New genetic environments of the macrolide-lincosamide-streptogramin resistance determinant erm(X) and their influence on potential horizontal transferability in bifidobacteria

•Three new genetic environments of erm(X) were retrieved in bifidobacteria.•Genetic environments influence the transferability of erm(X) in bifidobacteria.•The IS1249 and IS3 elements have a synergic effect in the transfer of erm(X).

With the abuse of macrolide, lincosamide, and streptogramin (MLS), the traditionally safe bifidobacterial strains in the human intestine could serve as a reservoir of MLS resistance genes. In this study, the erm(X) gene was detected in 29 MLS-resistant strains and one MLS-susceptible strain among 92 bifidobacterial strains of human origin. This study is the first to report erm(X)-mediated MLS resistance in Bifidobacterium pseudocatenulatum, Bifidobacterium breve and Bifidobacterium bifidum. The insertion sequences (ISs) flanking antibiotic resistance (AR) genes (i.e., the genetic environment of AR genes) could contribute to the horizontal spreading of AR. However, the potential transferability of erm(X) in bifidobacteria has not been previously verified. Here, we retrieved four genetic environments (I-IV) of erm(X) from 30 erm(X)-positive bifidobacterial strains. This study is the first to identify the erm(X) gene in three new genetic environments (II, III and IV) in bifidobacteria. The erm(X) gene was individually flanked by IS1249 or IS3 in genetic environments I, II and IV and was simultaneously flanked by IS1249 and IS3 elements in genetic environment III. Only the transfer of erm(X) from genetic environment III simultaneously flanked by IS1249 and IS3 elements was successfully observed in filter mating experiments. These findings indicate a synergic effect of IS1249 and IS3 elements in the transfer of erm(X) in bifidobacteria, and further reveal that the various genetic environments of erm(X) result in significant differences in the transferability of erm(X) in bifidobacteria.