Identification of Plasmid-Encoded sRNAs in a blaNDM-1-Harboring Multidrug-Resistance Plasmid pNDM-HK in Enterobacteriaceae

Abstract

Small RNAs (sRNAs) play significant roles in regulating gene expression post-transcriptionally in response to environmental changes in bacteria. In this work, we identified and characterized six novel sRNAs from an emerging multidrug-resistance (MDR) plasmid pNDM-HK, a New Delhi metallo-β-lactamase 1 gene (blaNDM−1)-carrying IncL/M plasmid that has caused worldwide threat in recent years. These sRNAs are located at different regions of pNDM-HK, such as replication, stability, and variable regions. Moreover, one of the plasmid-encoded sRNAs (NDM-sR3) functions in an Hfq-dependent manner and possibly plays roles in the fitness of pNDM-HK carrying bacteria. In addition, we attempted to construct the phylogenetic tree based on these novel sRNAs and surprisingly, the sRNA-phylogenetic tree provided significant information about the evolutionary pathway of pNDM-HK, including possible gene acquisition and insertion from relevant plasmids. Moreover, the sRNA-phylogenetic tree can specifically cluster the IncM2 type and distinguish it from other IncL/M subtypes. In summary, this is the first study to systematically identify and characterize sRNAs from clinically-isolated MDR plasmids. We believe that these newly found sRNAs could lead to further understanding and new directions to study the evolution and dissemination of the clinically MDR bacterial plasmids.

Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying blaNDM in Enterobacteriaceae Isolates in Geographically Widespread Areas

“…PCR assays were used to detect carbapenemase genes ( bla KPC , bla IMI , bla IMP , bla NDM , bla V IM , and bla OXA-48 ). The allele of the carbapenemase genes were determined by Sanger sequencing ( Ho et al, 2016 ; Kong et al, 2018 ). The isolates were surveyed for presence of the IncX1 to IncX5 subtypes plasmid replicons using previously described PCR procedures ( Lo et al, 2014 ).…”

Determination of incompatibility group plasmids and copy number of the bla NDM-1 gene in carbapenem-resistant Klebsiella pneumoniae strains recovered from different hospitals in Kerman, Iran

“…This difference between our results and those of Huang et al might be due to either plasmid type or the regulation of bla NDM-1 expression. Kong et al have reported an important role for bacterial small RNAs (sRNAs) in regulating bla NDM-1 expression for environmental changes [59]. In addition, other factors such as co-producing ESBLs and AmpC with carbapenemase, overactivation of efflux pumps, and loss or alteration of porins might contribute to the increase of MIC to imipenem among K.…”