Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce
Foodborne illnesses pose a significant global health threat, often caused by pathogens like <i>Escherichia coli</i>, <i>Listeria monocytogenes</i>, and <i>Salmonella</i> spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges....
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MDPI AG
2025-01-01
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| Series: | Foods |
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| author | Jerrald Jia Weai Quek Jun Leong Wong Joon Liang Tan Chew Chieng Yeo Seow Hoon Saw |
| author_facet | Jerrald Jia Weai Quek Jun Leong Wong Joon Liang Tan Chew Chieng Yeo Seow Hoon Saw |
| author_sort | Jerrald Jia Weai Quek |
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| description | Foodborne illnesses pose a significant global health threat, often caused by pathogens like <i>Escherichia coli</i>, <i>Listeria monocytogenes</i>, and <i>Salmonella</i> 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 <i>Listeria monocytogenes</i> identified in meats and vegetables and <i>Shigella flexneri</i> 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 <i>E. coli</i> and <i>Salmonella</i> 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. |
| format | Article |
| id | doaj-art-a53821254d7d4c608db44cecf7b82c79 |
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| issn | 2304-8158 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
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| series | Foods |
| spelling | doaj-art-a53821254d7d4c608db44cecf7b82c792025-08-20T02:12:25ZengMDPI AGFoods2304-81582025-01-0114335210.3390/foods14030352Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian ProduceJerrald Jia Weai Quek0Jun Leong Wong1Joon Liang Tan2Chew Chieng Yeo3Seow Hoon Saw4Department of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, MalaysiaDr. 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, MalaysiaFaculty of Information Science and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang 75450, Melaka, MalaysiaCentre for Research in Infectious Diseases & Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Jalan Sultan Mahmud, Kuala Terengganu 20400, Terengganu, MalaysiaDepartment of Allied Health Sciences, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar 31900, Perak, MalaysiaFoodborne illnesses pose a significant global health threat, often caused by pathogens like <i>Escherichia coli</i>, <i>Listeria monocytogenes</i>, and <i>Salmonella</i> 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 <i>Listeria monocytogenes</i> identified in meats and vegetables and <i>Shigella flexneri</i> 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 <i>E. coli</i> and <i>Salmonella</i> 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.https://www.mdpi.com/2304-8158/14/3/352foodborne pathogensmetagenomicsculture-complementary PCRpathogen detectionfood safetybacterial diversity |
| spellingShingle | Jerrald Jia Weai Quek Jun Leong Wong Joon Liang Tan Chew Chieng Yeo Seow Hoon Saw Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce Foods foodborne pathogens metagenomics culture-complementary PCR pathogen detection food safety bacterial diversity |
| title | Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce |
| title_full | Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce |
| title_fullStr | Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce |
| title_full_unstemmed | Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce |
| title_short | Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce |
| title_sort | integrating metagenomic and culture based techniques to detect foodborne pathogens and antimicrobial resistance genes in malaysian produce |
| topic | foodborne pathogens metagenomics culture-complementary PCR pathogen detection food safety bacterial diversity |
| url | https://www.mdpi.com/2304-8158/14/3/352 |
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