Supplementary text 1.1: Filter Sensitivity Analysis. Supplementary text 1.2: Investigating Highly Distinct Isolates. Supplementary text 1.3: Temporal Signal. Supplementary text 1.4: Hierarchical Model Selection. Supplementary text 1.5: Influence of the Priors. Table S1. Results from investigating highly distinct isolates. Table S2. Results from hierarchical model selection. (DOCX 36Â kb

Brent Paterson (3755230)

Desmond Collins (3755233)

Geoffrey de-Lisle (3755224)

Joseph Crispell (3755236)

Marian Price-Carter (2412403)

Mark Neill (3755221)

Paul Livingstone (3755227)

Roman Biek (21981)

Rowland Kao (330135)

Ruth Zadoks (2589703)

Samantha Lycett (3311286)

Simon Harris (137272)

BMC Genomics

PubMed

Joseph Crispell

Ruth N. Zadoks

Simon R. Harris

Brent Paterson

Desmond M. Collins

Geoffrey W. de-Lisle

Paul Livingstone

Mark A. Neill

Roman Biek

Samantha J. Lycett

Rowland R. Kao

Marian Price-Carter

Springer - Publisher Connector

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

BACKGROUND: Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being incorporated into routine bTB surveillance.RESULTS: A high rate of exchange was evident between the sampled wildlife and cattle populations but directional estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing methods, acts to endorse WGS as a typing tool.CONCLUSIONS: In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with the low prevalence of bTB in New Zealand's cattle population it is likely that, currently, wildlife populations are acting as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular typing data. The substitution rates estimated here will be an important part of epidemiological investigations using WGS data.</p

Crispell, Joseph

Zadoks, Ruth N.

Harris, Simon R.

Paterson, Brent

Collins, Desmond M

de-Lisle, Geoffrey W

Livingstone, Paul

Neill, Mark A

Biek, Roman

Lycett, Samantha J.

Kao, Rowland R.

Price-Carter, Marian

Edinburgh Research Explorer

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

FigShare

Additional file 1: of Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

Background: Bovine tuberculosis (bTB), caused by Mycobacterium bovis, is an important livestock disease raising public

health and economic concerns around the world. In New Zealand, a number of wildlife species are implicated in the

spread and persistence of bTB in cattle populations, most notably the brushtail possum (Trichosurus vulpecula). Whole

Genome Sequenced (WGS) M. bovis isolates sourced from infected cattle and wildlife across New Zealand were

analysed. Bayesian phylogenetic analyses were conducted to estimate the substitution rate of the sampled population

and investigate the role of wildlife. In addition, the utility of WGS was examined with a view to these methods being

incorporated into routine bTB surveillance.

Results: A high rate of exchange was evident between the sampled wildlife and cattle populations but directional

estimates of inter-species transmission were sensitive to the sampling strategy employed. A relatively high substitution

rate was estimated, this, in combination with a strong spatial signature and a good agreement to previous typing

methods, acts to endorse WGS as a typing tool.

Conclusions: In agreement with the current knowledge of bTB in New Zealand, transmission of M. bovis between

cattle and wildlife was evident. Without direction, these estimates are less informative but taken in conjunction with

the low prevalence of bTB in New Zealand’s cattle population it is likely that, currently, wildlife populations are acting

as the main bTB reservoir. Wildlife should therefore continue to be targeted if bTB is to be eradicated from New

Zealand. WGS will be a considerable aid to bTB eradication by greatly improving the discriminatory power of molecular

typing data. The substitution rates estimated here will be an important part of epidemiological investigations using

WGS data

Collins, Desmond M.

de-Lisle, Geoffrey W.

Neill, Mark A.

Enlighten

English

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

Crossref

http://dx.doi.org/10.1186/s12864-017-3569-x

Additional file 1: of Using whole genome sequencing to investigate transmission in a multi-host system: bovine tuberculosis in New Zealand

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