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Kate M. Thomas

Bio: Kate M. Thomas is an academic researcher from University of Otago. The author has contributed to research in topics: Food safety & One Health. The author has an hindex of 6, co-authored 15 publications receiving 90 citations.

Papers
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Journal ArticleDOI
TL;DR: Widespread prevalence of Campylobacter species and Salmonella serovars in African food animals and meat, particularly in samples of poultry and pig origin is demonstrated.

74 citations

Journal ArticleDOI
TL;DR: Risk factors identified for brucellosis included age and herding, with a greater probability of bru cellosis in individuals with lower age and who herded cattle, sheep or goats in the previous 12 months, and disease prevention activities targeting young herders have potential to reduce the impacts of human Brucellosis in Tanzania.
Abstract: Brucellosis is an endemic zoonosis in sub-Saharan Africa. Pastoralists are at high risk of infection but data on brucellosis from these communities are scarce. The study objectives were to: estimate the prevalence of human brucellosis, identify the Brucella spp. causing illness, describe non-Brucella bloodstream infections, and identify risk factors for brucellosis in febrile patients from a pastoralist community of Tanzania. Fourteen (6.1%) of 230 participants enrolled between August 2016 and October 2017 met study criteria for confirmed (febrile illness and culture positivity or ≥four-fold rise in SAT titre) or probable (febrile illness and single SAT titre ≥160) brucellosis. Brucella spp. was the most common bloodstream infection, with B. melitensis isolated from seven participants and B. abortus from one. Enterococcus spp., Escherichia coli, Salmonella enterica, Staphylococcus aureus and Streptococcus pneumoniae were also isolated. Risk factors identified for brucellosis included age and herding, with a greater probability of brucellosis in individuals with lower age and who herded cattle, sheep or goats in the previous 12 months. Disease prevention activities targeting young herders have potential to reduce the impacts of human brucellosis in Tanzania. Livestock vaccination strategies for the region should include both B. melitensis and B. abortus.

27 citations

Journal ArticleDOI
15 Oct 2019-PLOS ONE
TL;DR: The ssrA and gltA sequences obtained from rodent spleens and sSRA sequences from fleas reveal the presence of a diverse set of Bartonella genotypes and increase the understanding of the bartonellae present in Tanzanian.
Abstract: Three excel files that include rodent, flea and genotype level data (as indicated in file names). These together provide the source data for the work presented in the paper.

17 citations

Journal ArticleDOI
TL;DR: The findings suggest N. caninum is likely to be an important cause of abortion in cattle in Tanzania and management practices, such as restricted grazing, are likely to reduce the risk of infection and suggest contamination of communal grazing areas may be important for transmission.
Abstract: Neospora caninum is a protozoan intracellular parasite of animals with a global distribution. Dogs act as definitive hosts, with infection in cattle leading to reproductive losses. Neosporosis can be a major source of income loss for livestock keepers, but its impacts in sub-Saharan Africa are mostly unknown. This study aimed to estimate the seroprevalence and identify risk factors for N. caninum infection in cattle in northern Tanzania, and to link herd-level exposure to reproductive losses. Serum samples from 3,015 cattle were collected from 380 households in 20 villages between February and December 2016. Questionnaire data were collected from 360 of these households. Household coordinates were used to extract satellite derived environmental data from open-access sources. Sera were tested for the presence of N. caninum antibodies using an indirect ELISA. Risk factors for individual-level seropositivity were identified with logistic regression using Bayesian model averaging (BMA). The relationship between herd-level seroprevalence and abortion rates was assessed using negative binomial regression. The seroprevalence of N. caninum exposure after adjustment for diagnostic test performance was 21.5% [95% Credibility Interval (CrI) 17.9–25.4]. The most important predictors of seropositivity selected by BMA were age greater than 18 months [Odds ratio (OR) = 2.17, 95% CrI 1.45–3.26], the local cattle population density (OR = 0.69, 95% CrI 0.41–1.00), household use of restricted grazing (OR = 0.72, 95% CrI 0.25–1.16), and an increasing percentage cover of shrub or forest land in the environment surrounding a household (OR = 1.37, 1.00–2.14). There was a positive relationship between herd-level N. caninum seroprevalence and the reported within-herd abortion rate (Incidence Rate Ratio = 1.03, 95% CrI 1.00–1.06). Our findings suggest N. caninum is likely to be an important cause of abortion in cattle in Tanzania. Management practices, such as restricted grazing, are likely to reduce the risk of infection and suggest contamination of communal grazing areas may be important for transmission. Evidence for a relationship between livestock seropositivity and shrub and forest habitats raises questions about a potential role for wildlife in the epidemiology of N. caninum in Tanzania.

17 citations

Journal ArticleDOI
TL;DR: The findings suggest that the meat pathway may be an important source of human infection by some clades of Salmonella Enteritidis ST11 in East Africa, but not of humanSalmonella Typhimurium ST313 infection.
Abstract: BACKGROUND Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood. METHODS We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity. RESULTS We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources. CONCLUSIONS Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313. Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.

14 citations


Cited by
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01 Jun 2012
TL;DR: SPAdes as mentioned in this paper is a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler and on popular assemblers Velvet and SoapDeNovo (for multicell data).
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

10,124 citations

01 Jan 2013
TL;DR: In this paper, the authors present methods for the meta-analysis of prevalence of multiple sclerosis using logit and double arcsine transformations to stabilise the variance and propose solutions to the problems that arise.
Abstract: Meta-analysis is a method to obtain a weighted average of results from various studies. In addition to pooling effect sizes, meta-analysis can also be used to estimate disease frequencies, such as incidence and prevalence. In this article we present methods for the meta-analysis of prevalence. We discuss the logit and double arcsine transformations to stabilise the variance. We note the special situation of multiple category prevalence, and propose solutions to the problems that arise. We describe the implementation of these methods in the MetaXL software, and present a simulation study and the example of multiple sclerosis from the Global Burden of Disease 2010 project. We conclude that the double arcsine transformation is preferred over the logit, and that the MetaXL implementation of multiple category prevalence is an improvement in the methodology of the meta-analysis of prevalence.

725 citations

13 Nov 2018
TL;DR: In this paper, foodborne disease (FBD) in low and middle income countries (LMICs) is still limited, but important studies in recent years have broadened our understanding, suggesting that developing country consumers are concerned about FBD; that most of the known burden of FBD disease comes from biological hazards; and, most FBD is the result of consumption of fresh, perishable foods sold in informal markets.
Abstract: Evidence on foodborne disease (FBD) in low and middle income countries (LMICs) is still limited, but important studies in recent years have broadened our understanding. These suggest that developing country consumers are concerned about FBD; that most of the known burden of FBD disease comes from biological hazards; and, that most FBD is the result of consumption of fresh, perishable foods sold in informal markets. FBD is likely to increase in LMICs as the result of massive increases in the consumption of risky foods (livestock and fish products and produce) and lengthening and broadening value chains. Although intensification of agricultural production is a strong trend, so far agro-industrial production and modern retail have not demonstrated clear advantages in food safety and disease control. There is limited evidence on effective, sustainable and scalable interventions to improve food safety in domestic markets. Training farmers on input use and good practices often benefits those farmers trained, but has not been scalable or sustainable, except where good practices are linked to eligibility for export. Training informal value chain actors who receive business benefits from being trained has been more successful. New technologies, growing public concern and increased emphasis on food system governance can also improve food safety.

154 citations

Book ChapterDOI
28 Jul 2021

69 citations

Journal ArticleDOI
TL;DR: Three practical actions to minimize the impact of future pandemics are explored: better surveillance of pathogen spillover and development of global databases of virus genomics and serology, better management of wildlife trade, and substantial reduction of deforestation.
Abstract: The lives lost and economic costs of viral zoonotic pandemics have steadily increased over the past century. Prominent policymakers have promoted plans that argue the best ways to address future pandemic catastrophes should entail, “detecting and containing emerging zoonotic threats.” In other words, we should take actions only after humans get sick. We sharply disagree. Humans have extensive contact with wildlife known to harbor vast numbers of viruses, many of which have not yet spilled into humans. We compute the annualized damages from emerging viral zoonoses. We explore three practical actions to minimize the impact of future pandemics: better surveillance of pathogen spillover and development of global databases of virus genomics and serology, better management of wildlife trade, and substantial reduction of deforestation. We find that these primary pandemic prevention actions cost less than 1/20th the value of lives lost each year to emerging viral zoonoses and have substantial cobenefits.

68 citations