1
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Chen R, Yang L, Pajor MS, Wiedmann M, Orsi RH. Salmonella associated with agricultural animals exhibit diverse evolutionary rates and show evidence of recent clonal expansion. mBio 2024:e0191324. [PMID: 39287448 DOI: 10.1128/mbio.01913-24] [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: 07/22/2024] [Accepted: 08/18/2024] [Indexed: 09/19/2024] Open
Abstract
Most foodborne salmonellosis outbreaks are linked to agricultural animal products with a few serovars accounting for most Salmonella isolated from specific animal products, suggesting an adaptation to the corresponding animal hosts and their respective environments. Here, we utilized whole-genome sequence (WGS) data to analyze the evolution and population genetics of seven serovars frequently isolated from ground beef (Montevideo, Cerro, and Dublin), chicken (Kentucky, Infantis, and Enteritidis), and turkey (Reading) in the United States. In addition, publicly available metadata were used to characterize major clades within each serovar with regard to public health significance. Except for Dublin, all serovars were polyphyletic, comprising 2-6 phylogenetic groups. Further partitioning of the phylogenies identified 25 major clades, including 12 associated with animal or environmental niches. These 12 clades differed in evolutionary parameters (e.g., substitution rates) as well as public health relevant characteristics (e.g., association with human illness, antimicrobial resistance). Overall, our results highlight several critical trends: (i) the Salmonella generation time appears to be more dependent on source than serovar and (ii) all serovars contain clades and sub-clades that are estimated to have emerged after the year 1940 and that are enriched for isolates associated with humans, agricultural animals, antimicrobial resistance (AMR), and/or specific geographical regions. These findings suggest that serotyping alone does not provide enough resolution to differentiate isolates that may have evolved independently, present distinct geographic distribution and host association, and possibly have distinct public health significance. IMPORTANCE Non-typhoidal Salmonella are major foodborne bacterial pathogens estimated to cause more than one million illnesses, thousands of hospitalizations, and hundreds of deaths annually in the United States. More than 70% of Salmonella outbreaks in the United States have been associated with agricultural animals. Certain serovars include persistent strains that have repeatedly contaminated beef, chicken, and turkey, causing outbreaks and sporadic cases over many years. These persistent strains represent a particular challenge to public health, as they are genetically clonal and widespread, making it difficult to differentiate distinct outbreak and contamination events using whole-genome sequence (WGS)-based subtyping methods (e.g., core genome allelic typing). Our results indicate that a phylogenetic approach is needed to investigate persistent strains and suggest that the association between a Salmonella serovar and an agricultural animal is driven by the expansion of clonal subtypes that likely became adapted to specific animals and associated environments.
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Affiliation(s)
- Ruixi Chen
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Linghuan Yang
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Magdalena S Pajor
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Renato H Orsi
- Department of Food Science, Cornell University, Ithaca, New York, USA
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2
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Kong X, Chen J, Yang Y, Li M, Wang J, Jia Q, Wang Y, Yuan Q, Miao Y, Zhao P, You Y, Zhao X, Pei X, Zuo H, Meng J. Phenotypic and genotypic characterization of
salmonella
Enteritidis isolated from two consecutive
Food‐Poisoning
outbreaks in Sichuan, China. J Food Saf 2022. [DOI: 10.1111/jfs.13015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ximei Kong
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Jingxian Chen
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Yang Yang
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Ming Li
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Jian Wang
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Qu Jia
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Yao Wang
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Qiwu Yuan
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Yanfang Miao
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Pinnan Zhao
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Yiping You
- Chengdu Center for Disease Control and Prevention Chengdu China
| | - Xing Zhao
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
| | - Xiaofang Pei
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital Sichuan University Chengdu China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province Chengdu China
| | - Jiantong Meng
- Chengdu Center for Disease Control and Prevention Chengdu China
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3
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Davies CP, Jurkiw T, Haendiges J, Reed E, Anderson N, Grasso-Kelley E, Hoffmann M, Zheng J. Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper. Front Microbiol 2022; 13:970135. [PMID: 36160197 PMCID: PMC9507087 DOI: 10.3389/fmicb.2022.970135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
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Affiliation(s)
- Cary P. Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States
- *Correspondence: Cary P. Davies,
| | - Thomas Jurkiw
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Elizabeth Grasso-Kelley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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4
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The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems. NPJ Sci Food 2022; 6:35. [PMID: 35974024 PMCID: PMC9381742 DOI: 10.1038/s41538-022-00150-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/26/2022] [Indexed: 11/26/2022] Open
Abstract
The development and application of modern sequencing technologies have led to many new improvements in food safety and public health. With unprecedented resolution and big data, high-throughput sequencing (HTS) has enabled food safety specialists to sequence marker genes, whole genomes, and transcriptomes of microorganisms almost in real-time. These data reveal not only the identity of a pathogen or an organism of interest in the food supply but its virulence potential and functional characteristics. HTS of amplicons, allow better characterization of the microbial communities associated with food and the environment. New and powerful bioinformatics tools, algorithms, and machine learning allow for development of new models to predict and tackle important events such as foodborne disease outbreaks. Despite its potential, the integration of HTS into current food safety systems is far from complete. Government agencies have embraced this new technology, and use it for disease diagnostics, food safety inspections, and outbreak investigations. However, adoption and application of HTS by the food industry have been comparatively slow, sporadic, and fragmented. Incorporation of HTS by food manufacturers in their food safety programs could reinforce the design and verification of effectiveness of control measures by providing greater insight into the characteristics, origin, relatedness, and evolution of microorganisms in our foods and environment. Here, we discuss this new technology, its power, and potential. A brief history of implementation by public health agencies is presented, as are the benefits and challenges for the food industry, and its future in the context of food safety.
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Sithole TR, Ma YX, Qin Z, Wang XD, Liu HM. Peanut Butter Food Safety Concerns-Prevalence, Mitigation and Control of Salmonella spp., and Aflatoxins in Peanut Butter. Foods 2022; 11:1874. [PMID: 35804689 PMCID: PMC9265579 DOI: 10.3390/foods11131874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Peanut butter has a very large and continuously increasing global market. The food safety risks associated with its consumption are also likely to have impacts on a correspondingly large global population. In terms of prevalence and potential magnitude of impact, contamination by Salmonella spp., and aflatoxins, are the major food safety risks associated with peanut butter consumption. The inherent nature of the Salmonella spp., coupled with the unique chemical composition and structure of peanut butter, present serious technical challenges when inactivating Salmonella spp. in contaminated peanut butter. Thermal treatment, microwave, radiofrequency, irradiation, and high-pressure processing all are of limited efficacy in inactivating Salmonella spp. in contaminated peanut butter. The removal of aflatoxins in contaminated peanut butter is equally problematic and for all practical purposes almost impossible at the moment. Adopting good manufacturing hygiene practices from farm to table and avoiding the processing of contaminated peanuts are probably some of the few practically viable strategies for minimising these peanut butter food safety risks. The purpose of this review is to highlight the nature of food safety risks associated with peanut butter and to discuss the effectiveness of the initiatives that are aimed at minimising these risks.
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Affiliation(s)
| | | | | | - Xue-De Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou 450001, China; (T.R.S.); (Y.-X.M.); (Z.Q.); (H.-M.L.)
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