Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana.

Prevalence of foodborne pathogens in food from selected African countries - A meta-analysis.

Food safety information in the African region is insufficient and fragmented due to lack of surveillance, documentation and reporting, thereby resulting in inefficient utilization of resources, duplication of activities, and lack of synergy among the countries of the region. This paper reviews the prevalence of foodborne pathogens in seven African countries (Benin, Botswana, Ghana, Kenya, Nigeria, Sudan and Uganda) from papers in regional or international journals published between January 2000 and December 2015. One hundred and sixteen publications that dealt with food microbiology were reviewed for general analysis, while 66 papers on contamination of pathogenic bacteria were used for meta-analysis of prevalence. The food items were split into two categories: raw foods and ready-to-eat (RTE) foods (including street food and beverages) for meta-analysis. Majority of the reviewed studies (67.2%, 78/116) dealt with food of animal origin: 38.8% for meat and eggs, 17.2% for dairy products and 11.2% for aquatic products. Only 8.6% examined foods of plant origin (fruits and vegetables). The remaining 24.1% was the composite RTE food and beverages. Enterobacteriaceae, Escherichia coli, Salmonella, Staphylococcus aureus and Listeria monocytogenes were the most frequently reported organisms in those studies. Although the data were highly heterogeneous, a striking feature is high prevalence of the major pathogens in RTE foods, almost as high as in raw foods. E. coli averaged at 37.6% in raw foods and 31.6% in RTE foods. The corresponding prevalence for Salmonella was 19.9% vs 21.7%; S. aureus, 27.8% vs 25.1% and L. monocytogenes, 19.5% vs 6.7%. The average prevalence of foodborne pathogens in these countries was 34.2% (29.0-39.3%). Differences in food types as well as non-uniform protocols for sampling and identification might have contributed to high heterogeneity (I2 >97%) although some high prevalence data could be factual with extensive varieties of raw and RTE foods. Need for improved hygienic practices in handling of raw or RTE foods are suggested. Implementation of surveillance programs that use uniform laboratory protocols across the region could give homogeneous results.

Prevalence and antimicrobial susceptibility of Salmonella isolated from a variety of raw meat sausages in Gaborone (Botswana) retail stores.

The objective of the study was to provide baseline data on the prevalence and antimicrobial susceptibility of Salmonella in different types of raw meat sausages directly accessible to the consumers in Gaborone, Botswana. A total of 300 raw sausages comprising 79 beef, 78 pork, 72 chicken, and 71 mutton samples were concurrently analyzed for the presence of Salmonella using a conventional culture method and a validated PCR method. The PCR assay results were in full concordance with those of the conventional culture method for the detection of Salmonella. Sixty-five (21.7%) of 300 samples were positive for Salmonella by both the conventional culture method and PCR assay. Even though more chicken samples contained Salmonella than did any other sausage type, the difference in the presence of Salmonella among the four sausages types was not significant. Eleven serotypes were identified, and Salmonella enterica subsp. salamae II was most prevalent in all the sausage types. Beef sausages generally had higher mesophilic bacterial counts than did the other three sausage types. However, higher microbial counts were not reflective of the presence of salmonellae. Susceptibility of the Salmonella enterica serotypes to 20 antimicrobial agents was determined, and Salmonella Muenchen was resistant to the widest array of agents and was mostly isolated from chicken sausages. Regardless of the meat of origin, all 65 Salmonella isolates were resistant to at least four antimicrobial agents: amikacin, gentamicin, cefuroxime, and tombramycin. This resistance profile group was the most common in all four sausage types, comprising 90% of all Salmonella isolates from beef, 71% from pork, 63% from mutton, and 35% from chicken. These results suggest that raw sausages pose a risk of transmitting multidrug-resistant Salmonella isolates to consumers.

Detection and quantification of biogenic amines in fermented food products sold in Botswana.

The incidence and concentrations associated with four important biogenic amines in leading commercial fermented beverages consumed in Botswana were determined using high-performance liquid chromatography. In 87 sorghum brew and 84 sour milk (madila, amasi) samples tested, putrescine was the most prevalent biogenic amine (63 and 61%, respectively), while histamine was the least prevalent (24 and 8%, respectively). Cadaverine was the most frequently detected biogenic amine in 79 of the commercial sour maize beverage (mageu/mahewu) samples tested (found in 70% of the samples), while tyramine was the least detected (occurring in 3% of the samples). In sorghum brew and sour milk, tyramine was found to be the most concentrated (mean concentration of 2.08 mg/100 ml and 3.2 mg/100 ml, respectively), and histamine was found to be the least concentrated (mean concentration of 0.94 mg/100 ml and 0.31 mg/100 ml, respectively). Overall, the biogenic amine concentrations of all three fermented products were within acceptable limits. However, one sorghum brew sample had a histamine content of 5.8 mg/ 100 ml, which was above the 5.0 mg/100 g allowable limit suggested by the U.S. Food and Drug Administration.