Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics.

BACKGROUND: Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region.  RESULTS: The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. CONCLUSION: The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations.

Genetic variation of Nigerian cattle inferred from maternal and paternal genetic markers.

The African cattle provide unique genetic resources shaped up by both diverse tropical environmental conditions and human activities, the assessment of their genetic diversity will shade light on the mechanism of their remarkable adaptive capacities. We therefore analyzed the genetic diversity of cattle samples from Nigeria using both maternal and paternal DNA markers. Nigerian cattle can be assigned to 80 haplotypes based on the mitochondrial DNA (mtDNA) D-loop sequences and haplotype diversity was 0.985 + 0.005. The network showed two major matrilineal clustering: the dominant cluster constituting the Nigerian cattle together with other African cattle while the other clustered Eurasian cattle. Paternal analysis indicates only zebu haplogroup in Nigerian cattle with high genetic diversity 1.000 ± 0.016 compared to other cattle. There was no signal of maternal genetic structure in Nigerian cattle population, which may suggest an extensive genetic intermixing within the country. The absence of Bos indicus maternal signal in Nigerian cattle is attributable to vulnerability bottleneck of mtDNA lineages and concordance with the view of male zebu genetic introgression in African cattle. Our study shades light on the current genetic diversity in Nigerian cattle and population history in West Africa.

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

Bushmeat 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.

Pastoralists' Vulnerability to Trypanosomiasis in Maasai Steppe.

Trypanosomiasis is a neglected tropical disease of both livestock and humans. Although pastoral communities of the Maasai Steppe have been able to adapt to trypanosomiasis in the past, their traditional strategies are now constrained by changes in climate and land regimes that affect their ability to move with their herds and continually shape the communities' vulnerability to trypanosomiasis. Despite these constraints, information on communities' vulnerability and adaptive capacity to trypanosomiasis is limited. A cross-sectional study was therefore conducted in Simanjiro and Monduli districts of the Maasai Steppe to establish pastoralists' vulnerability to animal trypanosomiasis and factors that determined their adaptation strategies. A weighted overlay approach in ArcGIS 10.4 was used to analyze vulnerability levels while binomial and multinomial logistic regressions in R 3.3.2 were used to analyze the determinants of adaptation. Simanjiro district was the most vulnerable to trypanosomiasis. The majority (87.5%, n = 136) of the respondents were aware of trypanosomiasis in animals, but only 7.4% (n = 136) knew about the human form of the disease. Reported impacts of animal trypanosomiasis were low milk production (95.6%, n = 136), death of livestock (96.8%, n = 136) and emaciation of animals (99.9%, n = 136). Crop farming was the most frequently reported animal trypanosomiasis adaptation strategy (66%, n = 136). At a 95% confidence interval, accessibility to livestock extension services (ß = 7.61, SE = 3.28, df = 135, P = 0.02), years of livestock keeping experience (ß = 6.17, SE = 1.95, df = 135, P = 0.001), number of cattle owned (ß = 5.85, SE = 2.70, df = 135, P = 0.03) and membership in associations (ß = - 4.11, SE = 1.79, df = 135, P = 0.02) had a significant impact on the probability of adapting to animal trypanosomiasis.

Molecular prevalence of trypanosome infections in cattle and tsetse flies in the Maasai Steppe, northern Tanzania.

BACKGROUND: African trypanosomosis is a disease of public health and economic importance that poses a major threat to the livelihoods of people living in the Maasai Steppe, where there is a significant interaction between people, livestock and wildlife. The vulnerability of the Maasai people to the disease is enhanced by the interaction of their cattle, which act as vehicles for trypanosomes, and tsetse flies close to wildlife in protected areas. This study was aimed at identification of trypanosome infections circulating in cattle and tsetse flies in order to understand their distribution and prevalence in livestock/wildlife interface areas in the Maasai Steppe. METHODS: A total of 1002 cattle and 886 tsetse flies were sampled from June 2015 to February 2016 in five villages and PCR was conducted to amplify the internal transcribed spacer 1 (ITS1) from trypanosomes. All Trypanosoma brucei-positive samples were further tested for the presence of the serum resistance-associated (SRA) gene found in human-infective trypanosomes using the SRA-LAMP technique. RESULTS: The overall prevalence of trypanosome infections was 17.2% in cattle and 3.4% in tsetse flies. Using a nested PCR, prevalence and abundance of five trypanosome species, Trypanosoma vivax, T. brucei, T. simiae, T. theileri and T. congolense, were determined, which varied with season and location. The highest prevalence of the identified trypanosome species was recorded at the end of wet season with an exception of T. brucei which was high at the beginning of the wet season. No human-infective trypanosomes were detected in both cattle and tsetse fly DNA. CONCLUSIONS: This study confirms that seasonality and location have a significant contribution to the prevalence of trypanosome species in both mammalian and vector hosts. These results are important for designing of community-wide vector and disease control interventions and planning of sustainable regimes for reduction of the burden of trypanosomosis in endemic pastoral areas, such as the Maasai Steppe in northern Tanzania.

Patterns of tsetse abundance and trypanosome infection rates among habitats of surveyed villages in Maasai steppe of northern Tanzania.

BACKGROUND: Changes of land cover modify the characteristics of habitat, host-vector interaction and consequently infection rates of disease causing agents. In this paper, we report variations in tsetse distribution patterns, abundance and infection rates in relation to habitat types and age in the Maasai Steppe of northern Tanzania. In Africa, Tsetse-transmitted trypanosomiasis negatively impacted human life where about 40 million people are at risk of contracting the disease with dramatic socio-economical consequences, for instance, loss of livestock, animal productivity, and manpower. METHODS: We trapped tsetse flies in dry and wet seasons between October 2014 and May 2015 in selected habitats across four villages: Emboreet, Loiborsireet, Kimotorok and Oltukai adjacent to protected areas. Data collected include number and species of tsetse flies caught in baited traps, PCR identification of trypanosome species and extraction of monitored Normalized Difference Vegetation Index (NDVI) data from Moderate Resolution Imaging Spectrometer (MODIS). RESULTS: Our findings demonstrate the variation of tsetse fly species abundance and infection rates among habitats in surveyed villages in relation to NDVI and host abundance. Results have shown higher tsetse fly abundance in Acacia-swampy ecotone and riverine habitats for Emboreet and other villages, respectively. Tsetse abundance was inconsistent among habitats in different villages. Emboreet was highly infested with Glossina swynnertoni (68%) in ecotone and swampy habitats followed by G. morsitans (28%) and G. pallidipes (4%) in riverine habitat. In the remaining villages, the dominant tsetse fly species by 95% was G. pallidipes in all habitats. Trypanosoma vivax was the most prevalent species in all infected flies (95%) with few observations of co-infections (with T. congolense or T. brucei). CONCLUSIONS: The findings of this study provide a framework to mapping hotspots of tsetse infestation and trypanosomiasis infection and enhance the communities to plan for effective control of trypanosomiasis.

Variation of tsetse fly abundance in relation to habitat and host presence in the Maasai Steppe, Tanzania.

Human activities modify ecosystem structure and function and can also alter the vital rates of vectors and thus the risk of infection with vector-borne diseases. In the Maasai Steppe ecosystem of northern Tanzania, local communities depend on livestock and suitable pasture that is shared with wildlife, which can increase tsetse abundance and the risk of trypanosomiasis. We monitored the monthly tsetse fly abundance adjacent to Tarangire National Park in 2014-2015 using geo-referenced, baited epsilon traps. We examined the effect of habitat types and vegetation greenness (NDVI) on the relative abundance of tsetse fly species. Host availability (livestock and wildlife) was also recorded within 100×100 m of each trap site. The highest tsetse abundance was found in the ecotone between Acacia-Commiphora woodland and grassland, and the lowest in riverine woodland. Glossina swynnertoni was the most abundant species (68%) trapped throughout the entire study, while G. pallidipes was the least common (4%). Relative species abundance was negatively associated with NDVI, with greatest abundance observed in the dry season. The relationship with the abundance of wildlife and livestock was more complex, as we found positive and negative associations depending on the host and fly species. While habitat is important for tsetse distribution, hosts also play a critical role in affecting fly abundance and, potentially, trypanosomiasis risk.

Seasonal variation of tsetse fly species abundance and prevalence of trypanosomes in the Maasai Steppe, Tanzania.

Tsetse flies, the vectors of trypanosomiasis, represent a threat to public health and economy in sub-Saharan Africa. Despite these concerns, information on temporal and spatial dynamics of tsetse and trypanosomes remain limited and may be a reason that control strategies are less effective. The current study assessed the temporal variation of the relative abundance of tsetse fly species and trypanosome prevalence in relation to climate in the Maasai Steppe of Tanzania in 2014-2015. Tsetse flies were captured using odor-baited Epsilon traps deployed in ten sites selected through random subsampling of the major vegetation types in the area. Fly species were identified morphologically and trypanosome species classified using PCR. The climate dataset was acquired from the African Flood and Drought Monitor repository. Three species of tsetse flies were identified: G. swynnertoni (70.8%), G. m. morsitans (23.4%), and G.pallidipes (5.8%). All species showed monthly changes in abundance with most of the flies collected in July. The relative abundance of G. m. morsitans and G. swynnertoni was negatively correlated with maximum and minimum temperature, respectively. Three trypanosome species were recorded: T. vivax (82.1%), T. brucei (8.93%), and T. congolense (3.57%). The peak of trypanosome infections in the flies was found in October and was three months after the tsetse abundance peak; prevalence was negatively correlated with tsetse abundance. A strong positive relationship was found between trypanosome prevalence and temperature. In conclusion, we find that trypanosome prevalence is dependent on fly availability, and temperature drives both tsetse fly relative abundance and trypanosome prevalence.

Knowledge, attitudes and practices on malaria in relation to its transmission among primary school children in Bagamoyo district, Tanzania.

Background: Communities' knowledge, attitudes and practices on malaria disease often remain unobserved during malaria control efforts. In Tanzania, many studies focus on increasing community knowledge and awareness on malaria prevention but the potential participation and contribution of schoolchildren towards knowledge, attitudes and practices on malaria has received little attention. We investigated the knowledge and understanding of primary school children on malaria transmission, recognition of symptoms, treatment seeking behaviour, preventive measures and practices in order to potentially include this group in Tanzania's malaria control efforts. Materials and methods: 125 children were recruited from three purposively selected primary schools in Bagamoyo district, Tanzania. A semi-structured interview guide, including both closed and open-ended questions, was used to collect information from the participants to obtain their knowledge and understanding on malaria transmission, treatment and prevention. Results: More than half of the school children (79/125; 63.2% ) had knowledge on malaria as a disease and its transmission; 101/125 (80.8%) of the respondents reported that going to the hospital was their immediate care-seeking behaviour once they felt malaria symptoms, while 14/125 (11.2%) opted for self-medication. With regard to malaria prevention and control, 115/125 (92.0%) of the respondents reported using bednets as their main malaria prevention strategy, while 6/125 (4.8%) preferred the use of medicine, mostly artemether lumefantrine, as prophylaxis. Narratives obtained were able to explain clearly the rationale behind different options children took to treat and to protect themselves against malaria. Conclusions: Findings indicated that primary school children in Bagamoyo district are aware of malaria, its symptoms and preventive measures, although some had misconceptions and could not associate the disease with its transmission. We conclude that inclusion of school children on malaria control educational programmes could yield substantial benefits towards malaria elimination.

Prevalence of bacterial febrile illnesses in children in Kilosa district, Tanzania.

INTRODUCTION: 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. METHODS: 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. RESULTS: 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. CONCLUSION: The study has underscored the importance of febrile bacterial diseases including zoonoses such as leptospirosis and brucellosis in febrile 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.

Dengue and Chikungunya fever among viral diseases in outpatient febrile children in Kilosa district hospital, Tanzania.

INTRODUCTION: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.

Self-medication with anti-malarials is a common practice in rural communities of Kilosa district in Tanzania despite the reported decline of malaria.

BACKGROUND: Self-medication has been widely practiced worldwide particularly in developing countries including Tanzania. In sub-Saharan Africa high incidences of malaria have contributed to self-medication with anti-malarial drugs. In recent years, there has been a gain in malaria control, which has led to decreased malaria transmission, morbidity and mortality. Therefore, understanding the patterns of self-medication during this period when most instances of fever are presumed to be due to non-malaria febrile illnesses is important. In this study, self-medication practice was assessed among community members and information on the habit of self-medication was gathered from health workers. METHODS: Twelve focus group discussions (FGD) with members of communities and 14 in-depth interviews (IDI) with health workers were conducted in Kilosa district, Tanzania. The transcripts were coded into different categories by MaxQDA software and then analysed through thematic content analysis. RESULTS: The study revealed that self-medication was a common practice among FGD participants. Anti-malarial drugs including sulphadoxine-pyrimethamine and quinine were frequently used by the participants for treatment of fever. Study participants reported that they visited health facilities following failure of self-medication or if there was no significant improvement after self-medication. The common reported reasons for self-medication were shortages of drugs at health facilities, long waiting time at health facilities, long distance to health facilities, inability to pay for health care charges and the freedom to choose the preferred drugs. CONCLUSION: This study demonstrated that self-medication practice is common among rural communities in the study area. The need for community awareness is emphasized for correct and comprehensive information about drawbacks associated with self-medication practices. Deliberate efforts by the government and other stakeholders to improve health care services, particularly at primary health care facilities will help to reduce self-medication practices.

Community knowledge and attitudes and health workers' practices regarding non-malaria febrile illnesses in eastern Tanzania.

INTRODUCTION: Although malaria has been the leading cause of fever for many years, with improved control regimes malaria transmission, morbidity and mortality have decreased. Recent studies have increasingly demonstrated the importance of non-malaria fevers, which have significantly improved our understanding of etiologies of febrile illnesses. A number of non-malaria febrile illnesses including Rift Valley Fever, dengue fever, Chikungunya virus infection, leptospirosis, tick-borne relapsing fever and Q-fever have been reported in Tanzania. This study aimed at assessing the awareness of communities and practices of health workers on non-malaria febrile illnesses. METHODS: Twelve focus group discussions with members of communities and 14 in-depth interviews with health workers were conducted in Kilosa district, Tanzania. Transcripts were coded into different groups using MaxQDA software and analyzed through thematic content analysis. RESULTS: The study revealed that the awareness of the study participants on non-malaria febrile illnesses was low and many community members believed that most instances of fever are due to malaria. In addition, the majority had inappropriate beliefs about the possible causes of fever. In most cases, non-malaria febrile illnesses were considered following a negative Malaria Rapid Diagnostic Test (mRDT) result or persistent fevers after completion of anti-malaria dosage. Therefore, in the absence of mRDTs, there is over diagnosis of malaria and under diagnosis of non-malaria illnesses. Shortages of diagnostic facilities for febrile illnesses including mRDTs were repeatedly reported as a major barrier to proper diagnosis and treatment of febrile patients. CONCLUSION: Our results emphasize the need for creating community awareness on other causes of fever apart from malaria. Based on our study, appropriate treatment of febrile patients will require inputs geared towards strengthening of diagnostic facilities, drugs availability and optimal staffing of health facilities.