Research and analysis

Lincolnshire (low risk area) year end report 2022

Updated 20 November 2023

Introduction

The Low Risk Area (LRA) of England 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 2022 in cattle herds in Lincolnshire, which is part of the LRA. In 2022, 12% of all new TB incidents in the LRA were detected in Lincolnshire.

TB in cattle and other mammals is primarily caused by the bacterium Mycobacterium bovis (M. bovis) and the disease is subsequently referred to as TB in this report. 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 2022.

Types of TB incident

Unless otherwise specified, this report includes all new TB incidents detected during the reporting period, 1 January to 31 December 2022. This includes both ‘Officially Tuberculosis-Free Status Withdrawn’ (OTF-W) and ‘Officially Tuberculosis-Free Status Suspended’ (OTF-S) incidents.

OTF-W incidents are those involving at least one skin test reactor (an animal positive to the Single Intradermal Comparative Cervical Tuberculin, or SICCT test) with either typical lesions of TB identified at post-mortem (PM) meat inspection, or at least one animal 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 skin 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. Almost half of all herds are small (between 1 to 50 cattle), with only 3% of herds having more than 500 cattle.

There is one livestock market in Louth, which provides an outlet for store, breeding and fat cattle. There were 10 Licensed Finishing Units (LFUs) operating in the county, with no new units approved in 2022.

New TB incidents

During 2022 there were 17 new TB incidents in Lincolnshire, a decrease from 22 in 2021 (Figure 1). Whilst this reduction is a positive outcome, it is too early to establish if it is the beginning of a long-term decline. The number of OTF-W incidents increased marginally from 6 in 2021 to 7 in 2022 and the number of OTF-S incidents decreased from 16 in 2021 to 10 in 2022.

There were no incidents of TB reported in non-bovine species in Lincolnshire during 2022.

Figure 1: Annual number of new TB incidents (OTF-W and OTF-S) in Lincolnshire, from 2013 to 2022

Year	OTF-W incidents	OTF-S incidents	Total
2013	3	6	9
2014	4	5	9
2015	3	5	8
2016	1	5	6
2017	3	8	11
2018	6	6	12
2019	6	9	15
2020	11	11	22
2021	6	16	22
2022	7	10	17

The headline cattle TB statistics for Lincolnshire are summarised in Appendix 2.

Unusual TB incidents

One OTF-S incident that began in May 2019 was resolved after 1,055 days, and one OTF-W incident that began in April 2021 was still open at the end of 2022. The long duration of the OTF-W incident was down to the disclosure of reactors or inconclusive reactors at the short interval tests.

Disclosing test type

Six of the 17 (35%) TB incidents that began in 2022 were detected on radial surveillance testing (RAD), as displayed in Figure 2. This is a reduction from 2021, when 13 out of 22 (59%) were detected by RAD. This is likely due to the reduced number of radial tests carried out and the overall reducing prevalence in the county.

Three incidents (of which 2 became OTF-W) were detected by enhanced surveillance ‘hotspot tests’ in the confirmed TB hotspot area of the southwest of Lincolnshire (HS23). This shows that the current policy of enhanced testing within a 3km radius of OTF-W incidents and enhanced surveillance in hotspots is key for early disclosure of disease within the LRA.

Figure 2 also shows routine herd tests detected 4 new TB incidents, 12-month post incident testing detected 2 new TB incidents and post-movement tests and slaughterhouse tests detected one new TB incident each.

Figure 2: Number of new TB incidents (OTF-W and OTF-S) in Lincolnshire, in 2022 according to the surveillance method that detected them

Disclosing test type	Number of new TB incidents	Total
12 month test	2	2
Hotspot test	3	3
Post-movement test	1	1
Radial test	6	6
Routine herd test	4	4
Slaughterhouse	1	1

The headline cattle TB statistics for Lincolnshire are summarised in Appendix 2.

Duration of TB incidents

A total of 18 TB incidents were resolved during 2022. Of these, 7 were new TB incidents that started in 2022, 8 started in 2021, 2 were from 2020 and one started in 2019.

Most of the incidents that closed in 2022 (both OTF-W and OTF-S) were resolved within 550 days of detection. One OTF-S incident that started in 2019 and was resolved in 2022 after 1,055 days on restrictions. One OTF-W incident that was under movement restrictions for more than 550 days was still open at the end of 2022, as described in the unusual TB incidents section of this report.

The median duration of incidents that closed in 2022 in Lincolnshire was 198 days (interquartile range (IQR) 172 to 334), which was considerably longer than other counties in the LRA. It was also 46.5 days longer than the median of incidents that closed in 2021, which was 151.5 days (IQR 102 to 267).

The median length of incidents in the LRA, Edge Area and High Risk Area (HRA) were 150 (IQR 98 to 194), 185 days (IQR 160 to 266.5) and 190 (IQR 163 to 279), respectively.

Of the 17 new TB incidents that started in 2022, 10 were still ongoing at the end of 2022, and their duration will be assessed when they are resolved.

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 correspond with Confirmed Hotspot 23 (HS23) and Potential Hotspot Area 28 (PHA28) and are discussed below.

Whole genome sequencing (WGS) replaced genotyping at APHA in 2021. Of the 7 OTF-W incidents in Lincolnshire in 2022, 6 were due to infections with the WGS clade B3-11 of M. bovis. Four of these were within PHA28 and one within HS23 (Figure 3).

The homerange for clade B3-11 (the most common strain of M. bovis in Lincolnshire) traditionally included Staffordshire, Derbyshire, north Shropshire, Cheshire and north Leicestershire and, from 2022, the 2 TB hotspot areas in Lincolnshire HS23 and PHA28. It is broadly equivalent to genotype 25:a, which was 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 2022, and cattle holdings with pre-2022 OTF-W incidents still ongoing at the beginning of 2022, overlaid on a cattle density map. Note that ‘OTF-W Introduced 2022’ 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 2022 were attributed to different likely sources of infection. Spread to and from wildlife reservoirs of infection remains a concern in the south-west of the county. Local anecdotal observations of increasing wildlife populations (both wild deer and badgers) have been frequently reported in veterinary field investigations.

One OTF-W incident was most likely a purchased pathway (labelled 5 in Figure 4). The farm was a dealer with a high throughput of cattle and the reactor was detected at slaughter (the one slaughterhouse incident of 2022). WGS analysis showed that the reactor’s isolate was not related to any other incidents in the near vicinity but was most closely related to isolates from HS23 (from where it was purchased 12 months before it was found to be a reactor) and Derbyshire. Follow-up testing showed no further confirmed reactors on the farm.

The 4 OTF-W incidents in PHA28, were closely related genetically (labelled 1 to 4 in Figure 4). Further investigation is underway to elucidate the source and spread of these incidents.

It was not possible to isolate M. bovis in bacteriological culture for WGS analysis from one of the 2 OTF-W incidents detected in HS23 and so it remains classified as ‘undetermined’.

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 2022. 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.

Figure 5 provides an overview of the radial surveillance zones (both active and completed) around OTF-W incidents. Active radial zones are largely located within HS23 and PHA28.

Figure 5: Hotspot areas and radial surveillance zones around OTF-W incidents that were active, completed or not instigated in Lincolnshire during 2022, by year of initiation.

Potential or confirmed TB hotspots

Confirmed Hotspot 23

HS23 was initiated in 2018 in west Lincolnshire and north-east Leicestershire (WGS clade B3-11, genotype 25:a). 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 (WGS clade B3-11, genotype 25:a). 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 2022. Further information can be found in TB surveillance in wildlife – confirmed hotspots in the Low Risk Area of England.

The south-west cluster of incidents in Figure 3 is within HS23. In 2022, 2 new OTF-W incidents were detected in the Lincolnshire portion of HS23, unchanged from 2021.

In 2022, there were no collections of badger or wild deer carcases in the Lincolnshire portion of HS23. Although collections were suspended during part of the year due to prioritisation of the avian influenza outbreak, reports were still received from the public. One badger carcase was reported to APHA for collection in HS23, but this was not possible due to resource issues. It is concerning that reporting has reduced, as collection of ‘found-dead’ wildlife continues to help with the epidemiological picture in cattle herds.

Potential Hotspot Area 28

A cluster of seemingly unrelated OTF-W incidents around the town of Louth (WGS clade B3-11, genotype 25:a), 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 4 of them, APHA declared PHA28 on 1 September 2020. This cluster is most closely genetically related to M. bovis isolates from Cheshire, so undetected infected cattle brought in from this county may have been responsible for the original introduction of TB into the area.

Thirty-nine cattle incidents were disclosed between 2019 and 2022 in PHA28 (19 OTF-W and 20 OTF-S). In 2022 there were 4 new OTF-W incidents in PHA28, which was the same as 2021.

Since 2020, 73 badgers and 15 deer were reported in PHA28, of which 42 carcases were collected. During 2022, 7 wildlife carcases (4 badgers and 3 deer) were reported to APHA, of which 3 badgers were collected and examined. All 3 badger carcases tested negative for M. bovis infection. Investigations into the cluster of TB incidents in cattle herds continues. Phylogenetic analysis of WGS data from M. bovis isolates indicates that the cattle incidents are closely related, and so local spread of infection in PHA28 is likely.

Skin test reactors and interferon gamma test positive animals removed

During 2022, a total of 59 animals were removed as TB test reactors. Of these, 40 were skin test reactors and 19 were positive by the supplementary interferon gamma (IFN-γ) blood test, as shown in Figure 6.

Compared with 2021, this was a decrease on both the number of skin reactors (52) and IFN-γ test positive animals (56). Figure 6 shows how the total number of reactors removed in Lincolnshire increased from 37 in 2017, to a peak of 108 in 2021.

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 can also detect infection at an earlier stage of infection than the skin test.

Figure 6: Number of cattle that tested positive to the skin test or interferon gamma test and were removed by APHA for TB control reasons in Lincolnshire, from 2017 to 2022.

Year	Skin test	Interferon gamma test	Total
2017	21	16	37
2018	49	20	69
2019	36	29	65
2020	83	12	95
2021	52	56	108
2022	40	19	59

Main risk pathways and key drivers for TB infection

Evidence collected during APHA veterinary investigations into the source of infection within herds was used to inform this understanding. In 2022, 3 of 17 (12%) 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.

As there were only 3 new TB incidents that received an APHA veterinary investigation in 2022, it is not possible to make generalisations about the key drivers of the TB epidemic in Lincolnshire during 2022 from this evidence alone.

For one herd, located in HS23, exposure to probable infected badgers was identified as the most likely pathway of infection, either at grazing, or at housing where feed stores were accessible to badgers.

For another herd, located in PHA28, contact with contiguous infected cattle was assessed as the most likely risk pathway, with exposure to badgers or wild deer also identified as possible risk pathways.

A final herd, situated outside of HS23 and PHA28 received a desktop veterinary assessment into the likely source of infection. It was assessed that the infection was most likely bought in by purchased cattle due to a high throughput of cattle on the farm.

Forward look

Current surveillance and incident management measures are keeping the overall incidence of TB in Lincolnshire low and stable, with the number of OTF-W incidents falling in 2022 for the first time in 5 years.

Enhanced testing of cattle, predominantly through radial testing, is helping to detect infected herds earlier. With maintenance of this robust cattle TB testing regime, 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 and the clustering of incidents in PHA28.

Appendix 1: cattle industry demographics

Table 1: Number of cattle herds by size category in Lincolnshire as of 31 December 2022 (RADAR data)

Size of herds	Number of herds
Undetermined	4
1 to 50	332
51 to 100	118
101 to 200	119
201 to 350	59
351 to 500	26
Greater than 501	23
Total number of herds	681
Mean herd size	111
Median herd size	51

Table 2: Number (and percentage of total) of animals by breed purpose in Lincolnshire as of 31 December 2022

Breed purpose	Number (and percentage of total) cattle
Beef	64,371 (84%)
Dairy	10,237 (13%)
Dual purpose	1,317 (1%)
Unknown	0%
Total	75,925

Appendix 2: summary of headline cattle TB statistics

Table 3: Herd-level summary statistics for TB in cattle in Lincolnshire in 2022

Note (a) and (f) Cattle herd counts in Appendix 2 Table 3 and Appendix 1 Table 1 differ due to different data sources used. Appendix 1 Table 1 uses data from RADAR, while Appendix 2 Table 3 uses data from Sam.

Herd-level statistics	2020	2021	2022
(a) Total number of cattle herds live on Sam at the end of the reporting period	921	865	865
(b) Total number of cattle herds subject to annual TB testing (or more frequent) at the end of the reporting period (any reason)	199	208	195
(c) Total number of whole herd skin tests carried out at any time in the period	335	370	348
(d) Total number of OTF cattle herds having TB whole-herd tests during the period for any reason	269	257	276
(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)	867	820	818
(f) Total number of cattle herds that were not under restrictions due to an ongoing TB incident at the end of the report period	904	852	853
(g.1) Total number of new OTF-S TB incidents detected in cattle herds during the report period	11	16	10
(g.2) Total number of new OTF-W TB incidents detected in cattle herds during the report period	11	6	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?	1	3	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	2	3
(h.3) Of the new OTF-W herd incidents, how many were triggered by skin test reactors or 2 time inconclusive reactors (2xIRs) at routine herd tests?	0	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)?	10	5	0
(h.5) Of the new OTF-W herd incidents, how many were first detected through routine slaughterhouse TB surveillance?	0	0	1
(i.1) Number of new OTF-S incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	4	8	3
(i.2) Number of new OTF-W incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	6	5	3
(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)	10	9	7
(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 2022

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) Slaughterhouse (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.

Animal-level statistics (cattle)	2020	2021	2022
(a) Total number of cattle tested with tuberculin skin tests or additional IFN-γ blood tests in the period (animal tests)	45,374	55,128	54,241
(b.1) Reactors detected by tuberculin skin tests during the year	83	52	40
(b.2) Reactors detected by additional IFN-γ blood tests (skin-test negative or IR animals) during the year	12	56	19
(c) Reactors detected during year per incidents disclosed during year	4.32	4.91	3.47
(d) Reactors per 1,000 animal tests	2.09	1.96	1.09
(e.1) Additional animals slaughtered during the year for TB control reasons (dangerous contacts, including any first time IRs)	1	1	5
(e.2) Additional animals slaughtered during the year for TB control reasons (private slaughters)	5	10	4
(f) SLH cases (tuberculous carcases) reported by the Food Standards Agency (FSA) during routine meat inspection	1	3	9
(g) SLH cases confirmed by culture of M. bovis	0	0	2

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

In 2022, 3 of 17 (12%) of new TB incidents in Lincolnshire received a preliminary or final APHA veterinary investigation to identify the source of infection.

Each TB incident could have up to three 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)
• 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 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 2022.

Table 5: Suspected sources of M. bovis infection for the 3 new TB incidents that received a veterinary investigation in Lincolnshire in 2022.

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.

Source of infection	Possible (1)	Likely (4)	Most likely (6)	Definite (8)	Weighted contribution
Badgers	1	1	1	0	38%
Cattle movements	0	0	1	0	33%
Contiguous	0	0	1	0	25%
Residual cattle infection	0	0	0	0	0%
Domestic animals	0	0	0	0	0%
Non-specific reactor	0	0	0	0	0%
Fomites	0	0	0	0	0%
Other wildlife	1	0	0	0	4%
Other or unknown source	0	0	0	0	0%