Wei Xin Khong1, Kalisvar Marimuthu1,2, Jeanette Teo3, Yichen Ding4, Eryu Xia5, Jia Jun Lee1, Rick Twee-Hee Ong6, Indumathi Venkatachalam3, Benjamin Cherng7, Surinder Kaur Pada8, Weng Lam Choong8, Nares Smitasin3, Say Tat Ooi9, Rama Narayana Deepak9, Asok Kurup10, Raymond Fong11, My Van La12, Thean Yen Tan11, Tse Hsien Koh7, Raymond Tzer Pin Lin3,12, Eng Lee Tan13, Prabha Unny Krishnan14, Siddharth Singh15, Johann D Pitout16,17,18, Yik-Ying Teo5,6,19,20,21, Liang Yang4, Oon Tek Ng22. 1. Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore. 2. Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Rd 119228, NUHS Tower Block, Level 11, 117597, Singapore. 3. National University Hospital, 5 Lower Kent Ridge Rd, 119074, Singapore. 4. Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore. 5. NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Centre for Life Sciences (CeLS), #05-01Medical Drive, 117456, Singapore. 6. 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. 7. Singapore General Hospital, Outram Road, 169608, Singapore. 8. Ng Teng Fong General Hospital, 1 Jurong East Street 21, 609606, Singapore. 9. Khoo Teck Puat Hospital, 90 Yishun Central, 768828, Singapore. 10. Mount Elizabeth Hospital, 3 Mount Elizabeth, 228510, Singapore. 11. Changi General Hospital, 2 Simei Street 3, 529889, Singapore. 12. National Public Health Laboratory, College of Medicine Building, 16 College Road, 169854, Singapore. 13. Singapore Polytechnic, 500 Dover Road, 139651, Singapore. 14. Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, 308433, Singapore. 15. Pacbio Singapore Pte Ltd, 8 Boon Lay Way, 609964, Singapore. 16. Division of Microbiology, 1829 Ranchlands Blvd NW, Calgary, AB T3G 2A7, Canada. 17. Departments of Pathology and Laboratory Medicine, Microbiology Immunology and Infectious Diseases, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada. 18. Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. 19. Department of Statistics & Applied Probability, Block S16, Level 7, 6 Science Drive 2, Faculty of Science, National University of Singapore, 117546, Singapore. 20. Life Sciences Institute, National University of Singapore, Centre for Life 42 Sciences, #05-02, 28 Medical Drive, 117456, Singapore. 21. Genome Institute of Singapore, 60 Biopolis St, #02-01, 138672, Singapore. 22. Institute of Infectious Disease and Epidemiology, Communicable Disease Centre, 11 Jalan Tan Tock Seng, 308433, Singapore oon_tek_ng@ttsh.com.sg.
Abstract
OBJECTIVES: 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. METHODS: 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. RESULTS: In 20 (61%) isolates, blaNDM was 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. CONCLUSIONS: A combined sequencing-by-synthesis and SMRTS approach can determine effectively the transmission clusters of blaNDM and genetically characterize novel plasmids. Plasmid molecular epidemiology is important to understanding NDM spread as blaNDM-positive plasmids can conjugate extensively across species and STs.
OBJECTIVES: 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. METHODS: 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. RESULTS: In 20 (61%) isolates, blaNDM was 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. CONCLUSIONS: A combined sequencing-by-synthesis and SMRTS approach can determine effectively the transmission clusters of blaNDM and 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: David M Aanensen; Celia C Carlos; Silvia Argimón; Melissa A L Masim; June M Gayeta; Marietta L Lagrada; Polle K V Macaranas; Victoria Cohen; Marilyn T Limas; Holly O Espiritu; Janziel C Palarca; Jeremiah Chilam; Manuel C Jamoralin; Alfred S Villamin; Janice B Borlasa; Agnettah M Olorosa; Lara F T Hernandez; Karis D Boehme; Benjamin Jeffrey; Khalil Abudahab; Charmian M Hufano; Sonia B Sia; John Stelling; Matthew T G Holden Journal: Nat Commun Date: 2020-06-01 Impact factor: 14.919
Authors: Zena Lapp; Ryan Crawford; Arianna Miles-Jay; Ali Pirani; William E Trick; Robert A Weinstein; Mary K Hayden; Evan S Snitkin; Michael Y Lin Journal: Clin Infect Dis Date: 2021-10-20 Impact factor: 9.079
Authors: Yahua Chen; Kalisvar Marimuthu; Jeanette Teo; Indumathi Venkatachalam; Benjamin Pei Zhi Cherng; Liang De Wang; Sai Rama Sridatta Prakki; Weizhen Xu; Yi Han Tan; Lan Chi Nguyen; Tse Hsien Koh; Oon Tek Ng; Yunn-Hwen Gan Journal: Emerg Infect Dis Date: 2020-03 Impact factor: 6.883