Structural Genomics of repA, repB1-Carrying IncFIB Family pA1705-qnrS, P911021-tetA, and P1642-tetA, Multidrug-Resistant Plasmids from Klebsiella pneumoniae

Abstract

Background

Multidrug-resistant plasmids carrying replication genes have been widely present in various strains of Klebsiella pneumoniae. RepA and repB1 were found in plasmids belong to the IncFIB, but their detailed structural and genomic characterization was not reported yet. This is the first study that delivers structural and functional insights of repA- and repB1-carrying IncFIB plasmids.

Methods

Klebsiella pneumoniae strains A1705, 911021, and 1642 were isolated from the human urine samples and bronchoalveolar fluids collected from different hospitals of China. Antibacterial susceptibility and plasmid transfer ability were tested to characterize the resistant phenotypes mediated by the pA1705-qnrS, p911021-tetA, and p1642-tetA. The complete nucleotide sequences of these plasmids were determined through high-throughput sequencing technology and comparative genomic analyses of plasmids belong to the same incompatibility group were executed to extract the genomic variations and features.

Results

The pA1705-qnrS, p911021-tetA, and p1642-tetA are defined as non-conjugative plasmids, having two replication genes, repA and repB1 associated with IncFIB family, and unknown incompatible group, respectively. Comparative genomic analysis revealed that relatively small backbones of IncFIB plasmids integrated massive accessory module at one “hotspot” that was located between orf312 and repB1. These IncFIB plasmids exhibited the distinct profiles of accessory modules including one or two multidrug-resistant regions, many complete and remnant mobile elements comprising integrons, transposons and insertion sequences. The clusters of resistant genes were recognized in this study against different classes of antibiotics including β-lactam, phenicol, aminoglycoside, tetracycline, quinolone, trimethoprim, sulfonamide, tunicamycin, and macrolide. It has been observed that all resistant genes were located in multidrug resistance regions.

Conclusion

It is concluded that multidrug-resistant repA and repB1-carrying IncFIB plasmids are a key source to mediate the resistance through mobile elements among Klebsiella pneumoniae. Current findings provide a deep understanding of horizontal gene transfer among plasmids of the IncFIB family via mobile elements that will be utilized in further in vitro studies.

Keywords:

• plasmids
• repA
• repB1
• multidrug resistance
• structural genomics
• bioinformatics

Acknowledgments

This research was supported by a grant from The National Key Research and Development Program of China (2015AA020108, 2016YFC1202705, SKLPBS1518, AWS16J020 and AWS15J006), the National Natural Science Foundation of China (81572045, 81672001, and 81621005), National Science and Technology Major Project (Grant No. 2018ZX10201001). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Ethics Statement

Ethics approval and informed consent were not required. All the bacterial isolates involved in this study were part of the routine hospital laboratory procedure.

Disclosure

The authors state that they have no conflicts of interest.