scholarly journals Whole-Genome Sequencing Reveals the Origin and Rapid Evolution of an Emerging Outbreak Strain ofStreptococcus pneumoniae12F

2016 ◽  
Vol 62 (9) ◽  
pp. 1126-1132 ◽  
Author(s):  
Xianding Deng ◽  
Gisele Peirano ◽  
Erin Schillberg ◽  
Tony Mazzulli ◽  
Scott D. Gray-Owen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Rapid Evolution ◽  
Whole Genome ◽  
Outbreak Strain

scholarly journals Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate

2015 ◽  
Vol 144 (3) ◽  
pp. 576-581 ◽  
Author(s):  
M. MOHAMMED ◽  
N. DELAPPE ◽  
J. O'CONNOR ◽  
P. McKEOWN ◽  
P. GARVEY ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Gel Electrophoresis ◽  
Invasive Disease ◽  
Pulsed Field Gel Electrophoresis ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Salmonella Dublin ◽  
Source Of Infection ◽  
Human Salmonellosis

SUMMARYSalmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

scholarly journals In-Depth Study of a Nosocomial Outbreak Caused by Extensively Drug-Resistant Pseudomonas aeruginosa Using Whole Genome Sequencing Coupled With a Polymerase Chain Reaction Targeting Strain-Specific Single Nucleotide Polymorphisms

2020 ◽  
Vol 189 (8) ◽  
pp. 841-849
Author(s):  
Fermín Acosta ◽  
Ana Fernández-Cruz ◽  
Sandra R Maus ◽  
Pedro J Sola-Campoy ◽  
Mercedes Marín ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Outbreak Strain ◽  
Single Nucleotide ◽  
Specific Pcr ◽  
Extensively Drug Resistant ◽  
Polymerase Chain

Abstract In 2013–2014, an outbreak involving 14 patients infected by an extensively drug-resistant strain of Pseudomonas aeruginosa was detected in a hospital in Madrid, Spain. Our objective was to evaluate an alternative strategy for investigating the outbreak in depth by means of molecular and genomic approaches. Pulsed-field gel electrophoresis (PFGE) was applied as a first-line approach, followed by a more refined whole genome sequencing analysis. Single nucleotide polymorphisms identified by whole genome sequencing were used to design a specific polymerase chain reaction (PCR) for screening unsuspected cases infected by the outbreak strain. Whole genome sequencing alerted us to the existence of greater genetic diversity than was initially assumed, splitting the PFGE-associated outbreak isolates into 4 groups, 2 of which represented coincidental transmission unrelated to the outbreak. A multiplex allele-specific PCR targeting outbreak-specific single nucleotide polymorphisms was applied to 290 isolates, which allowed us to identify 25 additional cases related to the outbreak during 2011–2017. Whole genome sequencing coupled with an outbreak-strain-specific PCR enabled us to markedly redefine the initial picture of the outbreak by 1) ruling out initially suspected cases, 2) defining likely independent coincidental transmission events, 3) predating the starting point of the outbreak, 4) capturing new unsuspected cases, and 5) revealing that the outbreak was still active.

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 Utility of whole-genome sequencing during an investigation of multiple foodborne outbreaks of Shigella sonnei

2021 ◽  
Vol 149 ◽  
Author(s):  
Amy F. W. Mikhail ◽  
Monique Pereboom ◽  
Lara Utsi ◽  
Jeremy Hawker ◽  
Jonathan Lighthill ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Middle Eastern ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Food Samples ◽  
Shigella Sonnei ◽  
Whole Genome ◽  
Contributing Factors ◽  
Outbreak Strain

Abstract In April 2018, Public Health England was notified of cases of Shigella sonnei who had eaten food from three different catering outlets in England. The outbreaks were initially investigated as separate events, but whole-genome sequencing (WGS) showed they were caused by the same strain. The investigation included analyses of epidemiological data, the food chain and microbiological examination of food samples. WGS was used to determine the phylogenetic relatedness and antimicrobial resistance profile of the outbreak strain. Ultimately, 33 cases were linked to this outbreak; the majority had eaten food from seven outlets specialising in Indian or Middle Eastern cuisine. Five outlets were linked to two or more cases, all of which used fresh coriander although a shared supplier was not identified. An investigation at one of the venues recorded that 86% of cases reported eating dishes with coriander as an ingredient or garnish. Four cases were admitted to hospital and one had evidence of treatment failure with ciprofloxacin. Phylogenetic analysis showed that the outbreak strain was part of a wider multidrug-resistant clade associated with travel to Pakistan. Poor hygiene practices during cultivation, distribution or preparation of fresh produce are likely contributing factors.

scholarly journals Intensive infection control responses and whole genome sequencing to interrupt and resolve widespread transmission of OXA-181 Escherichia coli in a hospital setting

2019 ◽  
Author(s):  
Leah W. Roberts ◽  
Brian M. Forde ◽  
Andrew Henderson ◽  
E. Geoffrey Playford ◽  
Naomi Runnegar ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Infection Control ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Hospital Setting ◽  
Whole Genome ◽  
Outbreak Strain ◽  
E Coli ◽  
Public Data

AbstractBackgroundOXA-48-like carbapenemases have become increasingly prevalent in healthcare settings worldwide. Their low-level activity against carbapenems makes them difficult to identify, causing problems for infection control. Here we present an outbreak of Escherichia coli producing OXA-181 (part of the OXA-48 family of carbapenemases) in a Queensland Hospital, and describe how we used whole genome sequencing (WGS) to identify the outbreak strain, determine the extent of transmission within the hospital and support infection control responses.Methods116 isolates were collected and sequenced on an Illumina NextSeq to determine species, sequence type (ST) and presence of resistance genes. Core single nucleotide polymorphisms were used to determine strain relatedness. Three isolates were also sequenced on an Oxford Nanopore MinION to determine the context of the resistance genes.ResultsOf 116 isolates, 85 (84 E. coli and one K. pneumoniae) from 78 patients (and two environmental sources) were related to the ongoing outbreak. The outbreak E. coli strain was found to be ST38 and carried blaOXA-181, blaCTX-M-15 and qnrS1 genes. Long read sequencing revealed blaOXA-181 to be carried on an IncX3 plasmid with qnrS1. blaCTX-M-15 was chromosomally integrated (via ISEcp1 insertion) in close proximity to a second qnrS1 gene. A search of the laboratory database identified an isolate with an identical unusual antibiogram from a patient recently admitted to a hospital in Vietnam, suggesting that the strain was introduced to the hospital. This conclusion was supported by WGS, as comparison of the strain to public data identified a close match to an E. coli recovered from Vietnam in 2011.ConclusionA blaOXA-181-carrying E. coli ST38 strain was introduced to a Brisbane hospital and spread undetected throughout multiple wards over several months. Using WGS, we characterized the outbreak strain and unambiguously detected its presence throughout the hospital. We show how both WGS and infection control measures can be utilized to effectively terminate widespread transmission of an elusory pathogen.

A Novel Lineage of Ceftriaxone-resistant Salmonella Typhi From India That Is Closely Related to XDR S. Typhi Found in Pakistan

2019 ◽  
Vol 71 (5) ◽  
pp. 1327-1330 ◽  
Author(s):  
Ranjit Sah ◽  
Suzanne Donovan ◽  
Helena M B Seth-Smith ◽  
Guido Bloemberg ◽  
Daniel Wüthrich ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Typhi ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Indian Isolates

Abstract Two MDR Salmonella Typhi isolates from India were found by whole genome sequencing to be closely related to the 2016 XDR S. Typhi outbreak strain from Pakistan. The Indian isolates have no chromosomal antimicrobial resistance cassette but carry the IncY plasmid p60006. Both isolates are susceptible to chloramphenicol, azithromycin, and carbapenems.

scholarly journals Whole genome sequencing improved case ascertainment in an outbreak of Shiga toxin-producing Escherichia coli O157 associated with raw drinking milk

2016 ◽  
Vol 144 (13) ◽  
pp. 2812-2823 ◽  
Author(s):  
H. BUTCHER ◽  
R. ELSON ◽  
M. A. CHATTAWAY ◽  
C. A. FEATHERSTONE ◽  
C. WILLIS ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Phage Type ◽  
Dairy Farm ◽  
Whole Genome ◽  
The South ◽  
Outbreak Strain ◽  
Case Ascertainment ◽  
South West ◽  
Drinking Milk

SUMMARYFive cases of STEC O157 phage type (PT) 21/28 reported consumption of raw cows' drinking milk (RDM) produced at a dairy farm in the South West of England. STEC O157 PT21/28 was isolated from faecal specimens from milking cows on the implicated farm. Whole genome sequencing (WGS) showed that human and cattle isolates were the same strain. Further analysis of WGS data confirmed that sequences of isolates from an additional four cases (who did not report consumption of RDM when first questioned) fell within the same five single nucleotide polymorphism cluster as the initial five cases epidemiologically linked to the consumption of RDM. These four additional cases identified by WGS were investigated further and were, ultimately, associated with the implicated farm. The RDM outbreak strain encoded stx2a, which is associated with increased pathogenicity and severity of symptoms. Further epidemiological analysis showed that 70% of isolates within a wider cluster containing the outbreak strain were from cases residing in, or linked to, the same geographical region of England. During this RDM outbreak, use of WGS improved case ascertainment and provided insights into the evolution of a highly pathogenic clade of STEC O157 PT21/28 stx2a associated with the South West of England.

scholarly journals Retrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247

2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Mihkel Mäesaar ◽  
Rafael Mamede ◽  
Terje Elias ◽  
Mati Roasto
Keyword(s):  
Listeria Monocytogenes ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Core Genome ◽  
Clonal Complex ◽  
Antibiotic Resistance Genes ◽  
Whole Genome ◽  
Outbreak Strain ◽  
Determining Factors ◽  
Fish Product

Listeria monocytogenes sequence type 1247 clonal complex 8 caused a prolonged multicountry outbreak in five EU countries: Denmark, Estonia, Finland, France, and Sweden. A total of 22 disease cases were identified with onset of symptoms between July 2014 and February 2019. Five patients died due to, or with, the disease. The retrospective analysis of L. monocytogenes isolate VLTRLM2013 revealed the presence of an outbreak-related strain (cgMLST type L2-SL8-ST1247-CT4158) in ready-to-eat fish product more than a year prior to the first outbreak-related cases. Reference outbreak strain and VLTRLM2013 strain were compared using core genome and whole-genome multilocus sequence typing analyses. Genomic level differences of the persistent L. monocytogenes strains associated with a prolonged multicountry foodborne listeriosis outbreak are described. It was concluded that the persistent nature of the multicountry outbreak-related L. monocytogenes strain VLTRLM2013 together with stress island, virulence, and antibiotic resistance genes could potentially be the determining factors for the extensive and prolonged outbreak affecting five European Union countries. Our results support the systematic application of whole-genome sequencing in food and public health surveillance and further encourages its wide adoption.

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