Research and analysis

Lincolnshire (Low Risk Area) year end report 2023

Published 19 September 2024

Applies to England

Introduction

The Low Risk Area (LRA) was established in 2013, along with the Edge and High Risk Areas of England. In 2014 the 3 bovine tuberculosis (TB) risk areas were incorporated into the UK Government’s strategy to achieve Officially TB-Free (OTF) status for England by 2038. A key action was to recognise the different levels of TB in different parts of the country and to adjust the approaches to TB surveillance and control in each risk area accordingly. Overall, the LRA has a very low and stable incidence of TB-infected herds. The current strategy for the LRA seeks to mitigate the risk of TB incursions via cattle movements and rapidly contain and eradicate any foci of infection through:

• mandatory pre- and post- movement testing of cattle entering the LRA from higher risk areas of the UK
• more sensitive testing of infected herds
• temporarily enhanced TB surveillance (radial and hotspot testing) in the vicinity of herds experiencing lesion and/or Polymerase Chain Reaction (PCR) test (or culture)-positive incidents of TB

The aim of this combined approach 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 2023 in cattle herds in Lincolnshire, which is part of the LRA. In 2023, 14% of all new TB incidents in the LRA were detected in Lincolnshire.

TB in cattle and other mammals is primarily caused by infection with 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 those involved in the control of TB, both locally and nationally. This includes, but is not limited to:

• cattle farmers
• government and private veterinarians
• policy makers
• 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 2023.

Types of TB incident

Unless otherwise specified, this report includes all new TB incidents detected during the reporting period, 1 January to 31 December 2023. This includes both ‘Officially Tuberculosis-Free Status Withdrawn’ (OTF-W) and ‘Officially Tuberculosis-Free Status Suspended’ (OTF-S) incidents.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 [SICCT] test) with either

• typical lesions of TB identified at post-mortem (PM) meat inspection.
• and at least one animal with M. bovis-positive PCR test (or bacteriological culture) results in tissue samples collected from carcasses during the PM inspection

OTF-S incidents are triggered by reactors to the skin test, but without subsequent detection of TB lesions or positive PCR test (or 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 4% 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 2023.

The number of cattle markets in operation in 2023 is captured and maintained centrally by the Animal and Plant Health Agency (APHA) TB Customer Service Centre. Where possible, this data is then subject to further validation by APHA veterinarians subject to their best knowledge of the local area. Some small discrepancies may therefore exist where changes to markets were not captured in time for this report.

New TB incidents

During 2023 there were 19 new TB incidents in Lincolnshire, an increase of 12%, from 17 in 2022 (Figure 1), but a figure still lower than the 22 new TB incidents detected in 2021. The number of OTF-W incidents decreased marginally from 7 in 2022 to 6 in 2023, while the number of OTF-S incidents increased from 10 in 2022 to 13 in 2023.

The annual number of TB incidents identified in Lincolnshire has grown markedly since 2016, which only had 6 incidents (one OTF-W, 5 OTF-S). The annual number of incidents has more than tripled since, reaching a 10-year high in 2020 and 2021, with 22 incidents recorded in both years.

Year	OTF-W	OTF-S	Total
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
2023	6	13	19

Figure 1: Annual number of new TB incidents in Lincolnshire, from 2014 to 2023.

Figure 1 description: Stacked bar chart showing the number of new OTF-W and OTF-S incidents detected in Lincolnshire between 2014 and 2023. OTF-W incidents are shown in blue and OTF-S incidents are shown in green. There were 6 new OTF-W incidents and 13 new OTF-S incidents in 2023, as described in the main body of text.

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

Disclosing test type

Eight of the 19 (42%) TB incidents that began in 2023 were detected on radial surveillance testing (RAD), as displayed in Figure 2. This was an increase from 2022, when 6 out of 17 (35%) were detected by radial testing. Most of the incidents disclosed by radial testing (n=7) were in TB hotspot area HS28 (east Lincolnshire).

Five (26%) incidents (including 3 OTF-W) were detected by enhanced surveillance ‘hotspot tests’ in TB hotspot HS23 (south-west Lincolnshire).

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 (together those TB surveillance methods disclosed 68% of the total new TB incidents recorded in 2023 in Lincolnshire).

Figure 2 also shows routine (4-yearly) herd tests detected 2 new TB incidents, 6-month post incident testing detected 2 new TB incidents, post-movement tests detected one new TB incident and routine herd testing detected 2 new TB incidents in 2023.

Disclosing test type	Number of new TB incidents
6-monthy post-incident test	2
Hotspot test	5
New herd check test	1
Post-movement test	1
Radial test	8
Routine herd test	2

Figure 2: Number of new TB incidents (OTF-W and OTF-S) in Lincolnshire, in 2023 according to the surveillance method that detected them.

Figure 2 description: Bar chart showing which tests detected the new TB incidents in Lincolnshire in 2023. Most new incidents were detected by radial testing (8), followed by hotspot testing (5), 6-monthly testing (2) and routine herd testing (2).

Duration of TB incidents

A total of 20 TB incidents were resolved during 2023. Of these, 15 were new TB incidents that started in 2023, 4 started in 2022 and one started in 2021.

Of the 20 TB incidents that closed in the 2023, 7 were OTF-W incidents. Six of these were resolved within 550 days, and the other one lasted more than 551 days, and was considered a persistent TB incident.

Most OTF-S incidents (8 out of 13) were resolved within 150 days. There were 5 OTF-S incidents which were resolved within 550 days.

Ten TB incidents were ongoing at the end of 2023 in Lincolnshire.

Unusual TB incidents

There were no unusual TB incidents identified in 2023 in Lincolnshire.

TB in other species

There is no statutory routine TB surveillance of non-bovine species, apart from Post-Mortem Examination (PME) of animals slaughtered for human consumption, or carcasses submitted to veterinary laboratories for diagnostic investigation. Targeted TB testing takes place in non-bovine herds under TB movement restrictions due to laboratory-confirmed incidents of M. bovis infection, and in specific herds of camelids, goats and captive deer at an elevated risk of infection.

There were no TB incidents in 2023 reported in non-bovine species in Lincolnshire.

Recurring TB incidents

Three-year recurrence

In Lincolnshire, 2 of the 12 (17%) herds with a new OTF-S TB incident, and 3 of the 6 (50%) with an OTF-W incident in 2023, had experienced another TB incident in the previous 3 years, as shown in Figure 3. This was the third highest percentage of recurrent TB incidents (28%) of all the 7 LRA regions in 2023.

TB Incident	No history of TB in the last 3 years	History of TB in the last 3 years
OTF-S	10	2
OTF-W	3	3

Figure 3: Number of herds with a TB incident (by OTF-W and OTF-S) in Lincolnshire in 2023, with and without a history of any TB incident in the previous 3 years. This figure contains one less incident as in 2023, one herd experienced 2 incidents.

Figure 3 description: Bar chart showing the number of herds a TB incident, by OTF-W and OTF-S, in 2023 with and without a history of TB in the last 3 years. Herds with no history in the last 3 years are shown in blue, and those with a history of TB in the last 3 years are shown in orange. Ten herds with OTF-S incidents had no history, and 2 herds with an OTF-S incident had history of TB in the last 3 years. Three herds with OTF-W incidents had no history, and 3 herds with an OTF-W incident had history of TB in the last 3 years.

Overall recurrence

In 2023, 50% of incidents reported across the region were in herds with a history of TB at any time, including more than 3 years previously (6 out of 12 OTF-S and 3 out of 6 OTF-W), as shown in Figure 4.

Overall recurrence of TB decreased slightly compared to 2022 (63% overall, 5 out of 10 OTF-S and 5 out of 6 OTF-W).

TB Incident	No history of TB within the herd lifetime	History of TB within the herd lifetime
OTF-S	6	6
OTF-W	3	3

Figure 4: Number of herds with a TB incident (by OTF-W and OTF-S) in Lincolnshire in 2023, with and without a history of any TB incident at any point in time. This figure contains one less incident as in 2023 one herd experienced 2 incidents.

Figure 4 description: Bar chart showing the number of herds a TB incident, by OTF-W and OTF-S, in 2023 with and without a history of TB in the herd lifetime. Herds with no history of TB every are shown in blue, and those with a history of TB at any point in time are shown in green. Six herds with OTF-S incidents had no history, and 6 herds with an OTF-S incident had history of TB at any point in time. Three herds with OTF-W incidents had no history, and 3 herds with an OTF-W incident had history of TB at any point in time.

Geographical distribution of TB incidents

As in previous years, the new incidents in Lincolnshire were predominantly clustered into 2 areas of the county with a relatively high cattle density, one in the north-east and one in the south-west of the county (Figure 5). These 2 clusters correspond with Hotspot 23 (HS23) and Hotspot 28 (HS28) and are discussed below.

Whole Genome Sequencing (WGS) replaced genotyping at APHA in 2021. Of the 6 OTF-W incidents in Lincolnshire in 2023, 5 were due to infections with the WGS clade B3-11 (the most common strain of M. bovis in Lincolnshire) of M. bovis. Three of these were in HS28 and 2 in HS23 (Figure 5). There was also one OTF-W incident in HS23 due to infection with the WGS clade B6-62, which has a homerange centred on east of Gloucestershire, north-east of Wiltshire and the southern Edge Area (Oxfordshire, Warwickshire, Berkshire, west of Northamptonshire, north-west of Hampshire and West Buckinghamshire).

The homerange for clade B3-11 spans much of Staffordshire, Derbyshire, Cheshire, north-east of Shropshire and parts of Greater Manchester, Leicestershire, Lincolnshire and Nottinghamshire. It is broadly equivalent to genotype 25:a, which was detected in 17 incidents in Lincolnshire since 2017. WGS analysis through ViewBovis indicates that this is the clade that has been circulating in both HS23 and HS28. However, even though they belong to same clade of M. bovis, the cattle and badger isolates associated with each of those 2 hotspots are genetically distinct (the 2 TB hotspots in Lincolnshire are not epidemiologically linked).

Figure 5: Location of cattle holdings in Lincolnshire with new TB incidents (OTF-W and OTF-S) in 2023, and cattle holdings with pre-2023 OTF-W incidents still ongoing at the beginning of 2023, overlaid on a cattle density map. Note that ‘OTF-W Introduced 2023’ refers to OTF-W incidents in which cattle movements were the most likely source of infection.

Figure 5 description: A map of Lincolnshire showing the cattle density, the geographical location of cattle holdings with new TB incidents (OTF-W and OTF-S) in 2023, and OTF-W incidents pre-2023. Dark blue areas represent higher cattle density and light blue represent lower cattle density. New OTF-W incidents detected in 2023 are shown as triangles and colour-coded based on the WGS clade that was detected in the incident. Pink triangles represent clade B3-11, blue triangles represent clade B6-51, red represents clade B6-84, and white triangles represent incidents where the WGS clade was undetermined. OTF-S incidents in 2023 are shown as circles. OTF-W incidents detected pre-2023 are shown as squares. The geographical location of TB hotspots are shown as ‘brown hashed zones’. TB incidents in 2023 were located within the north-east and south-west of the county and are described in more detail in main body of text.

As can be seen from Figure 6 and Appendix 3 Table 5, OTF-W incidents in Lincolnshire in 2023 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 (such as HS23).

In 2023, wildlife reservoirs of infection were also recorded in 2 incidents in the north-east (HS28). Local anecdotal observations of increasing wildlife populations (both wild deer and badgers) have been frequently reported in veterinary field investigations.

Two OTF-W incidents were most likely attributed to introductions of undetected M. bovis-infected cattle. Both incidents were found in the south-west of Lincolnshire in HS23.

It was not possible to isolate M. bovis in bacteriological culture for WGS analysis from one OTF-W incident detected in HS28, and so it remains classified as ‘undetermined’.

Figure 6: 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 2023. 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 6 description: A map of Lincolnshire showing the geographical location of cattle holdings with new OTF-W incidents in 2023 and the most likely source of infection. OTF-W incidents are shown as circles in different colours which represent the source of infection. Blue represents local cattle, brown represents purchased cattle, and green represents wildlife. New OTF-S incidents in 2023 are shown as triangles. The geographical location of TB hotspots are shown as ‘brown hashed zones’. Most OTF-W incidents in 2023 had wildlife as the source of infection pathway with the highest level of certainty, followed by 2 attributed to purchased infection, and one undetermined.

Figure 7 provides an overview of the radial surveillance zones (both active and completed) around OTF-W incidents. Active radial zones in 2023 were largely located within HS23 and HS28.

Figure 7: Hotspot areas and radial surveillance zones around OTF-W incidents that were active, completed or not instigated in Lincolnshire during 2023, by year of initiation.

Figure 7 description: A map of Lincolnshire showing the geographical location of hotspots and radial surveillance zones around OTF-W incidents in 2023. The radial zones are shown as circles. Active radial zones are shown as solid line circles, completed radial zones are shown as dotted line circles, and radial zones that were not instigated are shown as orange triangles. The colour of the circles represents the year in which the radial zone was instigated: 2023 is green, 2022 is blue, 2021 is pink and 2014 to 2020 is orange. The geographical location of TB hotspots are shown as ‘yellow lines’ (to be updated). In 2023, there were new active radial zones, located in the HS28 in the north-east and HS23 in the south-west of Lincolnshire.

TB hotspots

Hotspot 23

Hotspot 23 (HS23) was launched in 2018 in west Lincolnshire and north-east Leicestershire (WGS clade B3-11, genotype 25:a). In June 2020 the original hotspot area was extended further into Leicestershire and Lincolnshire and included part of south-east Nottinghamshire (Figure 5). Two badger carcasses collected within the area tested positive for M. bovis in 2019 (WGS clade B3-11, genotype 25:a). The M. bovis isolates from both badgers had a close genetic relationship with those from 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. A further badger carcase was found in HS23 in 2020 with WGS clade B3-11. As a result, from September 2020, licensed culling of badgers for TB control purposes started in parts of HS23 and continued during 2022 and 2023. Further information can be found in TB surveillance in wildlife – confirmed hotspots in the Low Risk Area of England. HS23 had 21 new TB incidents in 2023 (including all 3 Lincolnshire, Leicestershire and Nottinghamshire sections), 10 of which were OTF-W and 11 were OTF-S.

As displayed in Figure 5, a cluster of 8 breakdowns (3 OTF-W, 5OTF-S) were disclosed in HS23 in the south-west of Lincolnshire. In 2023, 3 new OTF-W incidents were detected in the Lincolnshire portion of HS23, unchanged from 2022. There were 5 OTF-S incidents in 2023.

Hotspot 28

A cluster of seemingly unrelated OTF-W incidents caused by infection with WGS clade B3-11 of M. bovis (formerly genotype 25:a) were disclosed in 2019 and 2020 around the town of Louth in the east of the county. 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 and with no clear infection pathway for 4 of them, APHA declared a new potential hotspot 28 area (HS28) in July 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.

In February 2023 APHA identified M. bovis clade B3-11 (predominantly found in Cheshire, Derbyshire, Staffordshire, and north-east Shropshire) in a badger carcase collected within HS28 and the hotspot was confirmed. Additionally, M. bovis was isolated from a second badger carcase collected later in 2023 further east in HS28. Both badger isolates had likely epidemiological associations (based on the results of WGS analysis) with neighbouring cattle incidents caused by B3-11 clade of M. bovis. The boundary of HS28 was adjusted in 2023 according to the geographical distribution of cattle herds, cattle incidents, and location of the 2 positive badger carcasses. HS28 contains 201 cattle herds, with 178 beef herds (89%), 11 dairy herds (5%), 7 LFU, 4 calf rearers and one temporary gathering. Total head count is about 26,000, with the average head per unit of about 160 and with 1,900 in one single County Parish Herd Holding (CPHH) number. In 2023 there were three new OTF-W incidents in HS28, fewer than in 2022 and 2021 (4 incidents in each year). There were 7 new OTF-S incidents in HS28, which was an increase from 2022 (4 incidents). Overall, the number of cases over the last 3 years can be considered relatively stable and likely a consequence of enhanced controls in the area.

Since 2020, 73 badgers and 15 deer were reported in HS28, of which 42 carcasses were collected. During 2022, 7 wildlife carcasses (4 badgers and 3 deer) were reported to APHA, of which 3 badgers were collected and examined. All 3 badger carcasses tested negative for M. bovis infection.Further information can be found in TB surveillance in wildlife – confirmed hotspots in the Low Risk Area of England.

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 HS28 is likely.

Skin test reactors and interferon gamma test-positive animals removed

During 2023, a total of 90 animals were removed as TB test reactors from cattle herds affected by TB incidents in Lincolnshire. Of these, 59 were skin test reactors and 31 were positive by the supplementary interferon gamma (IFN-γ) blood test, as shown in Figure 8.

Compared with 2022, this was an increase on both the number of skin reactors (40) and IFN-γ test positive animals (19). Figure 8 shows how the total number of reactors removed in Lincolnshire increased from 65 in 2019, to a peak of 108 in 2021.

The IFN-γtest 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.

Year	Skin test reactors	Interferon gamma reactors	Grand total
2019	36	29	65
2020	83	12	95
2021	52	56	108
2022	40	19	59
2023	59	31	90

Figure 8: Number of skin test reactors and interferon gamma (IFN-γ) test positive cattle removed by APHA for TB control reasons in Lincolnshire, from 2019 to 2023.

Figure 8 description: Stacked bar chart showing the number skin test reactors and interferon gamma test positive animals removed from herds between 2019 and 2023 in Lincolnshire. Skin test reactors are shown in blue and interferon gamma test positive animals shown in green. There were 59 skin test reactors and 31 interferon gamma test positive animals removed from herds in 2023, as described in the main body of text.

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. Compared to 2022, there was a large increase in the number of new TB incidents in Lincolnshire that received a preliminary or final APHA veterinary investigation to identify the source of infection. In 2022, only 3 out of 17 (18%) incidents received a preliminary or final APHA veterinary investigation, whereas in 2023 17 out of 18 (94%) incidents were investigated.

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 2023.

The large increase during 2023 in APHA veterinary investigations carried out for new TB incidents facilitated the identification of potential key drivers.

The key drivers of the TB epidemic in Lincolnshire during 2023 were identified as follows:

• movement of undetected infected cattle
• exposure to potentially infected wildlife
• contact with other of unknown sources, including potential residual infection.

Exposure to probable infected badgers and other potential wildlife reservoirs was the main pathway of infection for cattle herds in 2023, with a weighted contribution of 50.2%, as shown in Appendix 3.

Potential exposure to infected badgers had a weighted contribution of 38.1%. This is similar to the weighted contribution in 2022 (38%) and more than double that in 2021 (11.8%).

Other infected wildlife had a higher weighted contribution compared with previous years, increasing to 12.1% in 2023 compared to 4.3% in 2022.

The movement of undetected infected cattle continued to be another important risk pathway. Compared to 2022, the weighted contribution decreased by 7.4% in 2023 (29.7% to 22.3%).

There was a high degree of uncertainty around the source of new incidents. Other or unknown sources had a weighted contribution of 22.5% in 2023. This category is added to those incidents in which there was high uncertainty around the selected pathways as alluded to earlier in the report (see explanatory supplement to the annual reports 2023 for methodology).

Forward look

The main concerns in Lincolnshire are the 2 active TB hotspots (HS23 and HS28). Enhanced TB surveillance and control measures will continue in 2024 as explained above, aiming at detecting any newly infected herds earlier. Monitoring of the epidemiological picture both in cattle and wildlife will also continue in 2024 in order to adapt controls as necessary. All these control measures in addition to improvements to biosecurity and education and encouragement of responsible cattle sourcing practices will be key to control and eradicate any local spread of TB and maintain the low risk TB status in Lincolnshire.

Appendix 1: cattle industry demographics

Table 1: Number of cattle herds by size category in Lincolnshire as of 31 December 2023 (RADAR data on number of holdings in the report year)

Size of herds	Number of herds
Undetermined	8
1 to 50	320
51 to 100	113
101 to 200	112
201 to 350	64
351 to 500	21
Greater than 500	25
Total number of herds	663
Mean herd size	114
Median herd size	52

Table 2: Number (and percentage of total) of animals by breed purpose in Lincolnshire as of 31 December 2023

Breed purpose	Number (and percentage of total) cattle
Beef	65,297 (86%)
Dairy	8,882 (11%)
Dual purpose	1,528 (2%)
Unknown	0 (0%)
Total	75,707

Appendix 2: summary of headline cattle TB statistics

Table 3: Herd-level summary statistics for TB in cattle in Lincolnshire in 2023. (Sam data showing the number of herds flagged as active at the end of the report year

Herd-level statistics	2021	2022	2023
(a) Total number of cattle herds live on Sam at the end of the reporting period	865	865	824
(b) Total number of cattle herds subject to annual TB testing (or more frequent) at the end of the reporting period (any reason)	213	198	302
(c) Total number of whole herd skin tests carried out at any time in the period	370	346	385
(d) Total number of OTF cattle herds having TB whole-herd tests during the period for any reason	257	276	295
(e) Total number of OTF cattle herds at the end of the report period (herds not under any type of TB movement restrictions)	820	818	782
(f) Total number of cattle herds that were not under restrictions due to an ongoing TB incident at the end of the report period	852	853	813
(g.1) Total number of new OTF-S TB incidents detected in cattle herds during the report period	16	10	13
(g.2) Total number of new OTF-W TB incidents detected in cattle herds during the report period	6	7	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 3 years?	3	6	2
(h.2) Of the new OTF-W herd incidents, how many could be considered secondary to a primary incident based on current evidence?	2	3	3
(h.3) Of the new OTF-W herd incidents, how many were triggered by skin test reactors or twice-inconclusive reactors (2xIRs) at routine herd tests?	0	1	0
(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)?	6	6	6
(h.5) Of the new OTF-W herd incidents, how many were first detected through routine slaughterhouse TB surveillance?	0	1	0
(i.1) Number of new OTF-S incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	8	3	4
(i.2) Number of new OTF-W incidents revealed by enhanced TB surveillance (radial testing) conducted around those OTF-W herds	5	3	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)	9	7	6
(k) Number of OTF-W herds still open at the end of the period that were on a finishing unit	1	1	1
(l) New laboratory-confirmed incidents of M. bovis infection in non-bovine domestic species or captive deer detected during the report period (indicate host species involved)	0	0	0

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.

Table 4: Animal-level summary statistics for TB in cattle in Lincolnshire during 2023.

Animal-level statistics (cattle)	2021	2022	2023
(a) Total number of cattle tested with tuberculin skin tests or additional IFN-γ blood tests in the period (animal tests)	55,129	54,233	59,101
(b.1) Reactors detected by tuberculin skin tests during the year	52	40	59
(b.2) Reactors detected by additional IFN-γ blood tests (skin-test negative or IR animals) during the year	56	19	31
(c) Reactors detected during year per incidents disclosed during year	4.91	3.47	4.74
(d) Reactors per 1,000 animal tests	1.96	1.09	1.52
(e.1) Additional animals slaughtered during the year for TB control reasons (dangerous contacts, including any first time IRs)	1	6	4
(e.2) Additional animals slaughtered during the year for TB control reasons (private slaughters)	10	4	0
(f) Slaughterhouse (SLH) cases (tuberculous carcasses) reported by the Food Standards Agency (FSA) during routine meat inspection	3	9	2
(g) SLH cases confirmed by M. bovis PCR testing or bacteriological culture	0	2	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

In 2023, 17 of 18 (94%) 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 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)
• 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 2023.

Table 5: Suspected sources of M. bovis infection for the 17 new TB incidents that received a veterinary investigation in Lincolnshire in 2023.

Source of infection	Possible (1)	Likely (4)	Most likely (6)	Definite (8)	Weighted contribution
Badgers	7	3	5	0	38.1%
Cattle movements	9	1	2	0	22.3%
Contiguous	1	1	0	0	3.6%
Residual cattle infection	1	0	0	0	0.8%
Domestic animals	0	0	0	0	0.0%
Non-specific reactor	0	0	0	0	0.0%
Fomites	1	0	0	0	0.5%
Other wildlife	8	2	0	0	12.1%
Other or unknown source	2	0	0	0	22.5%

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.