Prevalence and diversity of Staphylococcus aureus in the Zambian dairy value chain: A public health concern.

Staphylococcus aureus is an important opportunistic pathogen of both humans and animals. It can cause several diseases, including mastitis, as well as food poisoning by production of heat-stable enterotoxins in food. The aim of this study was to determine the prevalence of S. aureus and the diversity of strains circulating in the Zambian dairy value chain, which have not been studied in detail before. Three provinces were covered by the study (Lusaka, Southern, and Western) and almost 2000 samples along the dairy value chain, covering both the informal and formal market sectors, were taken at two time points (dry and wet season), with a special focus on raw milk. Nearly 300 presumptive S. aureus isolates were confirmed by MALDI-TOF MS and real-time PCR. Raw milk from traditional and smallholder farms was widely contaminated with S. aureus; prevalence was 33-46% depending on the study province. Raw milk from milk collection centres, informal traders, traditional market sellers, and processors were also frequently contaminated with S. aureus. In addition, S. aureus was detected in several milk bucket swabs and nasal and hand swabs of milkers. From industrially processed (heat-treated) milk and dairy products, no S. aureus was isolated. Methicillin-resistant S. aureus (MRSA) were not detected, but around 10% of the S. aureus isolates carried lukS-PV, a marker gene for the virulence factor Pantone-Valentine leucocidin (PVL), which has been associated with severe diseases in human. Molecular typing identified a total of 44 spa types including 13 novel types: t18396, t18397, t18398, t18399, t18400, t18402, t18416, t20459, t20460, t20461, t20462, t20463, and t20464. Furthermore, 12 novel multi-locus sequence types were identified: ST7012, ST7100, ST7101, ST7177, ST7291, ST7304, ST7305, ST7344, ST7596, ST7597, ST7598, and ST7599, of which ST7012, ST7177, and ST7596 fall into the bovine-associated clonal linage CC97. The spa types t084, t267, t355, and the novel type t20464 were common in all three study provinces. The predominant spa type varied depending on the province. Whole genome sequencing (WGS) and core genome multi-locus sequence typing (cgMLST) indicates transmission of strains along the Zambian dairy chain with possible persistence in the chain over time. cgMLST also revealed a very close relatedness between some isolates from milkers and from raw milk or milk buckets. The high prevalence and wide spa type diversity of S. aureus, as well as possible direct or indirect transmission of (potentially highly virulent) S. aureus to humans along the Zambian dairy value chain, are of public health concern, particularly as milk and milk products are often consumed raw by the Zambian population.