Revealing sRNA expression profiles of NDM-5-producing CRKP and explore the role of sRNA207 in NDM-5-producing CRKP resistance.

UNLABELLED

New Delhi metallo-beta-lactamase-5 (NDM-5)-producing carbapenem-resistant (CRKP) is characterized by high virulence, high morbidity, and mortality, and the detection rate in children has increased in recent years. Therefore, it is urgent to develop new therapeutic targets and strategies. Non-coding small RNA (sRNA)-mediated RNA-based therapies offer a new direction for the treatment of bacterial infections, especially resistant bacteria. This study first analyzed the transcriptional expression profiles of NDM-5-producing CRKP and Carbapenem-susceptible (CSKP) isolates from the clinic by RNA-seq. A total of 4,623 genes were obtained, of which 307 genes were differentially expressed in NDM-5-producing CRKP, and these differentially expressed genes are mainly related to metabolism. Then, by analyzing the length and secondary structure of genes that could not match the reference gene and non-redundant protein database, we obtained 268 sRNAs, of which 13 sRNAs were differentially expressed in NDM-5-producing CRKP. After the expression level of differentially expressed sRNA was verified by RT-PCR to be consistent with that of RNA-seq, we chose sRNA207 as our research target. By knockdown of sRNA207 and (the predicted target mRNA of sRNA207) in the strain, we found that increased expression of sRNA207 promoted biofilm formation by stabilizing expression of -1, which in turn affected the resistance of NDM-5-producing CRKP to carbapenems. This provides a new approach to treat CRKP infection.

IMPORTANCE

sRNAs form a regulatory network that regulates bacterial virulence, drug resistance, and other functions by targeting mRNAs. However, sRNA expression profile and function of NDM-5-producing carbapenem-resistant (CRKP) are still unknown. In this study, we analyzed the sRNA expression profiles of NDM-5-producing CRKP obtained from clinical by referring to the methods of previous articles. A total of 268 candidates sRNAs were obtained, of which 248 were newly discovered. More importantly, 13 sRNAs were differentially expressed in NDM-5-producing CRKP compared with CSKP. We knocked down sRNA207 in NDM-5-producing CRKP to validate its effect on -1, biofilm, and resistance of strains. We also confirmed the role of -1 in biofilm formation and drug resistance of NDM-5-producing CRKP by constructing -1-knockdown strain. The results suggest that -1 is the target gene of sRNA207. Increased expression of sRNA207 in NDM-5-producing CRKP stabilizes -1 expression, which in turn affects the resistance of the strains through biofilm formation.