Available Data

In accordance with EU Animal By-Product regulations (39), livestock that dies on British farms must be collected, identified and transported away as soon as is reasonably practical, by an approved transporter. Disposal must be via an approved, registered animal by-products premise (40). Exceptions are made for pet animals and horses, remote areas including large parts of the Scottish Highlands and Islands (41) and in cases of natural disaster. Livestock keepers can make arrangements themselves directly with one of the many companies that deal with collection and disposal, or the process can be facilitated by becoming a member of the National Fallen Stock Company (NFSCo) (40). A collection service or a disposal premise may operate privately and/or as a member of NFSCo.

NFSCo CIC is a not for profit Community Interest Company that acts as an intermediary between the farming community and fallen stock collectors across Great Britain (GB) (www.nfsco.co.uk). It provides a service; sets standards; promotes high levels of bio-security; creates competition; facilitates payments and simplifies invoicing and cash flow. Membership is voluntary and free. Data are, therefore, collected for business needs. When a collection is made from a members' property, receipts are provided for monthly invoicing purposes. The number of Species Service Units (SSUs) that are collected on date X, from postcode Y, belonging to member Z, are recorded.

The definition of “Fallen Stock” for NFSCo is “animals which were killed (euthanasia with or without definite diagnosis) or have died (including stillborn and unborn animals) on farm and which were not slaughtered for human consumption. This includes animals killed by routine culling as part of normal production arrangements, where no government support is applied and animals lost during events that would ordinarily be covered by existing insurance arrangements e.g., fires and road accidents.” (www.nfsco.co.uk). NFSCo collections are, therefore, an indication of the mortality experienced in the livestock populations that belong to NFSCo Members.

A full British postcode consists of two parts of up to eight specific alpha-numeric characters (i.e., AA00 00BB). The first two alphabetic characters define a postcode area e.g., IV—Inverness, CH—Cheshire. There are 124 postcode areas in the United Kingdom of Great Britain and Northern Ireland (UK); they do not equate to country boundaries. The unit code (i.e., the last two letters, AA00 00BB) part of the full postcode identifies a postal route (or walk) of up to 100 addresses, for delivery purposes. A property may, therefore, have its own unique full postcode, or there may be multiple properties per full postcode (42). Thus, in an area of high livestock holding density, or where the area that the unit code applies to is large, more than one collection point may have the same postcode. They may, or may not, belong to different members and members might have multiple collection points.

Stages 1 and 2: Separately for each of the three countries, Scotland, England and Wales, two datasets were provided: a membership file and a Species Services file for sheep.

Stage 4: Two Species Services files for sheep were provided; one for Scotland and one for England and Wales together.

These files provide an anonymized snapshot of the entire NFSCo membership, for each of the three countries, as of the date that the file was extracted. For Scotland this was “as of 31st October 2014,” whereas for England and for Wales it was “as of 31 July 2015.” Each member record had a unique identifier, a user status and postcodes for each of the addresses belonging to that member. There were no join, start, or stop dates and no other attribute data such as livestock species belonging to the member, livestock numbers, management type, or species collected from a member.

The sheep Species Services files contain aggregated Species Service Unit data (SSU).

Types of SSU: In the Stages 1 and 2 files up to 11 types of SSU were recorded, although not all types were present in every country's file (Table 1). In Stage 4, there were a small number of additional SSUs, mainly in the England and Wales dataset. These mainly occurred infrequently apart from Dolav® sheep per kilo. This refers to a type of industrial plastic pallet box that can be used to store material.

The 11 original SSUs recorded in the Sheep services files and what they consist of.

Time periods and aggregation:

In the original datasets (Stages 1 and 2), the time period available was January 2011 to December 2014, inclusive, for Scotland and January 2011 to July 2015 inclusive, for each of England and Wales. Only the period to the end of December 2014 was analyzed initially. SSUs were aggregated by full postcode and by calendar month. This level of aggregation was defined by the data providers.

In Stage 4, the time period provided was January 2015 to June 2018, inclusive, for both the Scotland and combined England and Wales datasets. SSUs were aggregated by a unique ID representing the membership number, full postcode and by date of collection. These data were combined with the Stages 1 and 2 data to produce a dataset for the full period 2011 to mid-2018 for Scotland and for England and Wales.

The SRUC Veterinary Services (VS) Disease Surveillance network consists of eight centers (DSCs) located around Scotland. They receive diagnostic submissions from livestock keepers, in conjunction with their veterinarians. These submissions are made to confirm, or elucidate, a diagnosis in cases where diagnostic uncertainty exists based on clinical examination. A submission may consist of single or multiple samples from single, or multiple animals. All submissions are recorded in a laboratory information management system (LIMS). For diagnostic samples, when a diagnosis is reached according to specific criteria then a standardized Veterinary Investigation Diagnosis Analysis (VIDA) code is applied to that submission. There are two fields in which such a diagnosis can be recorded (VIDA1 and VIDA2). These may refer to a primary and secondary diagnosis in the same animal, or to two primary diagnoses in two different animals included in the same submission.

Acute fasciolosis is often fatal in sheep (43). For exploration in parallel with the descriptive spatio-temporal analysis of fallen stock data, the interest in fasciolosis diagnoses is as a potential explanatory factor for statistical alarms indicating increased mortality. For sheep, the most appropriate submissions should be those diagnosed as VIDA CODE 372 Acute fasciolosis (VIDA372). Chronic fasciolosis is recorded as VIDA CODE 373 (VIDA373) (Table SM1).

All ovine diagnostic submission records between January 2011 and December 2014 inclusive that had VIDA372 or VIDA373 recorded as a diagnosis were extracted from LIMS. These submissions consisted of carcase, liver, and/or feces samples appropriate to the VIDA CODE assigned (Table SM1).