Emerging metronidazole resistance in Bacteroides spp. and its association with the nim gene: a study from North India

Bacteroides spp. are anaerobic resident intestinal flora but are also known to cause severe morbidity. They are resistant to a wide variety of antimicrobial agents, including metronidazole, which has been shown to be associated with specific nitroimidazole (nim) resistance genes. Metronidazole resistance is emerging worldwide, although presently it remains at ca. 5%. This study aimed to determine the metronidazole susceptibility and distribution of nim genes in Bacteroides spp. clinical isolates in India. The relationship among strains harbouring nim genes and their susceptibility to metronidazole was also analysed. A total of 42 Bacteroides spp. clinical isolates were identified using an advanced MALDI-TOF system. Minimum inhibitory concentrations (MICs) for metronidazole were determined by the agar dilution method. Bacterial DNA was extracted and was subjected to nim gene PCR and the amplified PCR products were sequenced to determine the prevalent nim types. Bacteroides fragilis was the most common isolate (64%) among all Bacteroides spp. isolates. Among the total 42 clinical Bacteroides spp. isolates, 29 (69%) were susceptible and 13 (31%) were resistant to metronidazole by the agar dilution method. nim gene PCR performed on 38 isolates showed positivity in 20 isolates (53%), of which 12 had high metronidazole MICs (χ2 test, P < 0.005). On sequencing, these nim genes were most closely related to nimE type. Resistance to metronidazole is consistently emerging worldwide. There is a significant association of the nim gene with metronidazole resistance. Periodic surveillance is needed to detect geographic and temporal trends in nim gene prevalence.