Real-time genomic and epidemiological investigation of a multi-institution outbreak of KPC-producing Enterobacteriaceae: a translational study
Jason C Kwong,Courtney R Lane,Finn Romanes,Anders Gonçalves da Silva,Marion Easton,Katie Cronin,Mary Jo Waters,Takehiro Tomita,Kerrie Stevens,Mark B. Schultz,Sarah L. Baines,Norelle L Sherry,Glen P. Carter,Andre Mu,Michelle Sait,Susan A Ballard,Torsten Seemann,Timothy P. Stinear,Benjamin P Howden +18 more
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TLDR
A real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive.Abstract:
Background: Until recently, KPC-producing Enterobacteriaceae were rarely identified in Australia. Following an increase in the number of incident cases across the state of Victoria, we undertook a real-time combined genomic and epidemiological investigation. The scope of this study included identifying risk factors and routes of transmission, and investigating the utility of genomics to enhance traditional field epidemiology for informing management of established widespread outbreaks. Methods and Findings: All KPC-producing Enterobacteriaceae isolates referred to the state reference laboratory from 2012 onwards were included. Whole-genome sequencing (WGS) was performed in parallel with a detailed descriptive epidemiological investigation of each case, using Illumina sequencing on each isolate. This was complemented with PacBio long-read sequencing on selected isolates to establish high-quality reference sequences and interrogate characteristics of KPC-encoding plasmids. Initial investigations indicated the outbreak was widespread, with 86 KPC-producing Enterobacteriaceae isolates (K. pneumoniae 92%) identified from 35 different locations across metropolitan and rural Victoria between 2012-2015. Initial combined analyses of the epidemiological and genomic data resolved the outbreak into distinct nosocomial transmission networks, and identified healthcare facilities at the epicentre of KPC transmission. New cases were assigned to transmission networks in real-time, allowing focussed infection control efforts. PacBio sequencing confirmed a secondary transmission network arising from inter-species plasmid transmission. Insights from Bayesian transmission inference and analyses of within-host diversity informed the development of state-wide public health and infection control guidelines, including interventions such as an intensive approach to screening contacts following new case detection to minimise unrecognised colonisation. Conclusions: A real-time combined epidemiological and genomic investigation proved critical to identifying and defining multiple transmission networks of KPC Enterobacteriaceae, while data from either investigation alone were inconclusive. The investigation was fundamental to informing infection control measures in real-time and the development of state-wide public health guidelines on carbapenemase producing Enterobacteriaceae management.read more
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SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Journal ArticleDOI
Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital.
Claire L. Gorrie,Mirjana Mirceta,Ryan R. Wick,Louise M. Judd,Kelly L. Wyres,Nicholas R. Thomson,Richard A. Strugnell,Nigel F. Pratt,Jill S. Garlick,Kerrie Watson,Peter Hunter,Steve A. McGloughlin,Denis Spelman,Adam Jenney,Kathryn E. Holt +14 more
TL;DR: Patients’ own gut microbiota were the major source of Klebsiella pneumoniae, but extended-spectrum β-lactamase strains were acquired in the referring hospital, highlighting the potential for rectal screening and the importance of the wider hospital network, for local risk management.
Posted ContentDOI
Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital
Claire L. Gorrie,Mirjana Mirceta,Ryan R. Wick,Louise M. Judd,Kelly L. Wyres,Nicholas R. Thomson,Richard A. Strugnell,Nigel F. Pratt,Jill S. Garlick,Kerrie Watson,Peter Hunter,Steve A. McGloughlin,Denis Spelman,Adam Jenney,Kathryn E. Holt +14 more
TL;DR: The data suggest the major source of K. pneumoniae was the patient’s own gut microbiome, but extended-spectrum beta-lactamase strains were acquired in the referring hospital, highlighting the need for rectal screening for ESBL organisms upon admission to geriatric wards.
outbreaker2: Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
TL;DR: This work introduces a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks, and is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker.
Dissertation
Population structure and carriage-infection dynamics of Klebsiella pneumoniae
TL;DR: In this article, the authors propose a method to solve the problem of "uniformity" and "uncertainty" in the context of video games.2.3.2
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