High-throughput sequencing of 16S rRNA Gene Reveals Substantial Bacterial Diversity on the Municipal Dumpsite

Background Multiple types of solid waste in developing countries is disposed of together in dumpsites where there is interaction between humans, animals and the bacteria in the waste. To study the bacteria at the dumpsite and the associated risks, previous studies have focused on culturable, leaving behind a great number of unculturable bacteria. This study focuses on a more comprehensive approach to study bacteria at the dumpsite. Since the site comprised of unsorted wastes, a qualitative survey was first performed to identify the variety of solid waste as this has influence on the microbial composition. Thus, domestic (Dom), biomedical (Biom), river sludge (Riv), and fecal material of pigs scavenging on the dumpsite (FecD) were sampled. Total DNA was extracted from 78 samples and the v4-16S rRNA amplicons was characterized using an Illumina MiSeq platform. Results A total of 8,469,294 sequences passed quality control. Catchall analysis predicted a mean of 8243 species per sample. Diversity was high with an average InvSimpson index of 44.21 ± 1.44. A total of 35 phyla were detected and the predominant were Firmicutes (38 %), Proteobacteria (35 %), Bacteroidetes (13 %) and Actinobacteria (3 %). Overall 76,862 OTUs were detected, however, only 20 % were found more than 10 times. The predominant OTUs were Acinetobacter (12.1 %), Clostridium sensu stricto (4.8 %), Proteinclasticum and Lactobacillus both at (3.4 %), Enterococcus (2.9 %) and Escherichia/Shigella (1.7 %). Indicator analysis (P ≤ 0.05, indicator value ≥ 70) shows that Halomonas, Idiomarina, Tisierella and Proteiniclasticum were associated with Biom; Enterococcus, Bifidobacteria, and Clostridium sensu stricto with FecD and Flavobacteria, Lysobacterand Commamonas to Riv. Acinetobacter and Clostridium sensu stricto were found in 62 % and 49 % of all samples, respectively, at the relative abundance of 1 %. None of OTUs was found across all samples. Conclusions This study provides a comprehensive report on the abundance and diversity bacteria in municipal dumpsite. The species richness reported here shows the complexity of this man-made ecosystem and calls for further research to assess for a link between human diseases and the dumpsite. This would provide insight into proper disposal of the waste, as well as, limit the risks to human health associated with the dumpsite

Assessing Risk Factors for Trypanosome Infections in Cattle in Wildlife Interface Areas in Northern Tanzania

This research article published by the Journal of Infectious Diseases and Epidemiology, 2019Trypanosomosis is a vector-borne, tropical disease that causes mortality and morbidity in livestock and humans. In this study we investigated the risk factors for trypanosome infection in cattle in the Maasai Steppe of northern Tanzania. We assessed the influence of age, sex, herd size and history of treatment against trypanosomosis as risk factors of trypanosome infection. Cattle blood samples were collected from 150 cattle in three villages in the vicinity of Tarangire National Park, which acts as a reservoir of tsetse flies, the trypanosome vector. Parasite species were identified using a nested Polymerase Chain Reaction (n-PCR). Smaller herd sizes, young age (1-2 years), and male sex significantly increased the risk of trypanosome infections. Efforts to control trypanosome infection should be strategically based on location and season while considering age, treatment and herd size as risk factors

Dengue and Chikungunya Fever among Viral Diseases in Outpatient Febrile Children in Kilosa District Hospital, Tanzania.

Viral etiologies of fever, including dengue, Chikungunya, influenza, rota and adeno viruses, cause major disease burden in tropical and subtropical countries. The lack of diagnostic facilities in developing countries leads to failure to estimate the true burden of such illnesses, and generally the diseases are underreported. These diseases may have similar symptoms with other causes of acute febrile illnesses including malaria and hence clinical diagnosis without laboratory tests can be difficult. This study aimed to identify viral etiologies as a cause of fever in children and their co-infections with malaria. A cross sectional study was conducted for 6 months at Kilosa district hospital, Tanzania. The participants were febrile children aged 2-13 years presented at the outpatient department. Diagnostic tests such as IgM and IgG ELISA, and PCR were used. A total of 364 patients were enrolled, of these 83(22.8%) had malaria parasites, 76 (20.9%) had presumptive acute dengue infection and among those, 29(38.2%) were confirmed cases. Dengue was more likely to occur in children ≥ 5 years than in <5 years (OR 2.28, 95% CI: 1.35-3.86). Presumptive acute Chikungunya infection was identified in 17(4.7%) of patients. We observed no presenting symptoms that distinguished patients with Chikungunya infection from those with dengue infection or malaria. Co-infections between malaria and Chikungunya, malaria and dengue fever as well as Chikungunya and dengue were detected. Most patients with Chikungunya and dengue infections were treated with antibacterials. Furthermore, our results revealed that 5(5.2%) of patients had influenza virus while 5(12.8%) had rotavirus and 2(5.1%) had adenovirus. Our results suggest that even though viral diseases are a major public health concern, they are not given due recognition as a cause of fever in febrile patients. Emphasis on laboratory diagnostic tests for proper diagnosis and management of febrile patients is recommended

Prevalence of Bacterial Febrile Illnesses in Children in Kilosa District, Tanzania.

Bacterial etiologies of non-malaria febrile illnesses have significantly become important due to high mortality and morbidity, particularly in children. Despite their importance, there are few reports on the epidemiology of these diseases in Tanzania, and the true burden of such illnesses remains unknown. This study aimed to identify the prevalence of leptospirosis, brucellosis, typhoid fever and urinary tract infections and their rate of co-infections with malaria. A cross-sectional study was conducted at Kilosa district hospital in Tanzania for 6 months. Febrile children aged from 2-13 years were recruited from the outpatient department. Patients were screened by serological tests such as IgM and IgG ELISA, and microscopic agglutination test. A total of 370 patients were enrolled; of these 85 (23.0%) had malaria parasites, 43 (11.6%) had presumptive acute leptospirosis and 26/200 (13%) had confirmed leptospirosis. Presumptive acute brucellosis due to B. abortus was identified among 26 (7.0%) of patients while B. melitensis was detected in 57 (15.4%) of the enrolled patients. Presumptive typhoid fever due to S. Typhi was identified in thirty eight (10.3%) of the participants and 69 (18.6%) had urinary tract infections. Patients presented with similar symptoms; therefore, the identification of these diseases could not be done based on clinical ground alone. Co-infections between malaria and bacterial febrile illnesses were observed in 146 patients (39.5%). Although antibacterials and/or anti-malarials were prescribed in most patients, some patients did not receive the appropriate treatment. The study has underscored the importance of febrile bacterial diseases including zoonoses such as leptospirosis and brucellosis infebrile children, and thus such illnesses should be considered by clinicians in the differential diagnoses of febrile diseases. However, access to diagnostic tests for discrimination of febrile illnesses is needed. This would allow febrile patients to receive the correct diagnoses and facilitation of accurate and prompt treatment

Influence of Land Cover and Host Species on Trypanosome Infection in Cattle and its Socio-Economic Impacts to Pastoralists of the Maasai Steppe, Tanzania

This research article published by the Journal of Infectious Diseases and Epidemiology, Volume 6 | Issue 1, 2020Introduction Trypanosome infections result into trypanosomosis in cattle and this is an infection detrimental to pastoralist income. The patterns of transmission are thought to be influenced by ecological factors including wildlife and land cover. We assessed the influence of the relative abundance of wildlife and land cover (cultivation and habitat type) on the presence of trypanosome infections in replicated cattle herds of the Maasai Steppe. Methodology We undertook a cohort field study in three villages of the Maasai Steppe: Sukuro, Kimotorok and Oltukai. The study took place in July 2017 and October 2017 and utilized 50 cattle from each village. Pastoralists were asked questions during each visit when blood sampled were taken to seek their viewpoint on the relative abundance of wildlife, habitat types and cultivation observed in the areas their cattle grazed. In addition, the percentage cover of cultivated land and habitat types in the grazing areas were determined during field visits and participatory mapping with pastoralists. A systematic review was used to understand the socio-economic importance of trypanosomosis. The species of trypanosomes in cattle were identified using nested Polymerase chain reaction (n-PCR). Results There was a significant and positive association between the presence of trypanosome infection and the abundance of wildlife within grazing areas, in particular the abundance of buffaloes (Odd Ratio > 1, P = 0.038, 95% CI 1.26 to 1.38) when cattle grazed in woodland habitats. Cultivation on grazing areas had a negative association with the presence of trypanosome infections (R < 1, P = 0.001, 95% CI 0.0614 to 0.0986) in cattle but this varied between villages. A systematic review showed that trypanosomosis had socio-economic impacts such as loss of income, reduced quality, and quantity of livestock products, management cost, and inadequate provisions of socio-services and potential zoonotic transmission to humans. Conclusion & recommendations The socio-economic impacts of trypanosomosis will continue to be a challenge to pastoralists when cattle are grazed close to wildlife areas which are infested with tsetse fly habitats. Control strategies for trypanosome infection in cattle on the Maasai Steppe should consider the interaction of cattle with ecological factors

Influence of Seasonal Cattle Movement on Prevalence of Trypanosome Infections in Cattle in the Maasai Steppe, Tanzania

This research article published by the Journal of Infectious Diseases and Epidemiology, 2019Animal African Trypanosomosis is a Neglected Tropical Disease with significant impacts to pastoral community livelihoods. Our study sought to determine the influence of seasonal cattle movements on the prevalence of trypanosome infections in cattle in the pastoral areas of the Maasai Steppe. Identification of spatial and temporal dynamics of trypanosome infections in cattle is essential for designing effective control strategies. To identify potential hotspots of trypanosome transmission, we worked with 5 pastoralists in each of 3 villages in the Maasai Steppe of northern Tanzania, and consecutively sampled 10 of each of their cattle in 3 periods, covering both wet and dry season grazing ranges (July 2017 to January 2018). Each time blood was collected from the cattle, a prophylactic dose of diminazene aceturate was administered to clear any parasites acquired in the previous 3 months. We then used participatory mapping techniques to identify the areas where the pastoralists had grazed their herds since the last sampling period, and interviewed them about any disease control methods they practice. Trypanosome infections in the sampled cattle blood were detected using nested polymerase chain reaction with ITS-1 primers. The overall prevalence of trypanosome infections across all sample periods and villages was 12%, though this varied distinctly by season and grazing area. Prevalence in July 2017 (19.33%) was significantly higher than prevalence in October 2017 (2%) (p < 0.05). A total of 45 grazing areas were identified and cattle acquired trypanosome infections in almost half of these (n = 21). Targeted awareness on seasonality and hotspot areas of trypanosome infections will help Maasai pastoralists to plan movement of their cattle strategically to avoid disease risk. These results also suggest enhanced control strategies for Trypanosomosis during the months of the year when cattle are moved further from homesteads to graze in hot spot areas

Data and tools to integrate climate and environmental information into public health

Background During the last 30 years, the development of geographical information systems and satellites for Earth observation has made important progress in the monitoring of the weather, climate, environmental and anthropogenic factors that influence the reduction or the reemergence of vector-borne diseases. Analyses resulting from the combination of geographical information systems (GIS) and remote sensing have improved knowledge of climatic, environmental, and biodiversity factors influencing vector-borne diseases (VBDs) such as malaria, visceral leishmaniasis, dengue, Rift Valley fever, schistosomiasis, Chagas disease and leptospirosis. These knowledge and products developed using remotely sensed data helped and continue to help decision makers to better allocate limited resources in the fight against VBDs. Main body Because VBDs are linked to climate and environment, we present here our experience during the last four years working with the projects under the, World Health Organization (WHO)/ The Special Programme for Research and Training in Tropical Diseases (TDR)-International Development Research Centre (IDRC) Research Initiative on VBDs and Climate Change to integrate climate and environmental information into research and decision-making processes. The following sections present the methodology we have developed, which uses remote sensing to monitor climate variability, environmental conditions, and their impacts on the dynamics of infectious diseases. We then show how remotely sensed data can be accessed and evaluated and how they can be integrated into research and decision-making processes for mapping risks, and creating Early Warning Systems, using two examples from the WHO TDR projects based on schistosomiasis analysis in South Africa and Trypanosomiasis in Tanzania. Conclusions The tools presented in this article have been successfully used by the projects under the WHO/TDR-IDRC Research Initiative on VBDs and Climate Change. Combined with capacity building, they are an important piece of work which can significantly contribute to the goals of WHO Global Vector Control Response and to the Sustainable Development Goals especially those on health and climate action

Molecular characterization of Theileria parva field strains derived from cattle and buffalo sympatric populations of Northern Tanzania

East coast fever is a disease of cattle caused by Theileria parva and is transmitted by the tick Rhipicephalus appendiculatus. Buffalos are a natural reservoir of the parasite. The objectives of this study were to determine the T. parva infection in buffalo and cattle field samples, to identify genotypes of T. parva infecting cattle and buffalo and finally to investigate the presence of buffalo-derived T. parva genotypes in cattle that graze in close proximity with infected buffalo. Real-Time PCR (RT-PCR) and Fluorescence Resonance Energy Transfer (FRET) was used to diagnose T.parva. Genotyping of T. parva was conducted by analysing p67, PIM and p104 genes . In addition, amplicons with unique PIM and p104 PCR-RFLP profiles were sequenced to identify shared genotypes. The results have shown the high occurrence of T. parva in buffalo and a much higher occurrence of T. parva in cattle from the Ngorongoro area. Analysis of the variable region of the p67 loci showed four different T. parva alleles in buffalo and cattle. PCR-RFLP analysis of the p104 loci revealed four allelic profiles in buffalo and two in cattle. PCR-RFLP analysis of PIM loci from buffalo gave profiles that were complex and difficult to interpret. On the contrary, cattle showed allelic profiles that resemble Muguga and Marikebuni isolate PIM gene profiles. Multi-locus genotypes (MLGs) and sequence analysis revealed that the majority of buffalo and cattle genotypes were distinct but there is an indication of some sharing of genotypes between buffalo and cattle.Belgian Directorate General for Development Co-operation Framework agreement ITM/DGCD and the Institute of Tropical Medicine (ITM).http://www.usa-journals.comam201

Detection of carrier state and genetic diversity of Theileria parva in ECF-vaccinated and naturally exposed cattle in Tanzania

This research article published by Elsevier B.V., 2019Infection and Treatment Method (ITM) has been practiced in Tanzania for over 20 years as a prevention measure against East Coast Fever disease. It is known that ITM, like natural ECF infection, leads to a carrier state, whereby vaccinated cattle become asymptomatic carriers of the parasite. It is expected that ECF vaccination using ITM also leads to generation of combinations of vaccine specific Theileria parva and local strains that circulate in the field what contributes to an unknown level of parasite diversity. Moreover, the long term impact of ITM on carrier state and parasite diversity in cattle are largely unknown. To address this question blood was collected from ECF-vaccinated (n = 239) and unvaccinated (n = 97) cattle from Loiborsoit, Emboreet, Esilalei, Manyara ranch and Mswakini villages in the Maasai steppe of northern Tanzania, as well as Mruazi and Leila farms in Tanga in eastern Tanzania. Screening for T. parva using nested PCR revealed an overall prevalence of T. parva to be 34.5%, with a significant higher prevalence among ECF-vaccinated cattle. Using three VNTR markers (ms2, ms5 and MS7) higher parasite genetic diversity in terms of higher number of alleles and expected heterozygosity was shown in vaccinated than unvaccinated cattle. These parameters were highest in cattle from Manyara ranch. Nevertheless, the principle component analysis (PCoA) showed no distinct clustering patterns as most T. parva alleles clustered together throughout the four quadrants implying parasite homogeneity among the sampled populations. However, some of the parasite alleles closely clustered with Muguga vaccine alleles in two of the quadrants, consistent with closer genetic relatedness between the vaccine strains and the T. parva populations from the Maasai steppe. Likewise analysis of molecular variance (AMOVA) revealed most of the genetic variation (93%) being contained within populations with only 7% being among populations. This study therefore confirms the role of ECF vaccination in enhancing carrier state and T. parva diversity in vaccinated cattle populations. Higher T. parva diversity may play an important role in carrier cattle by way of restricting breakthrough infections from field parasite strains

Molecular species identification of bushmeat recovered from the Serengeti ecosystem in Tanzania.

This research article published by PLOS ONE, 2020Bushmeat harvesting and consumption represents a potential risk for the spillover of endemic zoonotic pathogens, yet remains a common practice in many parts of the world. Given that the harvesting and selling of bushmeat is illegal in Tanzania and other parts of Africa, the supply chain is informal and may include hunters, whole-sellers, retailers, and individual resellers who typically sell bushmeat in small pieces. These pieces are often further processed, obscuring species-identifying morphological characteristics, contributing to incomplete or mistaken knowledge of species of origin and potentially confounding assessments of pathogen spillover risk and bushmeat offtake. The current investigation sought to identify the species of origin and assess the concordance between seller-reported and laboratory-confirmed species of origin of bushmeat harvested from in and around the Serengeti National Park in Tanzania. After obtaining necessary permits, the species of origin of a total of 151 bushmeat samples purchased from known intermediaries from 2016 to 2018 were characterized by PCR and sequence analysis of the cytochrome B (CytB) gene. Based on these sequence analyses, 30%, 95% Confidence Interval (CI: 24.4-38.6) of bushmeat samples were misidentified by sellers. Misreporting amongst the top five source species (wildebeest, buffalo, impala, zebra, and giraffe) ranged from 20% (CI: 11.4-33.2) for samples reported as wildebeest to 47% (CI: 22.2-72.7) for samples reported as zebra although there was no systematic bias in reporting. Our findings suggest that while misreporting errors are unlikely to confound wildlife offtake estimates for bushmeat consumption within the Serengeti ecosystem, the role of misreporting bias on the risk of spillover events of endemic zoonotic infections from bushmeat requires further investigation