ABSTRACT:
The South African National School Nutrition Programme (NSNP) services schools in low socioeconomic communities using voluntary food handlers. Numerous foodborne disease outbreaks have been reported in these schools. Municipal Health Services monitors compliance of all food premises as food contamination may occur during processing, handling and preparation. This study aimed to assess the compliance of the NSNP to national guidelines and to identify the presence of microbial pathogens on contact surfaces and hands of food handlers using a metagenomic approach. Primary schools in the NSNP (n=33) were randomly selected in KwaZulu-Natal and a standardised checklist assessed compliance of food preparation and storage areas. Swabs were collected from various food contact surfaces and from the hands of the food handlers. Microbial diversity was identified using 16S rRNA/18S rRNA based metagenomic analysis (Illumina, USA) Bioinformatics analysis for taxonomy and identification of genes was performed on the MG-RAST pipeline. Most schools were only partially compliant revealing poor pest and vector control, inadequate WASH provision and training of food safety principles for handlers, and poor waste management. The level of compliance was associated with increased bacterial diversity in various schools. Metagenomic analyses revealed that Pseudomonas, Stenotrophomonas, Acinetobacter, Rahnella and Pantoea were the most dominant genera. We found microbial species, previously undetected, thus introducing new potential contaminants for foodborne disease. The significant diversity and abundance of microbial species revealed by metagenomic analysis, despite the >50% compliance to the minimum standards for food premises, is a public health concern. Advanced molecular technology allows monitoring of all potential contaminants, and not just the “usual suspects.” This will allow a robust and comprehensive approach to improving food safety and mitigating food borne diseases.