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Ma X, Li K, Li F, Su J, Meng W, Sun Y, Sun H, Sun J, Yuan Y, Lin Y, Hu S, Xu X, He Z. Tracing Foodborne Botulism Events Caused by Clostridium botulinum in Xinjiang Province, China, Using a Core Genome Sequence Typing Scheme. Microbiol Spectr 2022; 10:e0116422. [PMID: 36377961 PMCID: PMC9769928 DOI: 10.1128/spectrum.01164-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
Foodborne botulism is a rare but life-threatening illness resulting from the action of a potent toxin mainly produced by Clostridium botulinum. It grows in an oxygen-deficient environment and is extremely viable in meat and soy products, making it one of the most virulent bacteria. How to track foodborne botulism events quickly and accurately has become a key issue. Here, we investigated two foodborne botulism events that occurred in Xinjiang in 2019 based on whole-genome sequencing and also successfully traced the relationship between clinical and food C. botulinum isolates using whole-genome core gene markers. All 59 isolates were classified as group I strains. Of the strains isolated in this study, 44 were found to be botulinum toxin A(B), and 15 isolates contained only the toxin B locus. Both the toxin A and B gene segments were located on the chromosome and organized in an ha cluster. Antibiotic resistance and virulence factors were also investigated. A set of 329 universal core gene markers were established using C. botulinum strains from a public database. These core gene markers were applied to the published C. botulinum genomes, and three outbreaks were identified. This work demonstrates that universal core gene markers can be used to trace foodborne botulism events, and we hope that our work will facilitate this effort in future. IMPORTANCE In this study, we analyzed 59 foodborne botulism (FB)-related strains isolated in Xinjiang Province, China. Our findings not only reveal the group classification, neurotoxin locus organization, antibiotic resistance and virulence factors of these strains but also establish a set of core gene markers for tracing foodborne botulism events, which was verified using published genomes. These findings indicate that these gene markers might be used as a potential tracing tool for FB events caused by C. botulinum group I strains, which have relatively stable genomic components.
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Affiliation(s)
- Xin Ma
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Kexin Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Engineering Medicine, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
| | - Fang Li
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Jing Su
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Weiwei Meng
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yanming Sun
- School of Engineering Medicine, Beihang University, Beijing, China
| | - Hui Sun
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, China
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiazheng Sun
- Criminal Investigation School, People's Public Security University of China, Beijing, China
| | - Yonghe Yuan
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yujia Lin
- Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xuefang Xu
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, Beijing, China
- National Institute for Communicable Diseases Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zilong He
- School of Engineering Medicine, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Interdisciplinary Innovation Institute of Medicine and Engineering, Beihang University, Beijing, China
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Umeda K, Hirai Y, Nakamura H, Amo K. Comparative whole-genome sequence analysis of a BoNT/B5-producing Clostridium botulinum isolate from an infant botulism case of unknown source in Osaka, Japan. FEMS Microbiol Lett 2022; 369:6653520. [PMID: 35918187 DOI: 10.1093/femsle/fnac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/19/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
A case of infant botulism of unknown origin, not involved in honey consumption, occurred in Osaka, Japan in 2020. A Clostridium botulinum type B strain named Osaka2020 was isolated from a stool sample of the patient. To clarify the epidemiology of the case, we performed whole-genome sequencing (WGS) of the isolate and compared it with strains from other sources. WGS analysis revealed that isolate Osaka2020 was classified into ST133 of a new sequence type, B5 subtype, and its toxin gene was encoded in a ∼274 kb plasmid. This plasmid was closely related to the pCLJ plasmid from strain 657Ba in the USA, reported to be conjugatively transferable to other strains. Moreover, isolate Osaka2020 also possesses another smaller plasmid that was common with some type A(B) infant botulism isolates in Japan. The phylogenetic tree from whole-genome SNP analysis showed that isolate Osaka2020 was the most closely related to a type B infant botulism isolate that occurred in Japan 10 years ago. Although no epidemiological connection among the two cases was confirmed, there is possibility that the cases are attributed to common causes such as some environmental substance.
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Affiliation(s)
- Kaoru Umeda
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Yuji Hirai
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Hiromi Nakamura
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kiyoko Amo
- Department of Pediatric Emergency Medicine, Osaka City General Hospital, Osaka, Japan
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Smith TJ, Williamson CHD, Hill KK, Johnson SL, Xie G, Anniballi F, Auricchio B, Fernández RA, Caballero PA, Keim P, Sahl JW. The Distinctive Evolution of orfX Clostridium parabotulinum Strains and Their Botulinum Neurotoxin Type A and F Gene Clusters Is Influenced by Environmental Factors and Gene Interactions via Mobile Genetic Elements. Front Microbiol 2021; 12:566908. [PMID: 33716993 PMCID: PMC7952441 DOI: 10.3389/fmicb.2021.566908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/08/2021] [Indexed: 12/30/2022] Open
Abstract
Of the seven currently known botulinum neurotoxin-producing species of Clostridium, C. parabotulinum, or C. botulinum Group I, is the species associated with the majority of human botulism cases worldwide. Phylogenetic analysis of these bacteria reveals a diverse species with multiple genomic clades. The neurotoxins they produce are also diverse, with over 20 subtypes currently represented. The existence of different bont genes within very similar genomes and of the same bont genes/gene clusters within different bacterial variants/species indicates that they have evolved independently. The neurotoxin genes are associated with one of two toxin gene cluster types containing either hemagglutinin (ha) genes or orfX genes. These genes may be located within the chromosome or extrachromosomal elements such as large plasmids. Although BoNT-producing C parabotulinum bacteria are distributed globally, they are more ubiquitous in certain specific geographic regions. Notably, northern hemisphere strains primarily contain ha gene clusters while southern hemisphere strains have a preponderance of orfX gene clusters. OrfX C. parabotulinum strains constitute a subset of this species that contain highly conserved bont gene clusters having a diverse range of bont genes. While much has been written about strains with ha gene clusters, less attention has been devoted to those with orfX gene clusters. The recent sequencing of 28 orfX C. parabotulinum strains and the availability of an additional 91 strains for analysis provides an opportunity to compare genomic relationships and identify unique toxin gene cluster characteristics and locations within this species subset in depth. The mechanisms behind the independent processes of bacteria evolution and generation of toxin diversity are explored through the examination of bacterial relationships relating to source locations and evidence of horizontal transfer of genetic material among different bacterial variants, particularly concerning bont gene clusters. Analysis of the content and locations of the bont gene clusters offers insights into common mechanisms of genetic transfer, chromosomal integration, and development of diversity among these genes.
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Affiliation(s)
- Theresa J Smith
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Charles H D Williamson
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Karen K Hill
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Gary Xie
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Fabrizio Anniballi
- Department of Food Safety, Nutrition and Veterinary Public Health, National Reference Centre for Botulism, Istituto Superiore di Sanità, Rome, Italy
| | - Bruna Auricchio
- Department of Food Safety, Nutrition and Veterinary Public Health, National Reference Centre for Botulism, Istituto Superiore di Sanità, Rome, Italy
| | - Rafael A Fernández
- Área Microbiología, Departamento de Patología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Patricia A Caballero
- Área Microbiología, Departamento de Patología, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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Smith TJ, Xie G, Williamson CHD, Hill KK, Fernández RA, Sahl JW, Keim P, Johnson SL. Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa. Genome Biol Evol 2021; 12:229-242. [PMID: 32108238 DOI: 10.1093/gbe/evaa043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2020] [Indexed: 11/14/2022] Open
Abstract
Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.
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Affiliation(s)
- Theresa J Smith
- Pathogen and Microbiome Institute, Northern Arizona University
| | - Gary Xie
- Bioscience Division, Los Alamos National Laboratory
| | | | - Karen K Hill
- Bioscience Division, Los Alamos National Laboratory
| | | | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University
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Wang S, Weller D, Falardeau J, Strawn LK, Mardones FO, Adell AD, Moreno Switt AI. Food safety trends: From globalization of whole genome sequencing to application of new tools to prevent foodborne diseases. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.09.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Anniballi F, Fillo S, Giordani F, Auricchio B, Tehran DA, di Stefano E, Mandarino G, De Medici D, Lista F. Multiple-locus variable number of tandem repeat analysis as a tool for molecular epidemiology of botulism: The Italian experience. INFECTION GENETICS AND EVOLUTION 2016; 46:28-32. [PMID: 27771520 DOI: 10.1016/j.meegid.2016.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 10/17/2016] [Accepted: 10/18/2016] [Indexed: 01/17/2023]
Abstract
Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions. Through clustering analysis isolates were grouped into 12 main clusters. No regional or temporal clustering was detected, demonstrating the high heterogeneity of strains circulating in Italy. This study confirmed that MLVA is capable of sub-typing C. botulinum strains. Moreover, MLVA is effective at tracing and tracking the source of contamination and is helpful for the surveillance system in terms of planning and upgrading of procedures, activities and data collection forms.
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Affiliation(s)
- Fabrizio Anniballi
- National Reference Centre for Botulism, Department of Veterinary Public Health and Food Safety. Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Silvia Fillo
- Histology and Molecular Biology Unit, Section Two, Army Medical and Veterinary Research Centre, 00184 Rome, Italy
| | - Francesco Giordani
- Histology and Molecular Biology Unit, Section Two, Army Medical and Veterinary Research Centre, 00184 Rome, Italy
| | - Bruna Auricchio
- National Reference Centre for Botulism, Department of Veterinary Public Health and Food Safety. Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Domenico Azarnia Tehran
- Histology and Molecular Biology Unit, Section Two, Army Medical and Veterinary Research Centre, 00184 Rome, Italy
| | - Enrica di Stefano
- Histology and Molecular Biology Unit, Section Two, Army Medical and Veterinary Research Centre, 00184 Rome, Italy
| | - Giuseppina Mandarino
- PENTA - The Joint Laboratory on Models and Methodology to Predict and Manage Large Scale Threats to Public Health - International Affair Unit. Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Dario De Medici
- National Reference Centre for Botulism, Department of Veterinary Public Health and Food Safety. Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Florigio Lista
- Histology and Molecular Biology Unit, Section Two, Army Medical and Veterinary Research Centre, 00184 Rome, Italy
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Abstract
C. botulinum Groups I and II form botulinum neurotoxin and cause foodborne botulism. Increased knowledge of C. botulinum Group I and II genomes and neurotoxin diversity. Impact on food safety via improved surveillance and tracing/tracking during outbreaks. New insights into C. botulinum biology, food chain transmission, evolution.
The deadly botulinum neurotoxin formed by Clostridium botulinum is the causative agent of foodborne botulism. The increasing availability of C. botulinum genome sequences is starting to allow the genomic diversity of C. botulinum Groups I and II and their neurotoxins to be characterised. This information will impact on microbiological food safety through improved surveillance and tracing/tracking during outbreaks, and a better characterisation of C. botulinum Groups I and II, including the risk presented, and new insights into their biology, food chain transmission, and evolution.
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Mazuet C, Legeay C, Sautereau J, Ma L, Bouchier C, Bouvet P, Popoff MR. Diversity of Group I and II Clostridium botulinum Strains from France Including Recently Identified Subtypes. Genome Biol Evol 2016; 8:1643-60. [PMID: 27189984 PMCID: PMC4943176 DOI: 10.1093/gbe/evw101] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2016] [Indexed: 01/31/2023] Open
Abstract
In France, human botulism is mainly food-borne intoxication, whereas infant botulism is rare. A total of 99 group I and II Clostridium botulinum strains including 59 type A (12 historical isolates [1947-1961], 43 from France [1986-2013], 3 from other countries, and 1 collection strain), 31 type B (3 historical, 23 recent isolates, 4 from other countries, and 1 collection strain), and 9 type E (5 historical, 3 isolates, and 1 collection strain) were investigated by botulinum locus gene sequencing and multilocus sequence typing analysis. Historical C. botulinum A strains mainly belonged to subtype A1 and sequence type (ST) 1, whereas recent strains exhibited a wide genetic diversity: subtype A1 in orfX or ha locus, A1(B), A1(F), A2, A2b2, A5(B2') A5(B3'), as well as the recently identified A7 and A8 subtypes, and were distributed into 25 STs. Clostridium botulinum A1(B) was the most frequent subtype from food-borne botulism and food. Group I C. botulinum type B in France were mainly subtype B2 (14 out of 20 historical and recent strains) and were divided into 19 STs. Food-borne botulism resulting from ham consumption during the recent period was due to group II C. botulinum B4. Type E botulism is rare in France, 5 historical and 1 recent strains were subtype E3. A subtype E12 was recently identified from an unusual ham contamination. Clostridium botulinum strains from human botulism in France showed a wide genetic diversity and seems to result not from a single evolutionary lineage but from multiple and independent genetic rearrangements.
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Affiliation(s)
| | - Christine Legeay
- Bactéries Anaérobies et Toxines, Institut Pasteur, Paris, France
| | - Jean Sautereau
- Bactéries Anaérobies et Toxines, Institut Pasteur, Paris, France
| | - Laurence Ma
- Plateforme Genomique-Pôle Biomics, Institut Pasteur, Paris, France
| | | | - Philippe Bouvet
- Bactéries Anaérobies et Toxines, Institut Pasteur, Paris, France
| | - Michel R Popoff
- Bactéries Anaérobies et Toxines, Institut Pasteur, Paris, France
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Williamson CHD, Sahl JW, Smith TJ, Xie G, Foley BT, Smith LA, Fernández RA, Lindström M, Korkeala H, Keim P, Foster J, Hill K. Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia. BMC Genomics 2016; 17:180. [PMID: 26939550 PMCID: PMC4778365 DOI: 10.1186/s12864-016-2502-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/18/2016] [Indexed: 11/24/2022] Open
Abstract
Background Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A–G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use comparative genomics to provide insights into the genetic diversity and evolutionary history of bacteria that produce the potent botulinum neurotoxin. Results Comparative genomic analyses of over 170 Clostridia genomes, including our draft genome assemblies for 59 newly sequenced Clostridia strains from six continents and publicly available genomic data, provided in-depth insights into the diversity and distribution of BoNT-producing bacteria. These newly sequenced strains included Group I and II strains that express BoNT/A,/B,/E, or/F as well as bivalent strains. BoNT-producing Clostridia and closely related Clostridia species were delineated with a variety of methods including 16S rRNA gene, concatenated marker genes, core genome and concatenated multi-locus sequencing typing (MLST) gene phylogenies that related whole genome sequenced strains to publicly available strains and sequence types. These analyses illustrated the phylogenetic diversity in each Group and the diversity of genomic backgrounds that express the same toxin type or subtype. Comparisons of the botulinum neurotoxin genes did not identify novel toxin types or variants. Conclusions This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria. Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2502-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charles H D Williamson
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jason W Sahl
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Theresa J Smith
- Molecular and Translational Sciences Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA.
| | - Gary Xie
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Brian T Foley
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
| | - Leonard A Smith
- Medical Countermeasures Technology, United States Army Medical Research and Material Command, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA.
| | - Rafael A Fernández
- Área Microbiología, Departamento de Patología, Facultad de Ciencias Médicas, Universidad Nacional de Cuyo, Centro Universitario, (5500), Mendoza, Argentina.
| | - Miia Lindström
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA.
| | - Jeffrey Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ, 86011, USA. .,Present Address: Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, 03824, USA.
| | - Karen Hill
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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