scholarly journals Cross-border outbreak of Yersinia enterocolitica O3 associated with imported fresh spinach, Sweden and Denmark, March 2019

2019 ◽  
Vol 24 (24) ◽  
Author(s):  
Laura Espenhain ◽  
Maximilian Riess ◽  
Luise Müller ◽  
Soledad Colombe ◽  
Steen Ethelberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Yersinia Enterocolitica ◽  
Whole Genome ◽  
Cross Border ◽  
Trace Back

In April 2019, a cross-border outbreak of Yersinia entercolitica O3 was identified in Sweden and Denmark and confirmed using whole genome sequencing. Close cross-border collaboration with representatives from human and food authorities helped direct resources and investigations. Combined epidemiological and trace-back investigations pointed to imported fresh spinach as the outbreak vehicle and highlight that other vehicles of Y. enterocolitica outbreaks than pork should be considered.

Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing

2018 ◽  
Vol 15 (5) ◽  
pp. 285-292 ◽  
Author(s):  
Laura Ford ◽  
Qinning Wang ◽  
Russell Stafford ◽  
Kelly-Anne Ressler ◽  
Sophie Norton ◽  
...  
Keyword(s):  
Salmonella Typhimurium ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Trace Back

scholarly journals Impact of whole genome sequencing on the investigation of food-borne outbreaks of Shiga toxin-producing Escherichia coli serogroup O157:H7, England, 2013 to 2017

2019 ◽  
Vol 24 (4) ◽  
Author(s):  
Claire Jenkins ◽  
Timothy J Dallman ◽  
Kathie A Grant
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Whole Genome ◽  
Trace Back ◽  
Food Borne ◽  
Evolutionary Context

We aim to provide insight and guidance on the utility of whole genome sequencing (WGS) data for investigating food-borne outbreaks of Shiga toxin-producing Escherichia coli (STEC) O157:H7 in England between 2013 and 2017. Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with multilocus variable number tandem repeat analysis. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured. There was evidence that phylogeny derived from WGS data can be used to trace the geographical origin of an isolate. Further analysis of the phylogenetic data provided insight on the evolutionary context of emerging pathogenic strains. Publically available WGS data linked to the clinical, epidemiological and environmental context of the sequenced strain has improved trace back investigations during outbreaks. Expanding the use of WGS-based typing analysis globally will ensure the rapid implementation of interventions to protect public health, inform risk assessment and facilitate the management of national and international food-borne outbreaks of STEC O157:H7.

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 Whole genome sequencing–based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent transmission in the host country and new importations

2019 ◽  
Vol 24 (4) ◽  
Author(s):  
Estefanía Abascal ◽  
Laura Pérez-Lago ◽  
Miguel Martínez-Lirola ◽  
Álvaro Chiner-Oms ◽  
Marta Herranz ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Host Country ◽  
Whole Genome ◽  
Cross Border ◽  
Recent Transmission ◽  
Allele Specific ◽  
Complex Cluster ◽  
Pcr Targeting ◽  
Border Surveillance

Background The analysis of transmission of tuberculosis (TB) is challenging in areas with a large migrant population. Standard genotyping may fail to differentiate transmission within the host country from new importations, which is key from an epidemiological perspective. Aim To propose a new strategy to simplify and optimise cross-border surveillance of tuberculosis and to distinguish between recent transmission in the host country and new importations Methods We selected 10 clusters, defined by 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR), from a population in Spain rich in migrants from eastern Europe, north Africa and west Africa and reanalysed 66 isolates by whole-genome sequencing (WGS). A multiplex-allele-specific PCR was designed to target strain-specific marker single nucleotide polymorphisms (SNPs), identified from WGS data, to optimise the surveillance of the most complex cluster. Results In five of 10 clusters not all isolates showed the short genetic distances expected for recent transmission and revealed a higher number of SNPs, thus suggesting independent importations of prevalent strains in the country of origin. In the most complex cluster, rich in Moroccan cases, a multiplex allele-specific oligonucleotide-PCR (ASO-PCR) targeting the marker SNPs for the transmission subcluster enabled us to prospectively identify new secondary cases. The ASO-PCR-based strategy was transferred and applied in Morocco, demonstrating that the strain was prevalent in the country. Conclusion We provide a new model for optimising the analysis of cross-border surveillance of TB transmission in the scenario of global migration.

scholarly journals A cross-border outbreak of Salmonella Bareilly cases confirmed by whole genome sequencing, Czech Republic and Slovakia, 2017 to 2018

2021 ◽  
Vol 26 (14) ◽  
Author(s):  
Klára Labská ◽  
Michaela Špačková ◽  
Ondřej Daniel ◽  
Josef Včelák ◽  
Veronika Vlasáková ◽  
...  
Keyword(s):  
Czech Republic ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Reference Laboratory ◽  
Production Plant ◽  
Surveillance Systems ◽  
Whole Genome ◽  
Cross Border ◽  
Typing Methods ◽  
Imported Foods

In August 2017, an increased incidence of Salmonella Bareilly was detected in the Czech Republic. An investigation was conducted with Slovakia to confirm the outbreak and identify the source. Probable outbreak cases were defined as cases with laboratory-confirmed S. Bareilly reported in either of the national surveillance systems, and/or the Czech and Slovak National Reference Laboratory databases from July 2017. Confirmed cases had the pulsed-field gel electrophoresis (PFGE) outbreak pulsotype or up to 5 alleles difference from outbreak cluster members by core genome multilocus sequence typing (cgMLST). PFGE and whole genome sequencing were used for isolate comparison. The same trawling questionnaire was used in both countries. By the end of October 2018, 325 cases were identified. Among 88 human S. Bareilly isolates analysed by PFGE, 82 (93%) shared an identical pulsotype; cgMLST of 17 S. Bareilly human isolates showed 1–2 allele difference. The trawling questionnaire excluded consumption of unusual or imported foods. In September 2018, an isolate closely related to the outbreak isolates was identified in a powdered egg product. A spray dryer was recognised as the contamination source and the production plant was closed. Using molecular typing methods, we detected a diffuse cross-border outbreak caused by S. Bareilly.

scholarly journals A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt

2017 ◽  
Vol 22 (2) ◽  
Author(s):  
Lena Fiebig ◽  
Thomas A Kohl ◽  
Odette Popovici ◽  
Margarita Mühlenfeld ◽  
Alexander Indra ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Universal Access ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
The European Union ◽  
Cross Border ◽  
Resistant Tuberculosis ◽  
Multidrug Resistant Tuberculosis ◽  
Mdr Tb

Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility. Ten isolates from 10 patients shared the same 24-loci MIRU-VNTR pattern. Within this cluster, WGS defined two subgroups of four patients each. The first comprised an MDR-TB patient from Romania who had sought medical care in Austria and two patients from Austria. The second comprised patients, two of them epidemiologically linked, who lived in three different countries but had the same city of provenance in Romania. Our findings strongly suggested that the two cases in Austrian citizens resulted from a newly introduced MDR-TB strain, followed by domestic transmission. For the other cases, transmission probably occurred in the same city of provenance. To prevent further MDR-TB transmission, we need to ensure universal access to early and adequate therapy and collaborate closely in tuberculosis care beyond administrative borders.

scholarly journals Use of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017–2019: an ECDC pilot study

2020 ◽  
Vol 57 (1) ◽  
pp. 2002272
Author(s):  
Elisa Tagliani ◽  
Richard Anthony ◽  
Thomas A. Kohl ◽  
Albert de Neeling ◽  
Vlad Nikolayevskyy ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Pilot Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance System ◽  
European Economic Area ◽  
Whole Genome ◽  
Cross Border ◽  
Lessons Learnt ◽  
Mdr Tb

Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system.WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability.A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 cross-border clusters with increased likelihood of recent transmission (≤5 SNPs distance) comprising 316 RR/MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries.This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGS-based surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters.

scholarly journals Genomic epidemiology of SARS-CoV-2 in Russia reveals recurring cross-border transmission throughout 2020

2021 ◽  
Author(s):  
Alina Matsvay ◽  
Galya Klink ◽  
Ksenia Safina ◽  
Elena Nabieva ◽  
Sofya Garushyants ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Genomic Epidemiology ◽  
Passenger Traffic ◽  
Cross Border ◽  
Regions Of Russia

Abstract SARS-CoV-2 has spread rapidly across the globe, with most nations failing to prevent or substantially delay its introduction. While many countries have imposed some limitations on trans-border passenger traffic, the effect of these measures on the spread of COVID-19 strains remains unclear. Here, we report an analysis of whole-genome sequencing of 3206 SARS-CoV-2 samples from 78 regions of Russia covering the period between March and November 2020. We describe recurring imports of multiple COVID-19 strains throughout this period, giving rise to 457 uniquely Russian transmission lineages, as well as repeated cross-border transmissions of local circulating variants out of Russia.

scholarly journals Cross-border spread of blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae: a European collaborative analysis of whole genome sequencing and epidemiological data, 2014 to 2019

2020 ◽  
Vol 25 (20) ◽  
Author(s):  
Catherine Ludden ◽  
Felix Lötsch ◽  
Erik Alm ◽  
Narender Kumar ◽  
Karin Johansson ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Epidemiological Data ◽  
Whole Genome ◽  
The European Union ◽  
Sequencing Data ◽  
The Public ◽  
Cross Border ◽  
Collaborative Analysis

Analysis of sequencing data for 143 bla NDM-1- and bla OXA-48-positive Klebsiella pneumoniae isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outside of the European Union including Egypt, Iran, Morocco, Russia, Serbia, Tunisia and Turkey. These findings highlight the benefit of European whole genome sequencing-based surveillance and data sharing for control of antimicrobial resistance.

scholarly journals Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017

2017 ◽  
Vol 22 (50) ◽  
Author(s):  
Susanne Schjørring ◽  
Sofie Gillesberg Lassen ◽  
Tenna Jensen ◽  
Alexandra Moura ◽  
Jette S Kjeldgaard ◽  
...  
Keyword(s):  
European Union ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
European Union Country ◽  
Human Isolate ◽  
Whole Genome ◽  
Genome Sequences ◽  
Cross Border ◽  
Smoked Salmon ◽  
Food Isolate

In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.

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