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 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 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.

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 Emergence of a New Highly Successful Acapsular Group A Streptococcus Clade of Genotype emm89 in the United Kingdom

mBio ◽  
2015 ◽  
Vol 6 (4) ◽  
Author(s):  
Claire E. Turner ◽  
James Abbott ◽  
Theresa Lamagni ◽  
Matthew T. G. Holden ◽  
Sophia David ◽  
...  
Keyword(s):  
United Kingdom ◽  
Hyaluronic Acid ◽  
Genome Sequencing ◽  
Virulence Factors ◽  
Invasive Disease ◽  
Whole Genome ◽  
The United Kingdom ◽  
Streptolysin O ◽  
Group A ◽  
Hyaluronic Acid Capsule

ABSTRACTGroup AStreptococcus(GAS) genotypeemm89 is increasingly recognized as a leading cause of disease worldwide, yet factors that underlie the success of thisemmtype are unknown. Surveillance identified a sustained nationwide increase inemm89 invasive GAS disease in the United Kingdom, prompting longitudinal investigation of this genotype. Whole-genome sequencing revealed a recent dramatic shift in theemm89 population with the emergence of a new clade that increased to dominance over previousemm89 variants. Temporal analysis indicated that the clade arose in the early 1990s but abruptly increased in prevalence in 2008, coinciding with an increased incidence ofemm89 infections. Although standard variable typing regions (emmsubtype,teetype,softype, and multilocus sequence typing [MLST]) remained unchanged, uniquely the emergent clade had undergone six distinct regions of homologous recombination across the genome compared to the rest of the sequencedemm89 population. Two of these regions affected known virulence factors, the hyaluronic acid capsule and the toxins NADase and streptolysin O. Unexpectedly, and in contrast to the rest of the sequencedemm89 population, the emergent clade-associated strains were genetically acapsular, rendering them unable to produce the hyaluronic acid capsule. The emergent clade-associated strains had also acquired an NADase/streptolysin O locus nearly identical to that found inemm12 and modernemm1 strains but different from the rest of the sequencedemm89 population. The emergent clade-associated strains had enhanced expression of NADase and streptolysin O. The genome remodeling in the new clade variant and the resultant altered phenotype appear to have conferred a selective advantage over otheremm89 variants and may explain the changes observed inemm89 GAS epidemiology.IMPORTANCESudden upsurges or epidemic waves are common features of group A streptococcal disease. Although the mechanisms behind such changes are largely unknown, they are often associated with an expansion of a single genotype within the population. Using whole-genome sequencing, we investigated a nationwide increase in invasive disease caused by the genotypeemm89 in the United Kingdom. We identified a new clade variant that had recently emerged in theemm89 population after having undergone several core genomic recombination-related changes, two of which affected known virulence factors. An unusual finding of the new variant was the loss of the hyaluronic acid capsule, previously thought to be essential for causing invasive disease. A further genomic adaptation in the NADase/streptolysin O locus resulted in enhanced production of these toxins. Recombination-related genome remodeling is clearly an important mechanism in group AStreptococcusthat can give rise to more successful and potentially more pathogenic variants.

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 Tracking Salmonella Enteritidis in the Genomics Era: Clade Definition Using a SNP-PCR Assay and Implications for Population Structure

2021 ◽  
Author(s):  
Dele Ogunremi ◽  
Ruimin Gao ◽  
Rosemarie Slowey ◽  
Shu Chen ◽  
Olga Andrievskaia ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enteritidis ◽  
Control Measures ◽  
Whole Genome Sequencing Data ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Salmonella Enterica Serovar Enteritidis ◽  
High Discrimination

Salmonella enterica serovar Enteritidis (or Salmonella Enteritidis, SE) is one of the oldest members of the genus Salmonella, based on the date of first description and has only gained prominence as a significant bacterial contaminant of food over the last three or four decades. Currently, SE is the most common Salmonella serovar causing foodborne illnesses. Control measures to alleviate human infections require that food isolates be characterized and this was until recently carried out using Pulsed-Field Gel Electrophoresis (PFGE) and phage typing as the main laboratory subtyping tools for use in demonstrating relatedness of isolates recovered from infected humans and the food source. The results provided by these analytical tools were presented with easy-to-understand and comprehensible nomenclature, however, the techniques were inherently poorly discriminatory, which is attributable to the clonality of SE. The tools have now given way to whole genome sequencing which provides a full and comprehensive genetic attributes of an organism and a very attractive and superior tool for defining an isolate and for inferring genetic relatedness among isolates. A comparative phylogenomic analysis of isolates of choice provides both a visual appreciation of relatedness as well as quantifiable estimates of genetic distance. Despite the considerable information provided by whole genome analysis and development of a phylogenetic tree, the approach does not lend itself to generating a useful nomenclature-based description of SE subtypes. To this end, a highly discriminatory, cost-effective, high throughput, validated single nucleotide based genotypic polymerase chain reaction assay (SNP-PCR) was developed focussing on 60 polymorphic loci. The procedure was used to identify 25 circulating clades of SE, the largest number so far described for this organism. The new subtyping test, which exploited whole genome sequencing data, displays the attributes of an ideal subtyping test: high discrimination, low cost, rapid, highly reproducible and epidemiological concordance. The procedure is useful for identifying the subtype designation of an isolate, for defining the population structure of the organism as well as for surveillance and outbreak detection.

scholarly journals Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota 2015–2017

2020 ◽  
Vol 148 ◽  
Author(s):  
J. M. Rounds ◽  
A. J. Taylor ◽  
D. Eikmeier ◽  
M. M. Nichols ◽  
V. Lappi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Cluster Size ◽  
Salmonella Enteritidis ◽  
Turnaround Time ◽  
Outbreak Detection ◽  
Polymorphism Analysis ◽  
Whole Genome ◽  
Case Definitions ◽  
Department Of Health

Abstract Clusters of Salmonella Enteritidis cases were identified by the Minnesota Department of Health using both pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) single nucleotide polymorphism analysis from 1 January 2015 through 31 December 2017. The median turnaround time for obtaining WGS results was 11 days longer than for PFGE (12 vs. 1 day). WGS analysis more than doubled the number of clusters compared to PFGE analysis, but reduced the total number of cases included in clusters by 34%. The median cluster size was two cases for WGS compared to four for PFGE, and the median duration of WGS clusters was 27 days shorter than PFGE clusters. While the percentage of PFGE clusters with a confirmed source (46%) was higher than WGS clusters (32%), a higher percentage of cases in clusters that were confirmed as outbreaks reported the vehicle or exposure of interest for WGS (78%) than PFGE (46%). WGS cluster size was a significant predictor of an outbreak source being confirmed. WGS data have enhanced S. Enteritidis cluster investigations in Minnesota by improving the specificity of cluster case definitions and has become an integral part of the S. Enteritidis surveillance process.

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.

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