Mapping of Mycobacterium tuberculosis Complex Genetic Diversity Profiles in Tanzania and Other African Countries

The aim of this study was to assess and characterize Mycobacterium tuberculosis complex (MTBC) genotypic diversity in Tanzania, as well as in neighbouring East and other several African countries. We used spoligotyping to identify a total of 293 M. tuberculosis clinical isolates (one isolate per patient) collected in the Bunda, Dar es Salaam, Ngorongoro and Serengeti areas in Tanzania. The results were compared with results in the SITVIT2 international database of the Pasteur Institute of Guadeloupe. Genotyping and phylogeographical analyses highlighted the predominance of the CAS, T, EAI, and LAM MTBC lineages in Tanzania. The three most frequent Spoligotype International Types (SITs) were: SIT21/CAS1-Kili (n = 76; 25.94%), SIT59/LAM11-ZWE (n = 22; 7.51%), and SIT126/EAI5 tentatively reclassified as EAI3-TZA (n = 18; 6.14%). Furthermore, three SITs were newly created in this study (SIT4056/EAI5 n = 2, SIT4057/T1 n = 1, and SIT4058/EAI5 n = 1). We noted that the East-African-Indian (EAI) lineage was more predominant in Bunda, the Manu lineage was more common among strains isolated in Ngorongoro, and the Central-Asian (CAS) lineage was more predominant in Dar es Salaam (p-value<0.0001). No statistically significant differences were noted when comparing HIV status of patients vs. major lineages (p-value = 0.103). However, when grouping lineages as Principal Genetic Groups (PGG), we noticed that PGG2/3 group (Haarlem, LAM, S, T, and X) was more associated with HIV-positive patients as compared to PGG1 group (Beijing, CAS, EAI, and Manu) (p-value = 0.03). This study provided mapping of MTBC genetic diversity in Tanzania (containing information on isolates from different cities) and neighbouring East African and other several African countries highlighting differences as regards to MTBC genotypic distribution between Tanzania and other African countries. This work also allowed underlining of spoligotyping patterns tentatively grouped within the newly designated EAI3-TZA lineage (remarkable by absence of spacers 2 and 3, and represented by SIT126) which seems to be specific to Tanzania. However, further genotyping information would be needed to confirm this specificity

Genetic diversity and risk factors for the transmission of antimicrobial resistance across human, animals and environmental compartments in East Africa: a review.

BACKGROUND The emergence and spread of antimicrobial resistance (AMR) present a challenge to disease control in East Africa. Resistance to beta-lactams, which are by far the most used antibiotics worldwide and include the penicillins, cephalosporins, monobactams and carbapenems, is reducing options for effective control of both Gram-positive and Gram-negative bacteria. The World Health Organization, Food and Agricultural Organization and the World Organization for Animal Health have all advocated surveillance of AMR using an integrated One Health approach. Regional consortia also have strengthened collaboration to address the AMR problem through surveillance, training and research in a holistic and multisectoral approach. This review paper contains collective information on risk factors for transmission, clinical relevance and diversity of resistance genes relating to extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-producing Enterobacteriaceae, and Methicillin-resistant Staphylococcus aureus (MRSA) across the human, animal and environmental compartments in East Africa. MAIN BODY The review of the AMR literature (years 2001 to 2019) was performed using search engines such as PubMed, Scopus, Science Direct, Google and Web of Science. The search terms included 'antimicrobial resistance and human-animal-environment', 'antimicrobial resistance, risk factors, genetic diversity, and human-animal-environment' combined with respective countries of East Africa. In general, the risk factors identified were associated with the transmission of AMR. The marked genetic diversity due to multiple sequence types among drug-resistant bacteria and their replicon plasmid types sourced from the animal, human and environment were reported. The main ESBL, MRSA and carbapenem related genes/plasmids were the CTX-Ms (45.7%), SCCmec type III (27.3%) and IMP types (23.8%), respectively. CONCLUSION The high diversity of the AMR genes suggests there may be multiple sources of resistance bacteria, or the possible exchange of strains or a flow of genes amongst different strains due to transfer by mobile genetic elements. Therefore, there should be harmonized One Health guidelines for the use of antibiotics, as well as regulations governing their importation and sale. Moreover, the trend of ESBLs, MRSA and carbapenem resistant (CAR) carriage rates is dynamic and are on rise over time period, posing a public health concern in East Africa. Collaborative surveillance of AMR in partnership with regional and external institutions using an integrated One Health approach is required for expert knowledge and technology transfer to facilitate information sharing for informed decision-making

A Survey of Bayesian Statistical Approaches for Big Data

The modern era is characterised as an era of information or Big Data. This has motivated a huge literature on new methods for extracting information and insights from these data. A natural question is how these approaches differ from those that were available prior to the advent of Big Data. We present a review of published studies that present Bayesian statistical approaches specifically for Big Data and discuss the reported and perceived benefits of these approaches. We conclude by addressing the question of whether focusing only on improving computational algorithms and infrastructure will be enough to face the challenges of Big Data

Certify or not? An analysis of organic food supply chain with competing suppliers

Customers expect companies to provide clear health-related information for the products they purchase in a big data environment. Organic food is data-enabled with the organic label, but the certification cost discourages small-scale suppliers from certifying their product. This lack of a label means that product that satisfies the organic standard is regarded as conventional product. By considering the trade-off between the profit gained from organic label and additional costs of certification, this paper investigates an organic food supply chain where a leading retailer procures from two suppliers with different brands. Customers care about both the brand-value and quality (more specifically, if food is organic or not) when purchasing the product. We explore the organic certification and wholesale pricing strategies for suppliers, and the supplier selection and retail pricing strategies for the retailer. We find that when two suppliers adopt asymmetric certification strategy, the retailer tends to procure the product with organic label. The supplier without a brand name can compensate with organic certification, which leads to more profits than the branded rival. As the risk of being abandoned by the retailer increases, the supplier without a brand name is more eager than the rival to obtain the organic label. If both suppliers certify the product, however, they will fall into a prisoner’s dilemma under situation with low health utility from organic label and high certification cost

Avaliação do efeito da cafeína no teste vestibular Evaluation of the caffeine effect in the vestibular test

Há controvérsias sobre a interferência da cafeína no teste vestibular. O café é a fonte mais rica em cafeína. Enquanto em alguns serviços os pacientes são orientados a suspender a ingestão de café 24 a 48 horas antes da realização do teste, outros não consideram necessária a suspensão da ingestão dessa bebida. OBJETIVO: Avaliar o efeito da cafeína no resultado do teste vestibular. FORMA DE ESTUDO: clínico com coorte transversal. MATERIAL E MÉTODO: Estudo comparativo, transversal, pareado. O teste vestibular foi realizado em duplicidade, com intervalo máximo de cinco dias entre um e outro exame. No primeiro teste, os pacientes foram orientados a não ingerir café 24 horas antes do exame; no segundo teste, os pacientes foram orientados a beber café como de costume. Todos os participantes tinham indicação clínica de se submeter ao teste vestibular e tinham o hábito de tomar café. RESULTADOS: Participaram do estudo 19 mulheres com idade média de 49,5 anos. O consumo médio de café foi de três xícaras por dia. As queixas de ansiedade e cefaléia foram associadas ao teste realizado com suspensão do café. Não houve diferença estatisticamente significante nos resultados dos exames realizados com e sem ingestão de café. CONCLUSÃO: A ingestão moderada de café não interferiu no resultado do teste vestibular. Considerando ser recomendável que o paciente esteja tranqüilo ao se submeter ao teste vestibular e que a meia-vida da cafeína é de apenas seis horas, sugerimos que a orientação para a suspensão súbita e completa da ingestão moderada de café antes do teste vestibular para os indivíduos habituados à ingestão diária seja reavaliada.<br>Exist controversy about the interference of the caffeine in the vestibular test. Coffee is the richest source of caffeine. While in some services, the patients were orient to suspend the ingestion of caffeine 24 to 48 hours before the vestibular test, other not consider the suspension of this drink necessary. AIM: To evaluate the effect of caffeine in the vestibular test result. STUDY DESIGN: clinical with transversal cohort. MATERIAL AND METHOD: Seccional and matched research. The vestibular test was performed twice in the same patient, with five days interval between the exams. In the first test, the patient did not drink coffee 24 hours before the exam; in the second, the patient drunk coffee as usual. All of the participants had clinical indication for vestibular test and were used to drinking coffee. RESULTS: Nineteen women, medium age of 49,5 years, participated. The average coffee consumption was three cups per day. The complaints of anxiety and headache were associated with the submission to the vestibular test without coffee. The exams were not statistically different comparing the results of the tests performed with and without the coffee ingestion. CONCLUSION: The moderate ingestion of coffee was not shown to interfere in the results of the vestibular test. Considering that it is recommended that the patient be calm to be submitted to the vestibular test and that the half-life of the caffeine is only of six hours, we suggest that the orientation of complete and abrupt drinking coffee suspension of moderate dose before the vestibular test for the individuals used to daily drinking coffee be reevaluated