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Bacterial Foodborne Pathogens (FBP) are the commonest cause of foodborne illness or foodborne diseases (FBD) worldwide. They contaminate food at any stages in the entire food chain, from farm to dining-table. Among these, the Diarrheagenic Escherichia coli (DEC), Non typhoidal Salmonella (NTS), Shigella spp. and Campylobacter spp. are responsible for a large proportion of illnesses, deaths; and, particularly, as causes of acute diarrheal diseases. Though existing studies indicate the problem may be severe in developing countries like Ethiopia, the evidence is commonly based on fragmented data from individual studies. A review of published and unpublished manuscripts was conducted to obtain information on major FBP and identify the gaps in tracking their source attributions at the human, animal and environmental interface. A total of 1753 articles were initially retrieved after restricting the study period to between January 2000 and July 2020. After the second screening, only 51 articles on the humans and 43 on the environmental sample based studies were included in this review. In the absence of subgroups, overall as well as human stool and environmental sample based pooled prevalence estimate of FBP were analyzed. Since, substantial heterogeneity is expected, we also performed a subgroup analyses for principal study variables to estimate pooled prevalence of FBP at different epidemiological settings in both sample sources. The overall random pooled prevalence estimate of FBP (Salmonella, pathogenic Escherichia coli (E. coli), Shigella and Campylobacter spp.) was 8%; 95% CI: 6.5–8.7, with statistically higher (P Salmonella and pathogenic E. coli contributed to 5.7% (95% CI: 4.7–6.8) and 11.6% (95% CI: 8.8–15.1) respectively, of the overall pooled prevalence estimates of FBD in Ethiopia. The result of meta-regression showed, administrative regional state, geographic area of the study, source of sample and categorized sample size all significantly contributed to the heterogeneity of Salmonella and pathogenic E. coli estimates. Besides, the multivariate meta- regression indicated the actual study year between 2011 and 2015 was significantly associated with the environmental sample-based prevalence estimates of these FBP. This systematic review and meta-analysis depicted FBP are important in Ethiopia though majority of the studies were conducted separately either in human, animal or environmental samples employing routine culture based diagnostic method. Thus, further FBD study at the human, animal and environmental interface employing advanced diagnostic methods is needed to investigate source attributions of FBD in one health approach.

As the cost of genome sequencing of foodborne pathogens decreases, it has become possible to sequence a large number of isolates and evaluate those using machine learning algorithms. This study aimed to utilize machine learning algorithms to predict the disease endpoints in untagged Salmonella genome sequences isolated from ground chicken. Our models recognized genetic patterns in the test dataset based on our training dataset obtained from an extensive literature review, using a semi-supervised approach. Using known genotypes as input features, the semi-supervised random forest model showed the highest overall accuracy of 0.94 (95% confidence interval: 0.85–0.99), and a Kappa value of 0.82, and predicted 87% of the disease endpoints. The model predicted genes associated with specific disease endpoints that were associated with virulence, which could be used as features in predictive modeling endeavors in the future. Our machine learning approach would be useful in different areas of food safety, including identifying pathogen sources, predicting antibiotic resistance, and risk assessment of foodborne pathogens.

The current study was designed to evaluate the potential impact of the level of regulation on the prevalence and patterns of antimicrobial agent resistance in bacteria isolated from fish. The study sites included two large lakes and both semiregulated and unregulated fish value chains. A total of 328 bacterial isolates belonging to 11 genera were evaluated for antimicrobial susceptibility testing using the disk diffusion method. The bacterial species were tested against 12 different antibiotics (trimethoprim-sulfamethoxazole, tetracycline, ampicillin, cefotaxime, chloramphenicol, nalidixic acid, amoxicillin, meropenem, ciprofloxacin, nitrofurantoin, cefuroxime, and kanamycin). Data analysis was done to assess the heterogeneity in proportion of resistant bacterial species within and between the two value chains using a random-effects model proposed by DerSimonian and Laird (Control Clin Trials 7:177–188, 1986). Statistical heterogeneity within and between groups was estimated using the Cochran chi-square test and the Cochrane I(2) index. The overall proportion of bacterial species resistant to antimicrobial agents in semiregulated and unregulated value chains ranged from 0.00 to 0.88 and 0.09 to 0.95, respectively. Shigella spp. had the highest proportion of bacteria that were resistant to most of the antimicrobial agents used. The bacterial species were highly resistant to ampicillin and amoxicillin, and the highest multidrug resistance capacity was observed in Shigella spp. (18.3%, n = 328), Vibrio spp. (18.3%), and Listeria monocytogenes (12.2%). We observed strong heterogeneity within and between the two value chains regarding proportion of resistant bacterial species. Sun-dried fish in both value chains had significantly high proportions of resistant bacterial species. Comparing the two value chains, the unregulated value chain had a significantly higher proportion of bacterial species that were resistant. In order to mitigate the risk of transmitting antimicrobial-resistant bacteria to consumers along the fish value chain, good manufacturing practices coupled with identification and management of possible sources of contamination are recommended for fish and potentially other foods distributed along the less regulated value chains. IMPORTANCE In order to mitigate the risk of transmitting antimicrobial-resistant bacteria to consumers along the fish value chain, good manufacturing practices coupled with identification and management of possible sources of contamination are recommended for fish and potentially other foods distributed along the less regulated value chains.

Scientific advances in pathogen decontamination offer great potential to reduce Campylobacter spp. during primary processing. The aim of this study was to collate data from eligible studies using systematic review, meta-analysis followed by meta-regression. Random effect meta-analysis revealed heterogenous (τ2 = 0.6, I2 = 98 %) pooled reduction in Campylobacter concentration of 0.6 log10 CFU/carcass and a decrease in relative risk of Campylobacter spp. prevalence in broiler carcasses by 57.2 %. Decontamination interventions during Inside-Outside-Carcass-Wash were most effective on concentration (0.8 log10 CFU/carcass) while those during evisceration were most effective on prevalence (78.0 % decrease in relative risk). Physical decontamination was more effective on Campylobacter prevalence (68.7 % decrease in relative risk) compared chemical treatment (30.3 %). Application through immersion was superior on Campylobacter concentration (0.9 log10 CFU/carcass odds reduction) to spraying (0.5 log10 CFU/carcass odds reduction). Publication bias and small study effect were observed in trials on Campylobacter prevalence but not for concentration. The meta-regression revealed four and seven potential modifier variables for concentration and prevalence respectively. This meta-analysis provides an overview of the expected magnitude in Campylobacter spp. concentration and prevalence with application of decontamination interventions on broiler carcasses along the slaughter process and forms a basis of quantitative microbial risk assessment and derivation of intervention measures. Even though modest microbial concentration reduction is reported there was a large decrease in contamination prevalence during processing interventions.

Nisin is a commonly used bacteriocin for controlling spoilage and pathogenic bacteria in food products. Strains possessing high natural nisin resistance that reduce or increase the potency of this bacteriocin against Listeria monocytogenes have been described. Our study sought to gather more insights into nisin resistance mechanisms in natural L. monocytogenes populations by examining a collection of 356 field strains that were isolated from different foods, food production environments, animals and human infections. A growth curve analysis-based approach was used to access nisin inhibition levels and assign the L. monocytogenes strains into three nisin response phenotypic categories; resistant (66%), intermediate (26%), and sensitive (8%). Using this categorization isolation source, serotype, genetic lineage, clonal complex (CC) and strain-dependent natural variation in nisin phenotypic resistance among L. monocytogenes field strains was revealed. Whole genome sequence analysis and comparison of high nisin resistant and sensitive strains led to the identification of new naturally occurring mutations in nisin response genes associated with increased nisin resistance and sensitivity in this bacterium. Increased nisin resistance was detected in strains harboring RsbUG77S and PBPB3V240F amino acid substitution mutations, which also showed increased detergent stress resistance as well as increased virulence in a zebra fish infection model. On the other hand, increased natural nisin sensitivity was detected among strains with mutations in sigB, vir, and dlt operons that also showed increased lysozyme sensitivity and lower virulence. Overall, our study identified naturally selected mutations involving pbpB3 (lm0441) as well as sigB, vir, and dlt operon genes that are associated with intrinsic nisin resistance in L. monocytogenes field strains recovered from various food and human associated sources. Finally, we show that combining growth parameter-based phenotypic analysis and genome sequencing is an effective approach that can be useful for the identification of novel nisin response associated genetic variants among L. monocytogenes field strains.

The accurate identification of Extended-Spectrum &beta, Lactamase (ESBL) genes in Gram-negative bacteria is necessary for surveillance and epidemiological studies of transmission through foods. We report a novel rapid, cheap, and accurate closed tube molecular diagnostic tool based on two multiplex HRM protocols for analysis of the predominant ESBL families encountered in foods. The first multiplex PCR assay targeted blaCTX-M including phylogenetic groups 1 (CTX-M-1-15, including CTX-M-1, CTX-M-3 and CTX-M-15), 2 (CTX-M-2), and 9 (CTX-M-9-14, including CTX-M-9 and CTX-M-14). The second assay involved blaTEM /bla CTX-M /blaSHV, including TEM variants (TEM-1 and TEM-2), SHV-1-56 (SHV-1, SHV-2 and SHV-56), and CTX-M-8-41 (CTX-M-8, CTX-M-25, CTX-M-26 and CTX-M-39 to CTX-M-41). The individual melting curves were differentiated by a temperature shift according to the type of ESBL gene. The specificity and sensitivity of the first assay were 100% and 98%, respectively. For the second assay, the specificity and sensitivity were 87% and 89%, respectively. The detection of ESBL variants or mutations in existing genes was also demonstrated by the subtyping of a variant of the CTXM-1-15. The HRM is a potential tool for the rapid detection of present &beta, lactamase genes and their characterization in a highly sensitive, closed-tube, inexpensive method that is applicable in high throughput studies.

Prevention of the emergence and spread of foodborne diseases is an important prerequisite for the improvement of public health. Source attribution models link sporadic human cases of a specific illness to food sources and animal reservoirs. With the next generation sequencing technology, it is possible to develop novel source attribution models. We investigated the potential of machine learning to predict the animal reservoir from which a bacterial strain isolated from a human salmonellosis case originated based on whole‐genome sequencing. Machine learning methods recognize patterns in large and complex data sets and use this knowledge to build models. The model learns patterns associated with genetic variations in bacteria isolated from the different animal reservoirs. We selected different machine learning algorithms to predict sources of human salmonellosis cases and trained the model with Danish Salmonella Typhimurium isolates sampled from broilers (n = 34), cattle (n = 2), ducks (n = 11), layers (n = 4), and pigs (n = 159). Using cgMLST as input features, the model yielded an average accuracy of 0.783 (95% CI: 0.77–0.80) in the source prediction for the random forest and 0.933 (95% CI: 0.92–0.94) for the logit boost algorithm. Logit boost algorithm was most accurate (valid accuracy: 92%, CI: 0.8706–0.9579) and predicted the origin of 81% of the domestic sporadic human salmonellosis cases. The most important source was Danish produced pigs (53%) followed by imported pigs (16%), imported broilers (6%), imported ducks (2%), Danish produced layers (2%), Danish produced cattle and imported cattle (

Camel milk provides a common source of nutrition but also a potential rich source of beneficial, pathogenic, and potentially pathogenic microorganisms. This chapter reviews lactic acid and probiotic bacteria from camel milk, product innovation using such bacteria, and potential areas of improvement in technical as well as practical aspects of fermentation technologies. Lactic acid bacteria fermentation helps mitigate the impact of poor handling and storage conditions by enhancing shelf life and food safety. Traditionally-fermented sour milk products are culturally accepted and widely distributed worldwide with product-specific microbiota responsible for aroma, flavor, and texture. Knowledge of microbiota and predominant, technologically important microorganisms associated with camel milk is critical in developing products with enhanced quality and safety, as well as sustainable interventions for these products, including camel milk specific starter culture development. This chapter presents occurrence of LAB and probiotic bacteria in camel milk and technological aspects of camel dairy.

In recent decades, the demand for ready-to-eat (RTE) food items prepared by the food catering sector has increased together with the value of cook-serve, cook-chill, and cook-freeze food products. The technologies by which foods are cooked, chilled, refrigerated for storage, and reheated before serving are of prime importance to maintain safety. Packaging materials and food containers play an important role in influencing the cooling rate of RTE foods. Food items that are prepared using improper technologies and inappropriate packaging materials may be contaminated with foodborne pathogens. Numerous research studies have shown the impact of deficient cooling technologies on the survival and growth of foodborne pathogens, which may subsequently pose a threat to public health. The operating temperatures and cooling rates of the cooling techniques applied must be appropriate to inhibit the growth of pathogens. Food items must be stored outside the temperature danger zone, which is between 5 and 60 °C, in order to inhibit the growth of these pathogens. The cooling techniques used to prepare potentially hazardous foods, such as cooked meat, rice, and pasta, must be properly applied and controlled to ensure food safety. This paper critically reviews the effects of cooling and its relationship to food containers on the safety of RTE foods produced and sold through the food service industry.

The microbial contamination level profiles (MCLPs) attributed to contamination of beef carcasses, personnel, and equipment in five Kenyan small and medium enterprise slaughterhouses were determined. Aerobic plate counts, Enterobacteriaceae, Staphylococcus, and Salmonella were used to determine contamination at four different slaughter stages, namely, dehiding, evisceration, splitting, and dispatch. Microbiological criteria of the four microorganisms were used to score contamination levels (CLs) as poor (0), poor to average (1), average (2), or good (3). MCLPs were further assigned to carcasses, personnel, and equipment at each stage by summing up the CL scores. The CL score attributed to aerobic plate count contamination was 2 or 3 for carcasses but 0 for personnel and equipment in almost all slaughterhouses. A score of 0 on carcasses was mostly attributed to Enterobacteriaceae at evisceration and to Salmonella at dehiding and evisceration. In addition, a score of 0 was mostly attributed to Staphylococcus contamination of personnel at dehiding. A score of 3 was attributed mostly to Enterobacteriaceae on hands at splitting, whereas a score of 2 was mostly attributed to the clothes at dehiding and evisceration. A CL score of 3 was mostly attributed to Enterobacteriaceae and Salmonella contamination of equipment at dehiding and splitting, respectively. Although CLs attributed to contamination of carcasses, personnel, and equipment ranged from 0 to 3, the maximum MCLP score of 9 was only attained in carcasses from two slaughterhouses at dehiding and from one slaughterhouse at dispatch. There is, therefore, a lot of room for small and medium enterprise slaughterhouses to improve their food safety objectives by improving food safety management systems at the points characterized by low CL scores.

An FSMS-Diagnostic Instrument was used to evaluate fifteen Kenyan dairy processors based on indicators and descriptive grids for context riskiness, FSMS activities, and microbial food safety (FS) output with respect to scale of production. Contextual riskiness was diagnosed as low, moderate or high. FSMS activities were diagnosed as absent, basic, average or advanced. FS output was diagnosed as not performed, poor, moderate or good. Four clusters with significantly different (p

Fresh beef and meat products have been implicated in outbreaks of Shiga toxin-producing Escherichia coli (STEC) worldwide. This study investigated the prevalence of E. coli O157: H7 and non-O157 STEC serogroups in fresh beef in the open market and street vended meat products (n = 180) in Lagos metropolis, Nigeria. A combination of culture media and immunomagnetic separation followed by typing for associated virulence factors and serotypes was performed. Antimicrobial susceptibility testing was performed on the isolated STEC serotypes using the disk diffusion method. A total of 72 STEC serogroup isolates were detected from 61 out of 180 samples. The O157 STEC serotypes were detected in fresh beef, suya, minced meat and tsire with prevalence of 20.8% while non-O157 STEC serogroups were detected in all the samples. Molecular typing revealed 25% (n = 18) of the STEC serogroups showed presence of all the stx1, stx2, eaeA, fliCH7 and rfbEO157 virulence factors while 54.2% (n = 39) possessed a combination of two virulence genes. Multidrug resistance was discovered in 23.6% (n = 17) of the total STEC serogroups. Locally processed ready-to-eat meat products in Lagos metropolis, Nigeria harbour potentially pathogenic multi-drug resistant STEC serogroups that can constitute public health hazard.

We investigated for virulence genes ( stx1 , stx2 and hlyA ), serotypes and extended-spectrum β-lactamases (ESBLs) producing capacity in O157 and non-O157 Escherichia coli isolated from producer-distributor bulk milk (PDBM). Fifteen different E. coli O-serogroups were observed from the isolates (n = 121). The prevalence of stx1 and stx2 genes among the E. coli isolates was 8.3% and 11.6%, respectively, while 5.8% harboured both stx1 and stx2 . Four E. coli isolates (3.3%) had ESBLs producing capacity, resisted multiple cephalosporins and aztreonam, and carried stx genes. Cluster analysis using GTG 5 finger printing revealed a diversity of E. coli seropathotypes in PDBM that are known to be associated with human diarrhoeal diseases. These results highlight a potential risk posed on human health by the consumption of PDBM contaminated with pathogenic E. coli . A further quantitative risk assessment of the impact of pathogenic E. coli contamination in PDBM on human health is therefore recommended.

The contribution of the fresh produce production environment to human exposure with bacteria bearing extended spectrum β-lactamases and AmpC β-lactamases (ESBL/AmpC) has not been reported. High prevalence of ESBLs/AmpC bearing E. coli as well as a high gene transfer efficiency of lettuce and irrigation water E. coli isolates was previously reported. This stochastic modeling was aimed at quantitatively assessing human exposure to ESBL/AmpC bearing E. coli through lettuce attributable to irrigation water and subsequent horizontal gene transfer. Modular process risk approach was used for the quantitative exposure assessment and models were constructed in Ms. Excel spreadsheet with farm to consumption chain accounted for by primary production, processing, retail and consumer storage. Probability distributions were utilised to take into account the variability of the exposure estimates. Exposure resulting from ESBL/AmpC positive E. coli and gene transfer was taken into account. Monte Carlo simulation was carried out using @Risk software followed by sensitivity and scenario analysis to assess most effective single or combinations of mitigation strategies for the ESBL/AmpC positive E. coli events from farm to fork. Three percent of South African lettuce consumers are exposed to lettuce contaminated with about 106.4±106.7 (95% CI: 105.1-107) cfu of ESBL/AmpC positive E. coli per serving. The contribution of originally positive isolates and conjugative genetic transfer was 106±106.7 (95% CI: 105-107) and 105.2±105.6 (95% CI: 103.9-105.8) cfu per serving respectively. Proportion of ESBL/AmpC positive E. coli (Spearman's correlation coefficient (ρ)=0.85), conjugative gene transfer (ρ=0.05-0.14), washing in chlorine water (ρ=0.18), further rinsing (ρ=0.15), and prevalence of E. coli in irrigation water (ρ=0.16) had highest influence on consumer exposure. The most effective single methods in reducing consumer exposure were reduction in irrigation water microbial quality variation (87.4% reduction), storage period (49.9-87.4% reduction) and growth rate reduction by 75% (90% reduction). Reduction in growth rate together with storage time (92.1-99.4%) and reduction in storage time combined with E. coli concentration in irrigation water (95-96% reduction) were most effective combinations of mitigation measures. The high variation in exposure reflected the high irrigation water quality variation. The exposure levels may impose higher consumer risk than acceptable for irrigation water risk. E. coli contamination and growth related measures, as well as measures to reduce contamination with antimicrobial resistant E. coli from lettuce production environment are recommended. This exposure model could form a basis for the development of similar models assessing the impact of contaminated irrigation water and gene transfer in other microbial hazards, antimicrobial resistance types and fresh produce types.

The current study was undertaken to characterize Escherichia coli and other Enterobacteriaceae in raw and pasteurized producer-distributor bulk milk (PDBM). A total of 258 samples were collected from purchase points in 8 provinces in South Africa. The samples were tested for antibiotic residues, phosphatase, total aerobic bacteria, coliforms, and E. coli counts. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used for identification of isolates. Escherichia coli isolates were characterized for virulence factors, antimicrobial resistance, serotypes, and presumptive E. coli O157:H7. Antibiotic residues and alkaline phosphatase were detected in 2% of both raw and pasteurized PDBM (n=258) and 21% pasteurized PDBM (n=104) samples, respectively. A total of 729 isolates belonging to 21 genera and 59 species were identified. Escherichia coli, Enterobacter cloacae, Klebsiella oxytoca, and Raoultella ornithinolytica were the most abundant species. Spoilage Enterobacteriaceae species exceeded 50% of the total isolates. Escherichia coli was detected and isolated from 36% of the milk samples. Thirty-one E. coli isolates harbored virulence genes stx1/stx2 and 38% (n=121) were presumptive O157:H7. The prevalence of samples with presumptive shigatoxin producing E. coli was 10%. Antimicrobial-resistant E. coli isolates were detected in 70% of the milk samples with 36% of stx1/stx2 positive E. coli showing multi-drug resistance. Information obtained from the study will be used for modeling the public health risk posed by milkborne pathogens in PDBM, which in many cases is consumed by poor and vulnerable members of the population.

Understanding the impact of climate change remains vital for food safety and public health. Of particular importance is the influence of climatic conditions on the growth of Aspergillus flavus and production of their toxins. Nevertheless, little is known about the actual impact of climate change on the issue. Setting up of relevant measures to manage the impact has therefore become a daunting task especially in developing nations. Therefore, this study aimed at providing adaptation and mitigation options to manage this risk with a special focus on Kenya where cases of aflatoxicosis have been recurrent. We used a systematic literature review of review and research articles, with limited searching but systematic screening to explore available qualitative and quantitative data. Projections from the data, showed that on average, a 58.9% increase of aflatoxin contamination in the Central and Western parts and a decrease of 44.6% in the Eastern and Southern parts is expected but with several possible scenarios. This makes the impact of climate change on aflatoxin contamination in Kenya complex. To protect the public and environment from the negative impact, a regulatory framework that allows for an integrated management of aflatoxins in a changing climate was proposed. The management practices in the framework are divided into agronomic, post-harvest and institutional levels. Given the multiple points of application, coordination amongst stakeholders along the chain is fundamental. We therefore proposed a complimentary framework that allows the food safety issues to be addressed in an integrated manner while allowing for transparent synergies and trade-offs (in implementing the measures). A policy-oriented foresight should be carried out to provide policy based evidence for the applicability of the proposed adaptation and mitigation measures.

Next‐generation sequencing (NGS) data present an untapped potential to improve microbial risk assessment (MRA) through increased specificity and redefinition of the hazard. Most of the MRA models do not account for differences in survivability and virulence among strains. The potential of machine learning algorithms for predicting the risk/health burden at the population level while inputting large and complex NGS data was explored with Listeria monocytogenes as a case study. Listeria data consisted of a percentage similarity matrix from genome assemblies of 38 and 207 strains of clinical and food origin, respectively. Basic Local Alignment (BLAST) was used to align the assemblies against a database of 136 virulence and stress resistance genes. The outcome variable was frequency of illness, which is the percentage of reported cases associated with each strain. These frequency data were discretized into seven ordinal outcome categories and used for supervised machine learning and model selection from five ensemble algorithms. There was no significant difference in accuracy between the models, and support vector machine with linear kernel was chosen for further inference (accuracy of 89% [95% CI: 68%, 97%]). The virulence genes FAM002725, FAM002728, FAM002729, InlF, InlJ, Inlk, IisY, IisD, IisX, IisH, IisB, lmo2026, and FAM003296 were important predictors of higher frequency of illness. InlF was uniquely truncated in the sequence type 121 strains. Most important risk predictor genes occurred at highest prevalence among strains from ready‐to‐eat, dairy, and composite foods. We foresee that the findings and approaches described offer the potential for rethinking the current approaches in MRA.

This study evaluated the microbiological safety of fresh Nile tilapia ( Oreochromis niloticus) from Kenyan fresh water fish value chains. One hundred seventy-six fish samples were analyzed. The microbial counts of hygiene indicators, total viable aerobic count (TVC), total coliforms, and fecal coliforms isolated by using culture techniques were enumerated, and microbial pathogens present in the fish samples were identified and characterized by using molecular methods. The diversity of bacterial isolates was determined by using the Shannon-Weaver diversity index. The mean of TVC in the samples was 4.44 log CFU/g. A comparison with the European Commission and International Commission on Microbiological Specifications for Foods standards showed two fish samples had counts above the 5.00 log CFU/g limit for TVC, and all the fish samples had total coliform and fecal coliform counts above 2.00 and 1.00 log CFU/g, respectively. Pathogenic strains, including Shiga toxin-producing and enteropathogenic Escherichia coli, Listeria monocytogenes, Yersinia enterocolitica, Klebsiella pneumoniae, and Salmonella enterica, were identified in the fish samples. The diversity of 1,608 bacterial isolates was higher in semiregulated chains than unregulated chains. The diversity was also high at the retail stage of the fish value chain. In conclusion, fresh Nile tilapia samples were above some of the set food safety standards and may be a source of foodborne pathogens. Further microbial risk assessment for detected pathogens is recommended to further support public health protection, taking into account growth, inactivation through cooking, processing, survival, and consumption.

The objective of this study was to estimate the risk associated with staphylococcal enterotoxin (SE) exposure from the consumption of Nile tilapia supplied through the semi-regulated and unregulated value chain in Kenya. The fish supply chain was modeled from landing to consumption of unprocessed (fresh) and processed (salted and sun dried, smoked, filleted) fish. Data related to prevalence of Staphylococcus aureus in fish, taking into account survey information on handling, storage, processing and consumption of Nile tilapia were collected from recently completed studies in Kenya. Other model inputs were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. The simulated levels of S. aureus in fish after handling and storage of salted and sun dried and smoked fish ranged between 4 log CFU/g and 9.01 log CFU/g (maximum population density), while in fillet, levels of S. aureus following growth during display at retail shops was between 3.10 log CFU/g (5% percentile) and 9.01 log CFU/g (95% percentile). Estimated SE dose per-serving in fish supplied after processing was significantly higher (p

In this study, the bacteriological quality and the presence of Staphylococcus aureus, Escherichia coli O157:H7, Bacillus cereus, Salmonella species, and Pseudomonas species were studied in raw milk, cultured milk, milk handlers and packaging containers. A total of 36 samples were collected over 3 months from three different farmers. Samples were analyzed for means of counts per milliliter of milk for total bacterial count (TBC), total coliform count (TCC), total E. coli count (TEC), S. aureus, B. cereus, Salmonella spp. and Pseudomonas spp. Microbial load ranged between 0.81 and 7.6 log10 cfu/ml for various critical sampling locations. Isolates of E. coli, S. aureus and B. cereus were taken for simple polymerase chain reaction (PCR) to investigate the presence of virulent genes, rfB, sei, and cytK with amplicon sizes of 1.0 kb, 500 bp and 320 bp, respectively. The sei gene was detected in 19% of the samples and 2.8% were found to have the cytK gene. The rfB gene could not be picked in E. coli. The results show poor hygienic practices at the processors and potential risk to the consumers. Key words: Fresh milk, fermented milk, packaging container, milk handler, pathogens.

Information asymmetry is often a characteristic present in food value chains. However, high information asymmetry reduces trust and may compromise food safety and quality. Traceability enhances information sharing and disclosure thereby reducing the imperfection. Qualitative and quantitative data was collected from Kenyan certified farmers and organic outlets to generate empirical information on the extent and factors that contribute to traceability along organic kale value chains. Interviews were conducted using a semi-structured questionnaire. Data was analysed using descriptive statistics and factor analysis. Majority (62 %) of smallholder producers had a functional traceability system. Factor analysis revealed that organizational activities and personnel perception contribute to traceability in an organization. Variables that contribute to organizational activities are documentation/record keeping (0.754), certification by other quality management standards (0.711), training on food safety and traceability management (0.444) and system monitoring (0.770). Such knowledge can be used by players along the value chain to reduce information asymmetry. The results suggest need for awareness creation among stakeholders on how organizational activities can be used to improve traceability through enhanced information flow for safer and better quality organic products. In addition, perception of personnel which plays an important role in traceability can be improved through training personnel on beneficial consequences of a traceability system.

The present study aimed at identifying and assessing antimicrobial resistance of Enterococcus spp. isolated from small and medium enterprise slaughterhouses in Kenya. In total, 67 isolates were recovered from 48 of 195 samples examined from beef carcasses, personnel, and cutting equipment in five small and medium enterprise slaughterhouses. The isolates were identified by using matrix-assisted laser desorption-ionization time of flight mass spectrometry and screened thereafter for their resistance against 12 antibiotics by using a disk diffusion assay. The isolates ( n = 67) included Enterococcus faecalis (41.8%), Enterococcus mundtii (17.9%), Enterococcus thailandicus (13.4%), Enterococcus faecium (9.0%), Enterococcus hirae (7.5%), Enterococcus casseliflavus (6.0%), and Enterococcus devriesei (4.5%). None of the isolates were resistant to ciprofloxacin, penicillin, ampicillin, vancomycin, nitrofurantoin, teicoplanin, linezolid, and levofloxacin. Resistance to rifampin (46.3%), erythromycin (23.9%), tetracycline (20.9%), and chloramphenicol (7.5%) was distributed among six of the seven species. All E. thailandicus were resistant to rifampin, erythromycin, and tetracycline. E. faecalis was resistant to rifampin (60.7%), tetracycline (17.9%), erythromycin (14.3%), and chloramphenicol (10.7%). Resistance to two or three antibiotics was observed in 26.9% of the enterococci isolates. The isolation of enterococci that are resistant to clinically relevant antibiotics, such as erythromycin, is of a serious concern given the role enterococci play in the transfer of antibiotic resistance genes.

As more microbiological data for indigenous fermented milk (IFM) becomes available, concern about their microbial safety becomes eminent. Nonetheless, these data are highly fragmented, and a tool is required to integrate existing data and to provide a basis for data-driven decision making for IFM&rsquo, s safety. Therefore, meta-analysis and meta-regression were conducted to estimate the prevalence of foodborne pathogens in IFM and to determine factors influencing the estimated values. Using Africa as a case, searches were systematically made for published data and relevant grey literature. Data from 18 studies in 15 countries were analyzed. Staphylococcus aureus (37%), pathogenic Escherichia coli (16%), Listeria monocytogenes (6%), and Salmonella spp. (3%) were the most prevalent pathogens with a pooled prevalence estimate of 12%. Heterogeneity among prevalence estimates was attributed to sampling point and microbial group but could be moderated by publication year, country cluster, and methods for microbial confirmation. The pooled prevalence estimates increased over time as more studies became available, whereby the odds were higher in studies from 2010 onwards than studies before 2010. From the analyses, S. aureus presented the greatest safety concern in African IFM. Future microbiological studies should take into consideration different IFM sampling points and advanced analytical methods to identify pathogens.

This study was conducted to estimate the hemolytic uremic syndrome (HUS) risk associated with consumption of producer-distributor bulk milk (PDBM) contaminated with Shiga toxin–producing Escherichia coli (STEC) in South Africa. Data were obtained from recently completed studies in South Africa taking into account prior collected prevalence data of STEC in raw and pasteurized PDBM and survey information from producer-distributor outlets and households. Inputs for the models were complemented with data from published and unpublished literature. A probabilistic exposure model was developed with Monte Carlo simulation in Excel add-in software using @Risk software. Hazard characterization was based on an exponential dose-response model to calculate the probability of illness from STEC infection in individuals 5 years and younger and individuals older than 5 years. The estimated mean STEC level was 0.12 CFU/mL (95% confidence interval [CI]: 0 to 1.2; r ¼ 0.34) for raw PDBM and 0.08 CFU/mL (95% CI: 0 to 1; r ¼ 0.27) for pasteurized PDBM. A higher risk of HUS cases per year was recorded in raw than in pasteurized PDBM and also in individuals younger than 5 years of age. For every 100,000 servings consumed, the expected median numbers of HUS cases per year from raw PDBM were 52 for 5 years and younger and 3.2 for older than 5 years. The median numbers of cases per year for pasteurized PDBM were 47 for 5 years and younger and 2.9 for older than 5 years. Sensitivity analysis revealed that serving volume and time taken to sell PDBM at producer-distributor outlets were the factors with the greatest impact on probability of illness. The models developed in this study are an example of risk assessments for milk produced and marketed from similar scenarios across the globe.

We present here draft genome sequences of Enterococcus mundtii strains K7-EM, P2-EM, C11-EM, and H18-EM, which were isolated from slaughterhouse equipment, carcasses, and personnel of small- and medium-sized beef slaughterhouses in Kenya.

Avian influenza virus (H5N1) is a rapidly disseminating infection that affects poultry and, potentially, humans. Because the avian virus has already adapted to several mammalian species, decreasing the rate of avian-mammalian contacts is critical to diminish the chances of a total adaptation of H5N1 to humans. To prevent the pandemic such adaptation could facilitate, a biology-specific disease surveillance model is needed, which should also consider geographical and socio-cultural factors. Here, we conceptualized a surveillance model meant to capture H5N1-related biological and cultural aspects, which included food processing, trade and cooking-related practices, as well as incentives (or disincentives) for desirable behaviours. This proof of concept was tested with data collected from 378 Egyptian and Nigerian sites (local [backyard] producers/live bird markets/village abattoirs/commercial abattoirs and veterinary agencies). Findings revealed numerous opportunities for pathogens to disseminate, as well as lack of incentives to adopt preventive measures, and factors that promoted epidemic dissemination. Supporting such observations, the estimated risk for H5N1-related human mortality was higher than previously reported. The need for multidimensional disease surveillance models, which may detect risks at higher levels than models that only measure one factor or outcome, was supported. To develop efficient surveillance systems, interactions should be captured, which include but exceed biological factors. This low-cost and easily implementable model, if conducted over time, may identify focal instances where tailored policies may diminish both endemicity and the total adaptation of H5N1 to the human species.

We acknowledge the TWAS Fellowship for Research and Advanced Training, National Research Foundation and Vice-Chancellor Postdoctoral Fellowship Programme at the University of Pretoria for financing P. M. K. Njage during the research work. The sequence analysis facility was funded by the National Research Foundation of South Africa.

Aflatoxicosis has repeatedly affected Kenyans, particularly in the eastern region, due to consumption of contaminated maize. However, save for the cases of acute toxicity, the levels of sub-lethal exposure have not been adequately assessed. It is believed that this type of exposure does exist even during the seasons when acute toxicity does not occur. This study, therefore, was designed to assess the exposure of households to aflatoxins through consumption of maize and maize products. Twenty samples each of maize kernels, muthokoi and maize meal were randomly sampled from households in Kibwezi District of Makueni County in Eastern Kenya and analysed for aflatoxin contamination. The samples were quantitatively analysed for aflatoxin contamination using HPLC. The uncertainty and variability in dietary exposure was quantitatively modelled in Ms Excel using Monte Carlo simulation in @Risk software. Aflatoxins were found in 45% of maize kernels at between 18 and 480 μg kg⁻¹, 20% of muthokoi at between 12 and 123 μg kg⁻¹, and 35% of maize meal at between 6 and 30 μg kg⁻¹. The mean dietary exposure to aflatoxin in maize kernels was 292 ± 1567 ng kg⁻¹ body weight day⁻¹, while the mean dietary exposure to aflatoxin in maize meal and muthokoi were 59 ± 62 and 27 ± 154 ng kg⁻¹ body weight day⁻¹ respectively. The results showed that the amount and frequency of consumption of the three foods is the more important contributing factor than the mean aflatoxin concentration levels, to the risk of dietary exposure to aflatoxins.

Limited knowledge is currently available on the influence of fish thawing and subsequent storage conditions on bacterial growth kinetics, succession, and diversity alongside the production of biogenic amines. This study aimed to address these factors during the thawing and subsequent storage of mackerel. Thawing was either done fast in 18°C water for 2 h or slowly at 30°C overnight. Subsequent storage was at 30°C (ambient) for 36 h and 2 to 5°C (refrigerated) for 12 days. The cultivation methods used were total viable counts, hydrogen sulfide-producing bacteria, and Pseudomonas . Maximum growth rate, population density, and lag time were fitted on the counts using the Baranyi model. The bacterial diversity and succession were based on sequencing of 16S rRNA amplicons, and biogenic amines were quantified on high-pressure liquid chromatography-UV. The results show that lag time of hydrogen sulfide-producing bacteria was significantly affected by both thawing methods, and further, the interaction between thawing and storage significantly affected the maximum growth rate of these bacteria. However, the maximum growth rate of Pseudomonas was higher during refrigerated storage compared with storage at ambient temperature. Total viable counts showed longer lag time and reduced growth rate under refrigerated storage. Higher bacterial diversity was correlated to slow thawing and storage at ambient temperature compared with slow thawing and refrigerated storage. Overall, Acinetobacter and Psychrobacter genera were the dominant bacterial populations. The amine levels were low and could not be differentiated along the thawing and storage approaches, despite a clear increase in bacterial load, succession, and diversity. This corresponded well with the low abundance of biogenic amine-producing bacteria, with the exception of the genus Proteus , which was 8.6% in fast-thawed mackerel during storage at ambient temperature. This suggests that the decarboxylation potential is dependent on both microbial load and microbial community structure.

Current approaches such as inspections, audits, and end product testing cannot detect the distribution and dynamics of microbial contamination. Despite the implementation of current food safety management systems, foodborne outbreaks linked to fresh produce continue to be reported. A microbial assessment scheme and statistical modeling were used to systematically assess the microbial performance of core control and assurance activities in five Kenyan fresh produce processing and export companies. Generalized linear mixed models and correlated random-effects joint models for multivariate clustered data followed by empirical Bayes estimates enabled the analysis of the probability of contamination across critical sampling locations (CSLs) and factories as a random effect. Salmonella spp. and Listeria monocytogenes were not detected in the final products. However, none of the processors attained the maximum safety level for environmental samples. Escherichia coli was detected in five of the six CSLs, including the final product. Among the processing-environment samples, the hand or glove swabs of personnel revealed a higher level of predicted contamination with E. coli , and 80% of the factories were E. coli positive at this CSL. End products showed higher predicted probabilities of having the lowest level of food safety compared with raw materials. The final products were E. coli positive despite the raw materials being E. coli negative for 60% of the processors. There was a higher probability of contamination with coliforms in water at the inlet than in the final rinse water. Four (80%) of the five assessed processors had poor to unacceptable counts of Enterobacteriaceae on processing surfaces. Personnel-, equipment-, and product-related hygiene measures to improve the performance of preventive and intervention measures are recommended.

UNLABELLED Fish-processing plants still face food safety (FS) challenges worldwide despite the existence of several quality assurance standards and food safety management systems/s (FSMSs). This study assessed performance of FSMS in fish exporting sector considering pressure from the context in which they operate. A FSMS diagnostic tool with checklist was used to assess the context, FSMS, and FS output in 9 Kenyan fish exporting companies. Majority (67%) companies operated at moderate- to high-risk context but with an average performance in control and assurance activities. This situation could be insufficient to deal with ambiguity, uncertainty, and vulnerability issues in the context characteristics. Contextual risk posed by product characteristics (nature of raw materials) and chain environment characteristics was high. Risk posed by the chain environment characteristics, low power in supplier relationships, and low degree of authority in customer relationships was high. Lack of authority in relationship with suppliers would lead to high raw material risk situation. Even though cooling facilities, a key control activity, was at an advanced level, there was inadequate packaging intervention equipment which coupled with inadequate physical intervention equipment could lead to further weakened FSMS performance. For the fish companies to improve their FSMS to higher level and enhance predictability, they should base their FSMS on scientific information sources, historical results, and own experimental trials in their preventive, intervention, and monitoring systems. Specific suggestions are derived for improvements toward higher FSMS activity levels or lower risk levels in context characteristics. PRACTICAL APPLICATION Weak areas in performance of control and assurance activities in export fish-processing sector already implementing current quality assurance guidelines and standards were studied taking into consideration contextual pressure wherein the companies operate. Important mitigation measures toward improved contextual risk, core assurance, and control activities irrespective of applied food safety management systems in fish industries were suggested.

Indigenous fermented milk products contain microbiota composed of technologically important species and strains which are gradually getting lost with new technologies. We investigated the microbial diversity in amabere amaruranu, a traditionally fermented milk product from Kenya. Sixteen samples of the product from different containers were obtained. One hundred and twenty isolates of lactic acid bacteria (LAB) and 67 strains of yeasts were identified using API 50 CH and API 20 C AUX identification kits, respectively. The average pH of all the traditional fermented samples was 4.00 ± 0.93. Lactobacilli, yeasts, and molds as well as Enterobacteriaceae counts from the plastic containers were significantly higher (P

Fish processing plants still face microbial food safety-related product rejections and the associated economic losses, although they implement legislation, with well-established quality assurance guidelines and standards. We assessed the microbial performance of core control and assurance activities of fish exporting processors to offer suggestions for improvement using a case study. A microbiological assessment scheme was used to systematically analyze microbial counts in six selected critical sampling locations (CSLs). Nine small-, medium- and large-sized companies implementing current food safety management systems (FSMS) were studied. Samples were collected three times on each occasion (n = 324). Microbial indicators representing food safety, plant and personnel hygiene, and overall microbiological performance were analyzed. Microbiological distribution and safety profile levels for the CSLs were calculated. Performance of core control and assurance activities of the FSMS was also diagnosed using an FSMS diagnostic instrument. Final fish products from 67% of the companies were within the legally accepted microbiological limits. Salmonella was absent in all CSLs. Hands or gloves of workers from the majority of companies were highly contaminated with Staphylococcus aureus at levels above the recommended limits. Large-sized companies performed better in Enterobacteriaceae, Escherichia coli, and S. aureus than medium- and small-sized ones in a majority of the CSLs, including receipt of raw fish material, heading and gutting, and the condition of the fish processing tables and facilities before cleaning and sanitation. Fish products of 33% (3 of 9) of the companies and handling surfaces of 22% (2 of 9) of the companies showed high variability in Enterobacteriaceae counts. High variability in total viable counts and Enterobacteriaceae was noted on fish products and handling surfaces. Specific recommendations were made in core control and assurance activities associated with sampling locations showing poor performance.

Food processors implement differing food safety and quality assurance standards and guidelines. This may result in variable performance of the food safety management systems (FSMS) due to differences in technological development, resource access and food safety legal frameworks. The aim of this study was to evaluate the performance of FSMS in the fresh produce export processing sector in Kenya as a case. The risk posed by the context in which they operate was assessed. An FSMS diagnostic instrument was used to evaluate thirteen fresh produce exporting processors based on indicators and descriptive grids for context factors, control and assurance activities and food safety output. Riskiness in context was diagnosed either as low risk, moderate risk or high risk. Performance of control and assurance activities was categorized as not conducted, basic, average or advanced. Food safety output was scored as either not done, poor, moderate or good. Majority of the processors (≥7) operate at moderate level in most (74%) of the context riskiness indicators. Seven out of the 13 processors indicated that susceptibility of initial material to microbial contamination posed the highest risk with respect to product characteristics. Even though majority of the companies had advanced level core control activities performance for 6 out of 29 of the activities, there was a moderate performance in 48% of the activities and 24% control activities were not applied. Core assurance activities for majority of the companies also performed moderately in 89% of the indicators. FSMS performance was poor for 53% and good for 37% of the processors. All the processors had advanced scores for monitoring of pesticide residues but five lacked sampling and subsequent criteria for microbial analysis. The FSMS implementation for 77% of the companies was poor to moderate and, given the moderate context riskiness, this therefore resulted in moderate FSMS-output. The mostly moderate FSMS activity levels when assessed in the context riskiness lower the food safety performance of the fresh produce sector. Several recommended control and assurance activities in fresh produce sector should be improved to advanced levels in order to realize a stable and predictable safety output subject to the riskiness of context situation.

Epidemiological studies show a definite connection between areas of high aflatoxin content and a high occurrence of human hepatocellular carcinoma (HCC). Hepatitis B virus in individuals further increases the risk of HCC. The two risk factors are prevalent in rural Kenya and continuously predispose the rural populations to HCC. A quantitative cancer risk assessment therefore quantified the levels at which potential pre- and postharvest interventions reduce the HCC risk attributable to consumption of contaminated maize and groundnuts. The assessment applied a probabilistic model to derive probability distributions of HCC cases and percentage reductions levels of the risk from secondary data. Contaminated maize and groundnuts contributed to 1,847 ± 514 and 158 ± 52 HCC cases per annum, respectively. The total contribution of both foods to the risk was additive as it resulted in 2,000 ± 518 cases per annum. Consumption and contamination levels contributed significantly to the risk whereby lower age groups were most affected. Nonetheless, pre- and postharvest interventions might reduce the risk by 23.0-83.4% and 4.8-95.1%, respectively. Therefore, chronic exposure to aflatoxins increases the HCC risk in rural Kenya, but a significant reduction of the risk can be achieved by applying specific pre- and postharvest interventions.

Aims: To pheno-and genotypically characterise Staphylococcus aureusisolated from raw and fermented camel milk from Kenya and Somali for their antibiotic resistance. Methodology: Microdilution assays to determine minimal inhibitory concentratio ns (MICs) were done using to 20 different antibiotics. Further tests with selected antibiotics were done using disk diffusion test. Genotypic antibiotic resistance was tested using by microarray hybridization with selected isolates and consequent screening of antibiotic resistance genes by PCR. Results: Prevalence of antibiotic resistance among the 47 S. aureus tested were ampicillin 26% (12), gentamicin 26% (12), streptomycin 11% (5), tetracycline 13% (6), trimethoprim 6% (3) and fusidic acid 2% (1). Multi -resistance was detected with three isolates resistant to two antibiotics, six to three antibiotics and six to four or more

Streptococcus infantarius subsp. infantarius belongs to the Streptococcus bovis/Streptococcus equinus complex (SBSEC) commonly associated with human and animal infections. We elucidated the lactose metabolism of S. infantarius subsp. infantarius predominant in African fermented milk products. S. infantarius subsp. infantarius isolates (n = 192) were identified in 88% of spontaneously fermented camel milk suusac samples (n = 24) from Kenya and Somalia at log10 8.2–8.5 CFU mL−1. African S. infantarius isolates excreted stoichiometric amounts of galactose when grown on lactose, exhibiting a metabolism similar to Streptococcusthermophilus and distinct from their type strain. African S. infantarius subsp. infantarius CJ18 harbors a regular gal operon with 99.7–100% sequence identity to S. infantarius subsp. infantarius ATCC BAA-102T and a gal-lac operon with 91.7–97.6% sequence identity to S. thermophilus, absent in all sequenced SBSEC strains analyzed. The expression and functionality of lacZ was demonstrated in a β-galactosidase assay. The gal-lac operon was identified in 100% of investigated S. infantarius isolates (n = 46) from suusac samples and confirmed in Malian fermented cow milk isolates. The African S. infantarius variant potentially evolved through horizontal gene transfer of an S. thermophilus-homologous lactose pathway. Safety assessments are needed to identify any putative health risks of this novel S. infantarius variant.

The microflora of 59 East African camel milk samples of unfermented raw milk supply chains and spontaneously fermented milk ( suusac ) was analyzed to describe the diversity of predominant lactic acid bacteria (LAB), identify potential health risks and study bacteriocin-like inhibitory substance (BLIS) production. Bacterial isolates ( n = 532) were identified using a genotypic approach incorporating rep-PCR, 16S rRNA gene sequencing, and species-specific PCR assays. The bacterial numbers on MRS and M17 agar exceeded log 10 6.5 colony forming units (CFU) mL −1 for raw milk supply chain samples and log 10 8 CFU mL −1 for suusac . Streptococcus agalactiae and Staphylococcus spp. were predominant in unfermented products, while suusac contained predominantly Streptococcus infantarius subsp. infantarius followed by Lactococcus lactis subsp. lactis, Streptococcus thermophilus , and lactobacilli. Fifty per cent of S. infantarius subsp. infantarius isolates originating from 15 out of 24 suusac samples produced a BLIS active against other LAB or Listeria and representing a potential selective advantage during fermentation. This study provides a detailed insight at the genotypic level into the LAB diversity of previously unstudied dairy products. It indicates potential health risks for consumers and the need for hygienic and manufacturing interventions and reports a potentially novel BLIS produced by S. infantarius subsp. infantarius .

The effects of existing food safety management systems and size of the production facility on microbiological quality in the dairy industry in Kenya were studied. A microbial assessment scheme was used to evaluate 14 dairies in Nairobi and its environs, and their performance was compared based on their size and on whether they were implementing hazard analysis critical control point (HACCP) systems and International Organization for Standardization (ISO) 22000 recommendations. Environmental samples from critical sampling locations, i.e., workers' hands and food contact surfaces, and from end products were analyzed for microbial quality, including hygiene indicators and pathogens. Microbial safety level profiles (MSLPs) were constructed from the microbiological data to obtain an overview of contamination. The maximum MSLP score for environmental samples was 18 (six microbiological parameters, each with a maximum MSLP score of 3) and that for end products was 15 (five microbiological parameters). Three dairies (two large scale and one medium scale; 21% of total) achieved the maximum MSLP scores of 18 for environmental samples and 15 for the end product. Escherichia coli was detected on food contact surfaces in three dairies, all of which were small scale dairies, and the microorganism was also present in end product samples from two of these dairies, an indication of cross-contamination. Microbial quality was poorest in small scale dairies. Most operations in these dairies were manual, with minimal system documentation. Noncompliance with hygienic practices such as hand washing and cleaning and disinfection procedures, which is common in small dairies, directly affects the microbial quality of the end products. Dairies implementing HACCP systems or ISO 22000 recommendations achieved maximum MSLP scores and hence produced safer products.

Streptococcus infantarius subsp. infantarius (Sii) and Streptococcus gallolyticus subsp. macedonicus are members of the Streptococcus bovis/Streptococcus equinus complex (SBSEC) associated with human infections. SBSEC-related endocarditis was furthermore associated with rural residency in Southern Europe. SBSEC members are increasingly isolated as predominant species from fermented dairy products in Europe, Asia and Africa. African variants of Sii displayed dairy adaptations to lactose metabolism paralleling those of Streptococcus thermophilus including genome decay. In this study, the aim was to assess the prevalence of Sii and possibly other SBSEC members in dairy products of East and West Africa in order to identify their habitat, estimate their importance in dairy fermentation processes and determine geographic areas affected by this potential health risk. Presumptive SBSEC members were isolated on semi-selective M17 and SM agar media. Subsequent genotypic identification of isolates was based on rep-PCR fingerprinting and SBSEC-specific16S rRNA gene PCR assay. Detailed identification was achieved through application of novel primers enhancing the binding stringency in partial groES/groEL gene amplification and subsequent DNA sequencing. The presence of S. thermophilus-like lacS and lacZ genes in the SBSEC isolates was determined to elucidate the prevalence of this dairy adaptation. Isolates (n = 754) were obtained from 72 raw and 95 fermented milk samples from Côte d'Ivoire and Kenya on semi-selective agar media. Colonies of Sii were not detected from raw milk despite high microbial titers of approximately 10(6)CFU/mL on M17 agar medium. However, after spontaneous milk fermentation Sii was genotypically identified in 94.1% of Kenyan samples and 60.8% of Kenyan isolates. Sii prevalence in Côte d'Ivoire displayed seasonal variations in samples from 32.3% (June) to 40.0% (Dec/Jan) and isolates from 20.5% (June) to 27.7% (Dec/Jan) present at titers of 10(6)-10(8)CFU/mL. lacS and lacZ genes were detected in all Kenyan and 25.8% (June) to 65.4% (Dec/Jan) of Ivorian Sii isolates. Regional differences in prevalence of Sii and dairy adaptations were observed, but no clear effect of dairy animal, fermentation procedure and climate was revealed. Conclusively, the high prevalence of Sii in Kenya, Côte d'Ivoire in addition to Somalia, Sudan and Mali strongly indicates a pivotal role of Sii in traditional African dairy fermentations potentially paralleling that of typical western dairy species S. thermophilus. Putative health risks associated with the consumption of high amounts of live Sii and potential different degrees of evolutionary adaptation or ecological colonization require further epidemiologic and genomic investigations, particularly in Africa.