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Countrywide multi-serotype outbreak of Salmonella Bovismorbificans ST142 and monophasic Salmonella Typhimurium ST34 associated with dried pork sausages in France, September 2020* to January 2021
The French National Reference Centre for Escherichia coli, Shigella and Salmonella (FNRC-ESS) detected two human clusters of 33 cases (median age: 10 years; 17 females) infected by Salmonella enterica serotype Bovismorbificans, ST142, HC5_243255 (EnteroBase HierCC‑cgMLST scheme) in September–November 2020 and of 11 cases (median age: 11 years; seven males) infected by S. enterica serotype 4,12:i:-, ST34, HC5_198125 in October–December 2020. Epidemiological investigations conducted by Santé publique France linked these outbreaks to the consumption of dried pork sausages from the same manufacturer. S. Bovismorbificans and S. 4,12:i:- were isolated by the National Reference Laboratory from different food samples, but both strains were identified in a single food sample only by qPCR. Three recalls and withdrawals of dried pork products were issued by the French general directorate of food of the French ministry for agriculture and food in November 2020, affecting eight supermarket chains. A notification on the European Rapid Alert System for Food and Feed and a European urgent enquiry on the Epidemic Intelligence Information System for Food and Waterborne Diseases and Zoonoses (EPIS-FWD) were launched. No cases were reported outside France. Outbreaks caused by multiple serotypes of Salmonella may go undetected by protocols in standard procedures in microbiology laboratories.
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A One Health real-time surveillance system for nowcasting Campylobacter gastrointestinal illness outbreaks, Norway, week 30 2010 to week 11 2022
BackgroundCampylobacter is a leading cause of food and waterborne illness. Monitoring and modelling Campylobacter at chicken broiler farms, combined with weather pattern surveillance, can aid nowcasting of human gastrointestinal (GI) illness outbreaks. Near real-time sharing of data and model results with health authorities can help increase potential outbreak responsiveness.
AimsTo leverage data on weather and Campylobacter on broiler farms to build a risk model for possible human Campylobacter outbreaks and to communicate risk assessments with health authorities.
MethodsWe developed a spatio-temporal random effects model for weekly GI illness consultations in Norwegian municipalities with Campylobacter monitoring and weather data from week 30 2010 to 11 2022 to give 1-week nowcasts of GI illness outbreaks. The approach combined a municipality random effects baseline model for seasonally-adjusted GI illness with a second model for peak deviations from that baseline. Model results are communicated to national and local stakeholders through an interactive website: Sykdomspulsen One Health.
ResultsLagged temperature and precipitation covariates, as well as 2-week-lagged positive Campylobacter sampling in broilers, were associated with higher levels of GI consultations. Significant inter-municipality variability in outbreak nowcasts were observed.
ConclusionsCampylobacter surveillance in broilers can be useful in GI illness outbreak nowcasting. Surveillance of Campylobacter along potential pathways from the environment to illness such as via water system monitoring may improve nowcasting. A One Health system that communicates near real-time surveillance data and nowcast changes in risk to health professionals facilitates the prevention of Campylobacter outbreaks and reduces impact on human health.
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Listeriosis outbreak caused by contaminated stuffed pork, Andalusia, Spain, July to October 2019
Between 1 July and 26 October 2019 in Andalusia, Spain, a large outbreak with 207 confirmed cases of listeriosis was identified. Confirmed cases had a median age of 44 years (range: 0–94) and 114 were women (55.1%). Most cases (n = 154) had mild gastroenteritis, 141 (68.1%) required hospitalisation and three died; five of 34 pregnant women had a miscarriage. The median incubation period was 1 day (range: 0–30), and was significantly shorter in cases presenting with gastroenteritis compared to those presenting without gastroenteritis (1 day vs. 3 days, respectively, p value < 0.001). Stuffed pork, a ready-to-eat product consumed unheated, from a single producer contaminated with Listeria monocytogenes ST388 was identified as the source of infection. The outbreak strain was identified in 189 human samples and 87 non-human (82 food and 5 environmental) samples. Notification of new cases declined abruptly after control measures were implemented. These included contaminated food recall, protocols for clinical management of suspected cases and for post-exposure prophylaxis in pregnant women and communication campaigns with concise messages to the population through social media. Given that there were 3,059 probable cases, this was the largest L. monocytogenes outbreak ever reported in Europe.
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Salmonella Typhimurium outbreak associated with frozen tomato cubes at a restaurant in western Finland, January to February 2021
Several individuals reported gastrointestinal symptoms following meals consumed in late January 2021 at a restaurant in western Finland. We conducted a retrospective cohort study and defined a case as a person who ate at the lunch restaurant between 27 and 29 January 2021 and had stomach pain, vomiting or diarrhoea and/or a laboratory-confirmed Salmonella Typhimurium infection within 2 weeks after the exposure. We collected faecal and food samples for microbiological analysis. Salmonella isolates were characterised in detail using whole genome sequencing (WGS) and cluster analysis by core genome multilocus sequence typing (cgMLST). Altogether, 393 meals were sold and 101 people (who ate 142 meals) participated in the cohort study. There were 49 cases; 23 were laboratory-confirmed infections with a multidrug-resistant S. Typhimurium. The S. Typhimurium isolates from cases and frozen tomato cubes used uncooked in salads were closely related and clustered together in cgMLST comparison. These salads were consumed by 76% of the cases. Based on the cgMLST clustering, they were the suggested source of the outbreak. Statistical association was not significant between eating the salads and being a case. Following the outbreak investigation, the producer decided to recommend cooking of their frozen tomato products before consumption.
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Changing epidemiology of Salmonella Enteritidis human infections in the Netherlands and Belgium, 2006 to 2019: a registry-based population study
BackgroundSalmonellosis remains the second most common zoonosis in the European Union despite a long-term decreasing trend. However, this trend has been reported to have stagnated in recent years, particularly for Salmonella enterica serotype Enteritidis (SE).
AimTo describe temporal changes in the incidence of SE human infections, and in its associated factors between 2006 and 2019. In addition, we aim to determine which factors influenced the stagnated trend seen in recent years.
MethodsData on culture-confirmed SE human infections from national surveillance registries in the Netherlands and Belgium between 2006 and 2019 were analysed using multivariable negative-binomial regression models with restricted cubic splines.
ResultsSE incidence was significantly higher in summer and autumn than winter, in persons aged 0–4 years and 5–14 years than in persons ≥ 60 years, and increased with increasing proportions of travel-related and resistant SE infections. SE incidence decreased significantly in both countries until 2015, followed by an increasing trend, which was particularly pronounced in the Netherlands. Potential SE outbreaks in both countries and invasive infections in the Netherlands also increased after 2015.
ConclusionThe increase in potential outbreaks and invasive infections since 2015 may partially explain the observed reversal of the decreasing trend. While these results provide insights into the possible causes of this trend reversal, attention should also be given to factors known to influence SE epidemiology at primary (animal) production and pathogen genomic levels.
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An outbreak of cryptosporidiosis associated with drinking water in north-eastern Italy, August 2019: microbiological and environmental investigations
Cryptosporidium is a leading global cause of waterborne disease, with many reported outbreaks related to main water supplies. In August 2019, an outbreak of cryptosporidiosis involving 80 cases occurred among 114 vacationers in a small municipality located in the Tuscan-Emilian Apennines, north-eastern Italy. After excluding a potential food-borne outbreak, the epidemiological investigation focussed on the hypothesis of a waterborne outbreak. This was confirmed by the finding of Cryptosporidium oocysts in stools of the cases and in water samples from the municipal water network. Molecular characterisation revealed the zoonotic species Cryptosporidium parvum as the causative agent. A single subtype (IIdA25G1) was found among all cases, and in one of two positive water samples. The municipality’s water supply used spring water that only received a disinfection treatment insufficient to inactivate the parasite. Possible entry means into the water mains were found through further environmental investigations. As these types of water supplies are particularly vulnerable to various environmental factors, a control system based on the risk assessment of each phase of the water supply chain is required to guarantee water safety. Effective methods for detection of protozoan pathogens, which are generally excluded from routine water supply analysis, should be applied.
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Epidemiological and microbiological investigation of a large increase in vibriosis, northern Europe, 2018
Ettore Amato , Maximilian Riess , Daniel Thomas-Lopez , Marius Linkevicius , Tarja Pitkänen , Tomasz Wołkowicz , Jelena Rjabinina , Cecilia Jernberg , Marika Hjertqvist , Emily MacDonald , Jeevan Karloss Antony-Samy , Karsten Dalsgaard Bjerre , Saara Salmenlinna , Kurt Fuursted , Anette Hansen and Umaer NaseerBackgroundVibriosis cases in Northern European countries and countries bordering the Baltic Sea increased during heatwaves in 2014 and 2018.
AimWe describe the epidemiology of vibriosis and the genetic diversity of Vibrio spp. isolates from Norway, Sweden, Denmark, Finland, Poland and Estonia in 2018, a year with an exceptionally warm summer.
MethodsIn a retrospective study, we analysed demographics, geographical distribution, seasonality, causative species and severity of non-travel-related vibriosis cases in 2018. Data sources included surveillance systems, national laboratory notification databases and/or nationwide surveys to public health microbiology laboratories. Moreover, we performed whole genome sequencing and multilocus sequence typing of available isolates from 2014 to 2018 to map their genetic diversity.
ResultsIn 2018, we identified 445 non-travel-related vibriosis cases in the study countries, considerably more than the median of 126 cases between 2014 and 2017 (range: 87–272). The main reported mode of transmission was exposure to seawater. We observed a species-specific geographical disparity of vibriosis cases across the Nordic-Baltic region. Severe vibriosis was associated with infections caused by Vibrio vulnificus (adjOR: 17.2; 95% CI: 3.3–90.5) or Vibrio parahaemolyticus (adjOR: 2.1; 95% CI: 1.0–4.5), age ≥ 65 years (65–79 years: adjOR: 3.9; 95% CI: 1.7–8.7; ≥ 80 years: adjOR: 15.5; 95% CI: 4.4–54.3) or acquiring infections during summer (adjOR: 5.1; 95% CI: 2.4–10.9). Although phylogenetic analysis revealed diversity between Vibrio spp. isolates, two V. vulnificus clusters were identified.
ConclusionShared sentinel surveillance for vibriosis during summer may be valuable to monitor this emerging public health issue.
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Outbreak of Salmonella Newport linked to imported frozen cooked crayfish in dill brine, Sweden, July to November 2019
In autumn 2019, the Public Health Agency of Sweden identified a cluster of Salmonella Newport cases by whole genome sequencing (WGS). Cases’ distribution in place and time indicated a nation-wide ongoing outbreak. An investigation was initiated to identify the source and prevent further cases. We conducted a case–case study based on notified salmonellosis cases and a Salmonella trawling questionnaire, comparing 20 outbreak cases and 139 control cases. Food exposures were compared by adjusted odds ratios (aOR) with 95% confidence interval (CI) using logistic regression. Implicated foods were sampled. Outbreak cases were more likely to have consumed crayfish (aOR = 26; 95% CI: 6.3–105). One specific brand of imported frozen, pre-cooked whole crayfish in dill brine was identified as the source. Salmonella Newport was later detected in different batches from retail and in one sample from border control. Isolates from food samples clustered with the human outbreak strain by WGS. Although the retailer made a complete recall, two more cases were identified long afterwards. This investigation demonstrated the successful use of a case–case study and targeted microbiological testing to identify the source. The immediate action taken by the retailer was important to confirm the source and stop the outbreak.
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Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022
Lesley Larkin , Maria Pardos de la Gandara , Ann Hoban , Caisey Pulford , Nathalie Jourdan-Da Silva , Henriette de Valk , Lynda Browning , Gerhard Falkenhorst , Sandra Simon , Raskit Lachmann , Rikard Dryselius , Nadja Karamehmedovic , Stefan Börjesson , Dieter van Cauteren , Valeska Laisnez , Wesley Mattheus , Roan Pijnacker , Maaike van den Beld , Joël Mossong , Catherine Ragimbeau , Anne Vergison , Lin Thorstensen Brandal , Heidi Lange , Patricia Garvey , Charlotte Salgaard Nielsen , Silvia Herrera León , Carmen Varela , Marie Chattaway , François-Xavier Weill , Derek Brown and Paul McKeownAn extensive multi-country outbreak of multidrug-resistant monophasic Salmonella Typhimurium infection in 10 countries with 150 reported cases, predominantly affecting young children, has been linked to chocolate products produced by a large multinational company. Extensive withdrawals and recalls of multiple product lines have been undertaken. With Easter approaching, widespread product distribution and the vulnerability of the affected population, early and effective real-time sharing of microbiological and epidemiological information has been of critical importance in effectively managing this serious food-borne incident.
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Molecular epidemiology of hepatitis A outbreaks and sporadic cases, Latvia, 2017 to 2019
More LessBackgroundHepatitis A is an acute infection of the liver caused by hepatitis A virus (HAV). Molecular detection and typing of the HAV VP1/P2A genomic region is used for genotyping and outbreak investigations. After a large hepatitis A outbreak in Latvia in 2007–08, only sporadic cases were registered until 2017 when a rise in cases occurred. During 2017–19, 179 laboratory-confirmed hepatitis A cases were notified in Latvia.
AimTo investigate the observed increase in hepatitis A cases during 2017 and to determine whether these cases were linked to one another, to risk groups, or to other outbreaks. The majority of HAV samples (69.8%) were typed.
MethodsThe VP1/P2A genomic region of HAV was amplified and sequenced for 125 case serum samples. Information about hepatitis-related symptoms, hospitalisation, vaccination, a possible source of infection and suspected countries of origin of the virus were analysed for sequenced cases.
ResultsMost HAV strains were subgenotype IA (n = 77), of which 41 were strains circulating among men who have sex with men (MSM) populations in Europe (VRD_521_2016 (n = 32), RIVM-HAV16–090 (n = 7) or V16–25801 (n = 2)). Forty-four cases were subgenotype IB and four cases subgenotype IIIA. However, other clusters and sporadic cases were detected with or without identifying the epidemiological link.
ConclusionThis work represents molecular epidemiological data of hepatitis A cases in Latvia from 2017 to 2019. Molecular typing methods allow identification of clusters for public health needs and establishing links with other outbreaks, and to compare Latvian strains with reported strains from other countries.
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Surveillance and characteristics of food-borne outbreaks in the Netherlands, 2006 to 2019
More LessBackgroundA wide variety of pathogens can cause disease in humans via consumption of contaminated food. Although food-borne outbreaks only account for a small part of the food-borne disease burden, outbreak surveillance can provide insights about the pathogens, food products implied as vehicle, points of contamination, and the settings in which transmission occurs.
AimTo describe the characteristics of food-borne outbreaks registered between 2006 and 2019 in the Netherlands.
MethodsAll reported outbreaks in which the first case occurred during 2006–19 were analysed. We examined the number of outbreaks, cases and setting by year, aetiology, type of evidence and food commodities.
ResultsIn total, 5,657 food-borne outbreaks with 27,711 cases were identified. The contaminated food product could be confirmed in 152 outbreaks (2.7%); in 514 outbreaks (9.1%), a pathogen was detected in cases and/or environmental swabs. Norovirus caused most outbreaks (205/666) and most related cases (4,436/9,532), followed by Salmonella spp. (188 outbreaks; 3,323 cases) and Campylobacter spp. (150 outbreaks; 601 cases). Bacillus cereus was most often found in outbreaks with a confirmed food vehicle (38/152). Additionally, a connection was seen between some pathogens and food commodities. Public eating places were most often mentioned as a setting where the food implicated in the outbreak was prepared.
ConclusionLong-term analysis of food-borne outbreaks confirms a persistent occurrence. Control and elimination of food-borne illness is complicated since multiple pathogens can cause illness via a vast array of food products and, in the majority of the outbreaks, the pathogen remains unknown.
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Healthcare-associated foodborne outbreaks in high-income countries: a literature review and surveillance study, 16 OECD countries, 2001 to 2019*
BackgroundHealthcare-associated foodborne outbreaks (HA-FBO) may have severe consequences, especially in vulnerable groups.
AimThe aim was to describe the current state of HA-FBO and propose public health recommendations for prevention.
MethodsWe searched PubMed, the Outbreak Database (Charité, University Medicine Berlin), and hand-searched reference lists for HA-FBO with outbreak onset between 2001 and 2018 from Organisation for Economic Co-operation and Development (OECD) countries and HA-FBO (2012–2018) from the German surveillance system. Additionally, data from the European Food Safety Authority were analysed.
ResultsThe literature search retrieved 57 HA-FBO from 16 OECD countries, primarily in the US (n = 11), Germany (n = 11) and the United Kingdom (n = 9). In addition, 28 HA-FBO were retrieved from the German surveillance system. Based on the number of outbreaks, the top three pathogens associated with the overall 85 HA-FBO were Salmonella (n = 24), norovirus (n = 22) and Listeria monocytogenes (n = 19). Based on the number of deaths, L. monocytogenes was the main pathogen causing HA-FBO. Frequently reported implicated foods were ‘mixed foods’ (n = 16), ‘vegetables and fruits’ (n = 15) and ‘meat and meat products’ (n = 10). Consumption of high-risk food by vulnerable patients, inadequate time-temperature control, insufficient kitchen hygiene and food hygiene and carriers of pathogens among food handlers were reported as reasons for HA-FBO.
ConclusionTo prevent HA-FBO, the supply of high-risk food to vulnerable people should be avoided. Well working outbreak surveillance facilitates early detection and requires close interdisciplinary collaboration and exchange of information between hospitals, food safety and public health authorities.
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Heatwave-associated Vibrio infections in Germany, 2018 and 2019
BackgroundVibrio spp. are aquatic bacteria that prefer warm seawater with moderate salinity. In humans, they can cause gastroenteritis, wound infections, and ear infections. During the summers of 2018 and 2019, unprecedented high sea surface temperatures were recorded in the German Baltic Sea.
AimWe aimed to describe the clinical course and microbiological characteristics of Vibrio infections in Germany in 2018 and 2019.
MethodsWe performed an observational retrospective multi-centre cohort study of patients diagnosed with domestically-acquired Vibrio infections in Germany in 2018 and 2019. Demographic, clinical, and microbiological data were assessed, and isolates were subjected to whole genome sequencing and antimicrobial susceptibility testing.
ResultsOf the 63 patients with Vibrio infections, most contracted the virus between June and September, primarily in the Baltic Sea: 44 (70%) were male and the median age was 65 years (range: 2–93 years). Thirty-eight patients presented with wound infections, 16 with ear infections, six with gastroenteritis, two with pneumonia (after seawater aspiration) and one with primary septicaemia. The majority of infections were attributed to V. cholerae (non–O1/non-O139) (n = 30; 48%) or V. vulnificus (n = 22; 38%). Phylogenetic analyses of 12 available isolates showed clusters of three identical strains of V. vulnificus, which caused wound infections, suggesting that some clonal lines can spread across the Baltic Sea.
ConclusionsDuring the summers of 2018 and 2019, severe heatwaves facilitated increased numbers of Vibrio infections in Germany. Since climate change is likely to favour the proliferation of these bacteria, a further increase in Vibrio-associated diseases is expected.
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Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019
BackgroundCampylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied.
AimTyping-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks.
MethodsWe performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat.
ResultsSeventy-two clusters were detected, 58 small clusters (2–4 cases) and 14 large clusters (5–91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak.
ConclusionOur WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.
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Hepatitis A outbreak associated with consumption of dates, England and Wales, January 2021 to April 2021
We report a national hepatitis A virus (HAV) outbreak linked to the consumption of Medjool dates. Twenty-nine cases of three genetically related sequences have been identified. Epidemiological investigations identified a suspected product (adjusted odds ratio: 47.36; 95% confidence interval: 1.79–1,256.07; p = 0.021). Microbiological testing has confirmed the presence of HAV on dates recovered from two cases and the product has been recalled. Date consumption is currently likely to be increased in connection with Ramadan, with potential ongoing contamination risk.
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Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019
Gabrielle Jones , Maria Pardos de la Gandara , Laura Herrera-Leon , Silvia Herrera-Leon , Carmen Varela Martinez , Roselyne Hureaux-Roy , Yasmine Abdallah , Athinna Nisavanh , Laetitia Fabre , Charlotte Renaudat , Joël Mossong , Wesley Mattheus , Cécile Huard , Caroline Le Borgne , Henriette de Valk , François-Xavier Weill and Nathalie Jourdan-Da SilvaWe describe a Salmonella Poona outbreak involving 31 infant cases in France. Following outbreak detection on 18 January 2019, consumption of rice-based infant formula manufactured at a facility in Spain was identified as the probable cause, leading to a recall on 24 January. Whole genome sequencing analysis linked present outbreak isolates to a 2010–11 S. Poona outbreak in Spain associated with formula manufactured in the same facility, indicating a persistent source of contamination.
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Whole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016
More LessIntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.
AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.
MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonellaenterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.
ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster. All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.
ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonellaenterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.
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Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016
Aymeric Ung , Amrish Y. Baidjoe , Dieter Van Cauteren , Nizar Fawal , Laetitia Fabre , Caroline Guerrisi , Kostas Danis , Anne Morand , Marie-Pierre Donguy , Etienne Lucas , Louise Rossignol , Sophie Lefèvre , Marie-Léone Vignaud , Sabrina Cadel-Six , Renaud Lailler , Nathalie Jourdan-Da Silva and Simon Le HelloOn 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.
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Hepatitis A outbreak linked to imported frozen strawberries by sequencing, Sweden and Austria, June to September 2018
Theresa Enkirch , Ronnie Eriksson , Sofia Persson , Daniela Schmid , Stephan W. Aberle , Emma Löf , Bengt Wittesjö , Birgitta Holmgren , Charlotte Johnzon , Eva X. Gustafsson , Lena M. Svensson , Lisa Labbé Sandelin , Lukas Richter , Mats Lindblad , Mia Brytting , Sabine Maritschnik , Tatjana Tallo , Therese Malm , Lena Sundqvist and Josefine Lundberg EderthBetween June–September 2018, 20 hepatitis A cases were notified in six counties in Sweden. Combined epidemiological and microbiological investigations identified imported frozen strawberries produced in Poland as the source of the outbreak. Sequence analysis confirmed the outbreak strain IB in the strawberries with 100 % identity and the respective batch was withdrawn. Sharing the sequence information internationally led to the identification of 14 additional cases in Austria, linked to strawberries from the same producer.
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Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015
Background and aimThe trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010–15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.
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