Population Structure and Antimicrobial Resistance in Campylobacter jejuni and C. coli Isolated from Humans with Diarrhea and from Poultry, East Africa.

Campylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.

Prevalence and risk factors for Q fever, spotted fever group rickettsioses, and typhus group rickettsioses in a pastoralist community of northern Tanzania, 2016-2017.

BACKGROUND: In northern Tanzania, Q fever, spotted fever group (SFG) rickettsioses, and typhus group (TG) rickettsioses are common causes of febrile illness. We sought to describe the prevalence and risk factors for these zoonoses in a pastoralist community. METHODS: Febrile patients ≥2 years old presenting to Endulen Hospital in the Ngorongoro Conservation Area were enrolled from August 2016 through October 2017. Acute and convalescent blood samples were collected, and a questionnaire was administered. Sera were tested by immunofluorescent antibody (IFA) IgG assays using Coxiella burnetii (Phase II), Rickettsia africae, and Rickettsia typhi antigens. Serologic evidence of exposure was defined by an IFA titre ≥1:64; probable cases by an acute IFA titre ≥1:128; and confirmed cases by a ≥4-fold rise in titre between samples. Risk factors for exposure and acute case status were evaluated. RESULTS: Of 228 participants, 99 (43.4%) were male and the median (interquartile range) age was 27 (16-41) years. Among these, 117 (51.3%) had C. burnetii exposure, 74 (32.5%) had probable Q fever, 176 (77.2%) had SFG Rickettsia exposure, 134 (58.8%) had probable SFG rickettsioses, 11 (4.8%) had TG Rickettsia exposure, and 4 (1.8%) had probable TG rickettsioses. Of 146 participants with paired sera, 1 (0.5%) had confirmed Q fever, 8 (5.5%) had confirmed SFG rickettsioses, and none had confirmed TG rickettsioses. Livestock slaughter was associated with acute Q fever (adjusted odds ratio [OR] 2.54, 95% confidence interval [CI] 1.38-4.76) and sheep slaughter with SFG rickettsioses case (OR 4.63, 95% CI 1.08-23.50). DISCUSSION: Acute Q fever and SFG rickettsioses were detected in participants with febrile illness. Exposures to C. burnetii and to SFG Rickettsia were highly prevalent, and interactions with livestock were associated with increased odds of illness with both pathogens. Further characterisation of the burden and risks for these diseases is warranted.

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

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

Prevalence and risk factors for human leptospirosis at a hospital serving a pastoralist community, Endulen, Tanzania.

BACKGROUND: Leptospirosis is suspected to be a major cause of illness in rural Tanzania associated with close contact with livestock. We sought to determine leptospirosis prevalence, identify infecting Leptospira serogroups, and investigate risk factors for leptospirosis in a rural area of Tanzania where pastoralist animal husbandry practices and sustained livestock contact are common. METHODS: We enrolled participants at Endulen Hospital, Tanzania. Patients with a history of fever within 72 hours, or a tympanic temperature of ≥38.0°C were eligible. Serum samples were collected at presentation and 4-6 weeks later. Sera were tested using microscopic agglutination testing with 20 Leptospira serovars from 17 serogroups. Acute leptospirosis cases were defined by a ≥four-fold rise in antibody titre between acute and convalescent serum samples or a reciprocal titre ≥400 in either sample. Leptospira seropositivity was defined by a single reciprocal antibody titre ≥100 in either sample. We defined the predominant reactive serogroup as that with the highest titre. We explored risk factors for acute leptospirosis and Leptospira seropositivity using logistic regression modelling. RESULTS: Of 229 participants, 99 (43.2%) were male and the median (range) age was 27 (0, 78) years. Participation in at least one animal husbandry practice was reported by 160 (69.9%). We identified 18 (7.9%) cases of acute leptospirosis, with Djasiman 8 (44.4%) and Australis 7 (38.9%) the most common predominant reactive serogroups. Overall, 69 (30.1%) participants were Leptospira seropositive and the most common predominant reactive serogroups were Icterohaemorrhagiae (n = 20, 29.0%), Djasiman (n = 19, 27.5%), and Australis (n = 17, 24.6%). Milking cattle (OR 6.27, 95% CI 2.24-7.52) was a risk factor for acute leptospirosis, and milking goats (OR 2.35, 95% CI 1.07-5.16) was a risk factor for Leptospira seropositivity. CONCLUSIONS: We identified leptospirosis in approximately one in twelve patients attending hospital with fever from this rural community. Interventions that reduce risks associated with milking livestock may reduce human infections.

Novel Escherichia coli-Infecting Bacteriophages Isolated from Uganda That Target Human Clinical Isolates.

Background: The antimicrobial resistance catastrophe is a growing global health threat and predicted to be worse in developing countries. Phages for Global Health (PGH) is training scientists in these regions to isolate relevant therapeutic phages for pathogenic bacteria within their locality, and thus contributing to making phage technology universally available. Materials and Methods: During the inaugural PGH workshop in East Africa, samples from Ugandan municipal sewage facilities were collected and two novel Escherichia coli lytic phages were isolated and characterized. Results: The phages, UP19 (capsid diameter ∼100 nm, contractile tail ∼120/20 nm) and UP30 (capsid diameter ∼70 nm, noncontractile tail of ∼170/20 nm), lysed ∼82% and ∼36% of the 11 clinical isolates examined, respectively. The genomes of UP19 (171.402 kb, 282 CDS) and UP30 (49.834 kb, 75 CDS) closely match the genera Dhakavirus and Tunavirus, respectively. Conclusion: The phages isolated have therapeutic potential for further development against E. coli infections.

Effect of awareness training to frontline health workers and the use of e-based technology on reporting of brucellosis cases in selected pastoral communities, Tanzania: a quasi-experimental study.

INTRODUCTION: Brucellosis is a serious community health problem and endemic disease in Tanzania in both humans and animals. Frontline health workers (FHWs) play a vital role in reporting and hence prevent and control brucellosis in rural settings. This study aims to evaluate the effect of awareness training to frontline health workers and use of electronic technology (e- technology) on reporting of brucellosis cases. METHODS: A quasi-experimental design was implemented in two pastoral communities in eastern part of Tanzania with one as control and another as treatment involving 64 FHWs who were purposively selected from May 2020 to December 2020. A total of 32 FHWs from treatment pastoral community were purposively selected for awareness training, rapid diagnosis using Rose Bengal test (RBT) and use of electronic technology (AfyaData app) for brucellosis reporting while nothing was done in control community. Before and after training information about their knowledge, attitude and practices were collected from all participants using a structured questionnaires uploaded in the mobile phone powered by AfyaData application. Blood samples were collected from 141 febrile patients attending the selected facilities in treatment community. Serum obtained from collected blood were analyzed using RBT and Competitive Enzyme Linked Immunosorbent Assay (c-ELISA) for brucellosis screening and confirmatory, respectively. Results from this analysis were reported back to the health facility using AfyaData app. Chi-square was used to analyze categorical variables and t-test and/Anova test was used to assess the effectiveness of the intervention. RESULTS: Results revealed that before the training majority of the participants were ignorant about brucellosis, although they had good attitude towards brucellosis prevention. Participant's awareness, practice and attitude increased significantly (p = 0.003, p = 0.001, p = 0.032) respectively, after the intervention. Total of 17(12.1%) patients were positive on RBT and four (2.8%) were confirmed by c-ELISA. AfyaData app was proven to provide quick reports regarding brucellosis in the study area. CONCLUSION: The training program was effective in increasing the level of knowledge and practice about brucellosis. Electronic based technology (AfyaData app) improved the reporting of brucellosis cases. There is a need for the use of electronic based technology to improve timely management of brucellosis in pastoral communities. Also, continuous training on FHWs regarding the disease is needed to improved their awareness and practices.

Scent detection of Brucella abortus by African giant pouched rats (Cricetomys ansorgei).

BACKGROUND: Brucellosis is a contagious zoonosis caused by bacteria of the genus Brucella. While the disease has been eradicated in most developed countries, it remains endemic in sub-Saharan Africa where access to reliable diagnostics is limited. African giant pouched rats (Cricetomys ansorgei) have been trained to detect the scent of Mycobacterium tuberculosis to increase case detection in sub-Saharan Africa. Given the similar diagnostic challenges facing brucellosis and tuberculosis, we explored the feasibility of training African giant pouched rats to detect Brucella. RESULTS: After 3 months of training, rats reliably identified cultured Brucella, achieving an average sensitivity of 93.56% (SD = 0.650) and specificity of 97.65% (SD = 0.016). Rats readily generalized to novel, younger Brucella cultures that presumably generated a weaker volatile signal and correctly identified at least one out of three fecal samples spiked with Brucella culture during a final test of feasibility. DISCUSSION: To our knowledge, these experiments are the first to demonstrate Brucella emits a unique odor profile that scent detection animals can be trained to identify. Importantly, cultured E. coli samples were included throughout training and test to ensure the rats learned to specifically identify Brucella bacteria rather than any bacteria in comparison to bacteria-free culture medium. E. coli controls therefore served a crucial function in determining to what extent Brucella abortus emits a unique odor signature. Further research is needed to determine if a Brucella-specific volatile signature is present within clinical samples. If confirmed, the present results suggest trained rats could serve as a valuable, novel method for the detection of Brucella infection.

Distribution and molecular identification of ixodid ticks infesting cattle in Kilombero and Iringa Districts, Tanzania.

BACKGROUND: Hard ticks infesting cattle are vectors of Tick-borne diseases that causes major public health problems and considerable socioeconomic losses to the livestock industry in tropical and subtropical countries. A repeated cross-sectional study was carried out by collecting ticks on cattle during the wet and dry seasons from January to August 2021 in order to determine hard tick prevalence, distribution, and abundance on cattle in Kilombero and Iringa Districts of Tanzania. The collected ticks were identified morphologically using published morphological keys under a stereomicroscope and confirmed by polymerase chain reaction (PCR) and sequencing. RESULTS: Out of 740 examined cattle, 304, (41.08%) were infested with ticks. In total, 1,780 ticks were counted on one side of the animal's body and doubled, whereby resulting in a total of 3,560 ticks were recorded. Individual tick burden ranged from n = 2 to 82 ticks per animal, with a mean tick burden of n = 11.7 ± 0.68 per animal. A total of 1,889 ticks were collected from infected cattle including 109 additional ticks observed while collecting ticks based on the animal's posture when restrained to the ground. Out of 1,889 ticks, nine species from three genera were identified morphologically: 1,377 fit in the genus Rhipicephalus, 459 to the genus of Amblyomma, and 53 to the genus Hyalomma. Rhipicephalus microplus was the most prevalent (n = 909, 48.1%), followed by Rhipicephalus evertsi (n = 310, 16.4%), Amblyomma lepidum (n = 310, 16.4%), Rhipicephalus appendiculatus (n = 140, 7.4%), Amblyomma gemma (n = 120, 6.4%), Hyalomma rufipes (n = 50, 2.6%), Amblyomma variegatum (n = 29, 1.5%), Rhipicephalus decoloratus (n = 18, 1.0%), while the least common was Hyalomma albiparmatum (n = 3, 0.2%). Tick diversity was higher in Iringa compared to Kilombero District. Tick prevalence was higher in wet season (n = 148, 41.11%). Ticks were widely distributed in different parts of the host body, with the highest distribution on zone 4 (n = 1,060, 56.11%), which includes groin, flank, abdomen, and around inner thigh of the hind legs and the lowest distribution on zone 2 (n = 14, 0.74%), which includes the back surface of the body. Both Amblyomma lepidum and Rhipicephalus microplus species were found in all the five body zones, and with the highest proportions recorded on zone 4: A. lepidum (n = 209, 67.42%) and R. microplus (n = 714, 78.55%). The nine tick species identified morphologically were also confirmed using molecular methods. However, during sequencing, two species (Rhipicephalus appendiculatus and R. decoloratus) had poor quality sequences and were excluded from the sequence analysis. Sequencing results indicated high nucleotide identity (96-100%) with sequences available in GenBank and Barcode of Life Database (BOLD). The phylogenetic analysis of partial mitochondrial COI and 16S rRNA gene sequences of ticks were used to confirm the morphological identification. CONCLUSION: The results showed a high burden of tick infestation on cattle, which could reduce animal production and potentially increase the risk of tick-borne diseases. Therefore, it is necessary to explore the epidemiological and molecular aspects of various tick species in other regions of Tanzania.

Integrating contact tracing and whole-genome sequencing to track the elimination of dog-mediated rabies: An observational and genomic study.

Background: Dog-mediated rabies is endemic across Africa causing thousands of human deaths annually. A One Health approach to rabies is advocated, comprising emergency post-exposure vaccination of bite victims and mass dog vaccination to break the transmission cycle. However, the impacts and cost-effectiveness of these components are difficult to disentangle. Methods: We combined contact tracing with whole-genome sequencing to track rabies transmission in the animal reservoir and spillover risk to humans from 2010 to 2020, investigating how the components of a One Health approach reduced the disease burden and eliminated rabies from Pemba Island, Tanzania. With the resulting high-resolution spatiotemporal and genomic data, we inferred transmission chains and estimated case detection. Using a decision tree model, we quantified the public health burden and evaluated the impact and cost-effectiveness of interventions over a 10-year time horizon. Results: We resolved five transmission chains co-circulating on Pemba from 2010 that were all eliminated by May 2014. During this period, rabid dogs, human rabies exposures and deaths all progressively declined following initiation and improved implementation of annual islandwide dog vaccination. We identified two introductions to Pemba in late 2016 that seeded re-emergence after dog vaccination had lapsed. The ensuing outbreak was eliminated in October 2018 through reinstated islandwide dog vaccination. While post-exposure vaccines were projected to be highly cost-effective ($256 per death averted), only dog vaccination interrupts transmission. A combined One Health approach of routine annual dog vaccination together with free post-exposure vaccines for bite victims, rapidly eliminates rabies, is highly cost-effective ($1657 per death averted) and by maintaining rabies freedom prevents over 30 families from suffering traumatic rabid dog bites annually on Pemba island. Conclusions: A One Health approach underpinned by dog vaccination is an efficient, cost-effective, equitable, and feasible approach to rabies elimination, but needs scaling up across connected populations to sustain the benefits of elimination, as seen on Pemba, and for similar progress to be achieved elsewhere. Funding: Wellcome [207569/Z/17/Z, 095787/Z/11/Z, 103270/Z/13/Z], the UBS Optimus Foundation, the Department of Health and Human Services of the National Institutes of Health [R01AI141712] and the DELTAS Africa Initiative [Afrique One-ASPIRE/DEL-15-008] comprising a donor consortium of the African Academy of Sciences (AAS), Alliance for Accelerating Excellence in Science in Africa (AESA), the New Partnership for Africa's Development Planning and Coordinating (NEPAD) Agency, Wellcome [107753/A/15/Z], Royal Society of Tropical Medicine and Hygiene Small Grant 2017 [GR000892] and the UK government. The rabies elimination demonstration project from 2010-2015 was supported by the Bill & Melinda Gates Foundation [OPP49679]. Whole-genome sequencing was partially supported from APHA by funding from the UK Department for Environment, Food and Rural Affairs (Defra), Scottish government and Welsh government under projects SEV3500 and SE0421.

Non-tuberculous mycobacterial pulmonary disease: Awareness survey of front-desk healthcare workers in Northern Tanzania.

Over the past decade, there have been increasing reports of non-tuberculous mycobacteria (NTM) species being implicated in tuberculosis (TB) treatment failure or misdiagnosed as TB. Inadequate awareness of NTM pulmonary disease among healthcare workers (HCWs) may contribute to a low index of suspicion for patients presenting to their hospitals. In this study, we assessed the awareness of NTM pulmonary disease (NTM-PD) among front desk HCWs in Northern Tanzania. A cross-sectional descriptive survey was carried out among front desk HCWs in four administrative regions of Northern Tanzania. A standardized questionnaire was administered to consented participants from four clusters; clinicians, laboratory scientists, nurses, and pharmacists serving TB patients from Regional and District Health Facilities. Each participant was asked a set of questions, scored and the total score for each participant was determined. An awareness score was used to measure the level of awareness. The average score for all participants was estimated including the 95% confidence interval (CI). The overall awareness score was 24.1%, 95% CI 22.0-26.2%. History of training, experience in TB care, level of health facilities, age group, and setting were found to be statistically associated with the level of awareness of study participants. More than two-thirds (67%) of participants believe that pulmonary NTM and TB are clinically similar and 60% are not aware that AFB Microscopy cannot distinguish between the two. Only 13% of participants could mention at least one risk factor for NTM pulmonary disease. The level of awareness of NTM pulmonary disease was poor among HCWs in the surveyed TB clinics. National TB Programs are advised to include a topic on NTM in various on-job TB training packages for HCWs.

Genetic diversity and genomic analysis of G3P[6] and equine-like G3P[8] in children under-five from Southern Highlands and Eastern Tanzania.

Rotavirus group A genomic characterization is critical for understanding the mechanisms of rotavirus diversity, such as reassortment events and possible interspecies transmission. However, little is known about the genetic diversity and genomic relationship of the rotavirus group A strains circulating in Tanzania. The genetic and genomic relationship of RVA genotypes was investigated in children under the age of five. A total of 169 Fecal samples were collected from under-five with diarrhea in Mbeya, Iringa and Morogoro regions of Tanzania. The RVA were screened in children under five with diarrhea using reverse transcription PCR for VP7 and VP4, and the G and P genotypes were determined using Sanger dideoxynucleotide cycle sequencing. Whole-genome sequencing was performed on selected genotypes. The overall RVA rate was 4.7% (8/169). The G genotypes were G3 (7/8) and G6 (1/8) among the 8 RVA positives, while the P genotypes were P[6] (4/8) and P[8] (2), and the other two were untypeable. G3P[6] and G3P[8] were the identified genotype combinations. The genomic analysis reveals that the circulating G3P[8] and G3P[6] isolates from children under the age of five with diarrhea had a DS-1-like genome configuration (I2-R2-C2-M2-axe-N2-T2-E2-H2). The phylogenic analysis revealed that all 11 segments of G3P[6] were closely related to human G3P[6] identified in neighboring countries such as Uganda, Kenya, and other African countries, implying that G3P[6] strains descended from a common ancestor. Whereas, G3P[8] were closely related to previously identified equine-like G3P[P8] from Kenya, Japan, Thailand, Brazil, and Taiwan, implying that this strain was introduced rather than reassortment events. We discovered amino acid differences at antigenic epitopes and N-linked glycosylation sites between the wild type G3 and P[8] compared to vaccine strains, implying that further research into the impact of these differences on vaccine effectiveness is warranted. The phylogenic analysis of VP7 also identified a bovine-like G6. For the first time in Tanzania, we report the emergence of novel equine-like G3 and bovine-like G6 RVA strains, highlighting the importance of rotavirus genotype monitoring and genomic analysis of representative genotypes.

A global analysis of One Health Networks and the proliferation of One Health collaborations.

There has been a renewed focus on threats to the human-animal-environment interface as a result of the COVID-19 pandemic, and investments in One Health collaborations are expected to increase. Efforts to monitor the development of One Health Networks (OHNs) are essential to avoid duplication or misalignment of investments. This Series paper shows the global distribution of existing OHNs and assesses their collective characteristics to identify potential deficits in the ways OHNs have formed and to help increase the effectiveness of investments. We searched PubMed, Google, Google Scholar, and relevant conference websites for potential OHNs and identified 184 worldwide for further analysis. We developed four case studies to show important findings from our research and exemplify best practices in One Health operationalisation. Our findings show that, although more OHNs were formed in the past 10 years than in the preceding decade, investment in OHNs has not been equitably distributed; more OHNs are formed and headquartered in Europe than in any other region, and emerging infections and novel pathogens were the priority focus area for most OHNs, with fewer OHNs focusing on other important hazards and pressing threats to health security. We found substantial deficits in the OHNs collaboration model regarding the diversity of stakeholder and sector representation, which we argue impedes effective and equitable OHN formation and contributes to other imbalances in OHN distribution and priorities. These findings are supported by previous evidence that shows the skewed investment in One Health thus far. The increased attention to One Health after the COVID-19 pandemic is an opportunity to focus efforts and resources to areas that need them most. Analyses, such as this Series paper, should be used to establish databases and repositories of OHNs worldwide. Increased attention should then be given to understanding existing resource allocation and distribution patterns, establish more egalitarian networks that encompass the breadth of One Health issues, and serve communities most affected by emerging, re-emerging, or endemic threats at the human-animal-environment interface.

Prevalence and genomic characterization of rotavirus group A genotypes in piglets from southern highlands and eastern Tanzania.

Animals have been identified as the potential reservoirs of rotavirus group A (RVA) for human infection. However, very little is known regarding the genotype and genomic profiles of circulating RVA in Tanzanian piglets. The rotavirus genetic diversity and genome analysis was assessed among piglets from Southern highlands and Eastern Tanzania. A total of 241 faecal samples were collected from piglets in the regions of Mbeya, Iringa, and Morogoro. RVA was detected and genotyped using reverse transcription polymerase chain reaction (RT-PCR). Sanger dideoxynucleotide cycle sequencing of the viral protein (VP) 4 and VP7 genes was afterwards performed to confirm the RT-PCR results. Selected genotypes were subjected to whole genome sequencing. The overall prevalence of RVA was 35.26% (85/241) in piglets (30.58% in Mbeya, 43.75% in Iringa and 31.16% in Morogoro). Upon genotyping, the G genotypes were G4 (26), G9 (10), G3 (6), G5 (3) and the remaining 40 were untypeable, while the P genotype, were P[6] (35), P[13] (3) and the remaining 47 were untypeable. The G4P[6] were the predominant genotype followed by G3P[6], G3P[13], G4P[13] and G5P[13] were most common genotypes combinations. On phylogenetic analysis, G4 was grouped to lineage V, sublineages VIIa and VIIc, G9 to lineage I, G5 to lineage II, G3 to lineage IV, P[6] to lineage V and sublineage Ic and the P[13] to lineage IV. We revealed amino acid differences between the circulating G4 and the G4 in the ProSystems RCE vaccine used in pigs. The whole genome reveals genomic constellation of G4-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1, G5-P[x]-I5-R1-C1-M1-A8-N1-Tx-E1-H1, G3/G4-P[13]/P[6]-Ix-R1-C1-M1-A8-N1-T1-E1-H1, G3-P[6]-Ix-R1-C1-M1-A8-N1-Tx-E1-H1 and G9-P[x]-Ix-R1-C1-M1-Ax-N1-Tx-E1-H1. The VP7 gene of G9, the VP4 gene of P[6] and NSP4 (E1) gene of some genotypes clustered together and closely related to humans origin or porcine-human reassortant strains with nucleotide similarities ranging from 97.90% to 99.74% from neighboring countries, implying possibility intragenogroup reassortment and interspecies transmission. The higher strain diversity observed within the gene segments highlight the importance of genomic analysis and continuous monitoring of RVA genotypes. Further research is needed to determine the risk factors associated with RVA infection in Tanzanian pigs in order to properly design a control program.

Seasonal shedding of coronavirus by straw-colored fruit bats at urban roosts in Africa.

The straw-colored fruit bat (Eidolon helvum) is a pteropodid whose conservation is crucial for maintaining functional connectivity of plant populations in tropical Africa. Land conversion has pushed this species to adapt to roosting in urban centers across its range. These colonies often host millions of individuals, creating intensive human-bat contact interfaces that could facilitate the spillover of coronaviruses shed by these bats. A better understanding of coronavirus dynamics in these roosts is needed to identify peak times of exposure risk in order to propose evidence-based management that supports safe human-bat coexistence, as well as the conservation of this chiropteran. We studied the temporal patterns of coronavirus shedding in E. helvum, by testing thousands of longitudinally-collected fecal samples from two spatially distant urban roosts in Ghana and Tanzania. Shedding of coronaviruses peaked during the second part of pup weaning in both roosts. Assuming that coronavirus shedding is directly related to spillover risk, our results indicate that exposure mitigation should target reducing contact between people and E. helvum roosts during the pup "weaning" period. This recommendation can be applied across the many highly-populated urban sites occupied by E. helvum across Africa.

Gendered asymmetry of access to knowledge for brucellosis control among pastoral communities in north-west Côte d'Ivoire.

Brucellosis is an infectious zoonotic disease considered as a threat to public health and pastoralist livelihoods. Symptoms of the disease can lead to gender-specific ailments such as abortions in women and orchitis in men. Pastoralists and their families are at high risk of contracting the disease. Access to health information reinforces existing knowledge and contributes to disease prevention. However, in developing countries, interventions for knowledge sharing on zoonotic diseases predominantly target men. This study aimed to describe mechanisms of knowledge production and transfer on brucellosis according to gender, by assessing the way knowledge affects behaviours of pastoral communities. A community-based cross-sectional survey was conducted among a pastoral community (PC) of the Folon region in north-west Côte d'Ivoire. The study included transhumant pastoralists, sedentary livestock owners, shepherds and their wives. By using mixed methods, 26 semi-structured interviews were conducted, and 320 questionnaires were completed. Statistical analysis with chi-square (χ 2) comparison tests was performed to compare variables between men and women. Findings were interpreted through the concept of specialisation of the social exclusion theory. We found that gender influences access to information on brucellosis and transfer of knowledge on brucellosis appeared gender-biased, especially from veterinarians towards men in the community. The social labour division and interventions of veterinarians through awareness reinforce the knowledge gap on brucellosis between men and women. Men and women consume raw milk, whilst only men in general handle animal discharges with bare hands. To improve the control of brucellosis, knowledge on best practice should be shared with pastoral communities using the One Health approach that encourages mutual learning. Innovative strategies based on gender daily tasks such as safe dairy processing by women and safe animal husbandry to expand their herd for men can be the entry point for the prevention of brucellosis.

Rabies shows how scale of transmission can enable acute infections to persist at low prevalence.

How acute pathogens persist and what curtails their epidemic growth in the absence of acquired immunity remains unknown. Canine rabies is a fatal zoonosis that circulates endemically at low prevalence among domestic dogs in low- and middle-income countries. We traced rabies transmission in a population of 50,000 dogs in Tanzania from 2002 to 2016 and applied individual-based models to these spatially resolved data to investigate the mechanisms modulating transmission and the scale over which they operate. Although rabies prevalence never exceeded 0.15%, the best-fitting models demonstrated appreciable depletion of susceptible animals that occurred at local scales because of clusters of deaths and dogs already incubating infection. Individual variation in rabid dog behavior facilitated virus dispersal and cocirculation of virus lineages, enabling metapopulation persistence. These mechanisms have important implications for prediction and control of pathogens that circulate in spatially structured populations.

Development of Dog Vaccination Strategies to Maintain Herd Immunity against Rabies.

Human rabies can be prevented through mass dog vaccination campaigns; however, in rabies endemic countries, pulsed central point campaigns do not always achieve the recommended coverage of 70%. This study describes the development of a novel approach to sustain high coverage based on decentralized and continuous vaccination delivery. A rabies vaccination campaign was conducted across 12 wards in the Mara region, Tanzania to test this approach. Household surveys were used to obtain data on vaccination coverage as well as factors influencing dog vaccination. A total 17,571 dogs were vaccinated, 2654 using routine central point delivery and 14,917 dogs using one of three strategies of decentralized continuous vaccination. One month after the first vaccination campaign, coverage in areas receiving decentralized vaccinations was higher (64.1, 95% Confidence Intervals (CIs) 62.1-66%) than in areas receiving pulsed vaccinations (35.9%, 95% CIs 32.6-39.5%). Follow-up surveys 10 months later showed that vaccination coverage in areas receiving decentralized vaccinations remained on average over 60% (60.7%, 95% CIs 58.5-62.8%) and much higher than in villages receiving pulsed vaccinations where coverage was on average 32.1% (95% CIs 28.8-35.6%). We conclude that decentralized continuous dog vaccination strategies have the potential to improve vaccination coverage and maintain herd immunity against rabies.

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.

Brucellosis testing patterns at health facilities in Arusha region, northern Tanzania.

BACKGROUND: Brucellosis is listed as one of six priority zoonoses in Tanzania's One Health strategic plan which highlights gaps in data needed for the surveillance and estimation of human brucellosis burdens. This study collected data on current testing practices and test results for human brucellosis in Arusha region, northern Tanzania. METHODS: Retrospective data were extracted from records at 24 health facilities in Arusha region for the period January 2012 to May 2018. Data were captured on: the test reagents used for brucellosis, procurement and testing protocols, the monthly number of patients tested for brucellosis and the monthly number testing positive. Generalised linear mixed models were used to evaluate relationships between health facility characteristics and the probability that brucellosis testing was conducted in a given month, and the proportion of individuals testing positive. RESULTS: Four febrile Brucella agglutination tests were used widely. The probability of testing for brucellosis in a given month was significantly associated with an interaction between year of testing and facility ownership. Test probability increased over time with more pronounced increases in privately owned as compared to government facilities. The proportion of individuals testing positive for brucellosis was significantly associated with facility type and district, with individuals tested in hospitals in Meru, Monduli and Ngorongoro districts more likely to test positive. CONCLUSIONS: Febrile Brucella agglutination tests, known for their poor performance, were the mainstay of brucellosis testing at health facilities in northern Tanzania. The study indicates that historical data on human brucellosis in Arusha and other regions are likely to provide an inaccurate measure of true disease burden due to poor performance of the tests used and variation in testing practices. Measures to address these identified shortcomings could greatly improve quality of testing and surveillance data on brucellosis and ultimately inform prevention and control of this priority disease.

Drug susceptibility profiles and factors associated with non-tuberculous mycobacteria species circulating among patients diagnosed with pulmonary tuberculosis in Tanzania.

BACKGROUND: While most Non-tuberculous mycobacteria (NTM) are saprophytic, several species have been associated with human diseases, from localized infection to disseminated diseases. Pulmonary NTM infections lead to TB-like disease called NTM pulmonary disease (NTM-PD). Due to variation in treatment options among NTM species, it is necessary to identify the species and determine drug susceptibility profiles to inform the choice of appropriate regimen for the disease. DESIGN: A total of 188 culture-positive isolates from patients diagnosed with TB were screened for NTM at the Central Tuberculosis Reference Laboratory. All NTM were further speciated using GenoType® Mycobacterium-Common Mycobacterium and Additional species (GenoType® CM/AS) kit. Mycobacteria avium complex (MAC) and Mycobacteria abscessus complex (MABC) which could not be identified with the test to species were subjected to GenoType® Mycobacteria NTM-DR for further speciation. Using the same test, identified MAC and MABC were genotyped to determine the drug susceptibility profile for each isolate to macrolide and aminoglycosides. RESULTS: Of all isolates identified as mycobacteria, 24 (13%) were NTM. Fifteen isolates could be identified to species level of which prevalent species was M. avium sub. intracellulare 4 (27%). A total of 10 isolates were MAC (n = 6) and MABC (n = 4) were subjected to GenoType® Mycobacteria NTM-DR for determination of macrolide and aminoglycoside susceptibility. Three of the four MABC had a mutation at the T28 position of the erm (41). All MAC were susceptible to both drugs. CONCLUSION: In this study, MAC was the most frequently isolated NTM species followed by MABC. While all MAC and MABC identified, were susceptible to aminoglycosides, three MABC were resistant to the macrolides due to mutation at position 28 of the erm (41) gene. For this, it is important for clinicians need to rule out NTM, understand species and their drug susceptibility for optimal case management.