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)a...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 strategy using single-molecule real-time(SMRT)sequencing was developed.This approach was applied to pooled conjugative plasmids from clinically isolated multidrug-resistant(MDR)Klebsiella pneumoniae 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 assembled plasmid fragments were obtained.In total,124 ARGs(responsible for resistance to b-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,IS903 B,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 duplications(TSDs).The landscape of the pooled plasmid sequences highlights the diversity and complexity of the relationship between MGEs and ARGs,underpinning the clinical value of dominant HGT profiles.展开更多
Acinetobacter baumannii has three clusters of genes for polysaccharide synthesis.Capsular polysaccharides and lipopolysaccharides are major virulence determinants in many Gram-negative bacteria,and play key roles in t...Acinetobacter baumannii has three clusters of genes for polysaccharide synthesis.Capsular polysaccharides and lipopolysaccharides are major virulence determinants in many Gram-negative bacteria,and play key roles in the overall fitness and virulence in A.baumannii,meanwhile poly-beta-1-6-N-acetylglucosamine was critical for biofilm formation.A variety of studies have been conducted which focused on the surveillance of antimicrobial resistance genes and clones in A.baumannii.However,a tool to perform serotype prediction in A.baumannii is still lacking.Here we present Bautype,a tool for whole genome sequencingbased K and O locus typing in A.baumannii.Using Bautype,users can upload and analyze the genome assembled in a web browser,with the results being displayed in a tabular or graphical format.We demonstrated the high accuracy of predicting K and O locus diversity using Bautype when analyzing more than 3000 A.baumannii genomes.Using our software,we were able to analyze K and O locus diversity among 593 genomes belonging to ST208(3 K and 8 O).These diverse loci can serve as epidemiological markers for Multi-drug Resistance(MDR)strain subtyping.We also identified 45 novel O locus types.Our findings highlight the importance in monitoring the capsule type and LOS of A.baumannii strains for which Bautype is a tailored clinical software.Bautype is available at http://BauType.net.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.81830069 and 81000756)the Key Research Program of the Science Technology Department of Zhejiang Province,China(Grant No.2015C03046)+1 种基金the Zhejiang Province Medical Platform Backbone Talent Plan,China(Grant No.2013RCA030)the Natural Science Foundation of Zhejiang Province,China(Grant No.LY17H190004)。
文摘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 strategy using single-molecule real-time(SMRT)sequencing was developed.This approach was applied to pooled conjugative plasmids from clinically isolated multidrug-resistant(MDR)Klebsiella pneumoniae 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 assembled plasmid fragments were obtained.In total,124 ARGs(responsible for resistance to b-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,IS903 B,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 duplications(TSDs).The landscape of the pooled plasmid sequences highlights the diversity and complexity of the relationship between MGEs and ARGs,underpinning the clinical value of dominant HGT profiles.
基金supported by the grants from the National Natural Science Foundation of China(31970128,31770142,81861138054,31670135)the Zhejiang Province Medical Platform(2020RC075).
文摘Acinetobacter baumannii has three clusters of genes for polysaccharide synthesis.Capsular polysaccharides and lipopolysaccharides are major virulence determinants in many Gram-negative bacteria,and play key roles in the overall fitness and virulence in A.baumannii,meanwhile poly-beta-1-6-N-acetylglucosamine was critical for biofilm formation.A variety of studies have been conducted which focused on the surveillance of antimicrobial resistance genes and clones in A.baumannii.However,a tool to perform serotype prediction in A.baumannii is still lacking.Here we present Bautype,a tool for whole genome sequencingbased K and O locus typing in A.baumannii.Using Bautype,users can upload and analyze the genome assembled in a web browser,with the results being displayed in a tabular or graphical format.We demonstrated the high accuracy of predicting K and O locus diversity using Bautype when analyzing more than 3000 A.baumannii genomes.Using our software,we were able to analyze K and O locus diversity among 593 genomes belonging to ST208(3 K and 8 O).These diverse loci can serve as epidemiological markers for Multi-drug Resistance(MDR)strain subtyping.We also identified 45 novel O locus types.Our findings highlight the importance in monitoring the capsule type and LOS of A.baumannii strains for which Bautype is a tailored clinical software.Bautype is available at http://BauType.net.
