There are multiple websites, blogs and pages on the internet with information about bovine TB. Given the highly polarised and political arguments surrounding the subject I would recommend that anyone approaches information they read online with a certain amount of caution, particularly if it is unclear who the author is, or where they are getting their information. Personally I would recommend www.Tbhub.co.uk which is supported by AHDB, BCVA, DEFRA, Landex and the NFU, as a key website with reliable information on bovine TB. Throughout my work I will aim to get the content I produce (articles, fact sheets etc) uploaded to the TBhub where possible. This page acts as a ‘Blog’ for me to talk about some of this work as it progresses and also highlight other information on the subject of bovine TB.
Impacts of badger culling in England: New paper published
October 11th 2019
Industry-led badger culling began in England in 2013 initially in two pilot areas in Gloucestershire and Somerset. A third cull area was licensed in Dorset in 2015, and then since then the number of cull areas has gradually increased.As of the end of 2018 there were 32 cull areas active in England, and this has now increased to a total of 43 (for a list of cull areas see here). Badger culling is hugely divisive and there is a lot of interest in what effect the culls are having on TB in cattle. Previous APHA reports have described the TB statistics for the cull areas (these are interesting but cannot prove if culling is having an impact – see here for the latest published data), and one previous paper has been published investigating the effects of the first two years of culling in the Gloucester and Somerset cull area (Brunton et al. 2017, summarised here).
A new study has just been published in the Journal Scientific Reports by Downs et al. which builds on this earlier work and gives us out best estimate yet of the impacts of the current badger culls. The study uses four years’ worth of data (2013 -2017) for the Gloucester and Somerset cull areas and two years’ worth of data for the Dorset cull area.
Assessing effects from four years of industry-led badger culling in England on the incidence of bovine tuberculosis in cattle, 2013–2017
I am one of the co-authors of this latest study, and together with the other authors I have created a two page summary of the paper which can be downloaded below and on the Tbhub.
It is always a challenge to summarise complex studies in just a few words, and much more detail can be found in the full paper, which I would recommend reading. I have also outlined some additional points relating to different aspects of the study below:
Why use complex multivariable analyses?
You may be thinking…why do the analyses need to be so complicated? Surely you can just look at the TB stats for the cull areas and show if TB is declining or not? Firstly, TB statistics go up and down all of the time (particularly at the scale of a cull area) so to understand effects of culling or any intervention you need to compare trends in the cull areas to comparison areas without culling. The comparison areas used in the current study are selected to be similar to the cull areas, but these areas will never be identical. This is potentially problematic, as TB in cattle is associated with a whole range of risk factors, many of which relate to cattle husbandry and have nothing to do with wildlife or culling (Skuce, Allen & McDowell 2012). This means that there could be differences between cull areas and comparison areas that are unrelated to culling, this could lead to differences in the level of TB in cattle. The multivariable analyses conducted aim test for an effect of culling, while controlling for these other differences. This means that when we describe the results of these analyses we do not simply say “TB declined by X amount” instead we talk about the effect of culling relative to the comparison areas (see below).
Incidence rate ratios (IRR)
The effect of culling and other factors on TB risk is described in the study using incidence rate ratios (IRR). An incidence rate is the rate that a given event (in this case TB breakdowns) happens over time. The statistics in the paper report the incidence rate RATIO (IRR) as this shows the rate of TB breakdowns in the cull areas RELATIVE to the comparison areas where no culling has taken place. For example an IRR of 0.3 would mean that the rate of breakdowns was 30% of that in comparison areas (ie 70% lower), 0.8 would mean it was 80% (or 20% lower) and so on. An IRR of more than one means an increase…..so 1.50 would mean a 50% increase (ie the rate was 150% of that the comparison areas) and 1.20 a 20% increase.
In the tables in the paper the IRR is reported for the intervention effect (culling) and also for several other variables (Table 4). For variables with a continuous scale (eg 1-100 rather than distinct categories) the IRR is the change in incidence rate associated with a 1 unit increase in that variable. For example, the IRR for the variable ‘percentage of herds that were dairy’ was 1.01. This means for every unit increase in that variable there was a 1% increase in the rate of TB breakdowns.
OTF-W, OTF-S or all TB incidents?
Bovine TB is reported in a number of different ways and this means that there are a number of possible statistics that can be analysed:
- OTF-W (Official TB Free Withdrawn): these are TB incidents where there was at least one test reactor or inconclusive reactor with post-mortem evidence of M. bovis infection (judged by the presence of visible lesions typical of TB and/or identification of M. bovis in culture), or at least one slaughterhouse case that yielded M. bovis on culture. In some studies these are referred to as ‘confirmed’ breakdowns.
- OTF-S (Official TB Free Suspended): these are TB incidents where at least one test reactor or two IRs have been identified but evidence of infection could not be confirmed through post-mortem examination or laboratory culture of tissue samples. In some studies these are referred to as ‘unconfirmed’ breakdowns.
- All TB incidents: – This includes both OTF-W and OTF-S incidents (ie all breakdowns regardless of if they were confirmed or not).
The paper largely focuses on changes in OTF-W incidence rates. This is partially because these breakdowns are confirmed as being caused by TB, while it is possible that OTF-S incidents may have been caused by something else. The analyses for the RBCT also focused on changes in confirmed (OTF-W) TB incidents, largely because no significant changes were observed when for all TB incidents or unconfirmed incidents (OTF-S) were analysed.
The paper and the supplementary materials of the paper (a range of extra details and tables published alongside the study) report the results of the analyses using OTF-W and all TB incidents. Analyses of changes in all TB incidents found a decline in the Gloucester and Somerset cull areas (although less than when focusing on OFT-W), but also a significant increase in the Dorset cull area.
Why is the data only up to 2017?
This paper summarises the data up to the end of 2017. This is now nearly two years ago, so why is there such a delay? This is partly because it takes a while to collate the enormous amount of TB data and statistics collected each year. For example the TB statistics covering the period up to the end of 2018 were only published (here) in March of 2019, which is after this paper was submitted for publication. Complex analyses like those reported in this paper also take time to complete, so it is not a simple task of updating the figures (particularly as the licensing of new cull areas may overlap with comparison areas used in the analysis). Finally, the paper also has to go through a process of peer review where it is assessed by anonymous reviewers (typically scientist with expert knowledge of the field). This peer review process is crucially important for ensuring that the science is robust, but it can take many months to complete (anywhere from 3/4 months up to a year or more in some cases).
A few final thoughts on the implications of this study
The key conclusions from the study are outlined at the end of the summary document. However, given the diverse views on badger culling it is inevitable that people will look at this study and come to very different conclusions. In my view it is important that any scientific studies such as these are looked at properly and the limitations and results are fully understood. This study does demonstrate that industry lead culling can result in benefits, measured as a drop in the rate of new breakdowns (relative to other areas without culling). This change in TB incidence is a standard way of evaluating disease management, partly because a fall in the rate of new disease incidents is likely to be the first change that can be detected. Whether culling leads to longer term reductions in disease in these areas, such as a reduction in prevalence (the % of herds under restrictions) we cannot definitively say from these data.
One important limitation of this study relates to the scale of the work. In an ideal world if you wanted to look at the effect of culling (or any disease intervention) you would carry out a randomised, replicated trial. This is what was conducted during the RBCT (for a summary of the RBCT see here) as there were 10 randomly selected areas for each culling treatment. The results from the RBCT analyses then give you an estimate of the average effect of culling (along with a range of uncertainty around this) if it were applied to a given random area. This essentially gives you the power to predict future impacts of culling, assuming it is done in a similar way, place and time (the RBCT was government cage trapping, in areas with high levels of TB in cattle, from 1998-2005).
The current badger culls in England are a programme of wildlife management with the aim of disease control, but they are not a scientific trial aimed specifically at investigating the effects of culling (like the RBCT). So while there may be opportunities to evaluate culling outcomes (like this study), it may be that we are limited in what we can conclude from the results. This latest study provides a good estimate of the effect of industry lead badger culling in the three specific areas studied. As mentioned in the summary document, these areas were not randomly selected and they could be very different from the other licensed cull areas in England. For example, the role that badgers play in cattle TB could be much smaller or larger. The effectiveness of the culling could also be very different due to differences in habitat, badger density, farmer behaviour, protestor activity or government support. This does not mean the results of this study are not valid, but it makes it difficult to predict what effects the culls will have in the other areas. For example, culling in other areas could have a large impact (like a Gloucester), a smaller impact (like Somerset), no impact (yet – as in Dorset) or a totally different impact we haven’t seen yet. It also means that these data cannot be used to confidently evaluate the whole culling policy, just those specific areas studied. Hopefully future analyses will help to shed light on the effect of culling in other areas, as well as the longer term impacts in Gloucester, Somerset and Dorset.
Latest TB trends in badger cull areas published
October 4th 2019
In September APHA published a report with the latest TB figures for the badger cull (control) areas.
The report shows the Officially Tuberculosis Free – withdrawn (OTF-W) incidence and OTF-W prevalence inside badger control areas and in the 2km buffer strip surrounding each area.
OTF-W (Official TB Free Withdrawn): these are TB incidents where there was at least one test reactor or inconclusive reactor with post-mortem evidence of M. bovis infection (judged by the presence of visible lesions typical of TB and/or identification of M. bovis in culture), or at least one slaughterhouse case that yielded M. bovis on culture. In some studies these are referred to as ‘confirmed’ breakdowns.
This data covers up to the end of 2018, which includes the first 21 badger control areas (ie those where culling started between 2013 and 2017). This means that 5 years’ worth of data is available for the first two licensed areas (Gloucestershire and Somerset) and one to three years of data for the other areas. New badger control areas will be included in subsequent reports once they have at least one year of follow-up data available.
The data in the report give raw trends in TB in cattle, but these data alone cannot demonstrate whether the badger control policy is effective in reducing bovine TB in cattle. All these data can provide is a description of the general patterns and trends. In a previous post (when last years numbers were published) I discussed this in more detail and also listed the published details of the current cull areas in England (see here).
The data from the latest report are displayed in the graphs below.
Tip: the below graphs are fully interactive. Pan your mouse curser over the graph to display the values for each point. You can zoom in/out, or export the graphs as images using the tools visible above the graphs (which are visible if you move your mouse curser over the graph).
These graphs are also viewable alongside other TB data as a page in the Bovine TB dashboard I have been developing.
Does badger vaccination reduce TB in cattle?
July 8th 2019
The injectable badger BCG vaccine (delivered to badgers caught in cage traps) has been licensed for use in badgers since 2010, based on evidence that the vaccine is safe and has a protective effect in badgers (Brown et al. 2013). Captive trials have shown that vaccination reduces the development and progression of disease (Chambers et al. 2011). Results from field trials also demonstrate that vaccination reduces the spread of disease within badger populations, as vaccinated badgers are much less likely to become infected with TB (Carter et al. 2012). Crucially, vaccination is also safe, the BCG bacteria is not excreted by badgers and the vaccination process does not cause perturbation (Lesellier et al. 2006; Woodroffe et al. 2017).
For a summary see the badger vaccination fact sheet, and for more information on perturbation read the fact sheet on the RBCT. The reviews by Chambers et al. (2014) and Godfray et al. (2013) also provide a good summary of the science on the subject.
Logically reducing disease spread in badger populations can only be a good thing for cattle, but are there any studies which prove one way or the other that vaccination does or doesn’t ‘work’?
The sort answer is no, there are no specific scientific trials or experiments that have been conducted with the explicit aim of investigating the effect of badger vaccination on TB in cattle. Such a trial would ideally need to be randomised (areas randomly selected to avoid potential bias), replicated (carried out in several locations to demonstrate how effects might vary) and with controls (matched comparison areas without vaccination), which was the case in the RBCT.
However, there are two areas in the UK where large scale badger vaccination has been conducted, these are the BVDP and IAA, which are often mentioned in discussions about badger vaccination.
The Badger Vaccine Deployment Project (BVDP) – England
This was a 100 km2 (approx.) area in Gloucestershire. Badgers vaccination was conducted from 2010 – 2015 by APHA staff, with an average of 7.6 badgers per km2 vaccinated each year (range = 5.4 to 10.0). The aims of the BVDP are outlined in the BVDP lessons learned report (APHA 2015):
“The BVDP was not set up as a scientific trial to investigate the effect of BadgerBCG deployment on TB in badgers or cattle. Rather, it aimed to provide the first use of a vaccine for bovine tuberculosis in badgers outside of research trials, to develop practical knowledge on the processes involved in vaccinating badgers and to facilitate training of lay vaccinators” – page 3.
The Intensive Action Area (IAA) – Wales
The IAA was a 288 km2 area primarily in Pembrokeshire, but with land also in Ceredigion and Carmarthenshire. The area was selected for a range of extra disease control measures due to having one of the highest rates of TB in Wales, as well as evidence of TB in the local badger population. The IAA was not a vaccination trial, a whole range of measures aimed at cattle and wildlife were applied to the IAA starting in 2010:
- stricter cattle controls and testing
- improved biosecurity measures
- testing all goats and camelids
- badger vaccination (2012 – 2015, delivered by government)
For more information see https://gov.wales/intensive-action-area-iaa
Approximately 3.9 – 4.9 badgers per km2 were vaccinated in the IAA each year. A road kill survey of badgers also recorded low levels of TB in the badger population, with the number of positive badgers declining during the project, but the sample size was too low to show a significant difference (APHA 2016).
Although neither of these areas were established as scientific studies to investigate the effects of badger vaccination, APHA has produced reports looking at changes in TB in cattle in both areas.
What do these reports tell us about the effectiveness of badger vaccination?
The BVPD report
The BVDP report investigated changes in cattle TB incidence rate (the rate of new breakdowns) in the BVDP and four comparison areas. These four comparison areas were selected using a process to identify areas similar to the BVDP in their TB history and cattle herd demographics.
The analyses conducted to investigate changes in TB in the BVDP and comparison areas was descriptive and relatively simple, in that the areas were not directly compared in a single analysis (ie vaccinated vs non-vaccinated, as was used during the RBCT). Rather separate individual analyses were conducted for each area and the trends (increasing or decreasing) were then described. The severe limitations of the analyses meant that it was unlikely any effects of badger vaccination would be detected, as clearly stated in the report:
“It is important to remember that this is a descriptive analysis, and that it is unlikely that any significant changes will be observed. Any analysis of the effect of vaccination is limited by the retrospective and non-randomised selection of comparison areas. In addition, the BVDP was only conducted in one intervention area so it is anticipated that there is the potential for selection bias and that there will be insufficient power to detect the effects of vaccination on cattle incidence in the area.” (page 5)
Did TB change in the BVDP area?
The TB incidence rate in cattle significantly declined throughout the course of the BVDP, with a reduction in OTF-W (official TB free withdrawn) breakdowns of more than 50% by the end of the five year project. However, there were also significant declines in three of the four comparison areas (see figure). This could suggest that the decline in the BVDP would have happened without vaccination, but it is difficult to be sure using the analyses used.
For example, when analyses similar to those in the BVDP report were applied to the Gloucestershire and Somerset cull areas (which are both 2-3 times larger) they found no effect of culling. Effects of culling were ONLY detected using much more sophisticated multivariable analyses (controlling for other non-cull effects) directly comparing the cull areas to TEN comparison areas (Brunton et al. 2017, read the fact sheet here). This highlights the importance of robust analyses, and the risks of coming to false conclusions if they are not conducted properly.
One other major problem is that the BVDP is a single area, and it is unclear whether this is representative of the wider landscape in relation to the role of badgers, or other factors relevant to TB (as many other factors influence TB risk ). TB was declining prior to vaccination in the BVDP and the similar matched areas experienced a drop in TB without any specific intervention. This could suggest that other non-wildlife factors were important in these areas, or changed during the trial.
The limitations of the analyses are described in detail in the report. The authors also make it clear that it would be wrong to come to firm conclusions about the general impacts of vaccination:
“The factors discussed here make assessing the impact of badger vaccination on cattle bTB incidence difficult and drawing firm conclusions from the data analysed here on the impacts of badger vaccination inappropriate.” – page 15
The IAA report
As with the BVDP report, the analyses conducted on the IAA were quite simple and descriptive in scope (ie they describe trends but make no attempt to identify the factors causing them). Trends in TB incidence (breakdown rate), prevalence (% of herds restricted) and a wide range of other TB metrics were compared for the IAA and a comparison area in west Wales.
Did TB change in the IAA?
Because of the range of different statistics calculated it is difficult to give a simple answer to this. Some metrics showed an improvement, for example the proportion of herds under restrictions in the IAA (prevalence) fell from 22-30% in the early part of the study to 14% by 2016. There was also a 35% reduction the TB incidence in the IAA, relative to a 22% reduction in the comparison area (these differences were reported by farminguk and the BVA). However the authors of the report do state that “Notable differences in indicators of TB incidence have not yet been seen” (as of 2016).
The IAA report makes no statement on the effects of badger vaccination, partly because vaccination was used alongside a wide range of other measures, which makes it impossible to determine which specific measures did or did not work.
Another reason it is difficult to draw conclusions is because the IAA is a quite different to the comparison area used in the analysis. This can be seen in the figure above, as the prevalence in the comparison area is much lower than the IAA. This issue is also further outlined by the authors:
“Selection of the IAA and the CA (comparison area) was not performed randomly, nor were either area replicated. There are known demographic differences between the IAA, the CA and the other areas which might influence TB trends in those regions independently of policy interventions. For example, there are a higher proportion of large dairy herds in the IAA than in other areas, and such herds are considered more likely than beef herds to see TB incidents, regardless of location. Consequently, it is not appropriate to use conventional statistical tests when making comparisons because the areas are not directly comparable.” – page 8
This is not surprising, as the IAA was not chosen to be representative of the wider welsh countryside. It was chosen due to the high levels of TB and for other differences which make controlling TB challenging, hence the ‘intensive’ approach taken. By definition the outcome of any intervention in the IAA is likely to be quite different to other areas, with different levels of TB in badgers and cattle.
So what can the IAA and BVDP tell us about the effect of badger vaccination on TB in cattle? Unfortunately very little. In both areas there was evidence of TB declining in the cattle population, but it is not possible to say whether vaccination contributed to this or not.
The authors of both the IAA and BVDP reports make it very clear that neither of these projects were intended as a scientific studies to prove or disprove the effects of badger vaccination. The authors also clearly outline several reasons why it would be wrong to use the descriptive analyses conducted to come to firm conclusions about vaccine effectiveness. Proving the effect of any intervention, whether its culling, vaccination, biosecurity or other cattle measures is extremely difficult, either requiring large replicated controlled trials (like the RBCT), or robust sophisticated statistical analyses. The contribution of badgers to TB in cattle likely varies hugely across the UK (Birch et al. 2018). This also means that impacts of vaccination (or any intervention) will also likely vary, and that the results from one area may not apply to other areas where the situation is very different.
Until further trials or analyses are conducted it is not possible the say definitively what effect badger vaccination will have on TB in cattle. There is however, good scientific evidence that vaccination is an effective means to reduce transmission and disease spread in badgers (as summarised here). If the aim is to have fewer infected badgers in the landscape, then vaccination is a potential tool to achieve this. Vaccination is also a viable option in parts of the country where the badger population is currently free of TB, as a way of reducing disease spread and future risk to cattle.
Badger visits to farm yards – new paper published
June 12th 2019
Several research studies have shown that badgers will enter farm yards where they may contaminate the farm environment (feed, water troughs etc) or come into close contact with cattle (Garnett, Delahay & Roper 2002; Tolhurst et al. 2009; Judge et al. 2011; O’Mahony 2015). Feeding opportunities seem to be a key driving factor behind this behaviour, as yards and buildings may contain high energy animal feeds which are attractive to badgers (click here to see a list of feed sources attractive to badgers).
Work by APHA has shown that practical measures such as sheet gates or electric fences can be used to keep badgers out of farm yards (Judge et al. 2011), and it is recommended that farmers use such measures where practical in their farms to reduce the risk of disease spread (see the TBhub). However, previous studies on badger activity in farm yards have shown that levels of activity can vary hugely (Mullen et al. 2015; Woodroffe et al. 2017). This raises the question as to how widespread this behaviour is and whether particularly farms are more likely to experience badger visits than others.
Recently we published a paper in the Journal PLOS One on the subject of badgers in farm buildings…
This study aimed to answer several questions:
- How widespread are badgers visits to farm yards?
- Which farm characteristics are associated with visits by badgers?
- Can we predict this behaviour and identify farms where visits occur?
The paper is open access (free to view), but I thought it would be useful to produce a short summary for those who want the key information.
What did the study involve?
The study involved monitoring badger activity at 155 farms across south-west England and Wales. Each farm was monitored for one month using trail cameras (click here for advice on using cameras to monitor badger activity).
Each farm was also surveyed for badger field signs (setts, latrines etc) and a range of other farm characteristics were recorded (farm type, number of cattle, numbers of different buildings etc).
A range of statistical analyses were then conducted to look at how common badgers visits were, and also determine which farm characteristics were associated with badger visits.
How widespread were badger visits to farm yards?
Overall 41% of farms had evidence of farm visits (badgers recorded on camera), although the level of activity (number of nights badgers were seen) was quite variable.
Which farm characteristics were associated with badger visits?
The presence/absence of badger visits was significantly related to several farm characteristics……
- Badger visits were more likely at farms with higher numbers of feed stores and cattle sheds (suggesting more feeding opportunities?)
- Badger visits were more likely at farms with higher numbers of badger setts (within 500m), and where the nearest active sett was located closer to the farm.
- Badger visits were less likely at farms which housed large numbers of cattle and where there was a farm house on dwelling on site. This could indicate that the farm was larger or had higher levels of human disturbance that may deter badgers?
The frequency of visits (ie the number of nights badgers were recorded) was related to only two factors:
- Number of cattle housed (higher number = fewer visits)
- Distance to the nearest active badger sett (closer sett = more visits
Can we predict this behaviour and identify farms where visits occur?
Statistical models (which identified the different relationships above) were used to predict badger visits at 40 farms with known levels of badger visitation which were intensively monitored as part of an earlier study (Judge et al. 2011). Much like when developing a new diagnostic test, different cut off values can be chosen (ie above this cut off farms are classed as being likely to experience badger visits) which affect the accuracy of the models predictions, along with the sensitivity and specificity.
- Sensitivity – the % of farms with badger visits that were correctly classified
- Specificity – the % of farms without badger visits that were correctly classified
Overall the models could predict the presence /absence of badger visits with a 72% accuracy (sensitivity = 62%, specificity= 81%). However these number could potentially be changed by using a different cut off value.
The models were less accurate at predicting the frequency of badger visits (ie not only identifying farms where badgers were present, but those which had lots of visits rather than just one or two). Although, farms predicted as having badgers present tended to be those with higher overall levels of activity.
We also created an interactive tool where users can enter the characteristics of a given farm and generate predictions.
What can we conclude from this study?
This study further confirms that badger visits to farm yards may be widespread, affecting a significant proportion of farms within the area studied (south west England and wales). Although it should be noted that the farms were not randomly selected, so the sample of farms could be slightly biased. The study also highlights that certain farms are more likely to be of visited than others, which could help to focus biosecurity measures in a more targeted way.
The results from the study differ from several recent studies, which suggest that badger visits to farm yards are uncommon or that badgers avoid farm yards. It is important to stress there are some important differences with this study and these earlier studies, both in their scale and in the way that badger activity was recorded. This study also demonstrates that certain types of farms are more/less likely to be visited, so it is possible that farms monitored in these earlier studies fall into a low risk/less likely to be visited category.
For further details on what this study involved and for a more thorough discussion of the results – read the full paper here.
TB in other livestock and domestic animals
March 1st 2019
Mycobacterium bovis (M. bovis) causes bovine TB in cattle and it can also infect badgers and a range of other wildlife (addressed in another fact sheet). But what about other livestock like sheep or pigs? Or domestic animals like dogs and cats? Can they also be infected? And if they can, is there a risk to cattle or wildlife?
To address these questions I have produced a fact sheet with input from veterinary experts from APHA. This can be downloaded by clicking the image below, or by going to the TB fact sheet page of this website.
In addition to this factsheet there are a number of other great information sources if you are interested in TB in other livestock or domestic animals.
Firstly the non-bovines section of the TBhub has really useful information and links to government advice.
The role of non-bovines is also discussed in length in the recent Godfray report (2018). See chapter 7 on page 80. Within this section there are also figures quoted of the numbers of other livestock found infected with M. bovis each year. As you can see below, the numbers are generally very low. To download spreadsheets containing these data go to the gov website here.
For a more in depth review of the subject there is a two part review by (Broughan et al. 2013). Part one reviews evidence/epidemiology of TB in other species. Part two then covers the different tests for TB available for non-bovines.
Broughan, J.M., Downs, S.H., Crawshaw, T.R., Upton, P.A., Brewer, J. & Clifton-Hadley, R.S. (2013) Mycobacterium bovis infections in domesticated non-bovine mammalian species. Part 1: Review of epidemiology and laboratory submissions in Great Britain 2004–2010. The Veterinary Journal, 198, 339-345.
Broughan, J.M., Crawshaw, T.R., Downs, S.H., Brewer, J. & Clifton-Hadley, R.S. (2013) Mycobacterium bovis infections in domesticated non-bovine mammalian species. Part 2: A review of diagnostic methods. The Veterinary Journal, 198, 346-351.
If you are interested, but cannot access these papers then feel free to contact me and I will be happy to send them to you.
Can M. bovis survive in silage?
February 11th 2019
TB transmission via contaminated feed
Bovine TB is caused by Mycobacterium bovis (M. bovis), but it is unclear how the bacteria spreads between hosts, whether that’s between cattle, or between cattle and wildlife. One potential route is by ‘indirect’ transmission, where an infected animal contaminates grass, stored feed, water or other parts of the farm environment, and then another animal interacts with this contamined material and becomes infected.
Studying these indirect transmission routes is very difficult, but research has shown that M. bovis can survive in different environments such as water, soil, and faeces and a range of stored feed types (Fine et al. 2011). Research from the United states has also shown that M. bovis can spread from infected deer to cattle via contaminated troughs and housing (Palmer, Waters & Whipple 2004). This is why current guidance in the UK is to keep badgers out of stored feed and housing to reduce opportunities for disease spread.
But what about silage?
Badgers may be attracted to open silage clamps, particularly those containing whole crop wheat or maize silage (click here for a list fo feed attractive to badgers), so it is advisable to reduce badger access if possible. BUT – silage could also potentially become contaminated in the field, either from infected badgers, or if contaminated slurry is spread on the field (click here for a factsheet about TB in slurry and faeces). Silage goes through an ensiling, or fermentation process, where oxygen levels are low and the pH becomes acidic. Previous reviews of the subject have highlighted that M. bovis could potentially survive in these conditions, but these reviews have also highlighted the lack of science in this area.
Recently a study was published in the United states by (Grooms et al. 2019), which directy addresses the question of M. bovis survival in silage:
Grooms et al. (2019) Survival of Mycobacterium bovis during forage ensiling. American Journal of Veterinary Research, 80, 87-94.
Given the interest in this subject, and the fact that this paper is a difficult to access journal, I have produced a summary of the paper below.
What did the study invovle?
The study involved experimentally adding M. bovis to samples of cut forage which was then ensiled in the lab.
Three different feed types were tested:
- Alfalfa – dry matter content at ensiling 36%
- ‘Mixed mostly grass’ – mainly orchard grass (not specified, but I believe this is cocks foot), with some alfalfa and clover. – 65% dry matter content at ensiling (this was higher than intended, the target was 40%)
- Maize (‘chopped corn’) – 32% dry matter content at ensiling Samples were spiked with M. bovis prior to ensiling, with samples arranged in replicate groups of six; four samples containing M. bovis and two with no M. bovis ( to act as controls).After each period of time the samples were then tested for M. bovis using two methods
Each group of six samples were then ensiled for one of ten different periods spanning 0 – 112 days (meaning 60 samples of each forage type). Samples (250g of each) were placed in thick vaccuum packed polythene bags, wrapped in black liners and and stored at room temperature (18-22°C) to simulate the ensiling process.
After each period of time the samples were then tested for M. bovis using two methods:
- Culture – M. bovis is grown in the lab
- PCR – tests for the presence of M. bovis DNA (click herefor a factsheet on PCR testing)
What did the study find?
This study had three key results:
- The study found that M. bovis could be cultured from Maize and Alfalfa silage up to two days into the ensiling process, and up to 28 days in grass silage. All samples tested after this period tested negative. The authors suggest that the longer survival in grass could be due to the higher (less acidic) pH recorded in these samples (pH was around 5 while maize and alfalfa was closer to 4). This could also be due to the higher dry matter content in the grass samples in the study.
- M. bovis DNA could be found in some samples of all three silage types up to the end of the study (day 112).
- None of the control samples tested positive on either culture or PCR
What do these results mean?
To quote the authors “these results suggest that properly ensiled forages would be an unlikely source for M bovis transmission to cattle”, as M. bovis could not be cultured after 28 days in any of the samples. M. bovis DNA was detected beyond this date, right up to the end of the study. However, it is not clear whether the bacteria are viable (ie if they could grow or infect an animal). One possibility is that the bacteria are ‘dormant’ and that changes in conditions in the future could make them infectious, but it is unclear if this is possible (and what condictions could causes this).
Although this study has some very interesting results, it is important to acknowledge that this is an experimental study, and no experiment is perfect. M. bovis was added at very high concentrations to the forage samples (tens of millions of backeria in each 250g sample), which is likely much higher than contamination would occur naturally. The primary method of testing for M. bovis (culture) is also not 100% perfect, so could potentially fail to detect the bacteria, even though it was present. It is therefore possible that M. bovis survival in natural conditions is longer or shorter than stated here. Nevertheless, this study provides the best information to date on the likely survival of M. bovis in silage.
Overall conclusion : The study suggests that properly ensiled forage is unlikely to be a source of infection in cattle, although the detection of M. bovis DNA up to the end of the experiment means that the risk cannot be totally ruled out.
The factsheet on TB survival in feed, water and soil has now been updated to reflect these new results.
What impact do badgers have on other wildlife?
January 22nd 2019
The badger population in England and Wales has increased in recent decades (Judge et al. 2014, Judge et al. 2017), although in cull areas in England there are likely to be declines. Badgers are our ‘largest predators’ and although their diet is mainly invertebrates (worms, snails etc) and plant matter, badgers will eat other mammals, amphibians and birds. Changes in badger numbers therefore have the potential to impact other species and this is an issue which receives a lot of attention in the ongoing debate around badgers and bovine TB. Much of the discussion is focused on hedgehogs and ground nesting birds, partly because while badger number have increased in recent decades, these species have undergone significant declines, and many people suggest these changes are connected.
So are badgers to blame for falling hedgehogs and ground nesting birds? And will culling badgers lead to changes in other species?
To address these questions I have produced a two-page fact sheet which can now be found on the factsheets page of this website, the TBhub and can also be downloaded by clicking the image below. This factsheet summarises the published literature on relationships between badgers with hedgehogs, ground nesting birds and also foxes.
Summarising these topics into two pages is always a challenge and it is not possibly to include every study or elaborate on every point. In addition to the contents of the fact sheet, below is some more details on hedgehogs and ground nesting birds.
Additional points on the effect of badger culling on hedgehogs.
Several studies have shown a negative association between badgers and hedgehog numbers (ie hedgehog numbers are lower in areas with higher badger activity/density), but the best evidence for the effects of badger culling on hedgehogs comes from this paper which I co-authored from Trewby et al. (2014)
Trewby, I.D., Young, R., McDonald, R.A., Wilson, G.J., Davison, J., Walker, N., Robertson, A., Doncaster, C.P. & Delahay, R.J. (2014) Impacts of Removing Badgers on Localised Counts of Hedgehogs. PLoS ONE, 9.
This paper involved conducting nocturnal spotlight surveys for hedgehog in RBCT cull areas. Hedgehog numbers were counted in pasture fields and amenity grassland (playing fields, village greens, parks etc), which is a key habitat for hedgehogs. Analysis of the data found that in cull areas there was a significant increase in hedgehog numbers in amenity grassland (hedgehog numbers roughly doubled), while in cull areas there was no such increase. This paper demonstrates that badger culling is likely to benefit hedgehog numbers. However, there are a couple of important points to consider:
- This increase was in amenity grassland only (essentially non-farmland). In pasture fields there were too few sightings of hedgehogs to conduct meaningful analyses, even after culling.
- The effect was significant (hedgehogs did increase), but the effect was quite variable (look at the figure).
So while culling does seem to benefit hedgehogs, it does not guarantee a doubling of hedgehog numbers across the whole cull area. Instead there is evidence for a variable increase in a specific habitat types.
Additional points on the causes of hedgehog declines
A recent study was published in nature scientific reports partly addresses this question.
Williams, B.M., Baker, P.J., Thomas, E., Wilson, G., Judge, J. & Yarnell, R.W. (2018) Reduced occupancy of hedgehogs (Erinaceus europaeus) in rural England and Wales: The influence of habitat and an asymmetric intra-guild predator. Scientific Reports, 8.
The study involved using tracking tunnels to survey for hedgehogs in areas where badger activity was also quantified in the recent national survey (Judge et al. 2014). The results found that hedgehog activity declined with increasing badger activity, consistent with badgers have a negative impact on hedgehogs. But this is not the whole story…
This study only found hedgehog activity in 22% of areas surveyed, suggesting hedgehogs were absent from a large part of the English countryside. The analyses also found that even in areas with no badgers present, hedgehogs were only present in 31% of areas surveyed, meaning around 70% of areas had no hedgehogs (even if there were no badgers recorded). This suggests that is a combination of factors affecting hedgehogs (ie badgers are important, but they are not the only factor) and the authors suggest that wider habitat changes are responsible. To quote the authors…..
“In summary, much of the blame for the perceived hedgehog decline in the UK has focussed upon the impacts of badgers as both a competitor but especially as a predator (e.g.34). Although our findings support the negative relationship between the two species, this relationship is likely to be complex, involving elements of predation, competition and avoidance; in the context of the latter, areas associated with human habitation appear to mitigate against some of the negative effects of badgers. At the same time, however, rates of hedgehog occupancy were low even in the absence of badgers, and badger setts were not recorded in 47.9% of sites surveyed. Collectively, this suggests that intensive management of rural areas is negatively impacting both these generalist terrestrial insectivores”
To further quote the authors….” the combined effects of increasing badger abundance and intensive agriculture may have provided a perfect storm for hedgehogs in rural Britain, leading to worryingly low levels of occupancy over large spatial scales.”
Additional points on badgers and ground nesting birds
The decline of farmland birds in the UK and the rest of Europe has been extensively studied for decades and there are a number of great reviews of the subject (see Donald, Green & Heath 2001; Newton 2004). Predation can be a factor for some species, but changes in the wider countryside are widely believed to be the primary factors driving declines in birds, as well as wildflowers, insects and other animals. For a summary of the factors affecting farmland birds see this page from the RSPB. For a summary of the factors driving changes in UK wildlife see the State of nature report, compiled by a large number of conservation and research organisations.
The British Trust for Ornithology (BTO) also has records of population trends, along with summaries of likely causes of population changes on the website ‘bird trends’, for example see this page on skylarks.
I stress that by mentioning the above I do not aim to ‘blame farmers’ for these changes, as changes in farming practices and the wider countryside are driven by many economic, social and political factors. There are also many good examples (contained in the report above) of how certain farming practices can have huge benefits for wildlife.
The above reports, papers and sources relate to large landscape changes in bird populations. As stated in the summary sheet there will be examples of localised areas (such as nature reserves or breeding colonies) where badgers, foxes and other predators can have impacts on breeding birds such as terns. This in part is because many bird species (particularly ground nesting species) are confined to small protected areas or fragments of suitable habitat, making them vulnerable to predators.
Bovine TB biosecurity videos
January 11th 2019
In 2011 FERA (now APHA) created a series of videos on bovine TB and farm biosecurity.
- Introduction –badger behaviour and TB infection in badgers.
- Identifying badger activity – badger setts, runs and latrines.
- Biosecurity at pasture – measures to reduce interactions between badgers and cattle at pasture.
- Biosecurity in farm buildings (part 1) – measures to reduce badger access to farm buildings and yards.
- Biosecurity in farm buildings (part 2) – measures to reduce badger access to farm buildings and yards.
The videos contain a wealth of useful information, especially the biosecurity at pasture and in farm building videos (videos 3-5), which feature several practical examples and interviews with farmers who have used measures on their farms. The effectiveness of measures at reducing badger activity in yards and buildings is largely based on a paper by Judge et al. (2011) and many of the measures are also outlined in a series of factsheets on the TB hub.
As these videos are now a few years old, there are a couple of areas which need updating based on research published in recent years (ie after the videos were created).
Video 1 – Introduction
Video 1 – corrections /updates
At 3:15 the video states…….
“Local badger population densities vary considerably throughout the country, from 20 adults per km2 in the Southwest to less than 1 adult per km2 in less favourable areas. The last national survey of the badger population in 1997 estimated that it was around 325,000. There is the perception that in some areas the badger population has increased dramatically since then, but there is no evidence currently available to support this.”
A national badger survey carried out from 2011-2013 (Judge et al. 2014; Judge et al. 2017) estimated that average badger densities in the south west were around 6 badgers per km. In particularly high density areas badger densities can be 20 per km2, as quoted in the video, but this is more the upper value, rather than the average across the whole south west region.
This more recent study estimates that the population is 424,000 for England and 61,000 for Wales (Judge et al. 2017). It is important to remember that this was conducted in 2011-2013, which was prior to the roll out of culling across England. These population estimates use modern genetic based methods (which makes it difficult to compare the numbers to previous studies), but as the authors state “our results are consistent with a marked increase in the badger population of England and Wales since the 1980s”. Comparisons of main sett numbers (comparing 2011-13 to the 1985-88 surveys) also suggest a large increase in the badger population, with a 103% increase in England, but no change in Wales (Judge et al. 2014).
Video 2 – Identifying badger activity
Video 2 – corrections / updates
At 1:10 the video states…
“The relationship between badgers, cattle and bovine TB is extremely complex. Badgers undoubtedly become infected with bovine TB and can pass it on, but what proportion of cattle herd breakdowns are caused by badgers is unknown.”
It is true that there is a lot of uncertainty over the proportion of breakdowns which are caused by badgers (as opposed to by infected cattle). A study published after this video has estimated the contribution of badgers to TB breakdowns using data from the RBCT (Donnelly & Nouvellet 2013). This study found the following:
- Badgers to cattle transmission is estimated to cause 6% (1-25%) of cattle breakdowns
- Further cattle to cattle transmission means that TB from badgers is then transmitted further, so that the overall contribution to cattle breakdowns is 52% (9-100%).
There is a lot of uncertainty around these numbers (hence the wide ranges in the brackets), for more details about this study see the fact sheet and post on this website.
At 4:02 the video states……
“In high density areas there are usually 3 to 6 setts per territory, but in lower density areas there can be up to 40.”
I think this statement must have been a slight mistake, of course there will not be almost 10 times the number of setts in low density areas. Although the density of badger groups (main setts) varies among land types in the UK (higher in the SW and lower in the N/E), numbers of setts per main sett (ie setts per group) recorded in the national sett survey are actually similar in high density and low density areas (Judge et al. 2014).
Video 3 – Biosecurity at pasture
Video 3 – corrections / updates
At 2: 30 the video states….
“While contact with faeces, urine and other excretions from infectious badgers are a real risk of disease transmission the M. bovis bacteria may only remain infectious on pasture for a few days to a few weeks depending on the weather. Therefore, it is highly unlikely that any faeces taken up during the silaging process will still be infectious by the time it is fed to cattle.”
Several different experimental studies have investigated the survival times of M. bovis in different environments, which are summarised in several fact sheets on this website.
Although it is true that risk from silage are probably lower than other sources, longer term survival of M. bovis in silage cannot be ruled out (at least based on the limited available science on the subject). See the survival of M bovis in feed water and soil fact sheet.
Video 4 & 5 Biosecurity in farm buildings (no updates required)
If you are interested in free biosecurity advice contact the TB advisory service at http://www.tbas.org.uk/
TB trends in the badger cull areas
October 31st 2018
Recently a report was published by APHA which contains summary TB statistics for the first 10 licensed ‘badger control’ or cull areas. Click here to download this report.
The report contains measures of cattle TB incidence (the rate that new breakdowns occur) and TB prevalence (the % of herds under restrictions). These statistics are provided for the three years prior to each cull starting (this gives an idea of any trends or patterns prior to culling) and for each year during the culls.
The report covers up to the end of 2017, so provides data for the first 10 badger cull areas which started between 2013 and 2016. Cull areas licensed in 2017 and 2018 have not been underway for long enough for the data to be available, but they will be included in subsequent reports. The map to the right and table below show the details of the current badger cull areas active in England (in 2018).
|County||Year started||size (km2)|
The statistics in this report are potentially quite interesting and give an idea of the TB trends in these areas, indicating whether TB is increasing, decreasing or stable. However, it is very important to note that on their own these data cannot tell us why these changes are occurring. This is clearly outlined by the authors of the report who state that “these data alone cannot demonstrate whether the badger control policy is effective in reducing bovine TB in cattle”. Unfortunately several organisations and individuals have ignored this and used these latest figures as evidence the cull are “working”. They may very well be working, but these latest statistics can not prove this for a number of important reasons.
If you look at any of the TB statistics (either in various reports, using the TB dashboard, or using ibTB) you can see that the numbers vary up and down over time and from area to area. It is therefore possible that TB could increase or decrease due to other factors which are unrelated to culling. This is clearly demonstrated by the fact that TB trends are often not stable in cull areas in the years prior to culling.
To demonstrate that culling is causing changes in TB in cattle we need to compare the rates or numbers of breakdowns in cull areas to areas without culling (see example below). There may be a benefit from culling (ie fewer TB breakdowns than would have occurred without culling) even if the raw trends in the data (ie the green arrow below) are decreasing, stable or even increasing (as the increase may be much less than in areas without culling, as in the bottom left graph – suggesting a benefit). Likewise, even if TB is decreasing this does not mean that culling is the cause, as it may have declined anyway due to other factors (as in the top middle and top right graphs).
The changes in TB incidence in the RBCT (randomised badger culling trial) were estimated by comparing areas with culling to matched controls without culling, producing the following results below (Taken from Godfray et al. (2013) ).
Again I stress that the above figures are changes in TB incidence (rate of new breakdowns) relative to the control areas without culling.
To date the only study that has compared TB incidence rates in cull areas to the comparison areas without culling is the study by Brunton et al. (2017) which uses only the first two years of data and is also summarised here. There are many limitations and caveats to this work, but to date this is the only evidence that that badger culling is causing changes in TB in cattle. An updated report/paper using four years of data is currently being prepared by APHA. Until then the data in this recent report may be interesting, but unfortunately they cannot answer the question “are the culls working?”.
Bovine TB in foxhounds
September 18th 2018
Back in 2017 there were several articles in the press on the subject of TB in foxhounds, specifically at the Kimblewick hunt. This resulted in an investigation by APHA, the results of which were published in a recent paper in the journal ‘Transboundary and Emerging diseases’’.
The publication of this paper resulted in a second wave of articles in the press and (rather predictably) a second wave of discussion on social media, much of it questioning whether fox hounds may play a significant role in the transmission of TB to cattle. The paper is open access, so available for anyone to read (click on the link above), but I still thought it might be useful to produce a quick summary of what the paper says and what the results mean for the spread of TB in the UK.
What did the study involve?
The investigation was triggered because a hound was put down (it was suffering from anorexia, excessive thirst and urination) and post mortem suggested that this animal was infected with Mycobacteria. APHA then became involved and confirmed that the animal was infected with Mycobacterium bovis (which causes TB in cattle), specifically genotype ‘10:a’.
Following this a “test and cull” policy was applied at the kennels (test the hounds and remove those with a positive reaction) with the aim of containing the spread and removing any other potentially infected animals. Hounds were tested using two tests:
- IGRA (interferon gamma release assay), essentially a modified version of the interferon gamma or blood test used on cattle (click here for factsheet on the gamma test).
- DPP (dual path platform) Vet TB test an antibody (serological) blood test developed for deer but regularly used by APHA to test badgers.
All dogs testing positive for either of these tests were euthanased and then subjected to gross post-mortem examination (PME – carcass inspected for lesions). Samples from some of these euthanased animals (but not all) were also taken for mycobacterial culture (where M. bovis is grown from samples in the lab).
Both the IGRA and DPP test for an immune response which indicates that the animal has been exposed to M. bovis. Although, it should be noted that neither of these tests have been specifically validated for use on dogs.
What where the results?
The results for this study are quite complicated as different numbers of hounds tested positive for various combinations of IGRA, DPP and culture. Overall the results suggest that large numbers of hounds at the kennels were infected with M. bovis and several were in advanced stages of the disease, with the bacteria cultured from several organs and also from urine. Several people in contact with the hounds were also tested, and one was diagnosed with TB (it is not possible to know if this was from the hounds or other sources). The main results are sumarised in the infographic below:
The testing at the kennels ran from the end of 2016 to July 2017. Following the results above it was deemed that the remaining 57 hounds were unlikely to be infected/infectious, so voluntary restrictions at the kennels were lifted.
How did the hounds become infected?
The hunt operates across several counties in the edge and low risk area in England, where TB incidence in cattle is relatively low (compared to the high risk area – for a map of the risk areas click here). It is difficult to identify an exact source of infection, but various options were considered and ranked as part of an epidemiological investigation conducted by the authors of the study.
The potential sources of infection were:
- Movement of infected hounds from other kennels within the high risk area. Hounds at these kennels may have become infected from eating fallen stock (raw meat from culled cattle) and then carried the infection with them. This was viewed as the most likely route.
- Feeding fallen stock infected with M. bovis. Rather than the infection moving in from other areas it is possible that the hounds at this kennel were directly fed meet from cattle infected with M. bovis. This was viewed as possible, but relatively unlikely, based on the TB history and status of where cattle fed to the hounds were sourced.
- Exposure to infected wildlife or cattle (either directly or by M. bovis contaminated environment). According to the authors, most of the area operated by the hunt has low levels of TB in cattle and no evidence of TB in wildlife (although little data is available on this). This was viewed as an unlikley source of infection, partly because it is very rare to find dogs infected with M .bovis, even in areas with high levels of TB in badgers and cattle (which suggest that transmission risks via these routes are low).
It seems likely that the feeding of infected fallen stock to hounds was a likely source. This has resulted in the following changes outlined in the paper….
“As a proportionate risk mitigation strategy, DEFRA has introduced tighter restrictions on the collection and feeding of fallen stock to hounds in registered kennels. Since 10 October 2017 the feeding of offal from livestock species to dogs from recognized kennels or packs of hounds has been banned in England (Anonymous, 2017). Hunt kennel operators must also carry out additional examinations for lesions of TB in fallen stock originating from “high risk” premises”
What do the results of this study mean?
TB has been previously found in small numbers of dogs, but the general assumption has been that dogs are dead end hosts which are unlikely to spread infection further. This study challenges this previous assumption – it provides evidence of transmission between dogs and demonstrates excretion of M. bovis by infected animals. BUT it is important to stress that this study is highly unusual and is the first example of such a large outbreak of TB with evidence of spread through a dog population. It may be that this was the result of the specific conditions at these kennels.
This study therefore raises the possibility that dogs may be able to infect other species such as cattle or wildlife. It also highlights that current practices of feeding fallen stock to dogs has a potential risk of disease transmission. However, it would be wrong to conclude from this one study that large numbers of hounds are infected in the British countryside and are contributing significantly to the hundreds of TB breakdowns that occur every year. If other kennels are infected to the same extent as in this study (with multiple animals with clinical signs of TB) then this should be detected, as happened here. Even if there is a risk from infected hounds, it seems likely that this risk is localised and significantly lower than the risks from other infected cattle, or from infected wildlife (principally badgers), both of which are far more numerous, widespread, and are the main sources of TB in the UK.