen is mainly due to the presence in its genome of genes encoding different resistance determinants, as several multidrug resistance (MDR) efflux pumps and antibiotic-modifying enzymes, and the quinolone resistance gene Smqnr (1, 2). Acquired resistance is mediated by the acquisition of mobile genetic elements containing antibiotic resistance genes and by the overexpression of chromosomal resistance genes encoding efflux pumps due to mutations in genes encoding the local regulators of these determinants (3-5).The combination of antibiotics that inhibit enzymes of the folate biosynthesis pathway, trimethoprim and sulfamethoxazole (co-trimoxazole), is one of the choices for S. maltophilia treatment. In 2005, S. maltophilia represented only 4.7% of co-trimoxazole-resistant isolates (6), although this percentage varies geographically and has increased in the last few years. While from 1998 to 2008, only 14.6% of isolates in Taiwan were co-trimoxazole resistant, nowadays, this number has increased to 31.1% (7). The rationale behind the use of antimicrobial combinations is that the frequency of resistant mutants will be lower than that for single-target drugs, since mutations at the genes encoding both targets will be required in the case of combined drugs (8). We reasoned that bacteria could overcome this situation if one efflux pump is able to extrude both antimicrobials, since a single mutation will lead to the overexpression of the efflux pump and confer resistance. This possibility was suggested in Pseudomonas aeruginosa, because strains overexpressing oprM, the gene encoding the outer membrane protein of the mexAB efflux pump, were less susceptible to sulfamethoxazole and trimethoprim (9). In addition, the study of clinical S. maltophilia isolates has shown a weak correlation between co-trimoxazole resistance and overexpression of the MDR efflux pumps SmeDEF and SmeABC (10). The overexpression of the efflux pump SmeABC reduces susceptibility to aminoglycosides, -lactams, and fluoroquinolones, but only the deletion of the smeC gene (outer membrane protein gene) has a direct effect on intrinsic resistance (11). The efflux pump Sme-DEF is responsible for intrinsic and acquired resistance to tetracycline, chl...