Comparative insights into multiple drug resistance determinants found in Stenotrophomonas maltophilia MER1

Abstract Objectives Stenotrophomonas maltophilia MER1, a multidrug resistant (MDR) bacterium was isolated from the wastewater from a hospital, Shandong province, China. We attempted to reveal the genetic determinants related to its striking MDR features for effective treatment to S. maltophilia. Methods Antibiotic susceptibility testing of strain MER1 was performed by using the disk diffusion method on the Mueller–Hinton agar plates, and the minimum inhibitory concentrations (MICs) were determined according to the Clinical Laboratory Standard Institute protocols. The genome of MER1 was sequenced and assembled with a PacBio RS II and a BGISEQ-500 platform. Antibiotic resistance agents together with other transferability or adaptability determinants were identified by comparative genomics. Phylogenetic and contextual assays for these identified elements were conducted to assess the spread risk of MER1. Results Susceptibility testing reveals that strain MER1 is strikingly resistant to nine different antibiotics, including ampicillin, meropenem, amikacin, erythromycin, vancomycin, tetracycline, tigecycline, polymyxin E and ceftazidime. Several genes were identified to encode efflux pumps and inactivation agents accounting for MER1 resistance to above antibiotics, including meropenem, tigecycline and colistin regarded as the last-line therapy for infections caused by multidrug-resistant Gram-negative bacteria. MER1 co-harbors two non-mobile mcr homologs. A novel genomic region of variability was demonstrated to confer bacterial robustness and adaptability upon strain MER1. Conclusion Collective efforts revealed the multiple drug resistance properties and potential genetic determinants of S. maltophilia MER1 isolated from the hospital sewage. Comparative genomic analysis of S. maltophilia MER1 may provide insights into prevention and treatment of its antimicrobial resistance. Our findings would prompt public concern that the MDR genes in the reservoir of S. maltophilia may further spread into various ecological niches or medically high-risk pathogens.