Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae
- Author:
Jiang YAN
1
,
2
;
Wang YANFEI
;
Hua XIAOTING
;
Qu YUE
;
Y.Peleg ANTON
;
Yu YUNSONG
Author Information
1. Department of Infectious Diseases,Sir Run Run Shaw Hospital,Zhejiang University School of Medicine,Hangzhou 310016,China
2. Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province,Hangzhou 310016,China
- Keywords:
Horizontal transfer profile;
Transconjugant;
Single-molecule real time sequencing;
Insertion sequence;
Plasmid
- From:
Genomics, Proteomics & Bioinformatics
2020;18(5):539-548
- CountryChina
- Language:Chinese
-
Abstract:
Plasmids remain important microbial components mediating the horizontal gene transfer (HGT) and dissemination of antimicrobial resistance. To systematically explore the relationship between mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), a novel strat-egy using single-molecule real-time (SMRT) sequencing was developed. This approach was applied to pooled conjugative plasmids from clinically isolated multidrug-resistant (MDR) Klebsiella pneu-moniae from a tertiary referral hospital over a 9-month period. The conjugative plasmid pool was obtained from transconjugants that acquired antimicrobial resistance after plasmid conjugation with 53 clinical isolates. The plasmid pool was then subjected to SMRT sequencing, and 82 assem-bled plasmid fragments were obtained. In total, 124 ARGs (responsible for resistance toβ-lactam, fluoroquinolone, and aminoglycoside, among others) and 317 MGEs [including transposons (Tns), insertion sequences (ISs), and integrons] were derived from these fragments. Most of these ARGs were linked to MGEs, allowing for the establishment of a relationship network between MGEs and/or ARGs that can be used to describe the dissemination of resistance by mobile elements. Key elements involved in resistance transposition were identified, including IS26, Tn3, IS903B, ISEcp1, and ISKpn19. As the most predominant IS in the network, a typical IS26-mediated multi-copy composite transposition event was illustrated by tracing its flanking 8-bp target site duplica-tions (TSDs). The landscape of the pooled plasmid sequences highlights the diversity and complex-ity of the relationship between MGEs and ARGs, underpinning the clinical value of dominant HGT profiles.
