Madlala, Sithembile S.Mchunu, NokuthulaDalasile, MonicaPierneef, Rian EwaldReddy, Poovendhree2025-06-252025-06-252025-06Madlala, S.S., Mchunu, N., Dalasile, M., Pierneef, R. & Reddy, P., 2025, ‘Metagenomic evaluation of food hygiene practices in the National School Nutrition Programme in KwaZulu Natal, South Africa’, Health SA Gesondheid 30(0), a2814. https://doi.org/10.4102/hsag.v30i0.2814.1025-9848 (print)2071-9736 (online)10.4102/hsag.v30i0.2814http://hdl.handle.net/2263/102978DATA AVAILABILITY : The data that support the findings of this study are available on request from the corresponding author, P.R. The data are not publicly available because of their containing information that could compromise the privacy of research participants.\ This article is partially based on the author’s thesis entitled ‘Food hygiene in the National Schools Nutrition Programme among primary schools in Vryheid, KwaZulu-Natal, South Africa’ towards the degree of Master of Health Science in Environmental Health in the Faculty of Health Sciences at the Durban University of Technology, South Africa on October 2022, with supervisor Prof. P. Reddy; co-supervisor Dr N. Mchunu and Ms M. Dalasile. It is available here: https://openscholar.dut.ac.za/server/api/core/bitstreams/5bf913ff-4f81-4bd6-a8b6-d79f2d181cb3/content.BACKGROUND : The National School Nutrition Programme (NSNP) provides meals to schools in low-income areas in South Africa, implemented by the Department of Basic Education (DBE) with food safety monitored by Municipal Health Services. AIM : To assess compliance of school kitchens with general hygiene requirements (R638 of 2018) and detect food pathogens on food contact surfaces using amplified metagenomics. SETTING : The study was conducted in quintile 1 and 2 primary schools in Vryheid, KwaZulu-Natal. METHODS : A quantitative cross-sectional study assessed the safety compliance of food preparation and storage areas in 33 primary schools against national legislation standards. Fifteen samples of food contact surfaces were collected from four schools and analysed using Illumina sequencing to identify prevalent bacterial genera. RESULTS : None of the schools possessed a Certificate of Acceptability. Significant structural issues include poor pest control, inadequate sanitary facilities, a lack of food safety training and inadequate waste management. Taxonomic analysis revealed several dominant bacterial genera, including Pseudomonas, Stenotrophomonas, Acinetobacter and Pantoea, indicating potential routes for food contamination and subsequent risks for foodborne illnesses. CONCLUSION : The study highlighted critical inadequacies in food preparation and storage areas requiring urgent intervention to ensure safe meal preparation. It emphasised the need for improved food safety monitoring and compliance in schools in low-income areas. Next-generation sequencing (NGS) techniques identified a broad spectrum of pathogens, offering a robust method for assessing environmental hygiene. CONTRIBUTION : This study provides insights into food safety risks in the NSNP, informing policies and interventions to improve food safety and reduce foodborne illnesses in schools.en© 2025. The Authors. Licensee: AOSIS. This work is licensed under the Creative Commons Attribution License.Amplified metagenomicsFood contact surfacesFood contaminationFood handlersFood hygieneNational School Nutrition Programme (NSNP)Department of Basic Education (DBE)Next-generation sequencing (NGS)Article