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Nemes K, Persson S, Simonsson M. Hepatitis A Virus and Hepatitis E Virus as Food- and Waterborne Pathogens-Transmission Routes and Methods for Detection in Food. Viruses 2023; 15:1725. [PMID: 37632066 PMCID: PMC10457876 DOI: 10.3390/v15081725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Foodborne viruses are an important threat to food safety and public health. Globally, there are approximately 5 million cases of acute viral hepatitis due to hepatitis A virus (HAV) and hepatitis E virus (HEV) every year. HAV is responsible for numerous food-related viral outbreaks worldwide, while HEV is an emerging pathogen with a global health burden. The reported HEV cases in Europe have increased tenfold in the last 20 years due to its zoonotic transmission through the consumption of infected meat or meat products. HEV is considered the most common cause of acute viral hepatitis worldwide currently. This review focuses on the latest findings on the foodborne transmission routes of HAV and HEV and the methods for their detection in different food matrices.
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Affiliation(s)
- Katalin Nemes
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Dag Hammarskjölds väg 56 A, 75237 Uppsala, Sweden; (S.P.); (M.S.)
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Pavoni E, Bertasi B, Galuppini E, Mangeri L, Meletti F, Tilola M, Carta V, Todeschi S, Losio MN. Detection of Hepatitis A Virus and Norovirus in Different Food Categories: A 6-Year Survey in Italy. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:69-76. [PMID: 34698989 DOI: 10.1007/s12560-021-09503-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
To observe the prevalence of contamination by hepatitis A virus (HAV) and norovirus (NoV) in different food types, 9242 samples were analyzed over a 6-year period (January 2014-December 2019). Samples were from routine official activities by Competent Authorities (CAs) and Food Business Operators, according to Hazard Analysis and Critical Control Points plans. Analyses were performed in accordance with European and Italian regulations. Food types were obtained from different production areas of Italy, and ranged from mollusks, ready-to-eat (RTE) and packaged vegetables, frozen berries, tap water, fruit and RTE fruit salads, and processed and preserved foods. No risk management plans were set by the authors' laboratory, because they were still adopted by conferring customers. Analyses were conducted according to ISO/TS 15216-2:2013 (ISO in Part 2: Method for Qualitative Detection. International Organization for Standardization, Geneva, 2013). The data showed that 2.25% (95% CI: 2.0-2.6) of samples were contaminated by at least one virus type, and that the most detected pathogen was NoV GII (89.50% of all positives). Mollusks (filter-feeding animals) were the most contaminated category (92.31% of all positives) not only by NoV or HAV individually, but also by multiple HAV/NoV contaminations consisting of 22.59% of all positives. For NoV, there was a significant correlation between shellfish positivity and season, with the autumn-winter period being the most associated with risk. Conversely, berries, drinking water and RTE vegetables, previously linked to several outbreaks, showed a low rate of contamination. These results from data collection have implications for the improvement of sampling plans for HAV and NoV by Italian CAs, and by food-producing and distribution operators. Moreover, these findings obtained by a standardized qualitative method contribute the collection of data aimed at establishing new microbiological criteria not yet foreseen (but advocated) by current European rules.
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Affiliation(s)
- Enrico Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy.
- Food Control Division, Food Safety Department, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini" (IZSLER), Via Bianchi 7/9, 25124, Brescia, Italy.
| | - Barbara Bertasi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Elisa Galuppini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Lucia Mangeri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Francesca Meletti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Michela Tilola
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Valentina Carta
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Silvia Todeschi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
| | - Marina-Nadia Losio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
- National Reference Centre for Emerging Risks in Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "B. Ubertini", via Bianchi 7/9, 25124, Brescia, Italy
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Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing. Microorganisms 2022; 10:microorganisms10010100. [PMID: 35056549 PMCID: PMC8779169 DOI: 10.3390/microorganisms10010100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 02/04/2023] Open
Abstract
Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness.
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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Desdouits M, de Graaf M, Strubbia S, Oude Munnink BB, Kroneman A, Le Guyader FS, Koopmans MPG. Novel opportunities for NGS-based one health surveillance of foodborne viruses. ONE HEALTH OUTLOOK 2020; 2:14. [PMID: 33829135 PMCID: PMC7993515 DOI: 10.1186/s42522-020-00015-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 05/15/2023]
Abstract
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.
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Affiliation(s)
- Marion Desdouits
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sofia Strubbia
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Bas B. Oude Munnink
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Annelies Kroneman
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Marion P. G. Koopmans
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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6
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Randazzo W, Sánchez G. Hepatitis A infections from food. J Appl Microbiol 2020; 129:1120-1132. [DOI: 10.1111/jam.14727] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/14/2022]
Affiliation(s)
- W. Randazzo
- Department of Preservation and Food Safety Technologies IATA‐CSIC Valencia Spain
- Department of Microbiology and Ecology University of Valencia Valencia Spain
| | - G. Sánchez
- Department of Preservation and Food Safety Technologies IATA‐CSIC Valencia Spain
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Fusco G, Anastasio A, Kingsley DH, Amoroso MG, Pepe T, Fratamico PM, Cioffi B, Rossi R, La Rosa G, Boccia F. Detection of Hepatitis A Virus and Other Enteric Viruses in Shellfish Collected in the Gulf of Naples, Italy. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E2588. [PMID: 31331104 PMCID: PMC6678136 DOI: 10.3390/ijerph16142588] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 12/28/2022]
Abstract
To assess the quality of shellfish harvest areas, bivalve mollusk samples from three coastal areas of the Campania region in Southwest Italy were evaluated for viruses over a three-year period (2015-2017). Screening of 289 samples from shellfish farms and other locations by qPCR and RT-qPCR identified hepatitis A virus (HAV; 8.9%), norovirus GI (NoVGI; 10.8%) and GII (NoVGII; 39.7%), rotavirus (RV; 9.0%), astrovirus (AsV; 20.8%), sapovirus (SaV; 18.8%), aichivirus-1 (AiV-1; 5.6%), and adenovirus (AdV, 5.6%). Hepatitis E virus (HEV) was never detected. Sequence analysis identified HAV as genotype IA and AdV as type 41. This study demonstrates the presence of different enteric viruses within bivalve mollusks, highlighting the limitations of the current EU classification system for shellfish growing waters.
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Affiliation(s)
- Giovanna Fusco
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, Portici, 80055 Naples, Italy
| | - Aniello Anastasio
- Department of Veterinary Medicine and Animal Production, Università degli Studi di Napoli Federico II, Via Federico Delpino 1, 80137 Naples, Italy
| | - David H Kingsley
- U.S. Department of Agriculture, Agricultural Research Service, Delaware State University, Dover, DE 19901, USA
| | - Maria Grazia Amoroso
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, Portici, 80055 Naples, Italy
| | - Tiziana Pepe
- Department of Veterinary Medicine and Animal Production, Università degli Studi di Napoli Federico II, Via Federico Delpino 1, 80137 Naples, Italy
| | - Pina M Fratamico
- USDA, Agricultural Research Service, Eastern Regional Research Center, 600 E. Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Barbara Cioffi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, Portici, 80055 Naples, Italy
| | - Rachele Rossi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute 2, Portici, 80055 Naples, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Federica Boccia
- Department of Veterinary Medicine and Animal Production, Università degli Studi di Napoli Federico II, Via Federico Delpino 1, 80137 Naples, Italy.
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Shin H, Park H, Seo DJ, Jung S, Yeo D, Wang Z, Park KH, Choi C. Foodborne Viruses Detected Sporadically in the Fresh Produce and Its Production Environment in South Korea. Foodborne Pathog Dis 2019; 16:411-420. [DOI: 10.1089/fpd.2018.2580] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Hansaem Shin
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Hyunkyung Park
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Dong Joo Seo
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Soontag Jung
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Daseul Yeo
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Zhaoqi Wang
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
| | - Ki Hwan Park
- Department of Food Science and Technology, Chung-Ang University, Anseong-si, Republic of Korea
- Bio and Environmental Technology Research Institute, Chung-Ang University, Anseong-si, Republic of Korea
| | - Changsun Choi
- Department of Food and Nutrition, Chung-Ang University, Anseong-si, Republic of Korea
- Bio and Environmental Technology Research Institute, Chung-Ang University, Anseong-si, Republic of Korea
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Sekse C, Holst-Jensen A, Dobrindt U, Johannessen GS, Li W, Spilsberg B, Shi J. High Throughput Sequencing for Detection of Foodborne Pathogens. Front Microbiol 2017; 8:2029. [PMID: 29104564 PMCID: PMC5655695 DOI: 10.3389/fmicb.2017.02029] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/04/2017] [Indexed: 12/23/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic "natural" strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.
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Affiliation(s)
- Camilla Sekse
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Arne Holst-Jensen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Gro S. Johannessen
- Department of Animal Health and Food Safety, Norwegian Veterinary Institute, Oslo, Norway
| | - Weihua Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Bjørn Spilsberg
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Oslo, Norway
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University–University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Application of next generation sequencing toward sensitive detection of enteric viruses isolated from celery samples as an example of produce. Int J Food Microbiol 2017; 261:73-81. [PMID: 28992517 DOI: 10.1016/j.ijfoodmicro.2017.07.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/15/2017] [Accepted: 07/30/2017] [Indexed: 02/06/2023]
Abstract
Next generation sequencing (NGS) holds promise as a single application for both detection and sequence identification of foodborne viruses; however, technical challenges remain due to anticipated low quantities of virus in contaminated food. In this study, with a focus on data analysis using several bioinformatics tools, we applied NGS toward amplification-independent detection and identification of norovirus at low copy (<103 copies) or within multiple strains from produce. Celery samples were inoculated with human norovirus (stool suspension) either as a single norovirus strain, a mixture of strains (GII.4 and GII.6), or a mixture of different species (hepatitis A virus and norovirus). Viral RNA isolation and recovery was confirmed by RT-qPCR, and optimized for library generation and sequencing without amplification using the Illumina MiSeq platform. Extracts containing either a single virus or a two-virus mixture were analyzed using two different analytic approaches to achieve virus detection and identification. First an overall assessment of viral genome coverage for samples varying in copy numbers (1.1×103 to 1.7×107) and genomic content (single or multiple strains in various ratios) was completed by reference-guided mapping. Not unexpectedly, this targeted approach to identification was successful in correctly mapping reads, thus identifying each virus contained in the inoculums even at low copy (estimated at 12 copies). For the second (metagenomic) approach, samples were treated as "unknowns" for data analyses using (i) a sequence-based alignment with a local database, (ii) an "in-house" k-mer tool, (iii) a commercially available metagenomics bioinformatic analysis platform cosmosID, and (iv) an open-source program Kraken. Of the four metagenomics tools applied in this study, only the local database alignment and in-house k-mer tool were successful in detecting norovirus (as well as HAV) at low copy (down to <103 copies) and within a mixture of virus strains or species. The results of this investigation provide support for continued investigation into the development and integration of these analytical tools for identification and detection of foodborne viruses.
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Abstract
Foodborne pathogens are causing a great number of diseases with significant effects on human health and economy. The characteristics of the most common pathogenic bacteria (Bacillus cereus, Campylobacter jejuni, Clostridium botulinum, Clostridium perfringens, Cronobacter sakazakii, Esherichia coli, Listeria monocytogenes, Salmonella spp., Shigella spp., Staphylococccus aureus, Vibrio spp. and Yersinia enterocolitica), viruses (Hepatitis A and Noroviruses) and parasites (Cyclospora cayetanensis, Toxoplasma gondii and Trichinella spiralis), together with some important outbreaks, are reviewed. Food safety management systems based on to classical hazard-based approach has been proved to be inefficient, and risk-based food safety approach is now suggested from leading researchers and organizations. In this context, a food safety management system should be designed in a way to estimate the risks to human health from food consumption and to identify, select and implement mitigation strategies in order to control and reduce these risks. In addition, the application of suitable food safety education programs for all involved people in the production and consumption of foods is suggested.
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Affiliation(s)
- Thomas Bintsis
- Department of International Trade, TEI of West Macedonia, Kastoria, Greece
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12
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Scavia G, Alfonsi V, Taffon S, Escher M, Bruni R, Medici DD, Pasquale SD, Guizzardi S, Cappelletti B, Iannazzo S, Losio NM, Pavoni E, Decastelli L, Ciccaglione AR, Equestre M, Tosti ME, Rizzo C, National Italian Task Force On Hepatitis A. A large prolonged outbreak of hepatitis A associated with consumption of frozen berries, Italy, 2013-14. J Med Microbiol 2017; 66:342-349. [PMID: 28086079 DOI: 10.1099/jmm.0.000433] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE In 2013/2014, Italy experienced one of the largest community-wide prolonged outbreaks of hepatitis A virus (HAV) throughout the country. The article provides a comprehensive description of the outbreak and the investigation carried out by a multidisciplinary National Task Force, in collaboration with regional and local public health authorities. Control strategies of food-borne HAV infection in both the human and food sectors are also described. METHODOLOGY Enhanced human epidemiological and microbiological surveillance together with microbiological monitoring of HAV in food and trace-back investigation were conducted. RESULTS A total of 1803 HAV cases were identified from 1 January 2013 to 31 August 2014, in Italy. Sequencing was possible for 368 cases (20.4 %), mostly collected between 1 January 2013 and 28 February 2014, and 246 cases (66.8 %) harboured an HAV outbreak strain. Imported frozen berries contaminated with HAV were identified as the vehicle of the outbreak which also involved many other European countries in 2013 and 2014. Epidemiological evidence obtained through a case-control study was supported by the finding of a 100 % nucleotide similarity of the VP1/2A sequences of HAVs detected in human and food samples. Trace-back investigation revealed an extremely complex supplying network with no possibility for a point source potentially explaining the vast contamination of berries found in Italy. CONCLUSION The investigation benefited from an excellent collaboration among different sectors who shared proactively the available information. Our findings highlight the importance of considering frozen berries among the highest risk factors for HAV.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Nadia Marina Losio
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Brescia, Italy
| | - Enrico Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Brescia, Italy
| | - Lucia Decastelli
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin, Italy
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13
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Terio V, Bottaro M, Pavoni E, Losio MN, Serraino A, Giacometti F, Martella V, Mottola A, Di Pinto A, Tantillo G. Occurrence of hepatitis A and E and norovirus GI and GII in ready-to-eat vegetables in Italy. Int J Food Microbiol 2017; 249:61-65. [PMID: 28319799 DOI: 10.1016/j.ijfoodmicro.2017.03.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 01/19/2017] [Accepted: 03/11/2017] [Indexed: 02/08/2023]
Abstract
Fresh vegetables and their ready-to-eat (RTE) salads have become increasingly recognized as potential vehicles for foodborne diseases. The EU Reg. 1441/2007 establishes microbiological criteria for bacterial pathogens for products placed on the market during their shelf-life (i.e. Salmonella spp., Listeria monocytogenes) for pre-cut fruits and vegetables (RTE) whilst it does not address the problem of contamination by enteric viruses. In this study we investigated the contamination by hepatitis A virus (HAV), hepatitis E virus (HEV) and norovirus (NoV) in 911 ready-to-eat vegetable samples taken from products at retail in Apulia and in Lombardia. The vegetable samples were tested using validated real-time PCR (RT-qPCR) assays, ISO standardized virological methods and ISO culturing methods for bacteriological analysis. The total prevalence of HAV and HEV was 1.9% (18/911) and 0.6% (6/911), respectively. None of the samples analysed in this study was positive for NoV, Salmonella spp. or Listeria monocytogenes. The detection of HAV and HEV in RTE salads highlights a risk to consumers and the need to improve production hygiene. Appropriate implementation of hygiene procedures is required at all the steps of the RTE vegetable production chain and this should include monitoring of emerging viral pathogens.
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Affiliation(s)
- V Terio
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy.
| | - M Bottaro
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - E Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi no. 9, 25124 Brescia, Italy
| | - M N Losio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna (IZSLER), Via Bianchi no. 9, 25124 Brescia, Italy
| | - A Serraino
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - F Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, via Tolara di Sopra 50, 40064 Ozzano Emilia, BO, Italy
| | - V Martella
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - A Mottola
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - A Di Pinto
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
| | - G Tantillo
- Department of Veterinary Medicine (DIMEV), University of Bari, Provincial Road to Casamassima, km 3, 70010 Valenzano, Bari, Italy
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14
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Ronholm J, Nasheri N, Petronella N, Pagotto F. Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing. Clin Microbiol Rev 2016; 29:837-57. [PMID: 27559074 PMCID: PMC5010751 DOI: 10.1128/cmr.00056-16] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generate in silico results for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.
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Affiliation(s)
- J Ronholm
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Neda Nasheri
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Nicholas Petronella
- Biostatistics and Modelling Division, Bureau of Food Surveillance and Science Integration, Food Directorate, Health Canada, Ottawa, ON, Canada
| | - Franco Pagotto
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada Listeriosis Reference Centre, Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, ON, Canada
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15
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Abstract
Enteric viruses are those human viruses that are primarily transmitted by the fecal-oral route, either by person-to-person contact or by ingestion of contaminated food or water. The importance of viral foodborne diseases is increasingly being recognized, and several international organizations have found that there is an upward trend in their incidence. Thus, in this review, state-of-the-art information regarding virus persistence in food and the environment is compiled.
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16
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Abstract
Among the wide variety of viral agents liable to be found as food contaminants, noroviruses and hepatitis A virus are responsible for most well characterized foodborne virus outbreaks. Additionally, hepatitis E virus has emerged as a potential zoonotic threat. Molecular methods, including an ISO standard, are available for norovirus and hepatitis A virus detection in foodstuffs, although the significance of genome copy detection with regard to the associated health risk is yet to be determined through viability assays. More precise and rapid methods for early foodborne outbreak investigation are being developed and they will need to be validated versus the ISO standard. In addition, protocols for next-generation sequencing characterization of outbreak-related samples must be developed, harmonized and validated as well.
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Affiliation(s)
- Albert Bosch
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
| | - Rosa M Pintó
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
| | - Susana Guix
- Enteric Virus Group, Department of Microbiology, University of Barcelona, Avda Diagonal 643, 08028 Barcelona, Spain
- Nutrition and Food Safety Research Institute (INSA-UB), University of Barcelona, Avda Prat de la Riba 171, 08921 Santa Coloma de Gramanet, Spain
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17
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Bruni R, Taffon S, Equestre M, Chionne P, Madonna E, Rizzo C, Tosti ME, Alfonsi V, Ricotta L, De Medici D, Di Pasquale S, Scavia G, Pavoni E, Losio MN, Romanò L, Zanetti AR, Morea A, Pacenti M, Palù G, Capobianchi MR, Chironna M, Pompa MG, Ciccaglione AR. Key Role of Sequencing to Trace Hepatitis A Viruses Circulating in Italy During a Large Multi-Country European Foodborne Outbreak in 2013. PLoS One 2016; 11:e0149642. [PMID: 26901877 PMCID: PMC4764681 DOI: 10.1371/journal.pone.0149642] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/03/2016] [Indexed: 12/15/2022] Open
Abstract
Background Foodborne Hepatitis A Virus (HAV) outbreaks are being recognized as an emerging public health problem in industrialized countries. In 2013 three foodborne HAV outbreaks occurred in Europe and one in USA. During the largest of the three European outbreaks, most cases occurred in Italy (>1,200 cases as of March 31, 2014). A national Task Force was established at the beginning of the outbreak by the Ministry of Health. Mixed frozen berries were early demonstrated to be the source of infection by the identity of viral sequences in patients and in food. In the present study the molecular characterization of HAV isolates from 355 Italian cases is reported. Methods Molecular characterization was carried out by PCR/sequencing (VP1/2A region), comparison with reference strains and phylogenetic analysis. Results A unique strain was responsible for most characterized cases (235/355, 66.1%). Molecular data had a key role in tracing this outbreak, allowing 110 out of the 235 outbreak cases (46.8%) to be recognized in absence of any other link. The data also showed background circulation of further unrelated strains, both autochthonous and travel related, whose sequence comparison highlighted minor outbreaks and small clusters, most of them unrecognized on the basis of epidemiological data. Phylogenetic analysis showed most isolates from travel related cases clustering with reference strains originating from the same geographical area of travel. Conclusions In conclusion, the study documents, in a real outbreak context, the crucial role of molecular analysis in investigating an old but re-emerging pathogen. Improving the molecular knowledge of HAV strains, both autochthonous and circulating in countries from which potentially contaminated foods are imported, will become increasingly important to control outbreaks by supporting trace back activities, aiming to identify the geographical source(s) of contaminated food, as well as public health interventions.
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Affiliation(s)
- Roberto Bruni
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
- * E-mail:
| | - Stefania Taffon
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Michele Equestre
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Paola Chionne
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Elisabetta Madonna
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Caterina Rizzo
- National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Maria Elena Tosti
- National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Valeria Alfonsi
- National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Lara Ricotta
- National Centre for Epidemiology, Surveillance and Health Promotion, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Dario De Medici
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Simona Di Pasquale
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Gaia Scavia
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Enrico Pavoni
- Reparto tecnologia acidi nucleici applicata agli alimenti, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Marina Nadia Losio
- Reparto tecnologia acidi nucleici applicata agli alimenti, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Luisa Romanò
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | | | - Anna Morea
- Azienda Ospedaliero-Universitaria Policlinico di Bari, Bari, Italy
| | - Monia Pacenti
- Microbiology and Virology Unit, Padua University Hospital, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Maria Chironna
- Azienda Ospedaliero-Universitaria Policlinico di Bari, Bari, Italy
| | - Maria Grazia Pompa
- Directorate General for Preventive Health Care, Ministry of Health, Rome, Italy
| | - Anna Rita Ciccaglione
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
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18
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Li D, De Keuckelaere A, Uyttendaele M. Fate of Foodborne Viruses in the "Farm to Fork" Chain of Fresh Produce. Compr Rev Food Sci Food Saf 2015; 14:755-770. [PMID: 32313514 PMCID: PMC7162173 DOI: 10.1111/1541-4337.12163] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022]
Abstract
Norovirus (NoV) and hepatitis A virus (HAV) are the most important foodborne viruses. Fresh produce has been identified as an important vehicle for their transmission. In order to supply a basis to identify possible prevention and control strategies, this review intends to demonstrate the fate of foodborne viruses in the farm to fork chain of fresh produce, which include the introduction routes (contamination sources), the viral survival abilities at different stages, and the reactions of foodborne viruses towards the treatments used in food processing of fresh produce. In general, the preharvest contamination comes mainly from soli fertilizer or irrigation water, while the harvest and postharvest contaminations come mainly from food handlers, which can be both symptomatic and asymptomatic. Foodborne viruses show high stabilities in all the stages of fresh produce production and processing. Low-temperature storage and other currently used preservation techniques, as well as washing by water have shown limited added value for reducing the virus load on fresh produce. Chemical sanitizers, although with limitations, are strongly recommended to be applied in the wash water in order to minimize cross-contamination. Alternatively, radiation strategies have shown promising inactivating effects on foodborne viruses. For high-pressure processing and thermal treatment, efforts have to be made on setting up treatment parameters to induce sufficient viral inactivation within a food matrix and to protect the sensory and nutritional qualities of fresh produce to the largest extent.
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Affiliation(s)
- Dan Li
- Laboratory of Food Microbiology and Food Preservation, Faculty of Bioscience Engineering Ghent Univ Coupure Links 653 B-9000 Ghent Belgium
| | - Ann De Keuckelaere
- Laboratory of Food Microbiology and Food Preservation, Faculty of Bioscience Engineering Ghent Univ Coupure Links 653 B-9000 Ghent Belgium
| | - Mieke Uyttendaele
- Laboratory of Food Microbiology and Food Preservation, Faculty of Bioscience Engineering Ghent Univ Coupure Links 653 B-9000 Ghent Belgium
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19
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Terio V, Bottaro M, Di Pinto A, Catella C, Chironna M, Bozzo G, Kingsley DH, Bonerba E, Morea A, Martella V. Outbreak of Hepatitis A in Italy Associated with Frozen Redcurrants Imported from Poland: A Case Study. FOOD AND ENVIRONMENTAL VIROLOGY 2015; 7:305-308. [PMID: 26001535 DOI: 10.1007/s12560-015-9199-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 05/11/2015] [Indexed: 06/04/2023]
Abstract
Hepatitis A virus (HAV) was detected in a batch of imported non-packaged frozen redcurrants purchased in a Bari grocery. Sequence and phylogenetic analysis showed the HAV strain clustered tightly with the HAV strain from the 2013 Italian epidemic, providing additional evidence that frozen redcurrants were the main vehicle of the HAV outbreak.
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Affiliation(s)
- V Terio
- Department of Veterinary Medicine, University of Bari "Aldo Moro", S.p. per Casamassima Km 3, Valenzano, 70010, Bari, Italy,
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20
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Sánchez G. Processing Strategies to Inactivate Hepatitis A Virus in Food Products: A Critical Review. Compr Rev Food Sci Food Saf 2015. [DOI: 10.1111/1541-4337.12154] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Gloria Sánchez
- Dept. of Microbiology and Ecology; Univ. of Valencia, Dr. Moliner; 50. Burjassot Valencia Spain
- Inst. of Agrochemistry and Food Technology (IATA); Spanish Council for Scientific Research (CSIC); Agustín Escardino, 7. Paterna Valencia Spain
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21
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Wenzel JJ, Schemmerer M, Oberkofler H, Kerschner H, Sinha P, Koidl C, Allerberger F. Hepatitis A Outbreak in Europe: Imported Frozen Berry Mix Suspected to be the Source of At least One Infection in Austria in 2013. FOOD AND ENVIRONMENTAL VIROLOGY 2014; 6:297-300. [PMID: 25183415 PMCID: PMC4228166 DOI: 10.1007/s12560-014-9165-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/23/2014] [Indexed: 06/03/2023]
Abstract
We tested 19 sera from Austrian patients with acute hepatitis A. A serum from a 48-year-old female patient yielded HAV-nucleic acid that showed 99.7% homology to the HAV-sequence obtained from samples taken during the current outbreak in several European countries, which is associated with consumption of frozen berries. So far, Austria was considered not to be affected by this hepatitis A outbreak.
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Affiliation(s)
- J J Wenzel
- Institute of Clinical Microbiology and Hygiene, University Medical Center Regensburg, Regensburg, Germany
| | - M Schemmerer
- Institute of Clinical Microbiology and Hygiene, University Medical Center Regensburg, Regensburg, Germany
| | - H Oberkofler
- Institut für Medizinisch-Chemische Labordiagnostik, Paracelsus Medizinische Privatuniversität Salzburg, Salzburg, Austria
| | - H Kerschner
- Analyse BioLab, Elisabethinen Hospital Linz, Linz, Austria
| | - P Sinha
- Institut für Labordiagnostik und Mikrobiologie, Klinikum Klagenfurt, Klagenfurt, Austria
| | - C Koidl
- Institut für Hygiene, Mikrobiologie und Umweltmedizin, Medizinische Universität Graz, Graz, Austria
| | - F Allerberger
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Spargelfeldstraße 191 A-1220, Vienna, Austria.
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22
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Tracing of food items in connection to the multinational hepatitis A virus outbreak in Europe. EFSA J 2014. [DOI: 10.2903/j.efsa.2014.3821] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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