The development of rapid food safety assessment methods to address the current limitations of food safety assessment methodologies

Foodborne diarrheal diseases remain a leading cause of global illness and death. A significant amount of disease burden is concentrated in low and middle-income countries (LMICs). The emergence of antimicrobial resistance (AMR) bacteria could complicate future diarrheal disease treatments. However, evidence on the risk for child exposure to foodborne enteric bacteria is limited in Kenya. Even when such evidence was available, the current food safety testing methods for detecting safety issues are time-consuming and inaccurate in determining where food safety and AMR steward interventions are needed. To address those gaps, we assessed the performance of species-specific Bacteroides microbial source tracking (MST) markers to determine if they are suitable indicators of enteric pathogen contamination in food. We found that Bacteroides MST markers are unsuitable for indicating enteric pathogen contamination in food due to the low sensitivity between MST markers and pathogen detections.

We developed a Salmonella enrichment and real-time polymerase chain reaction (qPCR) pathogen detection protocol that reduced the time needed for food safety assessment and provided a means for quantifying concentrations of viable bacteria. The time shortened 5-hour 37 °C enrichment protocol in peptone water was sufficient for Salmonella detection in milk by culture and qPCR. In addition, successive PCR measurements made qualitative and quantitative assessments of viable Salmonella possible.

Last, the AMR research in this dissertation highlighted the need for antibiotic stewardship in the milk supply chain and communities since the qPCR assay has detected resistance genes from Salmonella isolated from milk products and infant food that could express resistance to antimicrobials commonly used toward Kenyan farm animals. Additional molecular-based AMR testing should be conducted on other food products in Kenya to help policymakers design interventions to prevent the proliferation of AMR bacteria.