Identification of constrained sequence elements across 239 primate genomes

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3-9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct

BACKGROUND

Treponema pallidum subsp. pertenue (TPE) is the causative agent of human yaws. Yaws is currently reported in 13 endemic countries in Africa, southern Asia, and the Pacific region. During the mid-20th century, a first yaws eradication effort resulted in a global 95% drop in yaws prevalence. The lack of continued surveillance has led to the resurgence of yaws. The disease was believed to have no animal reservoirs, which supported the development of a currently ongoing second yaws eradication campaign. Concomitantly, genetic evidence started to show that TPE strains naturally infect nonhuman primates (NHPs) in sub-Saharan Africa. In our current study we tested hypothesis that NHP- and human-infecting TPE strains differ in the previously unknown parts of the genomes.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, we determined complete (finished) genomes of ten TPE isolates that originated from NHPs and compared them to TPE whole-genome sequences from human yaws patients. We performed an in-depth analysis of TPE genomes to determine if any consistent genomic differences are present between TPE genomes of human and NHP origin. We were able to resolve previously undetermined TPE chromosomal regions (sequencing gaps) that prevented us from making a conclusion regarding the sequence identity of TPE genomes from NHPs and humans. The comparison among finished genome sequences revealed no consistent differences between human and NHP TPE genomes.

CONCLUSION/SIGNIFICANCE

Our data show that NHPs are infected with strains that are not only similar to the strains infecting humans but are genomically indistinguishable from them. Although interspecies transmission in NHPs is a rare event and evidence for current spillover events is missing, the existence of the yaws bacterium in NHPs is demonstrated. While the low risk of spillover supports the current yaws treatment campaign, it is of importance to continue yaws surveillance in areas where NHPs are naturally infected with TPE even if yaws is successfully eliminated in humans.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Baboons (genus Papio) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high-coverage whole-genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and interspecies gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.

A global catalog of whole-genome diversity from 233 primate species

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboons

Baboons (genus Papio ) are a morphologically and behaviorally diverse clade of catarrhine monkeys that have experienced hybridization between phenotypically and genetically distinct phylogenetic species. We used high coverage whole genome sequences from 225 wild baboons representing 19 geographic localities to investigate population genomics and inter-species gene flow. Our analyses provide an expanded picture of evolutionary reticulation among species and reveal novel patterns of population structure within and among species, including differential admixture among conspecific populations. We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages. The results reveal processes, both ancient and recent, that produced the observed mismatch between phylogenetic relationships based on matrilineal, patrilineal, and biparental inheritance. We also identified several candidate genes that may contribute to species-specific phenotypes.

One-Sentence Summary

Genomic data for 225 baboons reveal novel sites of inter-species gene flow and local effects due to differences in admixture.

The landscape of tolerated genetic variation in humans and primates

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole genome sequencing data for 809 individuals from 233 primate species, and identified 4.3 million common protein-altering variants with orthologs in human. We show that these variants can be inferred to have non-deleterious effects in human based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases.

One Sentence Summary

Deep learning classifier trained on 4.3 million common primate missense variants predicts variant pathogenicity in humans.

Molecular detection of Coxiella burnetii infection in small mammals from Moshi Rural and Urban Districts, northern Tanzania

Coxiella burnetii is an obligate intracellular bacterium that causes Q fever, a zoonotic disease of public health importance. In northern Tanzania, Q fever is a known cause of human febrile illness, but little is known about its distribution in animal hosts. We used a quantitative real-time PCR (qPCR) targeting the insertion element IS1111 to determine the presence and prevalence of C. burnetii infections in small mammals trapped in 12 villages around Moshi Rural and Moshi Urban Districts, northern Tanzania. A total of 382 trapped small mammals of seven species were included in the study; Rattus rattus (n = 317), Mus musculus (n = 44), Mastomys natalensis (n = 8), Acomys wilson (n = 6), Mus minutoides (n = 3), Paraxerus flavovottis (n = 3) and Atelerix albiventris (n = 1). Overall, 12 (3.1%) of 382 (95% CI: 1.6-5.4) small mammal spleens were positive for C. burnetii DNA. Coxiella burnetii DNA was detected in five of seven of the small mammal species trapped; R. rattus (n = 7), M. musculus (n = 1), A. wilson (n = 2), P. flavovottis (n = 1) and A. albiventris (n = 1). Eleven (91.7%) of twelve (95% CI: 61.5-99.8) C. burnetii DNA positive small mammals were trapped within Moshi Urban District. These findings demonstrate that small mammals in Moshi, northern Tanzania are hosts of C. burnetii and may act as a source of C. burnetii infection to humans and other animals. This detection of C. burnetii infections in small mammals should motivate further studies into the contribution of small mammals to the transmission of C. burnetii to humans and animals in this region.

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

BACKGROUND

Tuberculosis (TB), particularly multi- and or extensive drug resistant TB, is still a global medical emergency. Whole genome sequencing (WGS) is a current alternative to the WHO-approved probe-based methods for TB diagnosis and detection of drug resistance, genetic diversity and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). This study compared WGS and clinical data in participants with TB.

RESULTS

This cohort study performed WGS on 87 from MTBC DNA isolates, 57 (66%) and 30 (34%) patients with drug resistant and susceptible TB, respectively. Drug resistance was determined by Xpert® MTB/RIF assay and phenotypic culture-based drug-susceptibility-testing (DST). WGS and bioinformatics data that predict phenotypic resistance to anti-TB drugs were compared with participant's clinical outcomes. They were 47 female participants (54%) and the median age was 35 years (IQR): 29-44). Twenty (23%) and 26 (30%) of participants had TB/HIV co-infection BMI < 18 kg/m2 respectively. MDR-TB participants had MTBC with multiple mutant genes, compared to those with mono or polyresistant TB, and the majority belonged to lineage 3 Central Asian Strain (CAS). Also, MDR-TB was associated with delayed culture-conversion (median: IQR (83: 60-180 vs. 51:30-66) days). WGS had high concordance with both culture-based DST and Xpert® MTB/RIF assay in detecting drug resistance (kappa = 1.00).

CONCLUSION

This study offers comparison of mutations detected by Xpert and WGS with phenotypic DST of M. tuberculosis isolates in Tanzania. The high concordance between the different methods and further insights provided by WGS such as PZA-DST, which is not routinely performed in most resource-limited-settings, provides an avenue for inclusion of WGS into diagnostic matrix of TB including drug-resistant TB.

One Health approach in the prevention and control of mycobacterial infections in Tanzania: lessons learnt and future perspectives

BACKGROUND

One Health (OH) is an integrated approach, formed inclusive of using multiple disciplines to attain optimal health for humans, animals, and the environment. The increasing proximity between humans, livestock, and wildlife, and its role in the transmission dynamics of mycobacterial infections, necessitates an OH approach in the surveillance of zoonotic diseases. The challenge remains as humans, livestock, and wildlife share resources and interact at various interfaces. Therefore, this review explores the potential of the OH approach to understand the impact of mycobacterial infections in Tanzania in terms of lessons learnt and future perspectives.

MATERIALS AND METHODS

Available literature on OH and mycobacterial infections in Tanzania was searched in PubMed, Google Scholar, and Web of Science. Articles on mycobacterial infections in Tanzania, published between 1997 to 2017, were retrieved to explore the information on OH and mycobacterial infections.

MAIN BODY

The studies conducted in Tanzania had have reported a wide diversity of mycobacterial species in humans and animals, which necessitates an OH approach in surveillance of diseases for better control of infectious agents and to safeguard the health of humans and animals. The close proximity between humans and animals increases the chances of inter-specific transmission of infectious pathogens, including drug-resistant mycobacteria. In an era where HIV co-infection is also the case, opportunistic infection by environmental non-tuberculous mycobacteria (NTM), commonly known as mycobacteria other than tuberculosis (MOTT) may further exacerbate the impact of drug resistance. NTM from various sources have greatest potential for diverse strains among which are resistant strains due to continued evolutional changes.

CONCLUSION

A collaborative interdisciplinary approach among professionals could help in solving the threats posed by mycobacterial infections to public health, particularly by the spread of drug-resistant strains.

Widespread Treponema pallidum Infection in Nonhuman Primates, Tanzania

We investigated Treponema pallidum infection in 8 nonhuman primate species (289 animals) in Tanzania during 2015-2017. We used a serologic treponemal test to detect antibodies against the bacterium. Infection was further confirmed from tissue samples of skin-ulcerated animals by 3 independent PCRs (polA, tp47, and TP_0619). Our findings indicate that T. pallidum infection is geographically widespread in Tanzania and occurs in several species (olive baboons, yellow baboons, vervet monkeys, and blue monkeys). We found the bacterium at 11 of 14 investigated geographic locations. Anogenital ulceration was the most common clinical manifestation; orofacial lesions also were observed. Molecular data show that nonhuman primates in Tanzania are most likely infected with T. pallidum subsp. pertenue-like strains, which could have implications for human yaws eradication.

Tuberculosis Infection: Occurrence and Risk Factors in Presumptive Tuberculosis Patients of the Serengeti Ecosystem in Tanzania

Background

Cross-species tuberculosis (TB) transmission between humans and animals has been reported for quite a long time in sub-Saharan Africa. Because humans and animals coexist in the same ecosystem, exploring their potential for cross-species transmission and the impact the disease may have on the health of humans, animals, and their products is critical.

Objectives

This study aimed to identify risk factors for transmission of TB (Mycobacterium tuberculosis) and to assess the potential for zoonotic TB (Mycobacterium bovis) transmission in the Serengeti ecosystem where humans and animals are in intense contact. Our aim is to create a base for future implementation of appropriate control strategies to limit infection in both humans and animals.

Methodology

We administered a semi-structured questionnaire to 421 self-reporting patients to gather information on risk factors and TB occurrence. In a parallel study, researchers screened sputum smears using Ziehl-Neelsen staining and confirmed by mycobacterial culture. We then performed descriptive statistics (Pearson's chi-square test) and logistic regression analysis to establish frequencies, association, and quantification of the risk factors associated with TB cases.

Results

Our findings showed 44% (95% confidence interval [CI], 0.40-0.49) of the results were positive from sputum samples collected over a 1-year duration in areas with a high TB burden, particularly the Bunda district, followed by the Serengeti and Ngorongoro districts. Of the culture-positive patients who also had infections other than TB (43/187 patients), 21 (49%) were HIV positive. Contact with livestock products (odds ratio [OR] 6.0; 95% CI, 1.81-19.9), infrequent milk consumption (OR 2.5; 95% CI, 1.42-4.23), cigarette smoking (OR 2.9; 95% CI, 1.19-7.1.2), and alcohol consumption (OR 2.3; 95% CI, 1.22-4.23) were associated with a higher likelihood of TB infection.

Conclusion

There was no evidence of direct cross-species transmission of either M tuberculosis or M bovis between humans and animals using the study methods. The absence of cross-species TB transmission could be due to limited chances of contact rather than an inability of cross-species disease transmission. In addition, not all people with presumptive TB are infected with TB, and therefore control strategies should emphasise confirming TB status before administering anti-TB drugs.

Isolation of Treponema DNA from Necrophagous Flies in a Natural Ecosystem

Background

Recently, the World Health Organization launched a campaign to eradicate the tropical disease yaws, caused by the bacterium Treponema pallidum subsp. pertenue; however, for decades researchers have questioned whether flies act as a vector for the pathogen that could facilitate transmission.

Methods

A total of 207 fly specimens were trapped in areas of Africa in which T. pallidum-induced skin ulcerations are common in wild baboons; 88 flies from Tarangire National Park and 119 from Lake Manyara National Park in Tanzania were analyzed by PCR for the presence of T. pallidum DNA.

Findings

We report that in the two study areas, T. pallidum DNA was found in 17–24% of wild-caught flies of the order Diptera. Treponemal DNA sequences obtained from many of the flies match sequences derived from nearby baboon T. pallidum strains, and one of the fly species with an especially high prevalence of T. pallidum DNA, Musca sorbens, has previously been shown to transmit yaws in an experimental setting.

Interpretation

Our results raise the possibility that flies play a role in yaws transmission; further research is warranted, given how important understanding transmission is for the eradication of this disfiguring disease.

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Treponema pallidum DNA was found in 17–24% of wild-caught flies in the Manyara region of Tanzania.

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Results further support the possibility that flies play a role in yaws transmission.

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New theoretic route of inter-species transmission for Treponema

The discovery of Treponema pallidum DNA on necrophagous flies in Africa supports historical reports on possible transmission of the bacterium by flies as a mechanical vector. The bacterium (subsp. pertenue) causes human yaws, which is currently subject to eradication efforts. It has been shown that African nonhuman primates are also found to be infected with T. pallidum strains that are closely related to human yaws causing strains. The ecology of T. pallidum infection in primates is not yet fully understood and intra- and interspecies transmission pathways, apart from skin-to-skin contact in humans, are largely unknown.

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.

Response to Rift Valley Fever in Tanzania: Challenges and Opportunities

Rift Valley Fever (RVF) is an arthropod borne viral disease affecting livestock (cattle, sheep, goats and camels), wildlife and humans caused by Phlebovirus. The disease occurs in periodic cycles of 4-15 years associated with flooding from unusually high precipitations in many flood-prone habitats. Aedes and Culex spp and other mosquito species are important epidemic vectors. Because of poor living conditions and lack of knowledge on the pathogenesis of RVF, nomadic pastoralists and agro-pastoralists are at high risk of contracting the disease during epidemics. RVF is a professional hazard for health and livestock workers because of poor biosafety measures in routine activities including lack of proper Personal Protective Equipment (PPE). Direct exposure to infected animals can occur during handling and slaughter or through veterinary and obstetric procedures or handling of specimens in laboratory. The episodic nature of the disease creates special challenges for its mitigation and control and many of the epidemics happen when the governments are not prepared and have limited resource to contain the disease at source. Since its first description in 1930s Tanzania has recorded six epidemics, three of which were after independence in 1961. However, the 2007 epidemic was the most notable and wide spread with fatal human cases among pastoralists and agro-pastoralists concurrent with high livestock mortality. Given all the knowledge that exist on the epidemiology of the disease, still the 2006/2007 epidemic occurred when the government of Tanzania was not prepared to contain the disease at source. This paper reviews the epidemiology, reporting and outbreak-investigation, public awareness, preparedness plans and policy as well as challenges for its control in Tanzania.

Stakeholders in One Health

The stakeholders in One Health include the ultimate beneficiaries (i.e. animals, people and the environment) and the organisations that work to protect them (i.e. research institutes, government ministries, international organisations and professional bodies). However, identifying these stakeholders who will contribute to One Health activities and develop solutions to complex health problems can be difficult, as these problems often affect all sectors of society. In addition, evolving concepts about health and its dependence on environmental resilience necessitate the inclusion of ministries, organisations and disciplines that may not have been traditionally considered to be related to health. The multilateral organisations with greatest responsibilities in the global health arena have recognised that the best way to protect health security and promote overall global well-being is to work together across disciplinary and jurisdictional boundaries. Permanent regional networks and ad hoc networks created to tackle specific issues (both of which require donor investment) are also facilitating improved disease surveillance and collaborative approaches to synchronised interventions across country borders. These networks necessarily involve the key ministries for One Health, those of health, agriculture/livestock, and natural resources/environment. Ministries play a critical role in the formulation and implementation of policies for the promotion of health and disease control. They contribute to all stages of the One Heath process, as do universities, which engage by generating knowledge and capacity through teaching, research and extension services. Similarly, non-governmental organisations have a key role in stewardship; resource mobilisation; generation of knowledge; capacity development; intervention design; and implementation. Finally, communities, including rural and indigenous peoples, particularly those that are in close proximity to natural areas, are at the heart of the One Health concept.

Genetic diversity of Mycobacterium tuberculosis isolated from tuberculosis patients in the Serengeti ecosystem in Tanzania

This study was part of a larger cross-sectional survey that was evaluating tuberculosis (TB) infection in humans, livestock and wildlife in the Serengeti ecosystem in Tanzania. The study aimed at evaluating the genetic diversity of Mycobacterium tuberculosis isolates from TB patients attending health facilities in the Serengeti ecosystem. DNA was extracted from 214 sputum cultures obtained from consecutively enrolled newly diagnosed untreated TB patients aged ≥18 years. Spacer oligonucleotide typing (spoligotyping) and Mycobacterium Interspersed Repetitive Units and Variable Number Tandem Repeat (MIRU-VNTR) were used to genotype M. tuberculosis to establish the circulating lineages. Of the214 M. tuberculosis isolates genotyped, 55 (25.7%) belonged to the Central Asian (CAS) family, 52 (24.3%) were T family (an ill-defined family), 38 (17.8%) belonged to the Latin American Mediterranean (LAM) family, 25 (11.7%) to the East-African Indian (EAI) family, 25 (11.7%) comprised of different unassigned (‘Serengeti’) strain families, while 8 (3.7%) belonged to the Beijing family. A minority group that included Haarlem, X, U and S altogether accounted for 11 (5.2%) of all genotypes. MIRU-VNTR typing produced diverse patterns within and between families indicative of unlinked transmission chains. We conclude that, in the Serengeti ecosystem only a few successful families predominate namely CAS, T, LAM and EAI families. Other types found in lower prevalence are Beijing, Haarlem, X, S and MANU. The Haarlem, EAI_Somalia, LAM3 and S/convergent and X2 subfamilies found in this study were not reported in previous studies in Tanzania.

Species diversity of non-tuberculous mycobacteria isolated from humans, livestock and wildlife in the Serengeti ecosystem, Tanzania

BACKGROUND

Non-tuberculous mycobacteria (NTM), which are ubiquitous micro-organisms occurring in humans, animals and the environment, sometimes receive public health and veterinary attention as opportunistic disease-causing agents. In Tanzania, there is limited information regarding the diversity of NTM species, particularly at the human-livestock-wildlife interface such as the Serengeti ecosystem, where potential for cross species infection or transmission may exist.

METHODS

Mycobacterial DNA was extracted from cultured isolates obtained from sputum samples of 472 suspect TB patients and 606 tissues from wildlife species and indigenous cattle. Multiplex PCR was used to differentiate NTM from Mycobacterium tuberculosis complex (MTBC) members. NTM were further identified to species level by nucleotide sequencing of the 16S rRNA gene.

RESULTS

A total of fifty five (55) NTM isolates representing 16 mycobacterial species and 5 isolates belonging to the MTBC were detected. Overall, Mycobacterium intracellulare which was isolated from human, cattle and wildlife, was the most frequently isolated species (20 isolates, 36.4%) followed by M. lentiflavum (11 isolates, 20%), M. fortuitum (4 isolates, 7.3%) and M. chelonae-abscessus group (3 isolates, 5.5%). In terms of hosts, 36 isolates were from cattle and 12 from humans, the balance being found in various wildlife species.

CONCLUSION

This study reveals a diversity of NTM species in the Serengeti ecosystem, some of which have potential for causing disease in animals and humans. The isolation of NTM from tuberculosis-like lesions in the absence of MTBC calls for further research to elucidate their actual role in causing disease. We are also suggesting a one health approach in identifying risk factors for and possible transmission mechanisms of the NTM in the agro-pastoral communities in the Serengeti ecosystem.

Prevalence and risk factors for infection of bovine tuberculosis in indigenous cattle in the Serengeti ecosystem, Tanzania

Background

Bovine tuberculosis (bTB) is a chronic debilitating disease and is a cause of morbidity and mortality in livestock, wildlife and humans. This study estimated the prevalence and risk factors associated with bovine tuberculosis transmission in indigenous cattle at the human-animal interface in the Serengeti ecosystem of Tanzania.

Results

A total of 1,103 indigenous cattle from 32 herds were investigated for the presence of bTB using the Single Intradermal Comparative Tuberculin Test. Epidemiological data on herd structure, management and grazing system were also collected.

The apparent individual animal prevalence of tuberculin reactors was 2.4% (95% confidence interval (CI), 1.7 – 3.5%), whereas the true prevalence was 0.6% CI, 0.6 – 0.7% as indicated by a reaction to avian tuberculin purified protein derivatives (PPD) which is more than 4 mm greater than the reaction to avian tuberculin PPD. The results showed that 10.6% (117/1,103) showed non-specific reactions (atypical mycobacterium). The herd prevalence of 50% (16/32) was found. Tuberculin skin test results were found to be significantly associated with age, location, size of the household and animal tested. Of 108 respondents, 70 (64.8%) individuals had not heard about bovine tuberculosis at all. Thirty five percent (38/108) of respondents at least were aware of bTB. About 60% (23/38) of respondents who were aware of bTB had some knowledge on how bTB is spread. Eighty one percent (87/108) of respondents were not aware of the presence of bTB in wildlife. There is regular contact between cattle and wild animals due to sharing of grazing land and water sources, with 99% (107/108) of households grazing cattle in communal pastures.

Conclusion

The study has demonstrated a high reported interaction of livestock with wildlife and poor knowledge of most cattle owners concerning bTB and its transmission pathways among people, livestock and wildlife. Although the overall proportion of animals with bTB is relatively low, herd prevalence is 50% and prevalence within herds varied considerably. Thus there is a possibility of cross transmission of bTB at wildlife-livestock interface areas that necessitates use of genetic strain typing methods to characterize them accurately.

Tuberculosis cross-species transmission in Tanzania: towards a One-Health concept

For centuries, tuberculosis, which is a chronic infection caused by the bacillus Mycobacterium tuberculosis has remained a global health problem. The global burden of tuberculosis has increased, particularly in the Southern African region, mainly due to HIV, and inadequate health systems which has in turn given rise to emergent drug resistant tuberculosis (TB) strains. Bovine tuberculosis (BTB) has also emerged as a significant disease with the tendency for inter-species spread. The extent of interspecies BTB transmission both in urban and rural communities has not been adequately assessed. The phenomenon is of particular importance in rural communities where people share habitats with livestock and wildlife (particularly in areas near national parks and game reserves). Aerosol and oral intake are the major routes of transmission from diseased to healthy individuals, with health care workers often contracting infection nosocomially. Although TB control has increasingly been achieved in high-income countries, the disease, like other poverty-related infections, has continued to be a disaster in countries with low income economies. Transmission of infections occurs not only amongst humans but also between animals and humans (and occasionally vice versa) necessitating assessment of the extent of transmission at their interface. This review explores tuberculosis as a disease of humans which can cross-transmit between humans, livestock and wildlife. The review also addresses issues underlying the use of molecular biology, genetic sequencing and bioinformatics as t tools to understand the extent of inter-species cross-transmission of TB in a 'One Health' context.

'One Health' infectious diseases surveillance in Tanzania: are we all on board the same flight?

Infectious diseases account for nearly 40% of the burden of human mortality and morbidity in low-income countries, of which 7% is attributable to zoonoses and 13% to recently emerging diseases from animals. One of the strategic approaches for effective surveillance, monitoring and control of infectious diseases compromising health in both humans and animals could be through a combination of multiple disciplines. The approach can be achieved through a joint effort from stakeholders comprising health professionals (medical and veterinary), social, economic, agricultural, environmental and other interested parties. With resource scarcity in terms of number of staff, skills and facility in low-income countries, participatory multi- sectoral and multidisciplinary approaches in limiting the burden of zoonotic diseases could be worthwhile. We review challenging issues that may limit the 'One Health' approach for infectious diseases surveillance in Tanzania with a focus on Health Policy and how best the human and animal health systems could be complemented or linked to suit the community in need for disease control under the theme's context.

Bovine tuberculosis at the human-livestock-wildlife interface: is it a public health problem in Tanzania? A review

Despite the apparent public health concern about Bovine tuberculosis (BTB) in Tanzania, little has been done regarding the zoonotic importance of the disease and raising awareness of the community to prevent the disease. Bovine tuberculosis is a potential zoonotic disease that can infect a variety of hosts, including humans. The presence of multiple hosts including wild animals, inefficient diagnostic techniques, absence of defined national controls and eradication programs could impede the control of bovine TB. In Tanzania, the diagnosis of Mycobacterium bovis in animals is mostly carried out by tuberculin skin testing, meat inspection in abattoirs and only rarely using bacteriological techniques. The estimated prevalence of BTB in animals in Tanzania varies and ranges across regions from 0.2% to 13.3%, which is likely to be an underestimate if not confirmed by bacteriology or molecular techniques. Mycobacterium bovis has been detected and isolated from different animal species and has been recovered in 10% of apparently healthy wildebeest that did not show lesions at post-mortem. The transmission of the disease from animals to humans can occur directly through the aerosol route and indirectly by consumption of raw milk. This poses an emerging disease threat in the current era of HIV confection in Tanzania and elsewhere. Mycobacterium bovis is one of the causative agents of human extra pulmonary tuberculosis. In Tanzania there was a significant increase (116.6%) of extrapulmonary cases reported between 1995 and 2009, suggesting the possibility of widespread M. bovis and Mycobacterium tuberculosis infection due to general rise of Human Immunodeficiency virus (HIV). This paper aims to review the potential health and economic impact of bovine tuberculosis and challenges to its control in order to safeguard human and animal population in Tanzania.

Species identification of Tanzanian antelopes using DNA barcoding

Efficient tools for consistent species identification are important in wildlife conservation as it can provide information on the levels of species exploitation and assist in solving forensic-related problems. In this study, we evaluated the effectiveness of the mitochondrial cytochrome c oxidase subunit I (COI) barcode in species identification of Tanzanian antelope species. A 470 base-pair region of the COI gene was examined in 95 specimens representing 20 species of antelopes, buffalo and domestic Bovidae. All the Tanzanian species showed unique clades, and sequence divergence within species was <1%, whereas divergence between species ranged from 6.3% to 22%. Lowest interspecific divergence was noted within the Tragelaphus genus. Neighbour-joining phylogenetic analyses demonstrated that the examined COI region provided correct and highly supported species clustering using short fragments down to 100 base-pair lengths. This study demonstrates that even short COI fragments can efficiently identify antelope species, thus demonstrating its high potential for use in wildlife conservation activities.

Effectiveness of strategic anthelmintic treatments in the control of gastrointestinal nematodes and Fasciola gigantica in cattle in Iringa region, Tanzania

A longitudinal field trial was conducted to determine the effectiveness of strategic anthelmintic treatments in the control of gastrointestinal (GI) nematodes and Fasciola gigantica in cattle. A total of 167 cattle (6-18 months) from three large-scale dairy farms, four traditional farms and nine small-scale dairy farms were randomly selected. The selected animals on each farm were ear tagged and allocated into three groups based on live weight and treated as follows: Group T4 was treated with albendazole 10% drench at 10 mg/kg four times a year (mid rainy, end of the rain, mid dry and late dry/early rainy season). Group T2 was treated with albendazole 10% drench at 10 mg/kg two times a year (mid rainy and late dry/early rainy season). Group UT remained as untreated control. Faecal, blood and pasture samples were taken every month for 13 months. In addition, individual body weight (BWT) was measured on every sampling date. Results showed that two and four strategic treatments significantly reduced faecal egg counts (FEC) by 49.5% and 62.3% respectively compared to untreated control animals (P < 0.001). Two and four strategic treatments per year significantly reduced the proportion of animals passing Fasciola eggs in faeces by 30.6% and 51.7% (P < 0.001), respectively. Animals treated two and four times a year significantly outgained untreated animals by 14.8 kg and 17.7 kg respectively at the end of the trial (P < 0.05). The management system had a significant effect on packed cell volume and the proportion of animals passing Fasciola eggs in faeces (P < 0.05). The programme of two strategic treatments per year was only effective in controlling GI nematodes. It is concluded that a programme of four strategic treatments per year was effective in controlling GI nematodes and F. gigantica and improved weight gain.

Cross-sectional prevalence of helminth infections in cattle on traditional, small-scale and large-scale dairy farms in Iringa district, Tanzania

A cross-sectional study was carried out to determine the prevalence of gastrointestinal (GI) nematodes and flukes (Fasciola and amphistomes) infection in communally grazed traditional cattle, zero-grazed small-scale dairy cattle and intensively grazed large-scale dairy cattle through examination of helminth eggs in faeces. Results indicated that the type of management, especially the grazing habit, has a significant influence on the prevalence and intensity of GI nematodes and flukes. The prevalence of GI nematodes in traditional, large-scale dairy and small-scale dairy cattle was 67%, 44.4% and 37%, respectively, with the highest faecal egg counts in calves. The overall prevalence of Fasciola gigantica in traditional, large-scale dairy and small-scale dairy cattle was 63.8%, 46.2% and 28.4%, respectively. The prevalence of amphistomes was 81.9%, 55.5% and 41.1% in traditional, large-scale dairy and small-scale dairy cattle, respectively. The high prevalence of flukes in the traditional system was attributed to communal grazing and watering management practices. Stomach flukes recovered in examined cattle at the abattoir were Calicophoron microbothrium and Cotylophoron jacksoni. About 42.1% of infected animals had both Fasciola and amphistomes. The prevalence of both GI nematodes and flukes varied greatly among villages and farms. The prevalence of both Fasciola and amphistomes was higher in adults (58.5%, 75.2%) than in yearlings (36.5%, 51.5%) or calves (24.9%, 47.2%). The variation in the prevalence of both GI nematodes and flukes among management and age groups within systems can be used as an entry point towards rational use of anthelmintics for each management system. More studies on seasonal transmission pattern of all these parasites are required in order to design rational, economic and locally sustainable parasite control programmes.

Epidemiology of Fasciola gigantica and amphistomes in cattle on traditional, small-scale dairy and large-scale dairy farms in the southern highlands of Tanzania

A longitudinal descriptive study was conducted to determine the prevalence and distribution of flukes (Fasciola gigantica and amphistomes) on traditional, large-scale and small-scale dairy cattle farms in Iringa district, southern highlands of Tanzania. Coprological examinations of different cohorts for the presence of fluke eggs were recorded monthly. Results indicated a significant influence of the type of management on the prevalence of both Fasciola and amphistomes. The prevalence of flukes was highest in the traditional system, moderate in the large-scale dairy system and lowest in the small-scale dairy system in most parts of the year. Adults and yearlings had the highest prevalence of flukes in all management systems throughout the year. The proportion of animals excreting amphistome eggs was always higher than that of animals excreting Fasciola eggs in all zones, villages, management systems, farms and age groups. The proportion of animals passing fluke eggs increased gradually from the early dry season and peaked at the end of the dry season and the early part of the rainy season. Strategic treatments against flukes are recommended in adults and yearlings only in traditional and large-scale dairy farms. Routine treatments of calves/weanlings in large-scale and traditional farms and zero-grazed small-scale dairy cattle farms might be unnecessary. For a cost-effective helminth control programme in the area, strategic treatments at the beginning of the dry season (June) and at the end of the dry/early rainy season (November/December) are recommended.

Epidemiology of gastrointestinal nematodes in cattle on traditional, small-scale dairy and large-scale dairy farms in Iringa district, Tanzania

A longitudinal study was carried out to determine the prevalence, distribution and intensity of gastrointestinal (GI) nematodes in traditional, small-scale dairy and large-scale dairy cattle farms in Iringa district, Southern highlands of Tanzania. Coprological examination of cohorts for GI nematode eggs in faeces, tracer worm counts and pasture larval counts were performed monthly for 1 year. Results indicated that the type of management, especially the grazing habit has a significant influence on the prevalence and intensity of GI nematodes. The predominant nematodes were Cooperia spp. (51.6%), Oesophagostomum radiatum (35.7%) and Haemonchus placei (10.2%). The worm burden in tracers was mainly composed of Cooperia spp. (83%) in large-scale dairy farms, while O. radiatum was dominant (60.8%) in traditional farms. Faecal egg counts (FEC) and tracer worm counts were generally low and FEC peaked only in calves and weaners/yearlings. Adults and all age groups in small-scale dairy farms had very low FEC throughout the year. Pasture larval counts, FEC and tracer worm counts peaked towards the end of the rainy season. Based on conditions of the study area, farmers could save substantial amount of money through strategic treatments as opposed to the previous routine of treating the whole herd at least four times a year. Strategic treatments are recommended in calves and weaners only in traditional and large-scale dairy farms. Strategic treatment of adults and small-scale dairy cattle might be not necessary. Strategic treatments at the end of the rainy/early dry season (May/June) and at the end of the dry/early rainy season (November/December) are recommended in the district. An additional treatment against GI nematodes in calves during the mid rainy season (February/March) might be important.

Gastrointestinal nematodes in indigenous Zebu cattle under pastoral and nomadic management systems in the lower plain of the southern highlands of Tanzania

This study aimed to determine the prevalence and intensity of gastrointestinal nematode infections in indigenous Zebu cattle in the lower plain (lowland zone) of the southern highlands of Tanzania. Gastrointestinal tracts were randomly purchased at the Iringa regional abattoir and at Kihesa and Ipogolo slaughter slabs in different seasons of the year. The contents of the abomasum, small intestine and large intestine were processed separately to recover the worms. The results indicated that 140 out of 144 (97.2%) of the examined animals were infected. The mean (+/-SE) total worm burden was 1284 +/- 183 (range 10-12,600) worms per animal and most infected animals contained more than one nematode species. The nematode species present, their prevalence and mean burden were as follows: Haemonchus placei, 84.7%, 316; H. similis, 5.6%, 1; Oesophagostomum radiatum, 79.2%, 66; Cooperia pectinata, 55.6%, 713; C. punctata, 44.4%, 157; Bunostomum phlebotomum, 5.6%, 5; Trichuris globulosa, 5.6%, 2; and Trichostrongylus colubriformis, 1.4%, 24. The burdens were mainly composed of Cooperia pectinata (55.5%), Haemonchus placei (24.6%), Cooperia punctata (12.3%) and Oesophagostomum radiatum (5.1%). The highest burdens occurred at the end of the rainy/early dry season, while the lowest burdens were found at the end of the dry/early rainy season. There was no difference in the burdens between male and female animals. Immature cattle (< 3 years) had significantly higher worm burdens than mature cattle (p < 0.01). A poor grade for a live animal was associated with higher worm burdens only in immature cattle and then especially during the dry season (r = 0.456, p < 0.001). Anthelmintic treatments in the late rainy/early dry season and early rainy season are recommended in order to prevent outbreaks of helminthosis during the dry season and to reduce carryover of infection into the next rainy season. An additional wet season treatment is advisable in immature cattle, but may not be needed for mature cattle owing to the availability of plenty of mature, good quality pasture.

Worm control practices and anthelmintic usage in traditional and dairy cattle farms in the southern highlands of Tanzania

Worm control practices and anthelmintic usage in 177 cattle farms in Iringa district in the southern highlands of Tanzania was determined through a questionnaire survey. A total of 76 traditional, 92 small-scale dairy and 9 large-scale dairy cattle farms were included in the survey. Results indicated that 87.7% traditional, 97.8% small-scale dairy and 100% large-scale farmers relied solely on the use of anthelmintics, 2.7% traditional farmers used traditional medicines while 9.6% traditional farmers had not any form of worm control practice. Worm infection was ranked the second most important constraint of productivity in cattle in the three production systems. Most farms (57.6% traditional, 35.8% small-scale dairy, 66.7% large-scale dairy) used anthelmintics with a combination of levamisole and oxyclozanide. Benzimidazoles were used only in traditional (25.4%) and small-scale dairy (32.1%) farms while nitroxynil (Trodax) was mostly used in large-scale dairy farms (33.3%). Generally, 40% of farmers treated three or four times a year and the frequency in some farms was surprisingly high for resource poor small-scale farmers. The frequency of anthelmintic treatment was mostly the same regardless of the management system. Treatments in most farms depended on availability of money and drugs and not the epidemiology of parasites. A significant proportion (46.3%, P=0.007) of farmers especially in rural areas failed to follow their pre-planned treatment schedules due to lack of money (86%) and unavailability of drugs (6.6%). Many farmers (58.9%) had used the same type of anthelmintic for four or more consecutive years and 85.3% of them would continue with the same anthelmintic. Farmers in all management systems mostly purchased anthelmintics from private veterinary drug shops and about 43% traditional and 33.3% small-scale dairy farmers mostly in rural areas obtained anthelmintics from village extension officers. Despite the fact that all farmers were aware of worm infection and the associated signs in cattle, 42.5% had poor knowledge on the source of worm infection. Small-scale dairy farmers allowed only a 1-day withdraw period for milk regardless of the type of anthelmintic used and there was no milk and slaughter clearance in traditional farms. It was concluded from this study that worm control in Iringa faces serious constrains and that education of farmers and farm hands is not adequate. Moreover, poor quality control and high price of potent anthelmintics, few extension workers, low income and low education among farmers contributed significantly to erratic worm control practices and anthelmintic usage in peri-urban and rural areas.

Distribution and density of cysticerci of Taenia solium by muscle groups and organs in naturally infected local finished pigs in Tanzania

The distribution and density of cysticerci of Taenia solium among distinct carcass sites was determined in 24 naturally infected finished pigs from Mbulu district, Tanzania. The heart, tongue, internal and external masseters, triceps brachii, lungs, liver, kidneys, psoas, diaphragm and brain of each pig as well as the muscles from the forelimb, hind limb, abdomen, head and thorax from one half of each pig carcass were all designated as distinct carcass sites and sliced in such a way that all fully developed cysts could be revealed and enumerated (i.e. each slice was less than 0.5 cm thick). The carcasses harboured from 76 to 80,340 cysts in total. Carcass sites which harboured the highest proportion of cysts were those of the hind and forelimbs (mean: 27.7 and 24.5%, respectively, of the total cysts in the carcass), while lower proportions were found in the tongue, heart, triceps brachii, and diaphragm (7, 3.6, 2 and 2, respectively). Relative cyst density was calculated for the different carcass sites by dividing the mean proportion of the total weight of the tissue groups into the mean proportion of cysts located in that site. The cysticerci in the examined distinct carcass sites were found in the following order of relative density: psoas muscles (10.5), internal masseter (8.1), external masseter (7.1), triceps brachii (4.9), forelimb (4.0), head muscles (3.8), tongue (3.4), hind limb (3.2), diaphragm (2.4), heart (1.9), abdominal muscles (1.3), trunk muscles (1.1), brain (1.0) and oesophagus (0.3). The proportion of cysts expected to be found at the surfaces exposed by visual examination or incision at meat inspection was calculated using an indirect method, which incorporated the area revealed by incision and visual inspection of an organ and the proportion of cysts located in the particular organ. It was estimated that 10.6% of the cysts would be located at inspected sites if regulations were followed carefully.

Efficacy of albendazole and levamisole against gastrointestinal nematodes of sheep and goats in Morogoro, Tanzania

A study was conducted to determine the efficacy of albendazole after it had been withdrawn from use due to the development of resistant strains of nematodes about ten years ago. The study also aimed to determine the present efficacy of levamisole, which had been recommended to replace albendazole. On one farm, the sheep and goats were divided into two groups, one group of each serving as the untreated control, while the other was treated with levamisole. The sheep on the other farm were divided into three groups, one serving as the untreated control group, the second being treated with levamisole and the third being treated with albendazole. Faecal samples were collected one day before treatment, and again 10 days after treatment. Anthelmintic efficacy was determined by the faecal egg count reduction test. Ten days after treatment, the sheep treated with levamisole on the first farm had a 98% reduction in faecal egg count, with a 95% confidence limit of 76%. The goats on the same farm had a 97% reduction in faecal egg count, with a 95% lower confidence limit of 81%. At the second farm, 10 days after treatment, sheep treated with levamisole had a 99.4% reduction in faecal egg count, with a 95% lower confidence limit of 88.9%, whereas the sheep treated with albendazole only had a 59.4% reduction in faecal egg count, with a 95% lower confidence limit of -19.6%. The study indicated that the gastrointestinal nematodes of sheep at the Department of Animal Science and Production farm were still resistant to albendazole about ten years after this anthelmintic had been withdrawn from use. A reduced efficacy of levamisole was suspected.

Peri-parturient helminthosis in strains of small East African goats in Tanzania

The effect of physiological status (e.g. pregnancy and lactation) on the susceptibility to gastrointestinal nematodes was studied in the Dodoma and Kigoma strains of small East African goats in Morogoro. Forty-six pregnant does (19 Dodoma and 27 Kigoma strain) and 123 non-pregnant/dry (68 Dodoma and 55 Kigoma) from a controlled-breeding programme were used. Does were grazed on naturally contaminated pastures at Sokoine University of Agriculture for 8 months. Faecal samples and whole blood for determination of faecal egg counts (FEC), packed-cell volume (PCV) and blood eosinophils (EOS) from each animal were collected at monthly intervals from the mating period (through the gestation period) to 3 months after kidding. From kidding to 3 months after kidding, lactating does had significantly higher FEC than non-lactating/dry does. From 1 month after kidding to 3 months after kidding, lactating does had significantly lower PCV than dry does. Blood eosinophils were higher in non-lactating/dry does than lactating does but only significant at 3 months after kidding. There were no significant differences in FEC, PCV and EOS between lactating Dodoma and lactating Kigoma does. We concluded that there was no difference in peri-parturient helminthosis between Dodoma and Kigoma strains and that blood eosinophilia decreased during peri-parturient helminthosis in both strains.