scholarly journals Interpretation of Whole-Genome Sequencing for Enteric Disease Surveillance and Outbreak Investigation

2019 ◽  
Vol 16 (7) ◽  
pp. 504-512 ◽  
Author(s):  
John M. Besser ◽  
Heather A. Carleton ◽  
Eija Trees ◽  
Steven G. Stroika ◽  
Kelley Hise ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Disease Surveillance ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Enteric Disease

scholarly journals Agrobacterium spp. nosocomial outbreak assessment using rapid MALDI-TOF MS based typing, confirmed by whole genome sequencing

2019 ◽  
Vol 8 (1) ◽  
Author(s):  
Carlo Casanova ◽  
Elia Lo Priore ◽  
Adrian Egli ◽  
Helena M. B. Seth-Smith ◽  
Lorenz Räber ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Point Sources ◽  
University Hospital ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Epidemiological Characteristics ◽  
Tof Ms

Abstract Background A number of episodes of nosocomial Agrobacterium spp. bacteremia (two cases per year) were observed at Bern University Hospital, Switzerland, from 2015 to 2017. This triggered an outbreak investigation. Methods Cases of Agrobacterium spp. bacteremias that occurred between August 2011 and February 2017 were investigated employing line lists, environmental sampling, rapid protein- (MALDI-TOF MS), and genome-based typing (pulsed field gel electrophoresis and whole genome sequencing) of the clinical isolates. Results We describe a total of eight bacteremia episodes due to A. radiobacter (n = 2), Agrobacterium genomovar G3 (n = 5) and A. pusense (n = 1). Two tight clusters were observed by WGS typing, representing the two A. radiobacter isolates (cluster I, isolated in 2015) and four of the Agrobacterium genomovar G3 isolates (cluster II, isolated in 2016 and 2017), suggesting two different point sources. The epidemiological investigations revealed two computer tomography (CT) rooms as common patient locations, which correlated with the two outbreak clusters. MALDI-TOF MS permitted faster evaluation of strain relatedness than DNA-based methods. High resolution WGS-based typing confirmed the MALDI-TOF MS clustering. Conclusions We report clinical and epidemiological characteristics of two outbreak clusters with Agrobacterium. spp. bacteremia likely acquired during CT contrast medium injection and highlight the use of MALDI-TOF MS as a rapid tool to assess relatedness of rare gram-negative pathogens in an outbreak investigation.

OzFoodNet into the future: the rapid evolution of foodborne disease surveillance in Australia

2017 ◽  
Vol 38 (4) ◽  
pp. 179
Author(s):  
Ben Polkinghorne ◽  
Anthony Draper ◽  
Michelle Harlock ◽  
Robyn Leader
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Diagnostic Tests ◽  
Disease Surveillance ◽  
Rapid Evolution ◽  
Enteric Pathogens ◽  
Whole Genome ◽  
Foodborne Disease ◽  
Surveillance Network ◽  
Culture Independent

OzFoodNet is Australia's national enhanced foodborne disease surveillance network. OzFoodNet is currently evolving in order to meet the most significant challenges faced since it commenced in 2000: the transition to culture independent diagnostic tests and the introduction of whole genome sequencing for typing of enteric pathogens. This has changed the nature of foodborne disease surveillance and outbreak investigation in Australia.

scholarly journals Enhanced tuberculosis outbreak investigation using whole genome sequencing and IGRA

2014 ◽  
Vol 45 (1) ◽  
pp. 276-279 ◽  
Author(s):  
Pieter W. Smit ◽  
Tuula Vasankari ◽  
Hanna Aaltonen ◽  
Marjo Haanperä ◽  
Nicola Casali ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Investigation ◽  
Whole Genome

scholarly journals Prospective Whole-Genome Sequencing in Tuberculosis Outbreak Investigation, France, 2017–2018

2019 ◽  
Vol 25 (3) ◽  
pp. 589-592 ◽  
Author(s):  
Charlotte Genestet ◽  
Caroline Tatai ◽  
Jean-Luc Berland ◽  
Jean-Baptiste Claude ◽  
Emilie Westeel ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Investigation ◽  
Whole Genome

scholarly journals Evaluation of Rapid Library Preparation Protocols for Whole Genome Sequencing Based Outbreak Investigation

2019 ◽  
Vol 7 ◽  
Author(s):  
Helena M. B. Seth-Smith ◽  
Ferdinando Bonfiglio ◽  
Aline Cuénod ◽  
Josiane Reist ◽  
Adrian Egli ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Library Preparation
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