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Garrido-Palazuelos LI, Aguirre-Sánchez JR, Castro-Del Campo N, López-Cuevas O, González-Torres B, Chaidez C, Medrano-Félix JA. Genomic characteristics of Salmonella Montevideo and Pomona: impact of isolation source on antibiotic resistance, virulence and metabolic capacity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-16. [PMID: 38576268 DOI: 10.1080/09603123.2024.2336597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024]
Abstract
Salmonella enterica is known for its disease-causing serotypes, including Montevideo and Pomona. These serotypes have been found in various environments, including river water, sediments, food, and animals. However, the global spread of these serotypes has increased, leading to many reported infections and outbreaks. The goal of this study was the genomic analysis of 48 strains of S. Montevideo and S. Pomona isolated from different sources, including clinical. Results showed that environmental strains carried more antibiotic resistance genes than the clinical strains, such as genes for resistance to aminoglycosides, chloramphenicol, and sulfonamides. Additionally, the type 4 secretion system, was only found in environmental strains. .Also many phosphotransferase transport systems were identified and the presence of genes for the alternative pathway Entner-Doudoroff. The origin of isolation may have a significant impact on the ability of Salmonella isolates to adapt and survive in different environments, leading to genomic flexibility and a selection advantage.
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Affiliation(s)
- Lennin Isaac Garrido-Palazuelos
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Roberto Aguirre-Sánchez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Nohelia Castro-Del Campo
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Osvaldo López-Cuevas
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Berenice González-Torres
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - Cristóbal Chaidez
- Laboratorio Nacional Para la Investigación En Inocuidad Alimentaria (LANIIA), Centro de Investigación En Alimentación y Desarrollo A.C (CIAD), Culiacán, México
| | - José Andrés Medrano-Félix
- Investigadoras e investigadores por México Centro de Investigación En Alimentación y Desarrollo A.C. Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán, México
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2
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Aguirre-Sánchez JR, Quiñones B, Ortiz-Muñoz JA, Prieto-Alvarado R, Vega-López IF, Martínez-Urtaza J, Lee BG, Chaidez C. Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen. Microorganisms 2023; 11:2114. [PMID: 37630674 PMCID: PMC10457828 DOI: 10.3390/microorganisms11082114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/27/2023] Open
Abstract
Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.
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Affiliation(s)
- José R. Aguirre-Sánchez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - José A. Ortiz-Muñoz
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Rogelio Prieto-Alvarado
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Inés F. Vega-López
- Parque de Innovación Tecnológica de la Universidad Autónoma de Sinaloa, Culiacan 80040, Mexico; (J.A.O.-M.); (R.P.-A.); (I.F.V.-L.)
| | - Jaime Martínez-Urtaza
- Departament de Genètica i de Microbiologia, Universitat Autờnoma de Barcelona, 08193 Bellaterra, Spain;
| | - Bertram G. Lee
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA 94710, USA; (B.Q.); (B.G.L.)
| | - Cristóbal Chaidez
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Culiacan 80110, Mexico;
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3
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González-López I, Medrano-Félix JA, Castro-del Campo N, López-Cuevas O, González-Gómez JP, Valdez-Torres JB, Aguirre-Sánchez JR, Martínez-Urtaza J, Gómez-Gil B, Lee BG, Quiñones B, Chaidez C. Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico. Microorganisms 2022; 10:microorganisms10061214. [PMID: 35744732 PMCID: PMC9228531 DOI: 10.3390/microorganisms10061214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/18/2022] Open
Abstract
Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.
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Affiliation(s)
- Irvin González-López
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - José Andrés Medrano-Félix
- Investigadoras e Investigadores por México, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico;
| | - Nohelia Castro-del Campo
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - Osvaldo López-Cuevas
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - Jean Pierre González-Gómez
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - José Benigno Valdez-Torres
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - José Roberto Aguirre-Sánchez
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
| | - Jaime Martínez-Urtaza
- Department of Genetics and Microbiology, Universitat Autờnoma de Barcelona, 08193 Bellaterra, Spain;
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Mazatlán, Acuicultura y Manejo Ambiental, Mazatlán 82100, Sinaloa, Mexico;
| | - Bertram G. Lee
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, USA; (B.G.L.); (B.Q.)
| | - Beatriz Quiñones
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA 94710, USA; (B.G.L.); (B.Q.)
| | - Cristóbal Chaidez
- Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Coordinación Regional Culiacán, Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Culiacán 80110, Sinaloa, Mexico; (I.G.-L.); (N.C.-d.C.); (O.L.-C.); (J.P.G.-G.); (J.B.V.-T.); (J.R.A.-S.)
- Correspondence: ; Tel.: +52-(667)-480-6950
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Morasi RM, Rall VLM, Dantas STA, Alonso VPP, Silva NCC. Salmonella spp. in low water activity food: Occurrence, survival mechanisms, and thermoresistance. J Food Sci 2022; 87:2310-2323. [PMID: 35478321 DOI: 10.1111/1750-3841.16152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 03/04/2022] [Accepted: 03/22/2022] [Indexed: 01/17/2023]
Abstract
The occurrence of disease outbreaks involving low-water-activity (aw ) foods has gained increased prominence due in part to the fact that reducing free water in these foods is normally a measure that controls the growth and multiplication of pathogenic microorganisms. Salmonella, one of the main bacteria involved in these outbreaks, represents a major public health problem worldwide and in Brazil, which highlights the importance of good manufacturing and handling practices for food quality. The virulence of this pathogen, associated with its high ability to persist in the environment, makes Salmonella one of the main challenges for the food industry. The objectives of this article are to present the general characteristics, virulence, thermoresistance, control, and relevance of Salmonella in foodborne diseases, and describe the so-called low-water-activity foods and the salmonellosis outbreaks involving them.
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Affiliation(s)
- Rafaela Martins Morasi
- Department of Food Sciences And Nutrition, Faculty of Food Engineering, State University of Campinas (UNICAMP), Monteiro Lobato Street, 80, Campinas, São Paulo, Brazil
| | - Vera Lúcia Mores Rall
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Stéfani Thais Alves Dantas
- Sector of Microbiology and Immunology, Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Vanessa Pereira Perez Alonso
- Department of Food Sciences And Nutrition, Faculty of Food Engineering, State University of Campinas (UNICAMP), Monteiro Lobato Street, 80, Campinas, São Paulo, Brazil
| | - Nathália Cristina Cirone Silva
- Department of Food Sciences And Nutrition, Faculty of Food Engineering, State University of Campinas (UNICAMP), Monteiro Lobato Street, 80, Campinas, São Paulo, Brazil
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5
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Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL, Thompson FL, Gomez-Gil B, Sawabe T. Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach. Curr Microbiol 2021; 79:10. [PMID: 34905112 DOI: 10.1007/s00284-021-02725-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
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Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayo Nishikawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, España
| | - Fabiano L Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC, Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, México
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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6
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Bell RL, Kase JA, Harrison LM, Balan KV, Babu U, Chen Y, Macarisin D, Kwon HJ, Zheng J, Stevens EL, Meng J, Brown EW. The Persistence of Bacterial Pathogens in Surface Water and Its Impact on Global Food Safety. Pathogens 2021; 10:1391. [PMID: 34832547 PMCID: PMC8617848 DOI: 10.3390/pathogens10111391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Water is vital to agriculture. It is essential that the water used for the production of fresh produce commodities be safe. Microbial pathogens are able to survive for extended periods of time in water. It is critical to understand their biology and ecology in this ecosystem in order to develop better mitigation strategies for farmers who grow these food crops. In this review the prevalence, persistence and ecology of four major foodborne pathogens, Shiga toxin-producing Escherichia coli (STEC), Salmonella, Campylobacter and closely related Arcobacter, and Listeria monocytogenes, in water are discussed. These pathogens have been linked to fresh produce outbreaks, some with devastating consequences, where, in a few cases, the contamination event has been traced to water used for crop production or post-harvest activities. In addition, antimicrobial resistance, methods improvements, including the role of genomics in aiding in the understanding of these pathogens, are discussed. Finally, global initiatives to improve our knowledge base of these pathogens around the world are touched upon.
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Affiliation(s)
- Rebecca L. Bell
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Julie A. Kase
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Lisa M. Harrison
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Kannan V. Balan
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Uma Babu
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, Laurel, MD 20708, USA; (L.M.H.); (K.V.B.); (U.B.)
| | - Yi Chen
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Dumitru Macarisin
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Hee Jin Kwon
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Jie Zheng
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
| | - Eric L. Stevens
- Office of the Center Director, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA;
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, MD 20742, USA;
| | - Eric W. Brown
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD 20740, USA; (J.A.K.); (Y.C.); (D.M.); (H.J.K.); (J.Z.); (E.W.B.)
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