title: Mapping the resistance-associated mobilome of a carbapenem-resistant Klebsiella pneumoniae strain reveals insights into factors shaping these regions and facilitates generation of a 'resistance-disarmed' model organism.
abstract: OBJECTIVE
  This study aims to investigate the landscape of the mobile genome, with a focus on antibiotic resistance-associated factors in carbapenem-resistant Klebsiella pneumoniae.
  
  
  METHODS
  The mobile genome of the completely sequenced K. pneumoniae HS11286 strain (an ST11, carbapenem-resistant, near-pan-resistant, clinical isolate) was annotated in fine detail. The identified mobile genetic elements were mapped to the genetic contexts of resistance genes. The blaKPC-2 gene and a 26 kb region containing 12 clustered antibiotic resistance genes and one biocide resistance gene were deleted, and the MICs were determined again to ensure that antibiotic resistance had been lost.
  
  
  RESULTS
  HS11286 contains six plasmids, 49 ISs, nine transposons, two separate In2-related integron remnants, two integrative and conjugative elements (ICEs) and seven prophages. Sixteen plasmid-borne resistance genes were identified, 14 of which were found to be directly associated with Tn1721-, Tn3-, Tn5393-, In2-, ISCR2- and ISCR3-derived elements. IS26 appears to have actively moulded several of these genetic regions. The deletion of blaKPC-2, followed by the deletion of a 26 kb region containing 12 clustered antibiotic resistance genes, progressively decreased the spectrum and level of resistance exhibited by the resultant mutant strains.
  
  
  CONCLUSIONS
  This study has reiterated the role of plasmids as bearers of the vast majority of resistance genes in this species and has provided valuable insights into the vital role played by ISs, transposons and integrons in shaping the resistance-coding regions in this important strain. The 'resistance-disarmed' K. pneumoniae ST11 strain generated in this study will offer a more benign and readily genetically modifiable model organism for future extensive functional studies.
authors.affiliation: State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China.
authors.forename: Dexi
authors.initials: D
authors.lastname: Bi
authors.affiliation: Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China.
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China.
authors.forename: Zi-Ke
authors.initials: ZK
authors.lastname: Sheng
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK.
authors.forename: David
authors.initials: D
authors.lastname: Ngmenterebo
authors.affiliation: State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China.
authors.forename: Cui
authors.initials: C
authors.lastname: Tai
authors.affiliation: Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China.
authors.forename: Minggui
authors.initials: M
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China.
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.affiliation: Department of Infection, Immunity and Inflammation, University of Leicester, Leicester LE1 9HN, UK.
authors.forename: Kumar
authors.initials: K
authors.lastname: Rajakumar
authors.affiliation: State Key Laboratory for Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai 200030, China Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiaotong University, Shanghai 200240, China hyou@sjtu.edu.cn.
authors.forename: Hong-Yu
authors.initials: HY
authors.lastname: Ou
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology*; D015780:Carbapenems / Q000494:pharmacology*; D002874:Chromosome Mapping; D004251:DNA Transposable Elements; D023061:Gene Order; D007711:Klebsiella pneumoniae / Q000187:drug effects* / Q000235:genetics*; D008826:Microbial Sensitivity Tests; D010957:Plasmids / Q000235:genetics; D018440:beta-Lactam Resistance
chemical_list: D000900:Anti-Bacterial Agents; D015780:Carbapenems; D004251:DNA Transposable Elements