Emergence of mobile RND-type efflux pump gene cluster tmexCD-toprJ on a broad-host-range IncC plasmid in Shewanella species in a water environment

The spread of the mobile resistance-nodulation-division (RND)-type efflux pump tmexCD-toprJ gene cluster that confers multidrug resistance (MDR), including tigecycline resistance, in gram-negative bacteria poses a global public health threat. However, the occurrence of such clinically important antimicrobial resistance genes (ARGs) in the natural environments has not yet been well investigated. In this study, we investigated MDR aquatic bacteria in Vietnam. A carbapenem- and tigecycline-resistant Shewanella xiamenensis isolate NUITM-VS2 was obtained from urban drainage in Hanoi, Vietnam, in October 2021. Antimicrobial susceptibility testing using agar dilution and whole-genome sequencing (WGS) was performed using both long-read and short-read sequencers. ARGs and plasmid replicons were detected using ResFinder and PlasmidFinder with the custom sequence database. NUITM-VS2 showed resistance to most antimicrobials tested, including tigecycline, tetracyclines, carbapenems, cephalosporins, fluoroquinolone, and aminoglycosides. WGS analysis resulted in the complete genome sequence consisting of one chromosome and five plasmids. A 152.2-kb IncC plasmid, pNUITM-VS2_2, co-carried two mobile tigecycline resistance genes, tet (X4) and tmexCD3-toprJ1b -like gene cluster. In addition, a 24.8-kb untypeable plasmid, pNUITM-VS2_4, carried the carbapenemase gene bla NDM-1 . pNUITM-VS2_2 was transferred to Escherichia coli by conjugation, which simultaneously conferred high-level resistance against many antimicrobials, including tigecycline. To the best of our knowledge, this is the first report of the detection of the mobile RND-type efflux pump gene cluster tmexCD-toprJ in Shewanella species. Our results provide genetic evidence of the complexity of the dynamics of clinically important ARGs among aquatic bacteria, which could be important reservoirs for ARGs in the natural environment.