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Quek JJW, Wong JL, Tan JL, Yeo CC, Saw SH. Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce. Foods 2025; 14:352. [PMID: 39941945 PMCID: PMC11817458 DOI: 10.3390/foods14030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 01/03/2025] [Accepted: 01/14/2025] [Indexed: 02/16/2025] Open
Abstract
Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.
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Affiliation(s)
- Jerrald Jia Weai Quek
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia;
- Dr. Wu Lien-Teh Centre of Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long Cheras, Kajang 43000, Selangor, Malaysia;
| | - Jun Leong Wong
- Dr. Wu Lien-Teh Centre of Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long Cheras, Kajang 43000, Selangor, Malaysia;
- Department of Pre-Clinical Sciences, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long Cheras, Kajang 43000, Selangor, Malaysia
| | - Joon Liang Tan
- Faculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang 75450, Melaka, Malaysia;
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases & Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Jalan Sultan Mahmud, Kuala Terengganu 20400, Terengganu, Malaysia;
| | - Seow Hoon Saw
- Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, Malaysia;
- Dr. Wu Lien-Teh Centre of Research in Communicable Diseases, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Jalan Sungai Long, Bandar Sungai Long Cheras, Kajang 43000, Selangor, Malaysia;
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Zhang Y, Lu Y, Chen F. Relationship between physicochemical properties and microbial structural distribution of Chinese-style and Salami fermented sausages. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2023.102583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Chen C, Fan X, Hu Y, Zhou C, Sun Y, Du L, Pan D. Effect of different salt substitutions on the decomposition of lipids and volatile flavor compounds in restructured duck ham. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Barcenilla C, Álvarez-Ordóñez A, López M, Alvseike O, Prieto M. Microbiological Safety and Shelf-Life of Low-Salt Meat Products-A Review. Foods 2022; 11:2331. [PMID: 35954097 PMCID: PMC9367943 DOI: 10.3390/foods11152331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Salt is widely employed in different foods, especially in meat products, due to its very diverse and extended functionality. However, the high intake of sodium chloride in human diet has been under consideration for the last years, because it is related to serious health problems. The meat-processing industry and research institutions are evaluating different strategies to overcome the elevated salt concentrations in products without a quality reduction. Several properties could be directly or indirectly affected by a sodium chloride decrease. Among them, microbial stability could be shifted towards pathogen growth, posing a serious public health threat. Nonetheless, the majority of the literature available focuses attention on the sensorial and technological challenges that salt reduction implies. Thereafter, the need to discuss the consequences for shelf-life and microbial safety should be considered. Hence, this review aims to merge all the available knowledge regarding salt reduction in meat products, providing an assessment on how to obtain low salt products that are sensorily accepted by the consumer, technologically feasible from the perspective of the industry, and, in particular, safe with respect to microbial stability.
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Affiliation(s)
- Coral Barcenilla
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of León, 24071 León, Spain
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of León, 24071 León, Spain
- Institute of Food Science and Technology, University of León, 24007 León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of León, 24071 León, Spain
- Institute of Food Science and Technology, University of León, 24007 León, Spain
| | - Ole Alvseike
- Animalia—Norwegian Meat and Poultry Research Centre, NO-0513 Oslo, Norway
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Faculty of Veterinary Medicine, University of León, 24071 León, Spain
- Institute of Food Science and Technology, University of León, 24007 León, Spain
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Muchaamba F, Eshwar AK, Stevens MJA, Stephan R, Tasara T. Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles. Front Microbiol 2022; 12:792162. [PMID: 35058906 PMCID: PMC8764371 DOI: 10.3389/fmicb.2021.792162] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Listeria monocytogenes is a public health and food safety challenge due to its virulence and natural stress resistance phenotypes. The variable distribution of L. monocytogenes molecular subtypes with respect to food products and processing environments and among human and animal clinical listeriosis cases is observed. Sixty-two clinical and food-associated L. monocytogenes isolates were examined through phenome and genome analysis. Virulence assessed using a zebrafish infection model revealed serotype and genotype-specific differences in pathogenicity. Strains of genetic lineage I serotype 4b and multilocus sequence type clonal complexes CC1, CC2, CC4, and CC6 grew and survived better and were more virulent than serotype 1/2a and 1/2c lineage II, CC8, and CC9 strains. Hemolysis, phospholipase activity, and lysozyme tolerance profiles were associated with the differences observed in virulence. Osmotic stress resistance evaluation revealed serotype 4b lineage I CC2 and CC4 strains as more osmotolerant, whereas serotype 1/2c lineage II CC9 strains were more osmo-sensitive than others. Variable tolerance to the widely used quaternary ammonium compound benzalkonium chloride (BC) was observed. Some outbreak and sporadic clinical case associated strains demonstrated BC tolerance, which might have contributed to their survival and transition in the food-processing environment facilitating food product contamination and ultimately outbreaks or sporadic listeriosis cases. Genome comparison uncovered various moderate differences in virulence and stress associated genes between the strains indicating that these differences in addition to gene expression regulation variations might largely be responsible for the observed virulence and stress sensitivity phenotypic differences. Overall, our study uncovered strain and genotype-dependent variation in virulence and stress resilience among clinical and food-associated L. monocytogenes isolates with potential public health risk implications. The extensive genome and phenotypic data generated provide a basis for developing improved Listeria control strategies and policies.
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Affiliation(s)
- Francis Muchaamba
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Athmanya K Eshwar
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Marc J A Stevens
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
| | - Taurai Tasara
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zürich, Zurich, Switzerland
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Gomes MDSA, Kato LS, Carvalho APAD, Almeida AECCD, Conte-Junior CA. Sodium replacement on fish meat products – A systematic review of microbiological, physicochemical and sensory effects. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.10.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Effect of Salt Content Reduction on Food Processing Technology. Foods 2021; 10:foods10092237. [PMID: 34574347 PMCID: PMC8469246 DOI: 10.3390/foods10092237] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/19/2021] [Accepted: 09/15/2021] [Indexed: 12/21/2022] Open
Abstract
Higher salt intake is associated with the risk of cardiovascular and kidney diseases, hypertension and gastric cancer. Salt intake reduction represents an effective way to improve people’s health, either by the right choice of food or by a reduction of added salt. Salt substitutes are often used and also herb homogenates are treated by high pressure technology. Salt reduction significantly influences the shelf life, texture, pH, taste, and aroma of cheese. The composition of emulsifying salts or starter cultures must be modified to enact changes in microbial diversity, protease activity and the ripening process. The texture becomes softer and aroma atypical. In bakery products, a salt reduction of only 20–30% is acceptable. Water absorption, dough development, length and intensity of kneading and stability of dough are changed. Gluten development and its viscoelastic properties are affected. The salt reduction promotes yeast growth and CO2 production. Specific volume and crust colour intensity decreased, and the crumb porosity changed. In meat products, salt provides flavour, texture, and shelf life, and water activity increases. In this case, myofibrillar proteins’ solubility, water binding activity and colour intensity changes were found. The composition of curing nitrite salt mixtures and starter cultures must be modified.
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