Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa

Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent

Complete genome sequence of Brucella abortus isolated from a human blood culture sample in Tanzania

This research articles was published in the microbiology resource announcementsBrucella abortus causes infections in humans and livestock. Bacterial isolates are challenging to obtain, and very little is known about the genomic epidemiology of this species in Africa. Here, we report the complete genome sequence of a Brucella abortus isolate cultured from a febrile human in northern Tanzani

Childhood vaccination trends during 2019 to 2022 in Tanzania and the impact of the COVID-19 pandemic

ABSTRACTThe COVID-19 pandemic has significantly disrupted healthcare systems at all levels globally, notably affecting routine healthcare services, such as childhood vaccination. This study examined the impact of these disruptions on routine childhood vaccination programmes in Tanzania. We conducted a longitudinal study over four years in five Tanzanian regions: Mwanza, Dar es Salaam, Mtwara, Arusha, and Dodoma. This study analyzed the trends in the use of six essential vaccines: Bacille Calmette-Guérin (BCG), bivalent Oral Polio Vaccine (bOPV), Diphtheria Tetanus Pertussis, Hepatitis-B and Hib (DTP-HepB-Hib), measles-rubella (MR), Pneumococcal Conjugate Vaccine (PCV), and Rota vaccines. We evaluated annual and monthly vaccination trends using time-series and regression analyses. Predictive modeling was performed using an autoregressive integrated moving average (ARIMA) model. A total of 32,602,734 vaccination events were recorded across the regions from 2019 to 2022. Despite declining vaccination rates in 2020, there was a notable rebound in 2021, indicating the resilience of Tanzania’s immunization program. The analysis also highlighted regional differences in vaccination rates when standardized per 1000 people. Seasonal fluctuations were observed in monthly vaccination rates, with BCG showing the most stable trend. Predictive modeling of BCG indicated stable and increasing vaccination coverage by 2023. These findings underscore the robustness of Tanzania’s childhood immunization infrastructure in overcoming the challenges posed by the COVID-19 pandemic, as indicated by the strong recovery of vaccination rates post-2020. We provide valuable insights into the dynamics of vaccination during a global health crisis and highlight the importance of sustained immunization efforts to maintain public health

Diagnostic validation of a portable whole slide imaging scanner for lymphoma diagnosis in resource-constrained setting: A cross-sectional study

Background: Telepathology utilizing high-throughput static whole slide image scanners is proposed to address the challenge of limited pathology services in resource-restricted settings. However, the prohibitive equipment costs and sophisticated technologies coupled with large amounts of space to set up the devices make it impractical for use in resource-limited settings. Herein, we aimed to address this challenge by validating a portable whole slide imaging (WSI) device against glass slide microscopy (GSM) using lymph node biopsies from suspected lymphoma cases from Sub-Saharan Africa. Material and methods: This was part of a multicenter prospective case–control head-to-head comparison study of liquid biopsy against conventional pathology. For the portable WSI scanner validation, the study pathologists evaluated 105 surgical lymph node specimens initially confirmed by gold-standard pathology between February and December 2021. The tissues were processed according to standard protocols for Hematoxylin and Eosin (H&E) and Immunohistochemistry (IHC) staining by well-trained histotechnicians, then digitalized the H& E and IHC slides at each center. The digital images were anonymized and uploaded to a HIPAA-compliant server by the histotechnicians. Three study pathologists independently accessed and reviewed the images after a 6-week washout. The agreement between diagnoses established on GSM and WSI across the pathologists was described and measured using Cohens’ kappa coefficient (κ). Results: On GSM, 65.5% (n=84) of specimens were lymphoma; 25% were classified as benign, while 9.5% were metastatic. Morphological quality assessment on GSM and WSI established that 79.8% and 53.6% of cases were of high quality, respectively. When diagnoses by GSM were compared to WSI, the overall concordance for various diagnostic categories was 93%, 100%, and 86% for lymphoma, metastases, and benign conditions respectively. The sensitivity and specificity of WSI for the detection of lymphoma were 95.2% and 85.7%, respectively, with an overall inter-observer agreement (κ) of 0.86; 95% CI (0.70–0.95). Conclusions: We demonstrate that mobile whole slide imaging (WSI) is non-inferior to conventional glass slide microscopy (GSM) for the primary diagnosis of malignant infiltration of lymph node specimens. Our results further provide proof of concept that mobile WSI can be adapted to resource-restricted settings for primary surgical pathology and would significantly improve patient outcomes

Traditional Knowledge, Use Practices and Conservation of Medicinal Plants for HIV/AIDS Care in Rural Tanzania

researchHIV/AIDS pandemic is currently the most socio-economic challenge that faces Tanzania as it affects mostly the young and most economically productive population. People living with HIV/AIDS in Tanzania are susceptible to fungal and bacterial opportunistic infections, which are a major cause of mortality and morbidity in the country. Despite the government’s intervention to provide ARVs to people living with HIV/AIDS, many of them especially those living in the rural areas can neither afford them due to poverty nor access them due to distance to health centers. Moreover, resistance of opportunistic microbial pathogens to conventional medicines and the serious side effects associated with antiretroviral drugs are also a major drawback to the management of HIV/AIDS in the country. Due to these factors, many people opt to use of traditional medicines. This paper highlights the use and conservation of herbal remedies to manage HIV/AIDS pandemic in Tanzania. Ethnobotanical surveys were carried out in Bukoba Rural District to explore the traditional ethno-medical knowledge, the use and conservation of medicinal plants in the management of HIV/AIDS opportunistic infections and to determine whether levels of harvesting are sustainable. The district is currently an epicenter of HIV/AIDS and although over 90% of the population in the district relies on traditional medicines to manage the disease, this traditional knowledge still remains largely unknown. Seventyfive plant species belonging to 66 genera and 40 families were found to be used to treat one or more HIV/AIDS related diseases in the district. Eight plant species were tested in-vitro for their antifungal activity against three major fungal pathogens, Candida albicans (C.P. Robin) Berkhout, Cryptococcus neoformans (San Felice) Vuill., and Aspergillus niger Tiegh. Three of them were further tested in-vivo for their anti-Candida activity. With decreasing natural stocks of medicinal plants, and based on the results, this study further provides concrete recommendations for the conservation of these important non-timber forest products and the region’s medicinal plant biodiversity

Prevalence of non-falciparum malaria infections among asymptomatic individuals in four regions of Mainland Tanzania

Abstract Background Recent studies point to the need to incorporate the detection of non-falciparum species into malaria surveillance activities in sub-Saharan Africa, where 95% of the world’s malaria cases occur. Although malaria caused by infection with Plasmodium falciparum is typically more severe than malaria caused by the non-falciparum Plasmodium species P. malariae, P. ovale spp. and P. vivax, the latter may be more challenging to diagnose, treat, control and ultimately eliminate. The prevalence of non-falciparum species throughout sub-Saharan Africa is poorly defined. Tanzania has geographical heterogeneity in transmission levels but an overall high malaria burden. Methods To estimate the prevalence of malaria species in Mainland Tanzania, we randomly selected 1428 samples from 6005 asymptomatic isolates collected in previous cross-sectional community surveys across four regions and analyzed these by quantitative PCR to detect and identify the Plasmodium species. Results Plasmodium falciparum was the most prevalent species in all samples, with P. malariae and P. ovale spp. detected at a lower prevalence (< 5%) in all four regions; P. vivax was not detected in any sample. Conclusions The results of this study indicate that malaria elimination efforts in Tanzania will need to account for and enhance surveillance of these non-falciparum species. Graphical Abstrac

Plasmodium falciparum pfhrp2 and pfhrp3 gene deletions among patients enrolled at 100 health facilities throughout Tanzania: February to July 2021

Abstract Plasmodium falciparum with the histidine rich protein 2 gene (pfhrp2) deleted from its genome can escape diagnosis by HRP2-based rapid diagnostic tests (HRP2-RDTs). The World Health Organization (WHO) recommends switching to a non-HRP2 RDT for P. falciparum clinical case diagnosis when pfhrp2 deletion prevalence causes ≥ 5% of RDTs to return false negative results. Tanzania is a country of heterogenous P. falciparum transmission, with some regions approaching elimination and others at varying levels of control. In concordance with the current recommended WHO pfhrp2 deletion surveillance strategy, 100 health facilities encompassing 10 regions of Tanzania enrolled malaria-suspected patients between February and July 2021. Of 7863 persons of all ages enrolled and providing RDT result and blood sample, 3777 (48.0%) were positive by the national RDT testing for Plasmodium lactate dehydrogenase (pLDH) and/or HRP2. A second RDT testing specifically for the P. falciparum LDH (Pf-pLDH) antigen found 95 persons (2.5% of all RDT positives) were positive, though negative by the national RDT for HRP2, and were selected for pfhrp2 and pfhrp3 (pfhrp2/3) genotyping. Multiplex antigen detection by laboratory bead assay found 135/7847 (1.7%) of all blood samples positive for Plasmodium antigens but very low or no HRP2, and these were selected for genotyping as well. Of the samples selected for genotyping based on RDT or laboratory multiplex result, 158 were P. falciparum DNA positive, and 140 had sufficient DNA to be genotyped for pfhrp2/3. Most of these (125/140) were found to be pfhrp2+/pfhrp3+, with smaller numbers deleted for only pfhrp2 (n = 9) or only pfhrp3 (n = 6). No dual pfhrp2/3 deleted parasites were observed. This survey found that parasites with these gene deletions are rare in Tanzania, and estimated that 0.24% (95% confidence interval: 0.08% to 0.39%) of false-negative HRP2-RDTs for symptomatic persons were due to pfhrp2 deletions in this 2021 Tanzania survey. These data provide evidence for HRP2-based diagnostics as currently accurate for P. falciparum diagnosis in Tanzania

Screening of traditionally used Tanzanian medicinal plants for antifungal activity

Kisangau DP, Hosea KM, Lyaruu HVM, et al. Screening of traditionally used Tanzanian medicinal plants for antifungal activity. PHARMACEUTICAL BIOLOGY. 2009;47(8):708-716.Fungal infections represent a significant cause of morbidity and mortality especially in immunocompromised patients in the world today. Dichloromethane (DM) and aqueous (W) extracts of nine plants used traditionally for the treatment of fungal infections in Bukoba rural district in Tanzania were screened for antifungal activity against Candida albicans, Cryptococcus neoformans, and Aspergillus niger using agar well and disk diffusion methods. Dichloromethane extracts of Capparis erythrocorpos [CE] Isert (Capparaceae), Cussonia arborea [CA] Hochst. Ex A. Rich (Araliaceae), Drocaena steudneri [DS] Engl. (Dracaenaceae), Lannea schimperi [LS] (A. Rich) Engl. (Anacardiaceae), Rouvolfia vomitoria [RV] Afz (Apocynaceae), and Sapium ellipticum [SE] (Krauss) Pax (Euphorbiaceae) showed activity against all three fungi. Extracts of Rumex usambarensis [RU] (Dammer) Dammer (Polygonaceae) and Zehneria scabro [ZS] (L.f.) Sond. (Cucurbitaceae) had an activity limited to only one or two of the test organisms. Rhoicissus tridentata [RT] (L.Q Wild & Drum (Vitaceae) was the only plant without activity. Fractions of the active extracts CE, CA, DS, LS, and SE exhibited higher antifungal activity against one or more of the three fungi. Four compounds isolated from S. ellipticum also exhibited antifungal activity against one or more of the three fungi. The minimum inhibitory concentrations (MICs) and minimum fungicidal concentrations (MFCs), determined using the microplate assay method, ranged between 0.4 and 50.0 mu g/mL for crude extracts, 1.6 and 50.0 mu g/mL for semi-purified fractions, and 0.12 and 1.0 mu g/mL for pure compounds, as compared to 0.016-1.5 mu g/mL for fluconazole. We confirm the potential of traditionally used plants as a source of new drugs for treatment of fungal infections