Biology subjects

Halliday, J. E. B.

Publications and source records attributed to Halliday, J. E. B..

4 recordsLinked to original sources

bioRxiv2022

Target-enrichment sequencing yields valuable genomic data for difficult-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 (>15X) 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 6 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. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. Scripts used in this study can be accessed on GitHub at https://github.com/tristanpwdennis/bactocap. All sequence data generated during this study have been deposited in the European Nucleotide Archive (ENA) Sequence Read Archive (SRA) under project accession numbers PRJEB46822 (B. anthracis) and PRJEB50216 (M. amphoriforme). Accession numbers for individual samples, along with metadata, laboratory parameters and sequence quality metrics, are available at the University of Glasgows data repository, Enlighten, at http://dx.doi.org/10.5525/gla.researchdata.1249.

molecular biology↗

bioRxiv2021

An outbreak of Rift Valley fever among peri-urban dairy cattle in northern Tanzania, 2018

Undetected Rift Valley fever (RVF) outbreaks are expected in endemic countries but little is known about their size or frequency. We describe a previously unreported RVF outbreak involving dairy cattle that appeared to be limited to the edge of the town of Moshi, Tanzania and occurred from May through August, 2018. The outbreak was detected retrospectively using samples collected as part of a cohort study investigating the causes of livestock abortion across northern Tanzania. A total of 14 RVF-associated cattle abortions were identified using a combination of serology and quantitative reverse transcription PCR (RT-qPCR). Milk samples from three (21%) of 14 cases were also RT-qPCR positive. Genotyping revealed circulation of RVF viruses from two lineages. The occurrence of an RVF outbreak among peri-urban dairy cattle, and evidence for RVF viral shedding in milk, highlights the potential for emerging zoonotic risks associated with the growth of urban and peri-urban livestock populations.

ecology↗

bioRxiv2021

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.

systems biology↗

bioRxiv2020

Classification and characterisation of livestock production systems in northern Tanzania

Livestock keepers in sub-Saharan Africa face a growing range of pressures, including climate change, land loss, restrictive policies, and population increase. Widespread adaptation in response to such pressures can lead to the emergence of new, non-traditional typologies of livestock production. We sought to characterise livestock production systems in northern Tanzania, a region undergoing rapid social, economic, and environmental change. Questionnaire and spatial data were collected from 404 livestock-keeping households in 21 villages in Arusha and Manyara Regions in 2016. Multiple factor analysis and hierarchical cluster analysis were used to classify households into livestock production systems based on household-level characteristics. Indicators of vulnerability, including household-level reports of hunger, illness, livestock loss, land loss and crop losses were compared between production systems. Three distinct clusters emerged through this process. The ethnic, environmental and livestock management characteristics of households in each cluster broadly mapped onto traditional definitions of pastoral, agro-pastoral and smallholder livestock production in the region, suggesting that this quantitative classification system is complementary to more qualitative classification methods. Our findings also suggest that traditional systems of livestock production continue to persist in northern Tanzania. Nonetheless, we found indicators of substantial change within livestock production systems, most notably the adoption of crop agriculture in the majority of pastoral households. Smallholder households were less likely than either pastoral or agro-pastoral households to report hunger, illness, and livestock, land or crop losses. Livelihoods that rely solely on livestock are relatively rare in northern Tanzania, which represents an important shift in production in the region, particularly among pastoralists. Policy initiatives to improve household and community well-being should recognise the continuing distinctiveness of traditional livestock production systems in the region.

systems biology↗