Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

Crispell, Joseph; Zadoks, Ruth N.; Harris, Simon R.; Paterson, B.M.; Collins, Desmond M.; Delisle, G. W.; Livingstone, Paul G; Neill, Mark A.; Biek, Roman; Lycett, Samantha; Kao, Rowland R.; Price-Carter, Marian

doi:10.1186/s12864-017-3569-x

Cited by 84 publications

(118 citation statements)

References 56 publications

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“…These additional SNPs may help evade the host immune responses to be able to infect more number of hosts. Hence, these observations can be attributed to the fact that M.bovis isolates belonging to NZ population are capable of zoonoses, which is in agreement with BTB infection in New Zealand reported by Crispell et al [47].…”

Section: Discussionsupporting

confidence: 89%

“…This indicated a rapidly evolving population, that is usually responsible for underlying subpopulations giving rise to heterogeneity within the population. This heterogeneous population is found to be polyphyletic in the distance-based tree and also has the capability of infecting hosts other than cattle as reported by Crispell et al [47]. UK isolates although were found to be sharing SNPs with other population M.bovis isolates, their occurrence was sporadic and were found as a monophyletic clade in the distance-based tree.…”

Section: Discussionsupporting

confidence: 60%

“…These polymorphisms could be used by other TB researchers for further addition and future reference of SNPs based on their unique rsids. The current study is the rst report of a comparative analysis of JVC approach versus single isolate variant detection in prokaryotes using homogenous and heterogenous cohort data, namely, M.bovis United Kingdom, henceforth abbreviated as UK [45,46], and New Zealand (NZ) isolates [47] respectively. JVC approach promises to improve consistency with fewer artefacts, and hence, more accurate variants were detected for homogenous as well as heterogeneous distribution of population [37,48], that have the potential to be used as biomarkers for diagnostics and treatment purposes apart from aiding in improvising our understanding of the pathogen in each population.…”

Section: Introductionmentioning

confidence: 99%

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Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

Banerjee¹,

Balamurugan²,

Joshi³

2020

Preprint

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BackgroundMycobacterium tuberculosis var. bovis is one of the causative agents of Tuberculosis primarily known to infect cattle and is a member of the Mycobacterium Tuberculosis Complex. M.bovis is zoonotic and infects human and other animals resulting in immense economic losses globally. M.bovis is often misdiagnosed and becomes a challenge for treatment and recovery, as M.bovis is intrinsically resistant to certain antibiotics. Hence, the need for accurate diagnostics for zoonotic tuberculosis. ResultsIn order to discern the differences which lie between M.tuberculosis and M.bovis isolates we collected a global collection of M.bovis isolates from NCBI and carried out variant identification studies keeping M.tuberculosis as the reference. Clustering approaches like Principal component analysis and distance-based UPGMA methods helped to segregate isolates into different clusters of homogeneous and heterogeneous populations, which were further analyzed for variant identification. Methods like Joint Variant Calling using population-based studies was adopted for the M.bovis strains, which helped to discern high confidence polymorphisms for each set of populations. Four different variant callers were used to predict SNPs present in their genomic regions. Based on the predicted SNPs, M.bovis samples isolated from New-Zealand were identified as a heterogeneous fast evolving population, whereas the UK samples were identified as a slow evolving homogeneous population. The core-SNP identified for each population revealed the “fixed” mutations present within the populations, whereas, the total-SNP for heterogeneous population indicated presence of clonal subpopulations. A methodology for assignment of genomic coordinates to the reference SNP cluster id of M.tuberculosis entries in dbSNP was also developed and implemented, which helped to identify the percentage of known variants in a population. ConclusionsPopulation-specific studies for global collection of M.bovis samples aided in identification of SNPs responsible for zoonosis. The core-SNP set identified across global M.bovis isolates provide a rationale for further studies to the underlying host-tropism along with aiding in as a robust genetic biomarker for distinguishing M.bovis form M.tuberculosis in addition to the already known RDs. The variation profile reported in this study can serve as potential biomarkers for identification of M.bovis isolates and provide a rationale for further studies to the underlying host-tropism.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionsupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

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Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

Banerjee¹,

Balamurugan²,

Joshi³

2020

Preprint

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“…More recently, studies based on WGS have brought deeper insights into the population dynamics of M. bovis and showed that unlike M. tuberculosis , wild animals act as M. bovis reservoirs in different regions of the world [15-18]. However, most studies using WGS have aimed at investigating local epidemics, and little is known about the global population structure and evolutionary history of M. bovis .…”

Section: Background and Objectivesmentioning

confidence: 99%

An African origin forMycobacterium bovis

Loiseau

Menardo

Aseffa

et al. 2019

Preprint

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Lay Summary: Mycobacterium bovis and M. caprae are both the most important agents 37 of tuberculosis in livestock and zoonotic tuberculosis in humans. Using phylogenetic and 38 molecular clock inferences based on an extensive collection of whole-genome sequences 39 we provide new insights into the global population structure, phylogeography and 40 evolutionary history of these pathogens. 41 42 Word count abstract: 180 43 Word count main text: 4366 44 Number of Figures: 3 45 46 ABSTRACT 47 48 Background and objectives 49 Mycobacterium bovis and Mycobacterium caprae are the two most important agents of 50 tuberculosis (TB) in livestock and the most important causes of zoonotic TB in humans. 51However, little is known about the global population structure, phylogeography and 52 evolutionary history of these pathogens. 53 Methodology 54We compiled a global collection of 3364 whole-genome sequences from M. bovis and M. 55 caprae originating from 35 countries and inferred their phylogenetic relationships, geographic 56 origins and age. 57 Results 58Our results resolve the phylogenetic relationship among the four previously defined clonal 59 complexes of M. bovis, and another eight newly described here. Our inferences indicate that 60 M. bovis emerged in East Africa likely between the 4 th and 10 th century. While some M. bovis 61 groups remained restricted to East-and West Africa, others have subsequently dispersed to 62 different parts of the world. 63 Conclusions and implications 64Our results allow a better understanding of the global population structure of M. bovis and its 65 evolutionary history. This knowledge can be used to define better molecular markers for 66 epidemiological investigations in settings where whole genome sequencing cannot easily be 67 implemented. 68 69 70 BACKGROUND AND OBJECTIVES 71 Tuberculosis (TB) remains an important burden for global health and the economy [1]. TB is 72 the number one cause of human death due to infection globally, with an estimated 10.0 73 million new cases and 1.6 million deaths occurring every year [1]. TB is caused by members 74 of the Mycobacterium tuberculosis complex (MTBC), which includes seven human-adapted 75 lineages, and several animal-adapted ecotypes including M. bovis and M. caprae. Animal TB 76 complicates the control of human TB due to the zoonotic transfer of TB bacilli from infected 77 animals to exposed human populations through e.g. the consumption of unpasteurized milk or 78 handling of contaminated meat [2]. M. bovis and M. caprae are the most important agents of 79 TB in livestock and the most important agents of zoonotic TB in humans, causing at least 147 80 000 new human cases and 12 500 deaths yearly [1, 3]. Zoonotic TB caused by M. bovis also 81 poses a challenge for patient treatment, due to its natural resistance to pyrazinamide (PZA), 82 one of the four first-line drugs used in the treatment of TB. In addition, TB in livestock 83 accounts for an estimated loss of three billion US dollars per year [4]. In Africa its prevalence 84 is highes...

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“…Another extension of the model may include the clinical and molecular data of the infected animals. But adding molecular data will require more investigation how to find who infects whom parameters from the phylogenetic analysis (62,63). The current model is adaptive in nature to add strain specific data for each individual animal.…”

Section: Methodsmentioning

confidence: 99%

A Data-driven Individual-based Model of Infectious Disease in Livestock Operation: A Validation Study for Paratuberculosis

Al-Mamun

Smith

Nigsch

et al. 2018

Preprint

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24Chronic livestock diseases cause large financial loss and affect the animal health and welfare. 25Controlling these diseases mostly requires precise information on both individual animal and 26 population dynamics to inform farmer's decision. Mathematical models provide opportunities to 27 test different control and elimination options rather implementing them in real herds, but these 28 models require valid parameter estimation and validation. Fitting these models to data is a 29 difficult task due to heterogeneities in livestock processes. In this paper, we develop an 30 infectious disease modeling framework for a livestock disease (paratuberculosis) that is caused 31 by Mycobacterium avium subsp. paratuberculosis (MAP). Infection with MAP leads to reduced 32 milk production, pregnancy rates, and slaughter value and increased culling rates in cattle and 33 causes significant economic losses to the dairy industry in the US. These economic effects are 34 particularly important motivations in the control and elimination of MAP. In this framework, an 35 individual-based model (IBM) of a dairy herd was built and a MAP infection was integrated on 36 top of it. Once the model produced realistic dynamics of MAP infection, we implemented an 37 evaluation method by fitting it to data from three dairy herds from the Northeast region of the 38 US. The model fitting exercises used least-squares and parameter space searching methods to 39 obtain the best-fitted values of selected parameters. The best set of parameters were used to 40 model the effect of interventions. The results show that the presented model can complement 41 real herd statistics where the intervention strategies suggested a reduction in MAP but no 42 elimination was observed. Overall, this research not only provides a complete model for MAP 43 infection dynamics in a cattle herd, but also offers a method for estimating parameter by fitting 44 IBM models.45 46 47 48 Chronic livestock diseases like paratuberculosis (PTB) and bovine tuberculosis (bTB) are 49 commonly reported worldwide (1,2). Bovine TB is caused by the pathogen Mycobacterium bovis 50 (M. bovis) while PTB is caused by Mycobacterium avium subsp. paratuberculosis (MAP). In the 51UK, bTB has been spreading over the last two decades, putatively due to the presence of a 52 wildlife reservoir in badgers(3). In United States (US), 68% of dairy herds have apparently at least 53 one cow that is infected with MAP (4). Both diseases pose a potential threat not only to animal 54 health and production, but also to public health. Historically, bTB has been a contributor to 55 human TB cases worldwide and PTB infections in humans have been associated with an 56 increased risk of Crohn's disease in humans(5). Recently, it has been reported that these 57 diseases may induce additional collateral risks for public health due to dispensed antibiotics as 58 a treatment in some cases can potentially contribute to the spread of antibiotic resistance(6). 60In the US cattle industry, the cost of PTB was estimated at...

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Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

Cited by 84 publications

References 56 publications

Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

Exploring the zoonotic potential of Mycobacterium bovis using variant calling approaches

An African origin forMycobacterium bovis

A Data-driven Individual-based Model of Infectious Disease in Livestock Operation: A Validation Study for Paratuberculosis

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