Antibiotic Resistance, Biofilm Genes, and <i>smeDEF</i> Efflux Pump in Clinical <i>Stenotrophomonas maltophilia</i> Isolates From Iran

Stenotrophomonas maltophilia is a nosocomial and opportunistic microorganism with increasing antibiotic resistance rates. This study aimed to assess its biofilm production capacity, antibiotic resistance distribution, and the prevalence of biofilm- and resistance-related genes in clinical isolates. In this multiinstitutional study, 230 isolates were collected from hospitals across Iran between 2022 and 2024. Resistance trends were evaluated using disc diffusion and minimal inhibitory concentration E test methods, per Clinical and Laboratory Standards Institute guidelines. Crystal violet staining assessed biofilm production, while polymerase chain reaction (PCR) sequencing identified biofilm- and resistance-related genes. Real-time PCR was used to evaluate the relative expression of the smeD, smeE, and smeT genes, calibrated against TMP/SMX-sensitive control strains. Susceptibility rates to trimethoprim/sulfamethoxazole (TMP/SMX), levofloxacin, and minocycline were 97.39%, 93.47%, and 93.04%, respectively. TMP/SMX-resistant strains showed 19.8- and 16-fold higher expression of smeD and smeE, compared with sensitive isolates. The spgM gene was detected in all isolates, and 93.04% (n = 214) were biofilm producers, with most showing moderate-biofilm formation (n = 89, 38.70%). Additionally, the rpfF gene was closely associated with strong-biofilm formation (p ≤ 0.05). The L2, L1, smqnr, sul2, and sul1 resistance genes were identified in 214 (93.04%), 181 (78.69%), 135 (58.7%), 136 (59.1%), and 127 (55.2%) isolates, respectively. Our findings demonstrate that most isolates remain sensitive to TMP/SMX, while resistance to alternative antibiotics is rising. Moreover, biofilm production appears significantly associated with the rpfF gene.