Research and analysis

Lincolnshire (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 Lincolnshire, 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 This includes ‘Officially Tuberculosis-Free Status Withdrawn’ (OTF-W) incidents and ‘Officially Tuberculosis-Free Status Suspended’ (OTF-S) incidents.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

The cattle industry in Lincolnshire is predominantly beef based, as shown in Appendix 1. Beef farms provide an outlet for the abundance of arable crop products and by-products grown in the county. There continues to be a decline in cattle numbers both in terms of farms and animals; those that remain are spread across the county. Almost half of all herds are small (between 1 to 50 cattle), with only 3% of herds having more than 500 cattle (see Appendix 1). There is one livestock market in Louth, which provides an outlet for store, breeding and fat cattle. There are 10 Licensed Finishing Units (LFUs) in the county, with 2 new units approved in 2021.

New TB incidents

During 2021, there were 22 new TB incidents in Lincolnshire. This figure was unchanged from 2020, as presented in Figure 1. However, the number of OTF-W incidents reduced by almost half, from 11 in 2020 to 6 in 2021. There were 16 OTF-S incidents (up from 11 in 2020). There were no unusual TB incidents in cattle or reports of TB in other farmed or captive non-bovine species in Lincolnshire during 2021.

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

Year	OTF-W	OTF-S	Total
2016	1	5	6
2017	3	8	11
2018	6	6	12
2019	6	9	15
2020	11	11	22
2021	6	16	22

Thirteen out of the 22 TB incidents in 2021 were detected on radial surveillance testing (RAD), as displayed in Figure 2. Four incidents were detected using routine surveillance testing of herds (RHT), three incidents by enhanced surveillance in potential or confirmed TB hotspot areas (HS), one by check testing (CT), and one by pre-movement testing (PRMT). This shows that the current policy of enhanced testing within a 3km radius of OTF-W incidents is key for early disclosure of disease within the LRA.

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

Disclosing test type	Number of new TB incidents
Check test (CT)	1
Pre-movement test (PRMT)	1
Radial test (RAD)	13
Routine herd test (RHT)	4
Hotspot test (HT)	3

Post-movement testing remains mandatory for animals bought into Lincolnshire from higher TB risk areas of GB. No TB herd incidents were disclosed at post-movement testing of cattle in 2021, even though a total of 8,912 post-movement tests were carried out, an increase of 1,800 on the number completed in 2020 (7,189). The figure for 2020 was unusually low, which is likely due to fewer movements due to COVID-19 restrictions. It is possible that Lincolnshire cattle farmers are increasingly considering the disease risks associated with the purchase of cattle and buying more animals from lower-risk farms than in the past.

Geographical distribution of TB incidents

As in previous years, the new incidents in Lincolnshire were predominantly clustered into 2 areas of the county (Figure 3). Both were areas with a relatively high cattle density, one in the north-east and one in the south-west of the county. These 2 clusters overlap with confirmed hotspot area HS23 and potential hotspot area HS28 and are discussed below.

Whole genome sequencing (WGS) replaced genotyping at the Animal and Plant Health Agency (APHA) in 2021. Four OTF-W incidents in Lincolnshire in 2021 were due to infections with the WGS clade B3-11 of M. bovis; 2 within Hotspot 23 and 2 within Potential Hotspot Area 28 (Figure 3). The homerange for clade B3-11 (the most common strain of M. bovis in HS23) includes Lincolnshire, Staffordshire, Derbyshire, and Cheshire. It is equivalent to genotype 25:a, which had been detected in 17 TB incidents in Lincolnshire since 2017.

Figure 3: Location of cattle holdings in Lincolnshire 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.

As can be seen from Figure 4 and Appendix 3 Table 5, OTF-W incidents in Lincolnshire in 2021 were attributed to different likely sources of infection, with a medium level of uncertainty. Spread into and from wildlife reservoirs of infection remains a concern in the south-west of the county.

Figure 4: Map of the source of infection pathway recorded with the highest level of certainty, for OTF-W incidents, and the location of OTF-S incidents in Lincolnshire 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

Confirmed Hotspot Area HS23

The south-west cluster of incidents in Figure 3 is within HS23. In 2021, 2 new OTF-W incidents were detected in the Lincolnshire portion of HS23, a decrease from 3 in 2020.

HS23 was initiated in 2018 in west Lincolnshire and north-east Leicestershire. In June 2020 the area was extended further into Leicestershire and Lincolnshire and included part of south-east Nottinghamshire (Figure 5). Two badger carcases collected within the area were M. bovis positive in 2020 (genotype 25:a, WGS clade B3-11). The M. bovis isolates from both badgers had a close genetic relationship with the local cluster of cattle incidents, based on WGS analysis. This showed that there was a credible epidemiological link between the cluster of cattle TB incidents and infected badgers in the area. As a result, what had been a potential hotspot area became a confirmed bovine TB Hotspot on 1 August 2020. From September 2020 licensed culling of badgers for TB control purposes started in parts of HS23, and continued during 2021. Further information can be found in TB surveillance in wildlife – confirmed hotspots in the Low Risk Area of England.

In 2021, 2 found-dead badgers were reported in the Lincolnshire portion of HS23. One of these was no longer present when APHA staff arrived, and the other was too decomposed for examination. Therefore, no further update is available on the presence of TB in road-kill wildlife.

Potential Hotspot Area HS28

A cluster of seemingly unrelated OTF-W incidents around the town of Louth, in the east of the county, were disclosed in 2019 and 2020. These incidents, and others in the area, could not reasonably be attributed to introductions of infected cattle. Following the disclosure of 5 TB incidents of the same genotype arising in close proximity over a short period of time and, with no clear infection pathway for four of them, a potential hotspot area (HS28) was declared on 1 September 2020. This cluster is most closely genetically related to isolates from Cheshire, so cattle bought from this county may have led to the original incursion.

In 2021 there were 4 new OTF-W incidents in HS28, a reduction from 6 in 2020. Of the 4 incidents, 2 were within herds with a previous incident in the preceding 2 years, indicating recurrent infection. No WGS analysis has yet been determined on the isolates from cattle removed from these farms to see if they are linked to the other cases within HS28. Samples from cattle removed from the other 2 incidents failed to yield M. bovis on culture, and no WGS data could be gathered.

Wildlife TB surveillance continued during 2021 in HS28 through post-mortem examination and bacteriological culture of samples from road-traffic accident (RTA) badgers and deer. Infection with M. bovis was not detected in any of the 32 RTA badger or 6 deer carcases examined in 2021. No extra cattle TB surveillance measures have been instigated over and above the existing radial TB surveillance regime around holdings with OTF-W incidents. Figure 5 provides an overview of the radial surveillance zones around OTF-W incidents in HS28 and HS23 of Lincolnshire.

Figure 5: Potential hotspot areas and radial surveillance zones around OTF-W incidents that were active, completed or not instigated in Lincolnshire 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 Lincolnshire 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 22 (100%) of new TB incidents in Lincolnshire 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 to the annual reports 2021.

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

• purchase of undetected infected cattle
• probably infected badgers (within HS23)

The movement of cattle with undetected infection continued to be the main pathway of infection for cattle herds in Lincolnshire in 2021, resulting in a weighted contribution of 30% to the likely sources of infection for herds with new TB incidents (see Appendix 3).

Within Hotspot 23 local spread between cattle and wildlife remains a key pathway. There is anecdotal suggestion of local spread in Hotspot 28, but no evidence yet to support this.

There was a high degree of uncertainty around the source of incidents in 2021, with other or unknown sources having 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). This is likely a reflection of the higher proportion of OTF-S incidents in this reporting period. OTF-S incidents are generally more difficult to ascribe to a definitive source of infection.

Skin test reactors and interferon gamma test positive animals removed

During 2021, a total of 108 animals were removed as TB test reactors. Of these, 52 were skin test reactors and 56 were positive by the supplementary interferon gamma (IFN-γ) blood test, as shown in Figure 6. Compared with 2020, this was a decrease on the number of skin reactors (83), and an increase in the number of IFN-γ test positive animals (12). The IFN-γ test has a higher sensitivity but lower specificity than the comparative skin test and so is likely to disclose more TB positive animals. It is able to detect infection at an earlier stage of infection.

Figure 6: Number of skin test reactors and interferon gamma (IFN-γ) test positive cattle removed by APHA for TB control reasons in Lincolnshire, from 2016 to 2021.

Year	Skin test reactors	Interferon gamma reactors	Total
2016	8	4	12
2017	21	16	37
2018	49	20	69
2019	36	29	65
2020	83	12	95
2021	52	56	108

The financial burden of TB in Lincolnshire to the taxpayer in 2021 was low in terms of the overall number of incidents and number of cattle slaughtered. Public money is predominately spent on paying for TB testing and compensation for compulsorily removed animals. The burden to the individual farmer is variable and dependent on the business type. The TB Advisory Service (TBAS) now offer visits to farmers in the LRA and represents an important tool in building resilience into the farm business.

Forward look

Current surveillance and incident management measures are keeping the incidence of TB in Lincolnshire stable. Overall, disease incidence remains low, with the number of OTF-W incidents falling in 2021 for the first time in 5 years. The total number of incidents was unchanged from 2020, after 4 consecutive years in which it increased. Enhanced testing of cattle, predominantly through radial testing, is helping to detect infected herds earlier. With maintenance of this robust testing, alongside improvements to biosecurity and education and encouragement of responsible cattle sourcing practices, the outlook for Lincolnshire maintaining its low TB risk status is positive despite the confirmed TB hotspot (HS23) in the south-west of the county.

Appendix 1: Cattle industry demographics

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

Size of herds	Number of herds in Lincolnshire
Undetermined	20
1-50	337
51-100	130
101-200	110
201-350	66
351-500	27
501+	21
Total number of herds	711
Mean herd size	108
Median herd size	50

Table 2: Number (and percentage of total) of animals by breed purpose in Lincolnshire at 1 January 2021.

Breed purpose	Number (and percentage of total) cattle in Lincolnshire
Beef	63,967 (83%)
Dairy	11,209 (14%)
Dual purpose	1,305 (1%)
Unknown	3
Total	76,484

Appendix 2: Summary of headline cattle TB statistics

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

Herd-level statistics	2019	2020	2021
(a) Total number of cattle herds live on Sam at the end of the reporting period	923	921	865
(b) Total number of cattle herds subject to annual TB testing (or more frequent) at the end of the reporting period (any reason)	145	199	208
(c) Total number of whole herd skin tests carried out at any time in the period	328	335	370
(d) Total number of OTF cattle herds having TB whole herd tests during the period for any reason	254	269	257
(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)	881	867	820
(f) Total number of cattle herds that were not under restrictions due to an ongoing TB incident at the end of the report period	910	904	852
(g.1) Total number of new OTF-S TB incidents detected in cattle herds during the report period	9	11	16
(g.2) Total number of new OTF-W TB incidents detected in cattle herds during the report period	6	11	6
(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?	5	1	3
(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	2
(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?	5	0	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)?	0	10	5
(h.5) Of the new OTF-W herd incidents, how many were first detected through routine slaughterhouse TB surveillance?	0	0	0
(i.1) Number of new OTF-S incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	4	4	8
(i.2) Number of new OTF-W incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	3	6	5
(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)	5	10	9
(k) Number of OTF-W herds still open at the end of the period that are within a finishing unit	1	1	1
(l) New confirmed (positive M. bovis culture) incidents in non-bovine species detected during the report period (indicate host species involved)	0	0	0

Table 4: Animal-level summary statistics for TB in cattle in Lincolnshire during 2021.

Animal-level statistics (cattle)	2019	2020	2021
(a) Total number of cattle tested in the period (animal tests)	47,697	45,374	55,128
(b.1) Reactors detected by tuberculin skin tests during the year	36	83	52
(b.2) Reactors detected by additional IFN-γ blood tests (skin-test negative or IR animals) during the year	29	12	56
(c) Reactors detected during year per incidents disclosed during year	4.33	4.32	4.91
(d) Reactors per 1,000 animal tests	1.36	2.09	1.96
(e.1) Additional animals slaughtered during the year for TB control reasons (dangerous contacts, including any first time IRs)	12	1	1
(e.2) Additional animals slaughtered during the year for TB control reasons (private slaughters)	5	5	10
(f) SLH cases (tuberculous carcases) reported by the Food Standards Agency (FSA) during routine meat inspection	3	1	3
(g) SLH cases confirmed by culture of M. bovis	0	0	0

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 or 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). WGS of M. bovis isolates can be a powerful tool in identifying a likely source of infection, however WGS clades are not 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 Lincolnshire in 2021.

Source of infection	Possible (1)	Likely (4)	Most likely (6)	Definite (8)	Weighted contribution
Badgers	11	0	3	0	11.8%
Cattle movements	13	0	5	3	29.7%
Contiguous	3	3	0	0	8.3%
Residual cattle infection	0	1	0	0	1.4%
Domestic animals	0	0	0	0	0.0%
Non-specific reactor	0	0	0	0	0.0%
Fomites	1	0	0	0	0.6%
Other wildlife	5	1	0	0	4.3%
Other or unknown source	1	4	7	0	43.8%

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 22 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 6 new OTF-W TB incidents in Lincolnshire in 2021, 2 were assessed to be 3B, 2 were assessed to be 4B and 2 were assessed to be 4C. None of these meet the eligibility criteria for removal from the county TB incidence calculations during an application for OTF status.