title: 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.
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 and within hospital and/or the community has implications for monitoring and controlling spread. Whole-genome sequencing (WGS) is the highest-resolution typing method available for transmission epidemiology. We sequenced carbapenem-resistant K. pneumoniae isolates from 26 individuals involved in several infection case clusters in a Nepali neonatal unit and 68 other clinical Gram-negative isolates from a similar time frame, using Illumina and PacBio technologies. Within-outbreak chromosomal and closed-plasmid structures were generated and used as data set-specific references. Three temporally separated case clusters were caused by a single NDM K. pneumoniae strain with a conserved set of four plasmids, one being a 304,526-bp plasmid carrying bla(NDM-1). The plasmids contained a large number of antimicrobial/heavy metal resistance and plasmid maintenance genes, which may have explained their persistence. No obvious environmental/human reservoir was found. There was no evidence of transmission of outbreak plasmids to other Gram-negative clinical isolates, although bla(NDM) variants were present in other isolates in different genetic contexts. WGS can effectively define complex antimicrobial resistance epidemiology. Wider sampling frames are required to contextualize outbreaks. Infection control may be effective in terminating outbreaks caused by particular strains, even in areas with widespread resistance, although this study could not demonstrate evidence supporting specific interventions. Larger, detailed studies are needed to characterize resistance genes, vectors, and host strains involved in disease, to enable effective intervention.
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom nicole.stoesser@ndm.ox.ac.uk adam.giess@ndm.ox.ac.uk.
authors.forename: N
authors.initials: N
authors.lastname: Stoesser
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom nicole.stoesser@ndm.ox.ac.uk adam.giess@ndm.ox.ac.uk.
authors.forename: A
authors.initials: A
authors.lastname: Giess
authors.affiliation: Wellcome Trust Center for Human Genetics, Oxford, United Kingdom.
authors.forename: E M
authors.initials: EM
authors.lastname: Batty
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: A E
authors.initials: AE
authors.lastname: Sheppard
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom.
authors.forename: A S
authors.initials: AS
authors.lastname: Walker
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom Wellcome Trust Center for Human Genetics, Oxford, United Kingdom.
authors.forename: D J
authors.initials: DJ
authors.lastname: Wilson
authors.affiliation: School of Public Health, Imperial College London, London, United Kingdom.
authors.forename: X
authors.initials: X
authors.lastname: Didelot
authors.affiliation: Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: A
authors.initials: A
authors.lastname: Bashir
authors.affiliation: Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: R
authors.initials: R
authors.lastname: Sebra
authors.affiliation: Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: A
authors.initials: A
authors.lastname: Kasarskis
authors.affiliation: Department of Pediatrics, Patan Hospital, Kathmandu, Nepal.
authors.forename: B
authors.initials: B
authors.lastname: Sthapit
authors.affiliation: Department of Pediatrics, Patan Hospital, Kathmandu, Nepal.
authors.forename: M
authors.initials: M
authors.lastname: Shakya
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom Oxford Vaccine Group, Center for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: D
authors.initials: D
authors.lastname: Kelly
authors.affiliation: NIHR Biomedical Research Center, University of Oxford/Oxford University Hospitals NHS Trust, Oxford, United Kingdom Oxford Vaccine Group, Center for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: A J
authors.initials: AJ
authors.lastname: Pollard
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: T E A
authors.initials: TE
authors.lastname: Peto
authors.affiliation: Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
authors.forename: D W
authors.initials: DW
authors.lastname: Crook
authors.affiliation: Wellcome Trust Center for Human Genetics, Oxford, United Kingdom.
authors.forename: P
authors.initials: P
authors.lastname: Donnelly
authors.affiliation: Department of Pediatrics, Patan Hospital, Kathmandu, Nepal.
authors.forename: S
authors.initials: S
authors.lastname: Thorson
authors.affiliation: Department of Pediatrics, Patan Hospital, Kathmandu, Nepal.
authors.forename: P
authors.initials: P
authors.lastname: Amatya
authors.affiliation: Department of Pediatrics, Patan Hospital, Kathmandu, Nepal.
authors.forename: S
authors.initials: S
authors.lastname: Joshi
mesh_terms: D000900:Anti-Bacterial Agents / Q000627:therapeutic use; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial / Q000737:chemistry* / Q000378:metabolism; D017714:Community-Acquired Infections / Q000188:drug therapy / Q000453:epidemiology / Q000382:microbiology; D003428:Cross Infection / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D024881:Drug Resistance, Bacterial; D019353:Endemic Diseases; D015870:Gene Expression; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006761:Hospitals; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D007363:Intensive Care Units, Neonatal; D007710:Klebsiella Infections / Q000188:drug therapy / Q000453:epidemiology* / Q000382:microbiology; D007711:Klebsiella pneumoniae / Q000187:drug effects / Q000201:enzymology / Q000235:genetics* / Q000302:isolation & purification; D009390:Nepal / Q000453:epidemiology; D010957:Plasmids / Q000737:chemistry / Q000378:metabolism; D001618:beta-Lactamases / Q000235:genetics* / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D001618:beta-Lactamases