# The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing

## TL;DR

This study uses whole genome sequencing to explore how Mycobacterium bovis spreads in Ireland, revealing regional strain patterns and the role of badgers in transmission.

## Contribution

The study provides new insights into M. bovis transmission pathways by integrating genomic data with spatial and movement data.

## Key findings

- Significant regional variation in M. bovis strain distribution was identified.
- Genetic similarities between cattle and badger isolates confirm badgers as infection reservoirs.
- Certain herds showed multi-strain infections linked to cattle movements rather than local spread.

## Abstract

Bovine tuberculosis (bTB), caused primarily by Mycobacterium bovis, remains a major challenge across the island of Ireland. Despite decades of an eradication programme that encompasses cattle testing, movement restrictions, and badger culling, bTB prevalence has increased in recent years. The epidemiology of bTB is complex, with inter-species (e.g. badger-cattle) and intra-species (e.g. cattle-cattle) transmission of infection. This study utilised whole-genome sequencing (WGS) to investigate the genetic diversity and spatial distribution of M. bovis across the island of Ireland as a route to help elucidate transmission of infection.

A total of 5,875 M. bovis isolates from cattle and badgers were analysed to identify strain diversity, geographic clustering, and patterns of strain sharing within and between host species. Our findings reveal significant regional variation in strain distribution, with certain clades predominantly confined to specific regions, while others are more widely dispersed. Strong genetic similarities between cattle and badger isolates support the role of badgers as infection reservoirs. Furthermore, a subset of herds contained multi-strain infections and amongst these herds there were ‘controlled finishing units’ (CFUs), where infection was more likely driven by inward cattle movements than local transmission.

By integrating phylogenetic analysis with spatial mapping and cattle movement data, this study provides new insights into M. bovis transmission pathways and highlights the value of WGS in refining Ireland’s bTB control strategies.

The online version contains supplementary material available at 10.1186/s13620-025-00324-0.