scholarly journals A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014

2015 ◽  
Vol 20 (16) ◽  
Author(s):  
T Inns ◽  
C Lane ◽  
T Peters ◽  
T Dallman ◽  
C Chatt ◽  
...  
Keyword(s):  
United Kingdom ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Chain ◽  
Salmonella Enteritidis ◽  
Phage Type ◽  
Whole Genome ◽  
Binary File ◽  
German Producer ◽  
Real Time Application

Binary file ES_Abstracts_Final_ECDC.txt matches

Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015

2018 ◽  
Vol 71 ◽  
pp. 32-38 ◽  
Author(s):  
Sanch Kanagarajah ◽  
Alison Waldram ◽  
Gayle Dolan ◽  
Claire Jenkins ◽  
Philip M. Ashton ◽  
...  
Keyword(s):  
United Kingdom ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enteritidis ◽  
Whole Genome ◽  
The United Kingdom

scholarly journals Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis

2016 ◽  
Vol 145 (2) ◽  
pp. 289-298 ◽  
Author(s):  
T. INNS ◽  
P. M. ASHTON ◽  
S. HERRERA-LEON ◽  
J. LIGHTHILL ◽  
S. FOULKES ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Food Chain ◽  
Salmonella Enteritidis ◽  
Common Source ◽  
Reference Laboratory ◽  
Whole Genome ◽  
Food History ◽  
The Uk ◽  
Chicken Eggs

SUMMARYSince April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

scholarly journals High-Resolution Analysis by Whole-Genome Sequencing of an International Lineage (Sequence Type 111) of Pseudomonas aeruginosa Associated with Metallo-Carbapenemases in the United Kingdom

2015 ◽  
Vol 53 (8) ◽  
pp. 2622-2631 ◽  
Author(s):  
Jane F. Turton ◽  
Laura Wright ◽  
Anthony Underwood ◽  
Adam A. Witney ◽  
Yuen-Ting Chan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
United Kingdom ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Type ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Evolutionary Analysis ◽  
Accessory Gene ◽  
The United Kingdom

Whole-genome sequencing (WGS) was carried out on 87 isolates of sequence type 111 (ST-111) of Pseudomonas aeruginosa collected between 2005 and 2014 from 65 patients and 12 environmental isolates from 24 hospital laboratories across the United Kingdom on an Illumina HiSeq instrument. Most isolates (73) carried VIM-2, but others carried IMP-1 or IMP-13 (5) or NDM-1 (1); one isolate had VIM-2 and IMP-18, and 7 carried no metallo-beta-lactamase (MBL) gene. Single nucleotide polymorphism analysis divided the isolates into distinct clusters; the NDM-1 isolate was an outlier, and the IMP isolates and 6/7 MBL-negative isolates clustered separately from the main set of 73 VIM-2 isolates. Within the VIM-2 set, there were at least 3 distinct clusters, including a tightly clustered set of isolates from 3 hospital laboratories consistent with an outbreak from a single introduction that was quickly brought under control and a much broader set dominated by isolates from a long-running outbreak in a London hospital likely seeded from an environmental source, requiring different control measures; isolates from 7 other hospital laboratories in London and southeast England were also included. Bayesian evolutionary analysis indicated that all the isolates shared a common ancestor dating back ∼50 years (1960s), with the main VIM-2 set separating approximately 20 to 30 years ago. Accessory gene profiling revealed blocks of genes associated with particular clusters, with some having high similarity (≥95%) to bacteriophage genes. WGS of widely found international lineages such as ST-111 provides the necessary resolution to inform epidemiological investigations and intervention policies.

scholarly journals First use of whole-genome sequencing to investigate a cluster of Yersinia enterocolitica, Liverpool, United Kingdom, 2017

2018 ◽  
Vol 67 (12) ◽  
pp. 1747-1752 ◽  
Author(s):  
Thomas Inns ◽  
Stephen Flanagan ◽  
David R. Greig ◽  
Claire Jenkins ◽  
Keeley Seddon ◽  
...  
Keyword(s):  
United Kingdom ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Yersinia Enterocolitica ◽  
Whole Genome

scholarly journals Genotyping Study of Salmonella 4,[5],12:i:- Monophasic Variant of Serovar Typhimurium and Characterization of the Second-Phase Flagellar Deletion by Whole Genome Sequencing

2020 ◽  
Vol 8 (12) ◽  
pp. 2049
Author(s):  
Ainhoa Arrieta-Gisasola ◽  
Aitor Atxaerandio-Landa ◽  
Victoria Garrido ◽  
María Jesús Grilló ◽  
Ilargi Martínez-Ballesteros ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enteritidis ◽  
Genomic Region ◽  
Second Phase ◽  
Whole Genome ◽  
Serovar Typhimurium ◽  
Selection Of

After Salmonella Enteritidis and S. Typhimurium, S. 4,[5],12:i:- is the most reported serovar in human clinical cases. During the past 20 years, many tools have been used for its typing and second-phase flagellar deletion characterization. Currently, whole genome sequencing (WGS) and different bioinformatic programs have shown the potential to be more accurate than earlier tools. To assess this potential, we analyzed by WGS and in silico typing a selection of 42 isolates of S. 4,[5],12:i:- and S. Typhimurium with different in vitro characteristics. Comparative analysis showed that SeqSero2 does not differentiate fljB-positive S. 4,[5],12:i:- strains from those of serovar Typhimurium. Our results proved that the strains selected for this work were non-clonal S. 4,[5],12:i:- strains circulating in Spain. Using WGS data, we identified 13 different deletion types of the second-phase flagellar genomic region. Most of the deletions were generated by IS26 insertions, showing orientation-dependent conserved deletion ends. In addition, we detected S. 4,[5],12:i:- strains of the American clonal line that would give rise to the Southern European clone in Spain. Our results suggest that new S. 4,[5],12:i:- strains are continuously emerging from different S. Typhimurium strains via different genetic events, at least in swine products.

scholarly journals Genetic relatedness of ceftriaxone-resistant and high-level azithromycin resistant Neisseria gonorrhoeae cases, United Kingdom and Australia, February to April 2018

2019 ◽  
Vol 24 (8) ◽  
Author(s):  
Amy V Jennison ◽  
David Whiley ◽  
Monica M Lahra ◽  
Rikki M Graham ◽  
Michelle J Cole ◽  
...  
Keyword(s):  
United Kingdom ◽  
Neisseria Gonorrhoeae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Relatedness ◽  
Whole Genome ◽  
The United Kingdom ◽  
High Level

Between February and April 2018, three ceftriaxone-resistant and high-level azithromycin-resistant Neisseria gonorrhoeae cases were identified; one in the United Kingdom and two in Australia. Whole genome sequencing was used to show that the isolates from these cases belong to a single gonococcal clone, which we name the A2543 clone.

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