Genome Sequencing of an Extended Series of NDM-Producing Klebsiella pneumoniae Isolates from Neonatal Infections in a Nepali Hospital Characterizes the Extent of Community- versus Hospital-Associated Transmission in an Endemic Setting

• DOI: 10.1128/aac.03900-14
• Publication Date: 2014-09-30T02:09:54Z
• Authors: N. Stoesser; A. Giess; E. M. Batty; A. E. Sheppard; A. S. Walker; D. J. Wilson; X. Didelot; A. Bashir; R. Sebra; A. Kasarskis; B. Sthapit; M. Shakya; D. Kelly; A. J. Pollard; T. E. A. Peto; D. W. Crook; P. Donnelly; S. Thorson; P. Amatya; S. Joshi
• Keywords: Molecular Epidemiology

ABSTRACT NDM-producing Klebsiella pneumoniae strains represent major clinical and infection control challenges, particularly in resource-limited settings with high rates of antimicrobial resistance. Determining whether transmission occurs at a gene, plasmid, or bacterial strain level within hospital and/or the community has implications for monitoring controlling spread. Whole-genome sequencing (WGS) is highest-resolution typing method available epidemiology. We sequenced carbapenem-resistant K. isolates from 26 individuals involved several case clusters Nepali neonatal unit 68 other Gram-negative similar time frame, using Illumina PacBio technologies. Within-outbreak chromosomal closed-plasmid structures were generated used as data set-specific references. Three temporally separated caused by single NDM conserved set four plasmids, one being 304,526-bp plasmid carrying bla NDM-1 . The plasmids contained large number antimicrobial/heavy metal resistance maintenance genes, which may have explained their persistence. No obvious environmental/human reservoir was found. There no evidence outbreak to isolates, although variants present different genetic contexts. WGS can effectively define complex Wider sampling frames are required contextualize outbreaks. Infection be effective terminating outbreaks particular strains, even areas widespread resistance, this study could not demonstrate supporting specific interventions. Larger, detailed studies needed characterize vectors, host disease, enable intervention.