From a healthy animal, raw milk is expected to harbour no pathogens at the point of collection. However, this is seldom the case. Generally, pathogenic microorganisms can contaminate raw milk in two ways. First, endogenous contamination occurs when milk is contaminated by a direct transfer of pathogens from the blood (systemic infection) of an infected animal into the milk, or via an infection in the udder. The second means by which fresh milk can be contaminated, known as exogenous contamination, occurs where milk is contaminated during or after collection by animal faeces, the exterior of the udder and teats, the skin, and other environmental sources ^[1]. Table 1 summarizes important risk factors and their implications for milk safety.

2. Risk Factors for Microbiological Hazards in Dairy Production and Processing in Africa

During the primary production stage, pathogens can contaminate milk through various routes. Animal feed and drinking water often serve as sources of microbial contamination. Predominant among the dairy production systems in Africa are the rural smallholder dairies in which farm animals are fed on grass, crop residues and cultivated fodder, or they roam the land in search of grazing grounds and water. Consequently, the microbiological quality of feed and water for dairy animals are not routinely assessed under these systems, and therefore there is a high risk for the ingestion of contaminated feed and water by dairy animals in Africa. Upon ingestion of contaminated water or feed, surviving (spore-formers) pathogens can be expelled into the farm environment and subsequently attach to teats and udder of dairy animals. Apart from contaminating the external surfaces of udder and teats, several potential pathogens including the genera Staphylococcus, Streptococcus, Bacillus, Micrococcus, and Corynebacterium can colonize the mammary glands of dairy animals even without any disease symptoms ^[2].

Mastitis, an inflammation of the mammary glands and udder tissues, is caused by a large variety of common bacteria, fungi, mycoplasmas and algae ^[3] infecting the mammary glands of dairy animals. Mastitis adversely affects animal health, milk quality, consumer safety, and can lead to great economic losses for milk production ^[4][5][6]. In sub-Sahara Africa, both subclinical mastitis (SCM) and clinical mastitis (CM) among dairy cows have been reported with prevalence rates in the range of 16.1%–90.3% and 4.8%–25.5%, respectively ^[7][8][9]. A recent report indicates that the prevalence of subclinical mastitis among dairy cows in some districts in Rwanda is 50.4% and the milk collected from positive mastitis cows were found to harbour coagulase negative Staphylococci (51.5%), Staphylococcus aureus (20.6%), Streptococcus species (10.3%), Bacillus species (10.3%), Streptococcus agalactiae (5.8%), and Escherichia coli (1.5%) ^[10]. Mastitis among dairy herds is a major constraint, and the disease has been identified as a primary cause of poor-quality and compromises the safety of raw milk in Ethiopia ^[11]. Generally, milk can easily become contaminated before it is secreted from the udder owing to mastitis. Although microbial contamination of milk during milking is difficult to completely avoid ^[12], it is of utmost importance to maintain a very high level of hygiene in dairy farming practices and proper cleaning of teats during milking for good udder health and optimum milk quality, and to ensure safety ^[13][14].

Once milk is secreted from the udder, it can be contaminated from several sources including air, faeces, bedding material, soil, feed, water, equipment, animal hides and people. A critical factor affecting milk safety is milking hygiene. Adequate milking hygiene potentially reduces the contaminating microorganisms and prevents them from inhabiting the immediate environment or skin of the animals, hands personnel and milking equipment, thereby minimizing their spread during milking ^[15]. High prevalence of pathogens in raw milk and occurrence of mastitis have previously been recorded in farms that practiced poor milking hygiene in Africa ^{[9][16][17][18]}. The dairy farm environment can be a reservoir of foodborne pathogens and serve as a major source of microbial contamination of raw milk due to direct contact with the milk. The use unsterilized collection vessels (containers) and other practices such as milking with unsanitized bare hands and allowing calves to feed without cleaning the teats of udders, expose milk to microbial contamination. In most small-scale milk production farms in Africa, there are no strict implementations of procedures for cleaning and disinfection of materials used during production processes, from milking to the sales of final products. While most foodborne pathogens such as E. coli, Salmonella spp. and Campylobacter spp. inhabit the ruminant intestinal tract, others including Listeria spp. and Bacillus spp. are widespread in nature and live in soils and plant environments. Thus, these environmental microorganisms can contaminate the milk by direct contact or through milking equipment and personnel on the farm if good hygiene management practices are not followed. Additionally, intentional adulterated of raw milk with contaminated water has been reported ^[19], a practice that potentially serves as another major source of pathogenic microorganisms in raw milk.

Storage and transportation of raw milk immediately after milking through to point of sale or processing are critical for safety and quality. In order to prevent proliferation of pathogens that contaminate freshly collected milk, there should be strict time and temperature controls between the milking and the processing of dairy products. Ideally, raw milk should be immediately cooled to below 4 °C to prevent microbial growth and ensure high-quality, safe milk for processing and consumption. This is in practice not possible for most small-scale producers in Africa, and therefore pasteurisation and sterilization of the milk are strongly recommended. This is unfortunately often not the case. Modern cooling facilities including mechanical refrigeration or cooling tanks are not available to the many small-scale dairy producers for reasons such as high initial investment and running costs and technical problems, including the lack or unreliable supply of electricity. Additionally, the majority of raw milk producers in Africa are mostly located in remote rural areas with poor road networks making it difficult to transport milk to urban markets and small-scale processing units. Subsequently, raw milk is often transported from the farm to small-scale processing units in urban market centres by bicycles, motorcycles, animals (donkeys), or by foot. The usual high ambient temperatures, often reaching 35–42 °C in most parts of sub-Sahara Africa, highlight the problem by accelerating the growth of spoilage and pathogenic microorganisms during transportation of raw milk.

The majority of milk produced in Africa is processed into a variety of traditional milk products by small-scale processing units or processors. The final products including spontaneously fermented yoghurt-like milk, traditional cheeses and butter, are produced with slight variations in processing methods depending on country or local region, which is affected by local tastes, dietary habits or culinary traditions ^[20][21]. The production of African traditional dairy products is based on recipes handed down from one generation to another, and processors often do not have access to formal training but learn by seeing, hearing and practicing ^[21]. Small-scale processors of traditional milk products often lack pasteurization, storage and packaging facilities and do not adhere to good manufacturing and hygiene practices (GMP/GHPs), including the implementation of starter culture procedures for milk fermentation. The processing of milk into yoghurts and other fermented products in most parts of Africa relies on spontaneous fermentation or back-slopping where a part of a previous batch of a fermented product is used to inoculate the new batch ^[21][22][23]. Consequently, traditional African fermented milk products may be susceptible to contamination with human pathogens of public health concerns due to the lack of proper control measures and adherence to good manufacturing practices (GMP) in the traditional fermentation processes.