Inter-epidemic Rift Valley fever virus infection incidence and risks for zoonotic spillover in northern Tanzania.

Rift Valley fever virus (RVFV) is a mosquito-borne pathogen that has caused epidemics involving people and animals across Africa and the Arabian Peninsula. A number of studies have found evidence for the circulation of RVFV among livestock between these epidemics but the population-level incidence of infection during this inter-epidemic period (IEP) is rarely reported. General force of infection (FOI) models were applied to age-adjusted cross-sectional serological data to reconstruct the annual FOI and population-level incidence of RVFV infection among cattle, goats, and sheep in northern Tanzania from 2009 through 2015, a period without reported Rift Valley fever (RVF) cases in people or animals. To evaluate the potential for zoonotic RVFV spillover during this period, the relationship between village-level livestock RVFV FOI and human RVFV seropositivity was quantified using multi-level logistic regression. The predicted average annual incidence was 72 (95% Credible Interval [CrI] 63, 81) RVFV infections per 10,000 animals and 96 (95% CrI 81, 113), 79 (95% CrI 62, 98), and 39 (95% CrI 28, 52) per 10,000 cattle, sheep, and goats, respectively. There was variation in transmission intensity between study villages, with the highest estimated village-level FOI 2.49% (95% CrI 1.89, 3.23) and the lowest 0.12% (95% CrI 0.02, 0.43). The human RVFV seroprevalence was 8.2% (95% Confidence Interval 6.2, 10.9). Human seropositivity was strongly associated with the village-level FOI in livestock, with the odds of seropositivity in an individual person increasing by around 1.2 times (95% CrI 1.1, 1.3) for each additional annual RVFV seroconversion per 1,000 animals. A history of raw milk consumption was also positively associated with human seropositivity. RVFV has circulated at apparently low levels among livestock in northern Tanzania in the period since the last reported epidemic. Although our data do not allow us to confirm human RVFV infections during the IEP, a strong association between human seropositivity and the FOI in cattle, goats, and sheep supports the hypothesis that RVFV circulation among livestock during the IEP poses a risk for undetected zoonotic spillover in northern Tanzania. We provide further evidence for the likely role of raw milk consumption in RVFV transmission from animals to people.

An outbreak of Rift Valley fever among peri-urban dairy cattle in northern Tanzania.

BACKGROUND: Human and animal cases of Rift Valley fever (RVF) are typically only reported during large outbreaks. The occurrence of RVF cases that go undetected by national surveillance systems in the period between these outbreaks is considered likely. The last reported cases of RVF in Tanzania occurred during a large outbreak in 2007-2008. METHODS: Samples collected between 2017 and 2019 from livestock suffering abortion across northern Tanzania were retrospectively tested for evidence of RVF virus infection using serology and reverse transcription quantitative polymerase chain reaction (RT-qPCR). RESULTS: A total of 14 RVF-associated cattle abortions were identified among dairy cattle in a peri-urban area surrounding the town of Moshi. RVF cases occurred from May to August 2018 and were considered to represent an undetected, small-scale RVF outbreak. Milk samples from 3 of 14 cases (21%) were found to be RT-qPCR positive. Genotyping revealed circulation of RVF viruses from two distinct lineages. CONCLUSIONS: RVF outbreaks can occur more often in endemic settings than would be expected on the basis of detection by national surveillance. The occurrence of RVF cases among peri-urban dairy cattle and evidence for viral shedding in milk, also highlights potentially emerging risks for RVF associated with increasing urban and peri-urban livestock populations.

Prospective cohort study reveals unexpected aetiologies of livestock abortion in northern Tanzania.

Livestock abortion is an important cause of productivity losses worldwide and many infectious causes of abortion are zoonotic pathogens that impact on human health. Little is known about the relative importance of infectious causes of livestock abortion in Africa, including in subsistence farming communities that are critically dependent on livestock for food, income, and wellbeing. We conducted a prospective cohort study of livestock abortion, supported by cross-sectional serosurveillance, to determine aetiologies of livestock abortions in livestock in Tanzania. This approach generated several important findings including detection of a Rift Valley fever virus outbreak in cattle; high prevalence of C. burnetii infection in livestock; and the first report of Neospora caninum, Toxoplasma gondii, and pestiviruses associated with livestock abortion in Tanzania. Our approach provides a model for abortion surveillance in resource-limited settings. Our findings add substantially to current knowledge in sub-Saharan Africa, providing important evidence from which to prioritise disease interventions.

Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance.

Genomic data contribute invaluable information to the epidemiological investigation of pathogens of public health importance. However, whole-genome sequencing (WGS) of bacteria typically relies on culture, which represents a major hurdle for generating such data for a wide range of species for which culture is challenging. In this study, we assessed the use of culture-free target-enrichment sequencing as a method for generating genomic data for two bacterial species: (1) Bacillus anthracis, which causes anthrax in both people and animals and whose culture requires high-level containment facilities; and (2) Mycoplasma amphoriforme, a fastidious emerging human respiratory pathogen. We obtained high-quality genomic data for both species directly from clinical samples, with sufficient coverage (>15×) for confident variant calling over at least 80% of the baited genomes for over two thirds of the samples tested. Higher qPCR cycle threshold (Ct) values (indicative of lower pathogen concentrations in the samples), pooling libraries prior to capture, and lower captured library concentration were all statistically associated with lower capture efficiency. The Ct value had the highest predictive value, explaining 52 % of the variation in capture efficiency. Samples with Ct values ≤30 were over six times more likely to achieve the threshold coverage than those with a Ct > 30. We conclude that target-enrichment sequencing provides a valuable alternative to standard WGS following bacterial culture and creates opportunities for an improved understanding of the epidemiology and evolution of many clinically important pathogens for which culture is challenging.

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.

Molecular detection and genetic characterization of Bartonella species from rodents and their associated ectoparasites from northern Tanzania.

BACKGROUND: Bartonellae are intracellular bacteria, which can cause persistent bacteraemia in humans and a variety of animals. Several rodent-associated Bartonella species are human pathogens but data on their global distribution and epidemiology are limited. The aims of the study were to: 1) determine the prevalence of Bartonella infection in rodents and fleas; 2) identify risk factors for Bartonella infection in rodents; and 3) characterize the Bartonella genotypes present in these rodent and flea populations. METHODS AND RESULTS: Spleen samples collected from 381 rodents representing six different species were tested for the presence of Bartonella DNA, which was detected in 57 individuals (15.0%; 95% CI 11.3-18.5), of three rodent species (Rattus rattus n = 54, Mastomys natalensis n = 2 and Paraxerus flavovottis n = 1) using a qPCR targeting the ssrA gene. Considering R. rattus individuals only, risk factor analysis indicated that Bartonella infection was more likely in reproductively mature as compared to immature individuals (OR = 3.42, p <0.001). Bartonella DNA was also detected in 53 of 193 Xenopsylla cheopis fleas (27.5%: 95% CI 21.3-34.3) collected from R.rattus individuals. Analysis of ssrA and gltA sequences from rodent spleens and ssrA sequences from fleas identified multiple genotypes closely related (≥ 97% similar) to several known or suspected zoonotic Bartonella species, including B. tribocorum, B. rochalimae, B. elizabethae and B. quintana. CONCLUSIONS: The ssrA and gltA sequences obtained from rodent spleens and ssrA sequences obtained from fleas reveal the presence of a diverse set of Bartonella genotypes and increase our understanding of the bartonellae present in Tanzanian. Further studies are needed to fully characterise the prevalence, genotypes and diversity of Bartonella in different host populations and their potential impacts on human health.

Taenia multiceps coenurosis in Tanzania: a major and under-recognised livestock disease problem in pastoral communities.

AbstractA neurological syndrome of small ruminants, known locally as 'ormilo', has been reported among pastoralist livestock keepers in Tanzania. This study was carried out in four affected pastoral communities to determine the prevalence and associated risk factors, characterise the clinical signs and investigate the aetiology of the syndrome. Questionnaires were administered at all households (n=480) within four study villages. Overall, 94 per cent of households reported at least one case in the previous 12 months. By village, the individual-level 12-month period prevalence ranged from 11 per cent to 34 per cent, equivalent to about 10,000 small ruminants across the four villages. Thirty-eight households were randomly selected for further investigation. Proprioceptive deficits and weakness were the most commonly observed clinical signs in affected animals. Brain and spinal cord cysts consistent with Taenia multiceps infection were detected in 32 (82 per cent) of 39 affected animals selected for postmortem examination. Feeding small ruminant brains to dogs was identified as an important risk factor for the syndrome, even in households that did not own dogs. This study confirms cerebral coenurosis as a major cause of small ruminant neurological disease in northern Tanzania and highlights the urgent need for further investigation to quantify the disease burden and to identify and implement control measures.

Assessment of animal hosts of pathogenic Leptospira in northern Tanzania.

Leptospirosis is a zoonotic bacterial disease that affects more than one million people worldwide each year. Human infection is acquired through direct or indirect contact with the urine of an infected animal. A wide range of animals including rodents and livestock may shed Leptospira bacteria and act as a source of infection for people. In the Kilimanjaro Region of northern Tanzania, leptospirosis is an important cause of acute febrile illness, yet relatively little is known about animal hosts of Leptospira infection in this area. The roles of rodents and ruminant livestock in the epidemiology of leptospirosis were evaluated through two linked studies. A cross-sectional study of peri-domestic rodents performed in two districts with a high reported incidence of human leptospirosis found no evidence of Leptospira infection among rodent species trapped in and around randomly selected households. In contrast, pathogenic Leptospira infection was detected in 7.08% cattle (n = 452 [5.1-9.8%]), 1.20% goats (n = 167 [0.3-4.3%]) and 1.12% sheep (n = 89 [0.1-60.0%]) sampled in local slaughterhouses. Four Leptospira genotypes were detected in livestock. Two distinct clades of L. borgpetersenii were identified in cattle as well as a clade of novel secY sequences that showed only 95% identity to known Leptospira sequences. Identical L. kirschneri sequences were obtained from qPCR-positive kidney samples from cattle, sheep and goats. These results indicate that ruminant livestock are important hosts of Leptospira in northern Tanzania. Infected livestock may act as a source of Leptospira infection for people. Additional work is needed to understand the role of livestock in the maintenance and transmission of Leptospira infection in this region and to examine linkages between human and livestock infections.