Research and analysis

Cumbria (low risk area) year end report 2021

Updated 16 February 2023

Introduction

The Low Risk Area (LRA) was established in 2013. In 2014 this area was incorporated into the UK government’s strategy to achieve Officially Tuberculosis-Free (OTF) status for England by 2038. A key action was to recognise the different levels of bovine tuberculosis (TB) in different parts of the country and to vary the approach to control accordingly. Overall, the LRA has a very low and stable incidence of infected herds. The current strategy seeks to rapidly control infection when it arises through:

• high sensitivity testing of affected herds
• temporarily enhanced local surveillance (radial and hotspot testing)
• mandatory pre- and post-movement testing of cattle entering the LRA from higher risk areas of the UK

The aim is to preserve the favourable disease status of this area so that its counties can be declared OTF as soon as possible.

This report describes the frequency and geographical distribution of TB in 2021 in cattle herds in the county of Cumbria, which is part of the LRA.

TB in cattle and other mammals is primarily caused by the bacterium Mycobacterium bovis (M. bovis) and the disease is subsequently referred to in this report as TB. Although other sources may refer to TB ‘breakdowns’, this report will use the term ‘incidents’ throughout.

This report is intended for individuals involved in the control of TB, both locally and nationally. This includes, but is not limited to farmers, veterinarians, policy makers and the scientific community.

Details of the data handling methodology used in this report, a glossary of terms, and the TB control measures adopted in the LRA, can be found in the Explanatory supplement for the annual reports 2021.

Types of TB incident

Unless otherwise specified, this report includes all new TB incidents detected during the reporting period. This includes ‘Officially Tuberculosis-Free Status Withdrawn’ (OTF-W) incidents and ‘Officially Tuberculosis-Free Status Suspended’ (OTF-S) incidents.

OTF-W incidents are those involving one or more test reactors with typical lesions of TB identified at post-mortem meat inspection, or one or more animals with M. bovis-positive culture results from tissue samples collected from carcases during the PM inspection, or both.

OTF-S incidents are triggered by reactors to the Single Intradermal Comparative Cervical Tuberculin (SICCT) test, but without subsequent detection of TB lesions or positive culture results in any of those animals.

Cattle industry

Cumbria has over 433,000 cattle, equally distributed between beef and dairy farms. Cattle herd sizes vary across the region, as shown in Appendix 1. There are 10 livestock markets in Cumbria, 6 of which hold TB-exempt approvals, but none of them hold TB slaughter gatherings at present. The county has one Licensed Finishing Unit (LFU). There is movement of cattle from Cumbria into Scotland as well as a significant number of cattle entering the county from Northern Ireland and the Republic of Ireland. These are generally destined for beef finishing or fattening units. Pedigree breeding bulls from Northern Ireland also move onto Cumbrian farms.

New TB incidents

In 2021, the total number of new TB incidents (18) decreased by 5 compared to 2020 (23). Total incident numbers have been decreasing in Cumbria over the past 5 years, from a high of 33 in 2017, as shown in Figure 1. In 2021, the number of OTF-S incidents decreased from 19 to 11, whilst OTF-W incidents nearly doubled compared to 2020 (from 4 to 7).

Figure 1: Annual number of new TB incidents in Cumbria from 2016 to 2021.

Year	OTF-W incidents	OTF-S incidents	Total
2016	16	16	32
2017	12	21	33
2018	9	18	27
2019	5	24	29
2020	4	19	23
2021	7	11	18

Most new TB incidents were identified through enhanced surveillance testing, including 8 by radial testing (RAD), and 4 by specific hotspot testing (HS), as displayed in Figure 2. Slaughterhouse surveillance, routine (4 yearly) herd testing, other check testing and post-movement testing each identified one new TB incident in 2021, as displayed in Figure 2 and Appendix 2.

Figure 2: Number of new TB incidents (OTF-W and OTF-S) in Cumbria 2021 according to the surveillance method that detected them.

Disclosing test type	Number of new TB incidents
12 month test (12M)	2
Check test (CT)	1
Radial test (RAD)	8
Routine herd test (RHT)	1
Slaughterhouse test (SLH)	1
Post-movement test (POSTMT)	1
Hotspot test (HS)	4

There were no incidents of M. bovis infection in non-bovine domestic species or captive deer in Cumbria in 2021.

Geographical distribution of TB incidents

All but one of the 18 new TB incidents detected in Cumbria during 2021 were in the eastern half of the county, along the Eden Valley and to the south of the Lake District National park where the land is more suitable for farming.

Whole Genome Sequencing (WGS) replaced genotyping at APHA in 2021. There were 2 new incidents in the Eden Valley in 2020, increasing to 6 in 2021 (4 OTF-W and 2 OTF-S) (Figure 3). These TB incidents were all within the Melmerby and Ousby area of Cumbria. For the 4 OTF-W in this area, all caused by clade B3-11 of M. bovis, exposure to infected badgers could not be ruled out and no clear evidence of introduction via animal movements was found (Figure 4).

Another of the new OTF-W cases was in the Brampton area further north and confirmed as clade B6-86 (Figure 3). Direct or indirect contact with a wildlife reservoir was the most likely source of infection for the affected herd. There was no relationship found with a previous OTF-W incident and 2021 OTF-S incident in the area (Figure 4).

There were fewer TB incidents towards the south of the county compared to 2020.

No TB incidents emerged in the north-west of Cumbria compared to 2020.

The county currently has two active TB Hotspot Areas: confirmed hotspot HS21 (central eastern area) and potential hotspot HS26 (southern area), as shown in Figure 3 and Figure 5.

Figure 3: Location of cattle holdings in Cumbria with new TB incidents (OTF-W and OTF-S) in 2021, and cattle holdings with pre-2021 OTF-W incidents still ongoing at the beginning of 2021, overlaid on a cattle density map. Note that ‘OTF-W Introduced 2021’ refers to OTF-W incidents in which cattle movements were the most likely source of infection.

Figure 4: Map of the source of infection pathway recorded with the highest level of likelihood, for OTF-W TB incidents, and the location of OTF-S incidents in Cumbria which started in 2021. Local cattle refer to residual infection and contiguous cattle risk pathways. Purchased refers to cattle movement risk pathways. Wildlife refers to both badger and other wildlife risk pathways.

Potential or confirmed TB hotspot areas

East Cumbria confirmed hotspot (HS21)

HS21 was established in 2016 and subsequently confirmed in the spring of 2017 after the detection in the carcases of badgers found dead of the same strain of M. bovis as that associated with the cattle incidents in the area (genotype 17:z, now termed clade B6:23) (Figure 5).

There were no new OTF-W herd incidents in 2021 and there were no B6:23 cattle isolates identified within the hotspot for 3 consecutive reporting periods (2019, 2020 and 2021). Similar to 2020, in 2021 there were 4 new OTF-S incidents, all of which remained open at the end of 2021. For one of these OTF-S TB incidents, exposure to infected badgers was considered to be the most likely risk pathway, with possible risk pathways including exposure to infected wild deer and unknown sources. For the other 3 OTF-S incidents, cattle movements from the LRA, contiguous cattle contact, exposure to infected badgers or other wildlife and unknown sources were all considered to be possible risk pathways, but there was no evidence to support any one of these ahead of the others.

Badger TB control measures have been taking place in the area since 2018 and there have been no M. bovis-culture positive badgers found since 2019.

In 2020, farms in the outer section of the hotspot were eligible to move to annual testing, instead of 6-monthly testing, subject to certain eligibility criteria. In 2021, the area within HS21 where this applies was extended to include more farms.

South Cumbria potential hotspot (HS26)

HS26 was established in 2019, following a cluster of TB incidents in South Cumbria near Cartmel Fell, between Kendal and Windermere (Figure 5). Wildlife surveillance has taken place since August 2019, however M. bovis has not been identified in local badgers or wild deer so far. No enhanced TB control measures have been applied to cattle herds in HS26 to date, apart from the radial testing zones triggered around the OTF-W incidents from 2019.

There was one new OTF-S case in HS26 in 2021. Exposure to infected badgers was the most likely risk pathway, with possible risk pathways including movements from the High Risk Area (HRA). Figure 5 provides an overview of the radial surveillance zones around OTF-W incidents in HS21 and HS26 of Cumbria.

Figure 5: Potential hotspot areas and radial surveillance zones around OTF-W incidents that were active, completed or not instigated in Cumbria during 2021, by year of initiation.

Main risk pathways and key drivers for TB infection

The main risk pathways and key drivers for TB infection within Cumbria in 2021 are considered here. Evidence collected during APHA veterinary investigations into the source of infection within herds was used to inform this understanding. In 2021, all 18 (100%) of new TB incidents in Cumbria received a preliminary or final APHA veterinary investigation to identify the source of infection.

It can be challenging to retrospectively establish the route of infection for a TB incident herd. Ideally this investigation includes a thorough on-farm investigation and scrutiny of routinely collected data; such as cattle movement records, and the results of WGS where available. Up to 3 hazards and risk pathways were selected for each incident investigated. Each of these potential sources were given a score that reflects the likelihood of that pathway being the true one, based on the available evidence.

Details of the protocol used for these investigations, and the subsequent methodology used to calculate the weighted contribution of the different suspected sources of M. bovis infection can be found in the Explanatory supplement for the annual reports 2021.

The key drivers of the TB epidemic in Cumbria during 2021 were identified as follows:

• purchase of undetected infected cattle
• exposure to probable infected badgers
• contact with contiguous infected cattle herds

The movement of undetected infected cattle continues to be the main pathway of infection for cattle herds, with a weighted contribution of 15%. All pathways and the weighted contributions are given in Table 5, Appendix 3.

Exposure to infected badgers was considered to be the second most important risk pathway, with a weighted contribution of 14%. This appears to be relatively less important in 2021 compared to 2020, when its contribution was 20%.

Finally, contact with contiguous infected cattle herds was the third most important risk pathway, weighted contribution 12%. This emphasises the need for improved biosecurity practices.

There was a high degree of uncertainty around the source of new incidents in 2021. Other or unknown sources had a weighted contribution of 44%. This category is added to those incidents in which there was high uncertainty around the selected pathways, (see explanatory supplement for methodology).

Skin test reactors and interferon gamma test positive animals removed

As presented in Figure 6, the number of reactors removed for TB control purposes in Cumbria increased compared to 2020 (from 39 to 106). Of the 106 cattle that were removed for TB control purposes in 2021, 37 were skin test reactors (unchanged from 2020) and 69 were positive on the interferon gamma (IFN-γ) test (up from 2 in 2020).

Figure 6: Number of skin test reactors and interferon gamma (IFN-γ) test positive cattle removed by the Animal and Plant Health Agency (APHA) for TB control reasons in Cumbria from 2016 to 2021.

Year	Skin test reactors	Interferon gamma reactors	Total
2016	107	134	241
2017	59	199	258
2018	57	225	282
2019	77	113	190
2020	37	2	39
2021	37	69	106

The increased number of IFN-γ test positive animals removed can be attributed to 2 incidents, which concluded in 2021. Each had 19 and 18 animals removed respectively. Additionally, the Melmerby-Ousby cluster of cases contributed 13 IFN-γ test positive animals.

Forward look

To further reduce the TB incidence and maintain LRA status, collectively, Cumbrian farmers need to remain vigilant with the cattle they bring on to their farms, herd biosecurity and adherence to TB surveillance measures. Persistent, as well as new clusters arising within the county, will be areas of particular focus, whilst aiming to resolve herd incidents as quickly as possible and with the least impact on farm businesses as possible.

Appendix 1: Cattle industry demographics

Table 1: Number of cattle premises by size band in Cumbria at 1 January 2021 (RADAR data).

Size of herds	Number of herds in Cumbria
Undetermined	46
1-50	1,029
51-100	506
101-200	561
201-350	399
351-500	169
501+	154
Total number of herds	2,864
Mean herd size	151
Median herd size	84

Table 2: Number (and percentage of total) animals by breed purpose in Cumbria at 1 January 2021, given as a percentage of total cattle in the county.

Breed purpose	Number (and percentage of total) cattle in Cumbria
Beef	213,094 (49%)
Dairy	203,075 (47%)
Dual purpose	16,950 (4%)
Unknown	10 (less than 0.01%)
Total	433,129

Appendix 2: Summary of headline cattle TB statistics

Table 3: Herd-level summary statistics for TB in cattle in Cumbria in 2021.

Herd-level statistics	2019	2020	2021
(a) Total number of cattle herds live on Sam at the end of the reporting period	3,398	3,386	3,242
(b) Total number of cattle herds subject to annual TB testing (or more frequent) at the end of the reporting period (any reason)	706	463	380
(c) Total number of whole herd skin tests carried out at any time in the period	1,715	1,389	1,207
(d) Total number of OTF cattle herds having TB whole herd tests during the period for any reason	1,386	1,141	947
(e) Total number of OTF cattle herds at the end of the report period (herds not under any type of Notice Prohibiting the Movement of Bovine Animals (TB02) restrictions)	3,355	3,345	3,201
(f) Total number of cattle herds that were not under restrictions due to an ongoing TB incident at the end of the report period	3,384	3,375	3,231
(g.1) Total number of new OTF-S TB incidents detected in cattle herds during the report period	24	19	11
(g.2) Total number of new OTF-W TB incidents detected in cattle herds during the report period	5	4	7
(h.1) Of the new OTF-W herd incidents, how many occurred in a holding affected by another OTF-W incident in the previous three years?	0	1	1
(h.2) Of the new OTF-W herd incidents, how many could be considered secondary to a primary incident based on current evidence?	1	1	0
(h.3) Of the new OTF-W herd incidents, how many were triggered by skin test reactors or 2x inconclusive reactors (IRs) at routine herd tests?	1	1	1
(h.4) Of the new OTF-W herd incidents, how many were triggered by skin test reactors or 2xIRs at other TB test types (such as forward and back-tracings, contiguous, check tests)?	3	3	5
(h.5) Of the new OTF-W herd incidents, how many were first detected through routine slaughterhouse TB surveillance?	1	0	1
(i.1) Number of new OTF-S incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	8	6	4
(i.2) Number of new OTF-W incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	3	0	4
(j) Number of OTF-W herds still open at the end of the period (including any ongoing OTF-W incidents that began in a previous reporting period)	6	3	3
(k) Number of OTF-W herds still open at the end of the period that are within a finishing unit	0	0	1
(l) New confirmed (positive M. bovis culture) incidents in non-bovine species detected during the report period (indicate host species involved)	0	1 (sheep)	0

Table 4: Animal-level summary statistics for TB in cattle in Cumbria from 2019 to 2021.

Animal-level statistics (cattle)	2019	2020	2021
(a) Total number of cattle tested in the period (animal tests)	285,775	224,679	204,786
(b.1) Reactors detected by tuberculin skin tests during the year	77	37	37
(b.2) Reactors detected by additional IFN-γ blood tests (skin-test negative or IR animals) during the year	113	2	69
(c) Reactors detected during year per incidents disclosed during year	6.55	1.70	5.89
(d) Reactors per 1,000 animal tests	0.66	0.17	0.52
(e.1) Additional animals slaughtered during the year for TB control reasons (dangerous contacts, including any first time IRs)	10	5	3
(e.2) Additional animals slaughtered during the year for TB control reasons (private slaughters)	3	5	2
(f) SLH cases (tuberculous carcases) reported by the Food Standards Agency (FSA) during routine meat inspection	7	6	6
(g) SLH cases confirmed by culture of M. bovis	1	0	1

Note (c) Reactors detected during year per incidents disclosed during year, reactors may be from incidents disclosed in earlier years, as any found through testing during the report year count here.

Note (g) SLH cases confirmed by culture of M. bovis, not all cases reported are submitted for culture analysis. All cases reported are from any period prior to or during restrictions.

Appendix 3: Suspected sources of M. bovis infection for all of the new OTF-W and OTF-S incidents identified in the report period

Each TB incident could have up to 3 potential risk pathways identified. Each risk pathway is given a score that reflects the likelihood of that pathway bringing TB into the herd. The score is recorded as either definite (score 8), most likely (score 6), likely (score 4) or possible (score 1). The sources for each incident are weighted by the certainty ascribed. Any combination of definite, most likely, likely, or possible can contribute towards the overall picture for possible routes of introduction into a herd. If the overall score for a herd is less than 6, then the score is made up to 6 using the ‘Other/Unknown Source’ option. Buffering up to 6 in this way helps to reflect the uncertainty in assessments where only ‘likely’ or ‘possible’ sources are identified.

Table 5 combines the data from multiple herds and provides the proportion of pathways in which each source was identified, weighted by the certainty that each source caused the introduction of TB. The output does not show the proportion of herds where each pathway was identified (this is skewed by the certainty calculation). Whole genome sequencing (WGS) of M. bovis isolates can be a powerful tool in identifying a likely source of infection, however WGS clades have not been determined for OTF-S herds. As a result of varying levels of uncertainty, only broad generalisations should be made from these data. A more detailed description of this methodology is provided in the Explanatory supplement for the annual reports 2021.

Table 5: Suspected sources of M. bovis infection for all new OTF-W and OTF-S incidents identified in Cumbria in 2021.

Source of infection	Possible (1)	Likely (4)	Most likely (6)	Definite (8)	Weighted contribution
Badgers	7	3	3	0	13.6%
Cattle movements	16	1	2	0	14.9%
Contiguous	2	3	3	0	12.0%
Residual cattle infection	0	0	1	0	2.3%
Domestic animals	0	0	0	0	0.0%
Non-specific reactor	1	2	0	0	3.9%
Fomites	1	0	0	0	0.5%
Other wildlife	7	4	0	0	8.8%
Other or unknown source	8	3	2	0	44.1%

Please note each TB incident could have up to 3 potential pathways so totals may not equate to the number of actual incidents that have occurred. In 2021, all 18 of the new TB incidents received a preliminary or final veterinary investigation to identify the source of infection.

Details of the methodology used to calculate the weighted contribution of the different suspected sources of M. bovis infection for all new incidents can be found in the Explanatory supplement for the annual reports 2021.

Appendix 4: Assessment of the origin of (and potential for spread of infection from) all the new OTF-W incidents identified in the report period

A risk matrix was used to identify isolated incidents that were likely to have been introduced to the LRA by cattle movements, while not causing any onward local spread. The following 2 questions were considered for each incident, and a score attributed. TB incidents with a score of 1A, 1B or 2A may be removed from the county TB incidence calculations during an application for OTF status (but remain in the incidence calculations in this report).

What is the probability of M. bovis infection being introduced to the LRA via infected cattle movements?

1. Definite - for example, traced reactors found in the LRA OTF-W incident herd in question as a result of spread tracings from another TB incident herd, genotype or WGS linked.
2. Likely - for example, a Reactor or IR originated from a previous incident herd (and the WGS or genotype does not suggest otherwise), other cattle were moved into the herd from previous incident herd (but were subsequently slaughtered without testing), or the trading practice of herd provides likely evidence (purchasing large numbers of cattle from the High Risk Area (HRA), or Edge Area, High and Intermediate TB areas of Wales, or from the island of Ireland).
3. Possible - not a closed herd, but cattle are purchased from the LRA, Scotland or EU Member States.
4. Not likely - indigenous infection is known in the locality, closed herd, genotype or WGS has been identified in local wildlife.

What is the probability of this being an isolated, sporadic (‘one-off’) incident, without secondary local spread from the index case?

A. Likely - no secondary incidents have been detected. There are no further incidents as a result of spread tracings anywhere and no genotype or WGS linked OTF-W incidents within 3km radial zone around the LRA OTF-W incident herd in question (or the 3km radial surveillance zone was not triggered).

B. Possible - no secondary incidents have been detected, but the dataset is incomplete. For example, incidents have occurred in the 3km radial zone, but only OTF-S ones, or if OTF-W, they were of an unknown or different genotype or WGS clade.

C. Not likely - secondary spread from the index case, or exposure to a common wildlife source has occurred. For example, OTF-W incidents have occurred in the 3km zone linked by genotype or WGS, or there is known wildlife infection in the area with this genotype or close WGS.

Of the 7 new OTF-W TB incidents in Cumbria in 2021, 4 were assessed to be 4C, 2 were assessed to be 3B and 1 was assessed to be 2B. None of these would be eligible for removal from the county TB incidence calculations during an application for OTF status.