title: Tracking inter-institutional spread of NDM and identification of a novel NDM-positive plasmid, pSg1-NDM, using next-generation sequencing approaches.
abstract: Owing to gene transposition and plasmid conjugation, New Delhi metallo-β-lactamase (NDM) is typically identified among varied Enterobacteriaceae species and STs. We used WGS to characterize the chromosomal and plasmid molecular epidemiology of NDM transmission involving four institutions in Singapore.
  
  
  
  Thirty-three Enterobacteriaceae isolates (collection years 2010-14) were sequenced using short-read sequencing-by-synthesis and analysed. Long-read single molecule, real-time sequencing (SMRTS) was used to characterize genetically a novel plasmid pSg1-NDM carried on Klebsiella pneumoniae ST147.
  
  
  
  In 20 (61%) isolates, blaNDMwas located on the pNDM-ECS01 plasmid in the background of multiple bacterial STs, including eight K. pneumoniae STs and five Escherichia coli STs. In six (18%) isolates, a novel blaNDM-positive plasmid, pSg1-NDM, was found only in K. pneumoniae ST147. The pSg1-NDM-K. pneumoniae ST147 clone (Sg1-NDM) was fully sequenced using SMRTS. pSg1-NDM, a 90 103 bp IncR plasmid, carried genes responsible for resistance to six classes of antimicrobials. A large portion of pSg1-NDM had no significant homology to any known plasmids in GenBank. pSg1-NDM had no conjugative transfer region. Combined chromosomal-plasmid phylogenetic analysis revealed five clusters of clonal bacterial NDM-positive plasmid transmission, of which two were inter-institution clusters. The largest inter-institution cluster involved six K. pneumoniae ST147-pSg1-NDM isolates. Fifteen patients were involved in transmission clusters, of which four had ward contact, six had hospital contact and five had an unknown transmission link.
  
  
  
  A combined sequencing-by-synthesis and SMRTS approach can determine effectively the transmission clusters of blaNDMand genetically characterize novel plasmids. Plasmid molecular epidemiology is important to understanding NDM spread as blaNDM-positive plasmids can conjugate extensively across species and STs.
authors: Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore.
authors: Wei Xin
authors: WX
authors: Khong
authors: Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore.|Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Rd 119228, NUHS Tower Block, Level 11, 117597, Singapore.
authors: Kalisvar
authors: K
authors: Marimuthu
authors: National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore.
authors: Jeanette
authors: J
authors: Teo
authors: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
authors: Yichen
authors: Y
authors: Ding
authors: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), #05-01Medical Drive, 117456, Singapore.
authors: Eryu
authors: E
authors: Xia
authors: Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore.
authors: Jia Jun
authors: JJ
authors: Lee
authors: Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, 117549, Singapore.
authors: Rick Twee-Hee
authors: RT
authors: Ong
authors: National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore.
authors: Indumathi
authors: I
authors: Venkatachalam
authors: Singapore General Hospital, Outram Road, 169608, Singapore.
authors: Benjamin
authors: B
authors: Cherng
authors: Ng Teng Fong General Hospital, 1 Jurong East Street 21, 609606, Singapore.
authors: Surinder Kaur
authors: SK
authors: Pada
authors: Ng Teng Fong General Hospital, 1 Jurong East Street 21, 609606, Singapore.
authors: Weng Lam
authors: WL
authors: Choong
authors: National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore.
authors: Nares
authors: N
authors: Smitasin
authors: Khoo Teck Puat Hospital, 90 Yishun Central, 768828, Singapore.
authors: Say Tat
authors: ST
authors: Ooi
authors: Khoo Teck Puat Hospital, 90 Yishun Central, 768828, Singapore.
authors: Rama Narayana
authors: RN
authors: Deepak
authors: Mount Elizabeth Hospital, 3 Mount Elizabeth, 228510, Singapore.
authors: Asok
authors: A
authors: Kurup
authors: Changi General Hospital, 2 Simei Street 3, 529889, Singapore.
authors: Raymond
authors: R
authors: Fong
authors: National Public Health Laboratory, College of Medicine Building, 16 College Road, 169854, Singapore.
authors: My
authors: M
authors: Van La
authors: Changi General Hospital, 2 Simei Street 3, 529889, Singapore.
authors: Thean Yen
authors: TY
authors: Tan
authors: Singapore General Hospital, Outram Road, 169608, Singapore.
authors: Tse Hsien
authors: TH
authors: Koh
authors: National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore.|National Public Health Laboratory, College of Medicine Building, 16 College Road, 169854, Singapore.
authors: Raymond Tzer Pin
authors: RT
authors: Lin
authors: Singapore Polytechnic, 500 Dover Road, 139651, Singapore.
authors: Eng Lee
authors: EL
authors: Tan
authors: Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore.
authors: Prabha Unny
authors: PU
authors: Krishnan
authors: Pacbio Singapore Pte Ltd, 8 Boon Lay Way, 609964, Singapore.
authors: Siddharth
authors: S
authors: Singh
authors: Division of Microbiology, 1829 Ranchlands Blvd NW, Calgary, AB T3G 2A7, Canada.|Departments of Pathology and Laboratory Medicine, Microbiology Immunology and Infectious Diseases, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada.|Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
authors: Johann D
authors: JD
authors: Pitout
authors: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), #05-01Medical Drive, 117456, Singapore.|Centre for Infectious Disease Epidemiology and Research, Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, 117549, Singapore.|Department of Statistics & Applied Probability, Block S16, Level 7, 6 Science Drive 2, Faculty of Science, National University of Singapore, 117546, Singapore.|Life Sciences Institute, National University of Singapore, Centre for Life 42 Sciences, #05-02, 28 Medical Drive, 117456, Singapore.|Genome Institute of Singapore, 60 Biopolis St, #02-01, 138672, Singapore.
authors: Yik-Ying
authors: YY
authors: Teo
authors: Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
authors: Liang
authors: L
authors: Yang
authors: Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore oon_tek_ng@ttsh.com.sg.
authors: Oon Tek
authors: OT
authors: Ng
mesh_terms: D004755:Enterobacteriaceae / Q000145:classification / Q000201:enzymology* / Q000235:genetics / Q000302:isolation & purification*; D004756:Enterobacteriaceae Infections / Q000453:epidemiology / Q000382:microbiology* / Q000635:transmission; D022761:Gene Transfer, Horizontal; D006268:Health Facilities; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017720:Molecular Epidemiology; D010957:Plasmids / Q000145:classification / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D012846:Singapore / Q000453:epidemiology; D001618:beta-Lactamases / Q000235:genetics*
chemical_list: D001618:beta-Lactamases; C552864:beta-lactamase NDM-1