New Statistical Methods for Integrating Epidemic and Genetic Data Within Spatio-Temporal Models Help to Control the Spread of Mycoplasma Bovis in New Zealand.

Description of impact

Methods for the simultaneous estimation of epidemic dynamics and pathogen evolution developed by researchers at Heriot Watt University were incorporated into a user-friendly computer package BORIS by scientists from the University of Melbourne.
From July 2018, the BORIS package has been used as an analytic tool within the New Zealand Ministry of Primary Industries (MPI) eradication programme for Mycoplasma Bovis, a bacterial disease that affects dairy and beef cattle, estimated to cost a total of NZD886,000,000. Specifically, BORIS has been used to identify potential times and sources for observed infections so that risk factors for transmission, or potential failures in biosecurity can be identified.
The eradication programme has been highly effective with only 4 premises out of more than 20,000 having active disease in July 2020 and infection having been successfully cleared from 246 premises by that time.

Narrative

Mycoplasma bovid is a bacterial disease that affects dairy and beef cattle, causing severe illness with major impact on production.
It is a disease of major significance to the New Zealand farming industry, which represents the second largest export market for the country.
The New Zealand epidemic was first detected in 2017, following which a major eradication programme was announced in May 2018. The total cost of the programme was estimated to be NZD886,000,000 (05-2018) [around GBP470,000,000], including NZD16,000,000 in lost production and NZD870,000,000 of response costs needed to fight the cattle disease over a 10-year period. According to researchers, had the epidemic been allowed to proceed unchecked the cost would have been approximately NZD1,300,000,000 (05-2018) [around GBP689,000,000] over 10 years, with ongoing productivity losses across the New Zealand farming sector.

As part of a wider programme of epidemiological work that included support (approximately AUD70,000) from New Zealand’s Ministry of Primary Industries (MPI), Firestone and colleagues developed a computer package BORIS (Bayesian Outbreak Reconstruction Inference and Simulation) which incorporated the methods of with the additional capacity to accommodate contact data and farm-level covariates. According to the team who developed BORIS, “The main benefits provided by your algorithm derive from its capacity to fit epidemic dynamics and pathogen phylodynamics within an integrated framework, to represent multiple introductions, and to cope with partial sampling scenarios – essentially allowing the state of unobserved nodes in a network to be inferred”.

The BORIS package, code for which is now freely available from GitHub, has subsequently been applied within the M bovis eradication programme since July 2018 as one of a suite of analytic tools, to analyse epidemiological and genomic data in order to inform the government of the timing of likely introduction of M bovis into New Zealand, whether there were multiple introductions, and the extent to which the case network could be determined. Specifically, BORIS is used to infer timing of infections, infectious periods for farms, and to identify likely transmission routes (who-infected-whom) for the ongoing epidemic. Such insights serve to identify possible infector-infectee links, and corresponding time periods, that should be scrutinised in order to understand the potential risk factors, or failures in biosecurity, that may lead to transmission of the disease. Unlike competing genomic methods, BORIS has the capacity to impute chains of infection that include farms for which genetic data on the pathogen may not be available.

Results of these analyses are key to providing confidence to MPI of their understanding of the outbreak. Since the eradication programme was initiated, the epidemic has been successfully controlled to the extent where, as of July 2020 (resp. November 2020), there were only 4 (resp. 6) properties (out of more than 20,000 dairy and beef farms) in New Zealand where the disease was known to be active, having been successfully cleared from 246 premises by that time. BORIS continues to be used as a decision-support tool for guiding surveillance teams within the programme as it moves towards eradication of the disease.

More widely, the techniques of have been promoted through a training programme delivered by Firestone on the use of the BORIS package to Australian government veterinarians at the Department of Agriculture, Water and the Environment (Canberra, November 2019). To date 20 scientists have received training in its use. BORIS has also helped improve the understanding of spread of foot-and-mouth disease in Japan, for example demonstrating the high transmissibility of the disease from farms holding predominantly pigs.

Impact status	Achieved
Impact date	1 Jul 2018 → 31 Dec 2020
Category of impact	Health
Impact level	National