Unraveling Mechanisms and Epidemic Characteristics of Nitrofurantoin Resistance in Uropathogenic Enterococcus faecium Clinical Isolates

PURPOSE: Multidrug-resistant (MDR) Enterococcus faecium is an important nosocomial pathogen causing urinary tract infection, and the reapplication of nitrofurantoin (NIT) in the clinic has attracted great attention. This study aims to explore the NIT resistance mechanisms and epidemiological characteristics of E. faecium clinical isolates. PATIENTS AND METHODS: A total of 633 E. faecium clinical isolates was obtained from urine samples in a clinical teaching hospital during 2017–2018. Among them, 40 NIT-resistant strains, and a similar number of -intermediate and -susceptible strains were isolated. The minimum inhibitory concentrations (MICs) of NIT were detected by agar dilution method. The prevalence and mutations of nitroreductase-encoding genes ef0404 and ef0648 were explored by polymerase chain reaction (PCR), followed by efflux pump inhibition test and quantitative real-time PCR (qRT-PCR) to investigate the resistance mechanisms of NIT. Furthermore, the epidemiological characteristics were detected by multilocus sequence typing (MLST). RESULTS: The carrying rates of nitroreductase in NIT-susceptible, -intermediate, and -resistant isolates were 100%, 50%, and 20%, respectively. After exposure to the efflux pump inhibitor, the MIC of 12 E. faecium decreased by ≥4-fold. However, the efflux pump genes efrAB, emeA, and oqxAB were not overexpressed in NIT-resistant E. faecium isolates. Moreover, MLST analysis revealed that all the NIT-resistant isolates belonged to CC17, of which 30 (75%) were associated with ST78. CONCLUSION: This study has established for the first time that the absence of EF0404 and EF0648 is the main mechanism of NIT resistance in E. faecium. Our findings are likely to fill the knowledge gap pertaining to the NIT resistance mechanism in E. faecium and provide important insights for molecular epidemiological characteristics analysis.