James O'KEeffe

Disturbance ecology refers to the study of discrete processes that disrupt the structure or dynamics of an ecosystem. Such processes can, therefore, affect wildlife species ecology, including those that are important pathogen hosts. We report on an observational before-and-after study on the association between forest clearfelling and bovine tuberculosis (bTB) herd risk in cattle herds, an episystem where badgers (Meles meles) are the primary wildlife spillover host. The study design compared herd bTB breakdown risk for a period of 1 year prior to and after exposure to clearfelling across Ireland at sites cut in 2015–2017. The percent of herds positive rose from 3.47% prior to clearfelling to 4.08% after exposure. After controlling for confounders (e.g., herd size, herd type), we found that cattle herds significantly increased their odds of experiencing a bTB breakdown by 1.2-times (95%CIs: 1.07–1.36) up to 1 year after a clearfell risk period. Disturbance ecology of wildlife reservoirs is an understudied area with regards to shared endemic pathogens. Epidemiological observational studies are the first step in building an evidence base to assess the impact of such disturbance events; however, such studies are limited in inferring the mechanism for any changes in risk observed. The current cohort study suggested an association between clearfelling and bTB risk, which we speculate could relate to wildlife disturbance affecting pathogen spillback to cattle, though the study design precludes causal inference. Further studies are required. However, ultimately, integration of epidemiology with wildlife ecology will be important for understanding the underlying mechanisms involved, and to derive suitable effective management proposals, if required.

Bovine tuberculosis (bTB) remains a significant endemic pathogen of cattle herds, despite multi-decadal control programmes being in place in several countries. Understanding the risks of future bTB breakdown (BD) and the associated characteristics of herds and index breakdowns could help inform risk categorisation. Such risk categories could then contribute to tailored management and policies. Here, we estimated the future risk of herd BD for the cohort of herds that were derestricted during 2013 in Ireland using multivariable logit regression models, with a dominance analysis approach. One third of herds that were derestricted in 2013 experienced a breakdown during the follow-up five year period (1469/4459; 33%). BD length was a significant predictor of future risk, primarily driven by long BDs > 230 days relative to short BDs < 130 days (OR 95%CI: 1.157–1.851), as was having had a previous BD (OR 95%CI: 1.012–1.366). Herd-size was the dominant predictor of future risk (accounted for 46% of predicted variance), suggesting significant increase in risk of future breakdown with increasing (log) herd-size (OR 95%CI: 1.378–1.609). There was significant spatial variation in future risk across counties, and it was the second most dominant predictor of future risk (25% of predicted variance). The size of index breakdowns was not a strong predictor of future risk over a 5-year period. These findings can inform a risk-based policy development.

Bovine tuberculosis (bTB) outbreaks, caused by Mycobacterium bovis infection, are a costly animal health challenge. Understanding factors associated with the duration of outbreaks, known as breakdowns, could lead to better disease management policy development. We undertook a retrospective observational study (2012–2018) and employed Finite Mixture Models (FMM) to model the outcome parameter, and to investigate how factors were associated with duration for differing subpopulations identified. In addition to traditional risk factors (e.g., herd size, bTB history), we also explored farm geographic area, parcels/farm fragmentation, metrics of intensity via nitrogen loading, and whether herds were designated controlled beef finishing units (CBFU) as potential risk factors for increased duration. The final model fitted log-normal distributions, with two latent classes (k) which partitioned the population into a subpopulation around the central tendency of the distribution, and a second around the tails of the distribution. The latter subpopulation included longer breakdowns of policy interest. Increasing duration was positively associated with recent (<3 years) TB history and the number of reactors disclosed, (log) herd size, beef herd-type relative to other herd types, number of land parcels, area, being designated a CBFU (“feedlot”) and having high annual inward cattle movements within the “tails” subpopulation. Breakdown length was negatively associated with the year of commencement of breakdown (i.e., a decreasing trend) and non-significantly with the organic nitrogen produced on the farm (N kg/hectare), a measure of stocking density. The latter finding may be due to confounding effects with herd size and area. Most variables contributed only moderately to explaining variation in breakdown duration, that is, they had moderate size effects on duration. Herd-size and CBFU had greater effect sizes on the outcome. The findings contribute to evidence-based policy formation in Ireland.

Reactivation of latent Gammaherpesvirus in the genital tract can lead to reproductive failure in domestic animals. Nevertheless, this pathophysiology has not received formal study in wild mammals. High prevalence of Mustelid gammaherpesvirus 1 (MusGHV-1) DNA detected in the genital tracts of European badgers (Meles meles) implies that this common pathogen may be a sexual transmitted infection. Here we used PCR to test MusGHV-1 DNA prevalence in genital swabs collected from 144 wild badgers in Ireland (71 males, 73 females) to investigate impacts on male fertility indicators (sperm abundance and testes weight) and female fecundity (current reproductive output). MusGHV-1 reactivation had a negative effect on female reproduction, but not on male fertility; however males had a higher risk of MusGHV-1 reactivation than females, especially during the late-winter mating season, and genital MusGHV-1 reactivation differed between age classes, where 3–5 year old adults had significantly lower reactivation rates than younger or older ones. Negative results in foetal tissues from MusGHV-1 positive mothers indicated that cross-placental transmission was unlikely. This study has broader implications for how wide-spread gammaherpesvirus infections could affect reproductive performance in wild Carnivora species.

In Ireland, every animal is examined at slaughter for its fitness for human consumption. The aim of this study was to determine the relative effectiveness of factories in submitting and subsequently in having suspect lesions confirmed as bovine tuberculosis (TB) lesions during the years 2005-2007. This work provides an update from previously published data for years 2003-2004. During 2005-2007 data were available on 4,401,813 cattle from attested herds (i.e. herds classified free of bovine TB), from which data for potential confounding factors were available for 3,344,057 slaughtered animals at one of the 37 export-licensed factories.

As part of ongoing culling operations, European badgers (Meles meles) were captured using stopped restraints in winter (October to December 2005) and summer (May to June 2006) in the Republic of Ireland. A subset of these badgers, those caught during four consecutive nights, was examined postmortem to determine the frequency and severity of physical injuries resulting from capture in the restraints. The skin and the tissues underlying the restraint of 343 badgers were assessed for injury by visual examination. There was an absence of skin damage or only minor skin abrasions in 88% of badgers; an absence of subcutaneous tissue injury or only localized subcutaneous tissue injury in 69%; and an absence of muscle injury or only slight muscle bruising in 99% of badgers. Only 2% of badgers had cuts to the skin and 5.5% had extensive subcutaneous edema, whereas 1.2% had areas of hemorrhage and tearing of the underlying muscle. Our results show that the majority of badgers examined sustained minimal injuries attributable to capture in stopped restraints.