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Assessing the value of surveillance information gathered at stock congregation points

Executive summaryThis report describes and appraises currently available data, such as that captured at livestock

‘congregation points’ (e.g. saleyards and abattoirs), that could be analysed to derive animal

health surveillance information. Additional data collection that may augment the application of

these data is then discussed.

In consultation with jurisdictional and departmental staff, potentially underutilised data

sources were identified: the National Livestock Identification System (NLIS) database; the

Export Production and Condemnation Statistics (EPACS) database; the National Sheep Health

Monitoring Project and Enhanced Abattoir Surveillance Program; the Victorian Pig Health

Monitoring Scheme; and diagnostic tests undertaken on animals destined for live export.

Beyond movement data, the NLIS database holds data relevant to ill-thrift syndromic

surveillance and carcase condemnation. However, these fields are optional and are currently not

sufficiently populated to derive robust surveillance information.

EPACS data could be utilised in a number of ways, including:

monitoring temporal trends in carcase condemnations, to aide in early detections of exotic

or emerging disease incursions

supporting arguments for proof-of-freedom from certain diseases

providing descriptive data of value to other surveillance projects

monitoring temporal trends in carcase condemnations to inform herd health strategies

regarding endemic conditions- though this is limited by the restriction of these data to

whole-carcase condemnations.

The surveillance value of the EPACS data could be improved by:

provision of resources to collect a sample of condemned tissues for follow-up laboratory

testing, to support proof-of-freedom claims of particular infections

a validation study of carcase condemnation, to support the use of these data in proof-of-

freedom arguments

Department of Agriculture and Water Resources 1

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production of reports of condemnation data, to provide benchmarks and temporal

monitoring information for herd health programmes (especially for industries with no

abattoir surveillance programs, e.g. beef).

Data from domestic abattoirs involved in the National Sheep Health Monitoring Project and

Enhanced Abattoir Surveillance Program, and the Victorian Pig Health Monitoring Scheme,

could augment EPACS data for the same purposes. This is particularly in consideration of the

broader scope of these data: the data result from specific monitoring of conditions, rather than

records of conditions only at a severity that warrants whole-carcass condemnation; and they

include data from domestic abattoirs, unlike EPACS.

Diagnostic tests results from animals destined for live export could be utilised strategically to

support proof-of-freedom arguments for certain diseases. The data may also support arguments

for investment in validation of diagnostic tests, or development of new diagnostic tests, for use

in surveillance. However, a method of regular collation of these data needs to be developed, as

there is no existing database.

Recommendations:

A project piloting the collation and analysis of abattoir carcase condemnation data (EPACS)

and abattoir monitoring data (National Sheep Health Monitoring Project and Enhanced

Abattoir Surveillance Program, and the Victorian Pig Health Monitoring Scheme). This

includes developing reference ranges of carcase condemnations and monitoring of

conditions in the absence of exotic or emerging disease outbreaks, to identify ‘trigger

points’ of exceptional upwards fluctuations that should prompt investigation to exclude an

exotic or emerging disease as the underlying cause.

A project piloting the collation and use of diagnostic test results from animals destined for

live export, to determine the feasibility and value in providing surveillance information.


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1 Background

The distribution of Australia’s surveillance system is well matched to the distribution of risk

associated with eight animal diseases of concern in Australia (East et al., 2013). However, an

opportunity may exist to make better use of data captured at livestock ‘congregation points’,

such as saleyards and abattoirs, to inform post-border surveillance and provide surveillance

evidence in support of Australia’s claims of freedom-from-disease.

Saleyards are known to be an important means of disease spread in disease outbreaks (e.g.

Gibbens et al., 2001; Mansley et al., 2003), and data of animal movement into and out of

saleyards are of interest in modelling disease spread and devising surveillance and disease

control strategies. Australian livestock saleyards are obliged to log livestock movements into

and out of the premises with the National Livestock Identification System (NLIS) (section 2.1).

There are no further obligatory data reporting requirements to any central databases. Stock

inspections at saleyards are usually not undertaken by registered veterinarians – though a

veterinarian may be called to inspect an animal identified as being sick, injured or diseased (e.g.

Department of Agriculture, 2003; Department of Economic Development, Jobs, Transport and

Resources, 2015). The large number of stock scanned at saleyards involves identifying and

removing overtly ill or injured animals, rather than determining the presence or absence of

certain lesions or infection(s). Augmenting livestock movement data with active disease

surveillance at Australian saleyards is neither feasible nor sufficiently sensitive to improve

time-to-detection, duration or size of a foot-and-mouth outbreak, compared to the passive

surveillance system currently in place (Garner et al., 2016). This is thought to also be true of

surveillance for other infectious disease of importance to Australia’s livestock production.

Data collected at slaughter can contribute to monitoring production animal health, particularly

regarding endemic diseases (Willeberg et al., 1984; Kaneene et al., 2006; Pointon et al., 2008;

Weber et al., 2011; Vial and Reist, 2014; Correia-Gomes et al., 2016), although it may be biased

as a representation of the production animal population (Vial and Reist, 2014). Data collected at

slaughter are also of value regarding syndromic surveillance (Dórea et al., 2011). However,

these data need to be interpreted carefully (Pointon et al., 2008; Alton et al., 2010). Data

collected at abattoirs may result from routine slaughter processes (for example, carcase

condemnation data), or be a result of specific monitoring projects investigating specific

conditions.

As part of the National Animal Health Surveillance and Diagnostics Business Plan 2016–2019

activity 2.8, this project aimed to:


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describe and appraise currently available data on livestock ‘congregation points’ that could

be analysed to derive surveillance information

make recommendations on what additional data (if any) would be required to support a

robust analysis of surveillance at congregation points, and the estimated costs of collecting

such data in an ad hoc or routine manner.

2 Potential data sources

In consultation with jurisdictional and departmental staff, potentially underutilised data

sources identified were: the NLIS database; the Export Production and Condemnation Statistics

database; the National Sheep Health Monitoring Project and Enhanced Abattoir Surveillance

Program; the Victorian Pig Health Monitoring Scheme; and diagnostic tests undertaken on

animals destined for live export.

2.1 The National Livestock Identification System databaseThe NLIS Mirror Database Data Dictionary v 2.0 (NLIS, 2016) and an NLIS Project Officer were

consulted to identify and investigate NLIS data of value to surveillance.

Australia’s NLIS is designed to enable tracing of livestock (including individual cattle, and sheep

and goat mobs) from the property of birth to the place of slaughter. The central NLIS database

holds logs of livestock movements, and also has the capacity to log carcase feedback from

abattoirs for cattle. The NLIS system involves:

compulsory registration of properties involved in the movement of cattle, sheep and goats,

using property identification codes (PICs)

compulsory tagging of animals

compulsory recording of movements of animals between PICs on a central database.

Under state and territory legislation in Australia, properties that run livestock are required to

have a PIC. Precise definitions of properties required to obtain a PIC vary between states and

territories, but always include all properties which run any cattle, sheep or goats. The ability to

apply one PIC to multiple properties owned by the same person/company varies between states

and territories, with different rules applying in different states. In some cases, multiple

properties will share a single PIC, and in other cases each property will have its own PIC.


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Cattle must be tagged with a NLIS-approved, machine readable, radio frequency identification

device (RFID) before they leave the property on which they were born. The RFIDs are contained

within an ear tag or a rumen bolus, and involve a microchip with a unique number for each

animal. The number is linked to the PIC of the animal’s property of birth. All RFIDs are

automatically registered to a PIC by the tag manufacturer when they are issued. If a cow loses

their RFID ear tag after leaving the property of its birth, it is required to be refitted with a ‘post

breeder’ ear tag.

All sheep and farmed goats must be tagged with an NLIS-approved ear tag prior to movement

off the property on which they were born. Ear tags are visually readable and are printed with

the PIC of the property on which the animal was born (this does not enable identification of

individual sheep). When combined with Sheep/Goat National Vendor Declaration (NVD) forms

or other approved movement documents, this allows trace-back of animals to the property of

birth, or property of last residence if the animal lost its original tag and required retagging with

a ‘post-breeder’ tag. The exception is that in Victoria, all lambs born from 2017 onwards are

required to be fitted with an electronic (individual) identification ear tag, as per cattle.

When cattle, sheep and goats are moved from one property to another, the movement must be

recorded in the NLIS database.

Movement of livestock bought, sold or moved through a saleyard must be recorded by the

saleyard (and uploaded into the NLIS database by the next working day).

For private sales not involving a saleyard, the buyer/ receiver of livestock must record the

movement onto their property. The vendor/ sender of the livestock may choose to do so,

but it is not compulsory.

For animals moved directly to an abattoir or export depot, the movement is recorded by the

abattoir or exporter.

For animals being exhibited at a show, the movement is recorded by the show.

For cattle (or individually identifiable sheep), compulsory recordings are:

NLISID (the visual number, printed on the electronic ear tag) or RFID numbers of all

animals moved

date of the movement

origin and destination PICs.


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For sheep and goats (mob-based movement), compulsory recordings are:

species (sheep or goat)

date of the movement

origin and destination PICs

number of head moved

NVD/waybill serial number

whether the stock were bred by the vendor

yes/no

if no, how long ago the livestock were obtained purchased (< 2 months, 2–6 months, 6–

12 months, or >12 months)

the PICs printed on the tags of those stock, if the mob includes stock not bred by the vendor.

Slaughterers are required to upload slaughter data to the NLIS. For cattle, compulsory data are:

slaughterer’s identification

NLISID or RFID numbers of the slaughtered cattle

kill date

body number.

For sheep and goats, compulsory data are:

species (sheep or goat)

kill date

processor PIC

number of head killed

source of the animals (direct or saleyard) and source PIC

the PICs printed on the tags of those stock, if the mob includes stock not bred by the vendor

NVD/waybill serial number

whether the stock were bred by the vendor

yes/no


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if no, how long ago the livestock were obtained or purchased (< 2 months, 2–6 months,

6–12 months, or >12 months).

Livestock movements and slaughter must be logged within a week of occurrence; though they

are typically automatically uploaded into the NLIS database by saleyard and abattoir software

programs. Additional (optional) data fields regarding the carcase characteristics also exist

within the database (Appendices 1 - 4).

There is also an NLIS system for pigs, and one is being developed for South American camelids,

but data on these livestock are not available on the central NLIS database.

Accessibility of NLIS data to the Department of Agriculture and Water Resources

The NLIS Mirror database allows departmental access to the NLIS data without impacting the

transactional database. However, departmental access to data by the Mirror site is bound by the

NLIS Terms of Use. These restrict departmental access to queries relating to compliance

monitoring and movement analyses for the purpose of biosecurity. Any further data access, such

as for surveillance purposes, relies on obtaining a specific permit, through the NLIS application

process.

2.2 The Export Production and Condemnation Statistics databaseStaff in the Exports Division were consulted to gain access to the Export Production and

Condemnation Statistics (EPACS) database and ascertain the categorisation of the data fields.

The EPACS database is a departmental database that contains throughput and whole-carcase

condemnation data from export-certified abattoirs. It does not include data of partial carcase

condemnations. It is primarily designed to confirm the number of animals processed for the

Commonwealth to bill processing plants. EPACS includes data from a range of species, which are

subcategorised into various ‘subtypes’ ().


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Table 1: Export Production and Condemnation Statistics (EPACS) database- species scope

Species category Species category ‘subtypes’1

Any - (RTE2 products)3

Beefalo (cattle/bison hybrid)- Calf- Cow/bull- Steer/heifer

Bovine

- Calf- Cow/bull- Steer/heifer- (Tripe)- (RTE2 products)

Bubaline (buffalo)- Calf3

- Cow/bull- Steer/heifer

Camels - Camels

Caprine

- Feral goat3

- Game goat3

- Goat skin off4

- Goat skin on4

- (Tripe3)

Cervine- Deer- Game deer

Equine- Donkey- Horse

Kangaroo- Game kangaroo5

- Kangaroo5

Ovine- Lamb- Sheep- (Tripe)

Porcine

- Feral pig3,6

- Game pig6

- Pig skin on- Pig skin off

Possums - Possums3

Poultry- Emu- Ostrich- Poultry3

Rabbits- Game rabbit3

- Hare- Rabbit3

1 Subtypes in brackets are not relevant to species throughput- for example, bovine tripe originates from calf, cow/bull or steer/heifer throughput2 RTE = Ready-to-eat: meat products that are in a form that is edible without additional preparation to achieve food safety. 3 Since 1/1/2012, no throughput of these subtypes has occurred.4 ‘Goat skin on’ and ‘goat skin off’ are of the same source population – ‘goat skin on’ is processed for niche markets.5 ‘Game kangaroo and ‘kangaroo’ are of the same source population – ‘game kangaroo’ are processed at plants that process various game; ‘kangaroo’ are processed at plants that exclusively process kangaroo.6 ‘Game pig’ is crossbred domestic pig and wild boar; ‘feral pig’ are differentiated from game by the on-plant vet counting the teats (12 teats differentiates a feral pig).


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All animals to be processed for the export meat market must go through an export-certified

abattoir or processing facility. Processing must include:

antemortem examination of animals undertaken by or verified by a Department of

Agriculture and Water Resources veterinarian (except for game)

post mortem examination of animals by suitably qualified meat safety inspectors

verification of post mortem inspection and processor hygiene practices by a Department of

Agriculture and Water Resources’ veterinarian.

Animals are inspected post-mortem according to departmental work instructions (e.g.

Department of Agriculture, Fisheries and Forestry, 2011, 2013; Department of Agriculture and

Water Resources, 2016). Post-mortem inspections vary depending on species, and in some

cases by species ‘subtypes’. Inspections are based around macroscopic examination of the

carcase, with sampling if certain conditions (such as Taenia saginata - cysticercus bovis in cattle)

are suspected. Condemnation type of the carcase is recorded according to the category of

condemnation (Table 2). Guidelines to condemning carcases are outlined in Department of

Agriculture, Fisheries and Forestry (2010), but the validity of assigning carcases to the listed

condemnation categories by gross examination on slaughter lines, and the reliability of doing so

between inspectors, have not been measured in Australian abattoirs.


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Table 2: ‘Condemnation type’ categories in the Export Production and Condemnation

Statistics (EPACS) database.

Condemnation type1

At antemortem Muscular dystrophy Dirofilaria roemeriNavel ill Fly strike

Abscess Neurofibroma Fly strike and gross contamTesticular abscess Peritonitis SparganosisAnaemia Pneumonia SarcosporidiaArthritis Septic pneumoniaPolyarthritis Xanthosis WoundsCancer eye Other causes Gunshot residueCellulitis Pot gut GunshotEcchymosis Pyaemia Body shotEmaciation Septic wounds Non head shotOff condition Septicaemia BruisingEnteritis Toxaemia Dog biteEosinophils myositis Uraemia Dog bitesErysipelas Actino ImmaturityFever AspergillosisFistula CLA Abnormal colour Gangrene Myxomatosis Abnormal odourJaundice Strangles Chemical residueMalignancy Tuberculosis Company condemnMelanosis C. bovis Processing damageMetritis C. ovis Gross contaminationMuscle conditions Hydatids Mould

1 Not all condemnation type categories are relevant to all species.

Trichinella spp. testing is undertaken for particular export markets. These data are held by the

processing plant.

Processing plants upload data to EPACS at least monthly, depending on plant size - some plants

with automated systems may update EPACS as frequently as daily.

Accessibility of EPACS data to the Department of Agriculture and Water Resources

The EPACS data are held by the department’s Exports Division, and with internal departmental

permission the database can be accessed by departmental staff.


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2.3 The National Sheep Health Monitoring Project and Enhanced Abattoir Surveillance Program

Staff at Animal Health Australia, and National Sheep Health Monitoring Project (NSHMP) annual

reports (e.g. Animal Health Australia, 2017), were consulted to describe the methodology

behind the NSHMP data and its accessibility to departmental staff.

The NSHMP involves collection of data on certain conditions at sheep abattoirs nationally (Table

3). The Enhanced Abattoir Surveillance Program (EASP) is an extended programme in South

Australian abattoirs that collects data on five additional conditions (Table 3). It is expected that

these programs will be harmonised in the near future, so all conditions listed in Table 3 will be

inspected for at all involved abattoirs.

Carcases are examined by certified meat inspectors that are employed by the NSHMP. The

presence or absence of pathology consistent with certain diseases and conditions is recorded.

Laboratory confirmation of conditions is not utilised, except for ovine Johne’s disease (OJD).

Where there are palpable lesions consistent with ovine Johne’s disease (e.g. enlarged

mesenteric lymph nodes, thickened intestine), the viscera of up to three animals per line which

have these lesions will be sampled and subject to confirmation by histopathology at the

respective jurisdictional laboratory. Remaining animals have the palpable abnormalities noted,

but are not sampled for histopathology.

Not all sheep are examined for all conditions, due to the time pressures of high-speed lines, but

there is a consistent attempt to monitor sheep for all conditions. Examinations for OJD lesions

are always done on carcases in the over-two-years-old age group; a lot of animals in the under-

two-years-old age group are not monitored for OJD, as many are lambs and infection (if present)

is unlikely to have yet manifested as grossly-detectable pathology.

Eighteen abattoirs were involved in the NSHMP from July 2015 – June 2016. This included two

abattoirs in South Australia who were also involved in the EASP. Abattoirs included a mix of

larger and smaller throughput establishments. Estimates are that a third of involved abattoirs

have NSHMP inspectors full time, a third of abattoirs have inspections equivalent to one week in

three, and the final third of abattoirs have occasional NSHMP inspections (Rob Barwell, Animal

Health Australia, pers comm). Ages of animals in abattoir lines are classified as >2yo, <2yo, or

mixed. The majority of examined carcases are lamb.


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Table 3: Conditions the National Sheep Health Monitoring Project and Enhanced Abattoir

Surveillance Program (EASP) collect data on. Unless indicated otherwise, conditions are

monitored under both projects.

Condition Case definition test

Arthritis Gross examination

Bladder worm (Taenia hydatigena cysts) Gross examination

Cancer Gross examination

Caseous lymphadenitis/cheesy gland (Corynebacterium pseudotuberculosis infection)

Gross examination

Dog bites Gross examination

Grass seeds Gross examination

Hydatids (Echinococcus granulosus cysts) Gross examination

Knotty gut (Oesophagostomum columbianum infection) Gross examination

Liver fluke (Fasciola hepatica infection) Gross examination

Ovine Johne’s diseaseScreening by gross examination, histopathology confirmatory test1

Pleurisy Gross examination

Pneumonia Gross examination

Sarcocystosis (Sarcocystis spp. cysts) Gross examination

Sheep measles (Taenia ovis cysts) Gross examination

Vaccination lesions Gross examination

Melanosis Gross examination

Cirrhosis (EASP only) Gross examination

Jaundice (EASP only) Gross examination

Nephritis (EASP only) Gross examination

Rib fractures (EASP only) Gross examination

Bruising (EASP only) Gross examination

Fever/ septicaemia (EASP only) Gross examination1 A maximum of three animals per line with gross pathology consistent with OJD will be tested histopathologically – the remainder will have clinical signs noted

Data collected at the abattoirs are typically available on the NSHMP database within 24 hours,

except for OJD results (these may take up to 2 weeks, given the histopathology confirmation).

Animal Health Australia manages the NSHMP database, and annually reports on the NSHMP (e.g.

Animal Health Australia, 2017). The NSHMP OJD results are reported on the National Animal

Health Information System database.

Accessibility of NSHMP data to the Department of Agriculture and Water

Resources

Access to NSHMP data is granted by application to the NSHMP Steering Committee.


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2.4 The Victorian Pig Health Monitoring SchemeStaff at the Department of Economic Development, Jobs, Transport and Resources (Victoria)

were consulted to describe the methodology behind the Victorian Pig Health Monitoring

Scheme, and the accessibility of data to departmental staff

The Victoria Pig Health Monitoring Scheme has been running for over 20 years. It was initially a

national program. Currently, pigs at two domestic abattoirs and one export abattoir in Victoria,

and one export abattoir in New South Wales, are included in the scheme. The scheme is run by

Victoria’s Chief Veterinary Officer Unit and is funded internally.

At inspection, the organs and carcase of slaughtered pigs are routinely examined for the

conditions listed in Table 4. Some conditions are scored as present / absent, whereas others are

scored according to an ordered categorical scale.

Table 4 – Conditions screened for as part of the Victorian Pig Health Monitoring Scheme

Condition Case definition test (data type) 1

Dermatitis Gross examination (scored)

Liver lesions (roundworm) Gross examination (present/ absent)

Pneumonia Gross examination (scored)

Pleuropneumonia Gross examination (present/absent)

Pleurisy Gross examination (scored)

Pericarditis Gross examination (present/absent)

Peritonitis Gross examination (present/absent)

Nephritis Gross examination (present/absent)

Ileitis Gross examination (present/absent)

Colitis Gross examination (present/absent)

Abscesses Gross examination (present/absent)

Arthritis Gross examination (present/absent)

Atrophic rhinitis Gross examination (scored)

Erysipelas (skin lesions only) Gross examination 1Present/absent = binary categorisation; scored = ordered categorical categorisation

50,000 – 60,000 pigs are inspected per year, across the four involved abattoirs.

Pigs that have died in the holding yards or are euthanised as a result of pre-slaughter inspection

are also examined opportunistically, if the inspector’s visit coincides. In these cases, samples are

taken for reporting back to the producer. Lung samples from pigs with pneumonia are subject to

culture and sensitivity testing.


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Accessibility of Victorian Pig Health Monitoring Scheme data to the Department of

Agriculture and Water Resources

The data are held by the Victorian Chief Veterinary Officer’s unit, and could be made accessible

to the Department of Agriculture and Water Resources in a collaborative effort.

2.5 Diagnostic tests undertaken on animals destined for exportStaff in the Exports Division of the department, and staff at the Elizabeth Macarthur Agricultural

Institute Laboratory, were consulted on the protocols for testing animals destined for live

export, and the accessibility of the associated data.

Animals intended for live export from Australia are tested for certain infections pre export. The

infections tested for varies between export consignments, depending on the requirements of the

importing country. For example, sheep may be tested for infections such as Brucella ovis,

bluetongue and Q fever; goats may be tested for infections such as leptospirosis and caprine

arthritis and encephalitis virus; cattle and pigs may be tested for infections such as brucellosis

and tuberculosis; donor flocks of poultry may be tested for infections such as Newcastle disease

and avian influenza; and horses may be tested for infections such as equine influenza and

equine viral arteritis. Animals may be tested serially for certain infections pre-export

(Department of Agriculture and Water Resources, n.d.). All testing is undertaken through

National Association of Testing Authorities-accredited laboratories- for example, Idexx and the

Elizabeth Macarthur Agricultural Institute (EMAI). Private laboratories undertake the majority

of pre-export testing.

Accessibility of diagnostic test data from animals destined for export to the

Department of Agriculture and Water Resources

Ownership of test results is not clear. It is believed that in New South Wales, test results are

owned by the jurisdiction, with exporters given unrestricted access to their results. Documents

that hold test results for particular export certificates are uploaded onto the Department of

Agriculture and Water Resources’ Tracking Animal Certification for Export (TRACE) database

system. Similarly, export certificates are uploaded onto the TRACE system, and may also contain

relevant data. The Department of Agriculture and Water Resources does not own a database

containing these test results.


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EMAI advised that specific data may be able to be extracted, deidentified and forwarded to the

department from their laboratory, to answer specific surveillance questions. Meaningful spatial

proxies would not be available with test results, due to the nature of livestock congregation

before testing prior to export. Data may require substantial cleaning after extraction, and it

would be difficult (perhaps impossible) to identify and filter out repeat tests from the same

animals where test protocols involve serial sampling of individuals.

3 Surveillance information that may be practicably

derived from these data sources, and additional

data that could be collected to augment this

Surveillance information that may be derived from existing data sources may support freedom-

from-disease claims, or support early detection of emerging disease or exotic disease incursions.

3.1 The National Livestock Identification System database

Carcase condemnation trends, and ill-thrift syndromic surveillance

For cattle, the NLIS database includes variables that could be of value in monitoring trends in

carcase condemnation and ill-thrift syndromic surveillance. Detecting exceptional fluctuations

in trends may contribute to early detection of exotic or emerging diseases. The relevant cattle

variables include:

variables related to carcase condemnation status, the part of the carcase condemned, and

the type of carcase damage (Appendices 1 & 2)

variables related to carcase weight, weight scores, muscle and fat scores, and fat depth

(Appendices 1 & 2)

variables related to potential confounders when evaluating temporal trends in ill-thrift

syndromic surveillance. These include estimates of age, sex, breed mix and number of days

on feed at a feedlot (Appendices 1 & 2). Additionally, data variables such as the date of

slaughter could be used to obtain data or derive proxies for other potential confounders,

including season and other environmental conditions prior to slaughter.


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However, there are currently substantial limitations associated with the use of these data to

monitor temporal trends:

Primary amongst these is that, given entry of carcase feedback data is voluntary, most of

these variables are not yet sufficiently populated in the NLIS database for reliable temporal

trend surveillance. Examples of the proportions of data fields populated in some relevant

slaughter variables for 36,986,874 cattle entries in the database at the time of this

assessment are given in Table 5.

Data access is relatively complicated – applications need to be very specific as to what data

is required and why, and applications are subject to NLIS approval with a non-refundable

application fee. In the case of following up ‘significant’ fluctuations, identifiable data may be

required. If access to such data is not granted, or is not granted in advance of the

occurrence of ‘significant’ fluctuations, this would preclude efficient follow up

investigations.

Permission would be required from farms associated with ‘significant’ fluctuations to

investigate causes.

Most of the carcase variables relevant to ill-thrift syndromic surveillance are based on AUS-

MEAT language (as per AUS-MEAT Ltd, 2011) - a classification system of meat products

used to provide industry standards for trade description. These data are only available

from AUS-MEAT accredited enterprises- all export abattoirs are AUS-MEAT accredited, but

the proportion of accredited domestic abattoirs is uncertain. Unaccredited abattoirs would

have differing carcase feedback (if any is provided), which is problematic in monitoring

trends.

Changes in technology used to measure carcases over time (e.g. the planned roll-out of

objective carcase measurements based on dual energy X-ray absorptiometry (DEXA) across

the Australian red meat industry, starting with AUS-MEAT registered facilities (Meat and

Livestock Australia, 2016) may have an impact on temporal monitoring.

The use of EPACS data (section 3.2) is considered a more valid source of carcase condemnation

data for monitoring temporal trends, given the consistent source population with sampling

applied across all of that population. The EPACS data are also more readily accessible to the

department.


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Table 5– Examples of NLIS database variables relevant to monitoring cattle carcase condemnation trends and ill-thrift syndromic surveillance: percentage of records that were entered as null values or were missing data (for time period 1st January 2012 to 31st December 2016)

Variable Explanation % null values or missing data

Killdate Kill date 0 %

Carcsex Sex characteristics of the carcase 7.2 %

Carcdent Number of teeth, either molar or incisor, of a carcase (age proxy) 31.2 %

Breed_mix Breed mix (parentage) of an animal 100 %

Days_on_feed The number of days on feed at a feedlot 100 %

Condemn Condemnation status for the carcase 41.6 %

Carc_ctg Carcase category 84.4 %

Live_Weight On-the-hoof weight in kg 76.3 %

HSCW Individual weight of a carcase/side in hot standard carcase weight (HSCW) 11.3 %

Weight_score AUS-MEAT defined weight scores based upon HSCW1 64.0 %

Cold_weight Individual weight of a carcase/side in cold weight kg 91.0 %

Trim_weight Individual weight of a carcase/side in trimmed weight kg 94.1 %

CAWeight Chiller assessment weight of carcase/side 100 %

Actual_yield Actual percentage yield of saleable meat 100 %

Mscl_score Muscle score as per AUS-MEAT Meat Language1 93.3 %

Fat_mm Fat depth (mm) 67.9 %

Fat_score Fat depth expressed as a score 88.7 %

Fat_site Site at which a fat measurement was taken 72.4 %

CAFatDepth Chiller assessment fat depth in mm 100 %

CAFatPercent Percentage of fat as determined by chiller assessment/video image analysis 100 %1 Aus-meat Ltd, 2011

Cattle movement data

The cattle movement data on the NLIS are comprehensive, though not without limitations

(Iglesias and East, 2015). These data could be of use in social network analyses – for example, to

identify compartments of particular epidemiological risk and ‘cut-points’ in infection

transmission for application to outbreak control strategies. However, augmenting movement

pattern data with active surveillance at saleyards is impractical (Garner et al., 2016).

Sheep data

As sheep and goats are not entered in the NLIS system at individual level, there are no data

available to monitor trends in condemnation status or for ill-thrift syndromic surveillance

(Appendices 3 and 4).


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3.2 The Export Production and Condemnation Statistics DatabaseThe EPACS database provides denominator data of animals inspected by certified inspectors

under the verification of a departmental veterinarian. For certain diseases that would be

expected to manifest on gross examination in at least a small proportion of cases, and which

inspectors would be likely to sample for laboratory confirmation in at least a small proportion

of cases (for example, bovine tuberculosis (Mycobacterium bovis) infection in cattle), the

absence of detections amongst these animals may support arguments of freedom from such

diseases. These data would not be adequate to support arguments for freedom-from-disease of

infections that do not have distinct macroscopic pathological manifestations, and infections

where there is not a protocol for follow-up laboratory confirmation of macroscopic findings.

The EPACS database could also provide information on trends in condemnation status, to

contribute to early detection of exotic and emerging disease incursions. For example,

exceptional upward fluctuations in pneumonia condemnations may provide an early indicator

of an incursion such as peste des petits ruminants infection in sheep, or classical swine fever or

African swine fever in pigs. The outbreak of classical swine fever in 1960-61 was detected after

an investigation prompted by increase in septicaemia condemnations in pigs (Seddon, 1966). An

example of such data is presented in Figure 1.

Figure 1 Percentage condemnations due to septic pneumonia amongst ‘Pig skin on’ and

‘Pig skin off’ species subtypes, from export abattoirs in Australia, 2016


ATTACHMENT A

Considerations for such temporal surveillance include:

Stratification by abattoir would ensure some sensitivity in detecting localised incursions,

control for potentially substantial variations in condemnation rates between smaller and

larger throughput abattoirs (Weber et al., 2011), and minimise the influence of

geographically related biases in monitoring trends.

A frequent data analysis interval would be required for an improvement in time-to-

detection of exotic/emerging disease incursions compared to passive surveillance. It seems

that a monthly interval would be the shortest interval available to collate and analyse data

from all processing plants, given that is the maximum interval of submission of data to

EPACS by processing plants.

Definitions as to what constitutes a ‘significant’ fluctuation would need to be

predetermined (particularly in view of the very large sample sizes), with protocols on how

a ‘significant’ fluctuation should be investigated to determine the cause. While approaches

to defining what constitutes a ‘significant’ fluctuation in equivalent data have been

described (Weber et al., 2011), the sensitivity and specificity of such an approach in an

Australian setting is not known. For certain species, there is over 17 years of condemnation

data in the EPACS system, which provides a range of condemnation statistics in absence of

outbreaks of exotic/emerging diseases. This would aide defining an ‘expected’ range of

variation.

Commitment to investigating ‘significant’ fluctuations would be required to justify the

surveillance.

Not all condemnation status categories are likely to be sufficiently valid, or relevant to

surveillance, to justify analysing trends over time. For example, condemnations such as

‘pneumonia’ and ‘hydatids’ may have relatively high validity by qualified meat safety

inspectors under veterinary supervision, and are relevant to production, some exotic or

emerging disease incursions, and/or public health; conversely ‘cancer’ and ‘pyaemia’ may

hold less validity in the absence of follow-up laboratory testing, and may not provide

information relevant to surveillance or public health. The high-speed nature of slaughter

lines limits the practicable extent of examination and thus is likely to impact accuracy of

condemnation status categorisation; this compounds the fact that, in some (or many) cases,

macroscopic findings alone are inherently lack sensitivity and/or specificity. This has been

demonstrated in regards to macroscopic examination to classify carcasses as fit for human

consumption, fit for pet food, or condemned (Uzal et al., 1990). Similarly, though this is not

a category in the above carcass condemnation categories, nor for the Victorian Pig Health


ATTACHMENT A

Monitoring Scheme (below), detection of Leptospira sp. infection by macroscopic lesions at

slaughter in pigs has been shown to lack sensitivity and specificity in Australian abattoirs

(Jones et al., 1987; Chappel et al., 1992). Conversely, papular skin lesions (hypersensitivity

reaction) detected on Australian pigs have been shown to be a highly specific indicator of

Sarcoptes scabiei var suis infection (Davies et al., 1991).

The EPACS data are prone to bias as a representation of the health and infection status of

the Australian livestock population (the source population is likely to represent a relatively

healthy population of animals, and whole-carcase condemnation data is expected to

generally represent only severe cases of a nominated condition). However, the internal

validity of temporal comparisons is preserved, given the same catchment of animals, with

relatively consistent approaches to condemnation, would be compared over time.

The EPACS data may also be of value in monitoring trends in certain endemic diseases to assess

their impact on the industry, and guide allocation of resources to address infections or

conditions of production significance. Regular summary reports of trends in condemnation by

abattoir may thus be of interest to the relevant industry, particularly regarding production

animal industries with limited or no existing abattoir-based monitoring that is reported on in a

broadly accessible way (e.g. cattle). Considerations and limitations of such temporal

surveillance are as described above for monitoring temporal trends in carcase condemnation

status. Of particular relevance, The EPACS whole-carcase condemnation data may only

represent severe cases of a condition (Pointon et al., 2008), and so may be biased in terms of

making comparisons of a condition’s overall impact on production.

Descriptive data associated with condemnation statistics may be of value in informing other

surveillance projects- for example, in providing data to inform scenario tree modelling or

Bayesian analyses.

Collation of EPACS data would be required for analysis, but this is expected to be relatively

straightforward. Creation of EPACS database reports for throughput, stratified by state, species

and species “subtypes”, and abattoir / processing establishment, for a nominated time period, is

simple. Similarly, reports on proportions of condemnations, stratified by condemnation type,

species and species “subtype” are easily created. When stratified by state, results are also

presented stratified by the different processing establishments within the state. Where species

subtypes are from the same source population, they should be combined for analysis (e.g. ‘game

kangaroos’ and ‘kangaroos’).


ATTACHMENT A

Additional data to support a robust analysis for surveillance purposes, and the

estimated costs

Additional data from laboratory testing of a sample of condemned tissues, and from processes

for investigating ‘significant’ fluctuations in trends (for example, tracing back and investigating

on-farm, or collecting and testing tissues from further consignments at the relevant abattoir(s)),

would provide more robust data for use in arguments for proof-of-freedom, and would aide

early detection of exotic/emerging disease incursions. Similarly, data from laboratory

investigation of unusual macroscopic findings on slaughter lines may also augment surveillance

for early detection of exotic or emerging diseases.

However, it must be considered that, in attempting to augment carcase inspection data for

surveillance purposes, the high-speed nature of slaughter lines limits the ability to incorporate

sampling for subsequent laboratory testing. In addition to funding laboratory expenses, funding

further staff may be required to support specific sampling efforts.

Validation of carcase condemnation data is important for its application to surveillance

(Willeberg et al., 1984). However, validity of EPACS condemnation data, and reliability between

inspectors and plants, have not been assessed. As previously described, a valuable

augmentation of carcase condemnation data would be to perform such studies, to validate the

use of these data, and the use of monitoring data, in surveillance activities (Pointon et al., 2008).

This is likely to be supported by industry, as a way of assessing current condemnation protocols

in relation to possible wastage.

3.3 The National Sheep Health Monitoring Project and Enhanced Abattoir Surveillance Program and the Victorian Pig Health Monitoring Scheme

The ovine Johnes disease results from the NSHMP are currently reported on the NAHIS

database, so are readily accessible for surveillance reporting purposes.

As for the EPACS data, certain post mortem inspection data may be of value if monitored

temporally, to detect exceptional fluctuations in conditions which may indicate an incursion of

exotic / emerging disease, or to monitor trends in endemic conditions. As monitoring data may

capture a broader scope of the impact of a condition in a particular species, rather than just the

most severe cases that warrant condemnation (as per EPACS data), it may provide more

accurate data for capturing trends in endemic diseases. Similar to the use of EPACS data, a

validation study would be of value in interpreting the data associated with these monitoring

schemes. The Victorian Pig Health Monitoring Scheme has been identified as providing data on


ATTACHMENT A

herd health trends over time, production limiting diseases in the Australian pig industry, and

the efficacy of interventions to limit the impact of herd health conditions (Pointon et al., 2008).

Data originating from domestic abattoirs could be stratified out of the NSHMP and Victorian Pig

Health Monitoring Scheme, to augment the EPACS (export abattoir) data, as well as be

presented across all involved abattoirs. Considerations and limitations associated with the use

of these data for surveillance purposes are similar to those discussed regarding the EPACS data

(section 3.2). These data originate from a subset of Australian abattoirs, and a subset of animals

slaughtered in those abattoirs, and so the external validity of findings as representation of the

Australian sheep and pig populations, respectively, is limited, However, temporal comparisons

are expected to be internally valid in considering data at abattoir level, if there is a consistent

approach to sampling in within abattoirs over time.

As for EPACS data, descriptive data associated with these programs may be of value in

informing other surveillance projects- for example, in providing data to inform scenario tree

modelling or Bayesian analyses.

These data are not of value of themselves in proof-of-freedom claims, in the absence of a

protocol for follow-up laboratory investigation of macroscopic pathological findings.


estimated costs

As for the EPACS data (section 3.2), additional data from laboratory testing of condemned

tissues, and from processes for investigating ‘significant’ fluctuations in trends (for example,

tracing back and investigating on-farm, or collecting and testing tissues from further

consignments at the abattoir), would be required to provide more robust data for use in

arguments for proof-of-freedom and early detection of disease incursions. Also as for EPACS

data, data from laboratory investigation of unusual macroscopic findings on slaughter lines may

also augment surveillance for early detection of exotic or emerging diseases.

As pigs are the only species inspected with their head and feet attached, it may be possible to

incorporate formal screening for vesicles to facilitate early detection of foot-and-mouth disease,

given that the head area is currently examined for atrophic rhinitis as part of the Victorian Pig

Health Monitoring Scheme. However, the cost-effectiveness of this (as compared to detection by

passive surveillance) would need to be demonstrated.


ATTACHMENT A

3.4 Diagnostic tests for animals destined for exportData of diagnostic tests undertaken on animals intended for live export would be best utilised

strategically, to provide specific data relevant to animal disease surveillance and market access.

For example, Chlamydophila abortus is a nationally notifiable disease (Department of

Agriculture and Water Resources, 2017) and is thought to be absent from the country (e.g.

Department of Primary Industries, n.d.; Department of Agriculture and Food, n.d.). However,

certain C. abortus serological tests in sheep return a high number of positive results, presumably

due to cross-reaction with the endemic C. pecorum. Where export markets expect animals to be

tested pre export, this may result in a substantial number of presumptive false-positive animals

being excluded from that export market (McCauley et al., 2010). Associated data may therefore

be of use in supporting the argument for diagnostic test validation studies for application to

surveillance. A validated test of high specificity would minimise market exclusions due to

inaccuracy, as well as facilitate the ability to obtain accurate data to support Australia’s proof-

of-freedom claims.

Additionally, data from tests for exotic infections could be of value in supporting Australia’s

freedom-from-disease claims. However, as tests are not taken to be proportionately

representative of the respective Australian livestock population, results would not be of stand-

alone value. Further complications in utilising these data include the likelihood of false positive

results in testing a large numbers of animals with diagnostic tests that are not 100% specific.

The approach to utilisation of these data would need to be precisely predefined in that regard.

There is currently no way of efficiently accessing diagnostic test results through internal

departmental means, and permission from the exporters may be required to use these data.

These data may be able to be utilised through collaborations, if laboratories are willing and able

to provide data, with the consent of the exporters or by deidentification prior to sharing.


estimated costs

As data would have to be obtained through the accredited laboratories, it may be necessary to

fund staff time to extract and forward required data.


ATTACHMENT A

4 ConclusionsThe NLIS system has the capacity to record information of value in monitoring trends in carcase

condemnation and ill-thrift syndromic surveillance over time. However, recording of these data

are voluntary and the data fields are not sufficiently populated to enable such surveillance at

this time. Data from the Export Production and Condemnation Statistics database, National

Sheep Health Monitoring Project and Enhanced Abattoir Surveillance Program, and the

Victorian Pig Health Monitoring Scheme, may allow for: monitoring temporal trends in carcase

condemnation, to facilitate early detection of exotic/ emerging disease incursions and monitor

conditions of production significance; provision of denominator data of inspected animals

without detections, to support claims of proof-of-freedom of certain diseases; and provision of

descriptive data, of value in informing other surveillance projects. Diagnostic tests of animals

destined for live export are a potential data source to be used strategically to support proof-of-

freedom claims of certain diseases. However, accessing these data may be complicated and is

dependent on exporter consent and laboratory consent and participation.


ATTACHMENT A

5 References

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carcass condemnation rates in provincially-inspected abattoirs in Ontario 2001-2007:

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2015/09/NSHMP-Annual-report-2015-2016_Final_170317.pdf (Accessed 7/4/2017).

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Department of Agriculture, 2003. Code of practice for animals at saleyards in Western Australia.

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Davies PR, Moore MJ, Pointon AM, 1991. Sarcoptic mite hypersensitivity and skin lesions in

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ATTACHMENT A

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decision%20notes.pdf (Accessed 15/05/2017).

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gov.au/team/IML/IML/Post-mortem%20-%20camelid%20(OPMS_WI_ 6.03.10).pdf (Accessed

22/5/2017).

Department of Agriculture, Fisheries and Forestry, 2013. Post-mortem – Calves, On-Plant

Management System. Biosecurity Work Instruction 6.03.03. Available online: http://mylink.

agdaff.gov.au/team/IML/IML/Post-mortem%20-%20calves%20(OPMS_WI_6.03.03).pdf

(Accessed 22/5/2017).

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welfare Standards and Guidelines – Livestock at Saleyards and Depots (v 1.0 – subject to

government endorsement). Available online: http://www.animalwelfarestandards.net.au/files/

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(Accessed 22/02/2017).

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first five months. The Veterinary Record, 149, 729-743.

Iglesias RM, East IJ, 2015. Cattle movement patterns in Australia: an analysis of the NLIS

database 2008–2012. Australian Veterinary Journal, 93, 394-403.


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Jones RT, Millar BD, Chappel RJ, Adler B, 1987. Macroscopic kidney lesions in slaughtered pigs

are an inadequate indicator of current leptospiral infection. Australian Veterinary Journal, 64,

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Kaneene JB, Miller R, Meyer RM, 2006. Abattoir surveillance: the U.S. experience. Veterinary

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disease virus through sheep marketing in February 2001. The Veterinary Record, 153, 43-50.

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Chlamydophila abortus in Australian sheep and implications for the rejection of breeder sheep

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abattoirs. Sydney: Meat and Livestock Australia

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and virus diseases’. Canberra: Department of Health.

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Veterinary Medicine, 3, 79-91.


ATTACHMENT A

Appendix 1: Schema of cattle information on the NLIS database (as per NLIS, 2016)


ATTACHMENT A

Appendix 2: Cattle NLIS data fields (as per NLIS, 2016)

Variable group Variable Definition

Device

TagID Unique identifier for a deviceNLISID NLIS identifier (printed on the ear tag/paired with bolus)RFID The right most 16 characters of the RFIDPICIDOfIssue PIC ID for the Property the device was issued toManufacturerCode Code which shows the device manufacturerDeviceTypeCode Type of device, breeder, post breeder, bolus etcManufactureYearCode Year of device manufactureDeviceColourCode Colour of deviceIssueDate Date of device manufacture LTStatus Lifetime traceable status (Y / N)LTLossReasonID The reason why the device’s lifetime traceability was lostUploadID Upload ID of the tag upload file used to add the deviceCurrentPICID PIC ID for the Property the device is currently inCurrentSaleyardPICID The PIC ID for the saleyard the device is currently in (if relevant)IsDeceased Set if the device is deceased, either through upload of a kill

record or by moving to the PIC “DECEASED”

Transfer

TransferID Unique identifier for each transferTagID The device that was movedSourcePICID PIC ID of the location the device has moved from DestinationPICID PIC ID of the location the device has moved toTransferDate Date the transfer occurredVendorDeclaration The Serial No. of the movement document for the movementUploadID The upload ID of the transaction that uploaded this movementRollbackFlag Set to 1 if the transfer has been rolled backRollbackUploadID If transfer has been rolled back, upload ID of rollback transaction

Kill

KillRowID Primary keyTagID The device (animal) that was killedEstablishmentNumber Establishment where the animal was slaughteredPICID PIC ID number of establishment where the animal was killedDeceaseDate The date the animal was killedBodyNumber Body number of this deviceLotNumber Lot number for this deviceOperatorNumber Operator code for the abattoirChainNumber The chain that the animal was slaughtered onPICIDOfConsignment The PIC ID of the PIC that consigned the animalAccountID The NLIS account ID of the user that uploaded the kill recordUploadID The upload ID of the upload used to set the device to killedRollbackFlag Set to 1 if the transfer has been rolled backRollbackUploadID If the transfer has been rolled back, the value of this field will be

the upload ID of the rollback transaction

DeviceStatus

StatusRowID Unique identifier for a status change of a deviceTagID The device to which the status appliesStatusID The status that was applied to the deviceStatusDate Date the status was setStatusDuration The time that status will remain active on the deviceUploadID The upload ID of the upload used to set the statusActiveFlag Denotes whether the status is active (1) or has been removed (0)DeactivationDate The date the status was removed (if active flag = 0)DeactivationUploadID The upload ID used to remove the status

Upload

UploadID The unique identifier of a transactionUserID The NLIS User ID of the user that submitted the transactionAccountID The Account ID of the user that uploaded the transactionTransactionTypeID Type of transactionUploadStatusID Status of processing from the standard NLIS transaction

processing typesUploadDate The date and time the upload was processed


ATTACHMENT A


ErrorLog

ErrorLogID Unique identifier of the error event loggedUploadId Unique identifier of the transaction that this row of processed

data belongs toTagID An integer that uniquely identifies each device ErrorID Unique number identifying the errorExtraInfo Extra Information

Property

PICID Unique identifier of a PICPIC The property identification code assigned to the propertyPICType The type assigned to the property (feedlot, saleyard, etc)SaleyardID Saleyard ID if the property is also a saleyardEUStatus The EU Status of the propertyEUStatusDate The date the property was set to EU eligible (if relevant)PICRegisterStatus Status of the property (A= active, B= blocked, D= disbanded, G=

amalgamated)

AccountAccountID The NLIS Account IDTradingName The name of the trading company or person

EstablishmentNumberPICLink

LinkID Unique identifier for a recordEstbNo The Processor establishment numberPICID The PICID of the ProcessorNLIS_AccID The NLIS Account ID assigned to the establishment

SightedCattle

TransferID Unique identifier for a sighted recordUpldID The UploadID that uploaded the sightingPIC The PIC the animal was sighted atSightingDate The date the animal was sightedNVD The movement document serial number (if appropriate)Comments Any comments entered regarding the sighting. Usually used to

identify a show or eventTagID The device that was sighted

lkpStatus

StatusID Primary key StatusCode Status codeStatusCodeID Status Code IDProgramCode Program Code ProgramCodeID Program Code IDERPCodeFlag Y = ERP/PIC status; N = Extended/Device statusDescription Description of the statusStatusTypeID Status Type ID

lkpTransactionTypeTransactionTypeID Unique identifier for a transaction typeDescription A description of the transaction type

lkpUploadStatusUploadStatusID Unique identifier for each upload statusUploadStatus Status of processing from the standard NLIS transaction

processing types

lkpErrorErrorID Unique identifier for an errorErrorType The type of the errorDescription A short description of the error

lkpLossOfLTReasonReasonID An integer that uniquely identifies each reasonReasonDescription A description of the reason for loss

CarcaseHeader CarcaseHeaderID Primary KeyKill_key Key used to link other carcase tablesSpecies The species of the carcase (C= cattle, S= sheep)Killdate Date the animal was slaughteredKilltime Time the animal was slaughteredBody_no The body number assigned by the ProcessorChain_no The chain the animal was slaughtered onLot A code allocated to group animals/carcases to bring them into a

single commercial transaction groupOperator A code used to identify an operator. An operator code often

identifies an 'owner'Estb_fed Abattoir / boning room establishment number allocated by AQIS


ATTACHMENT A


Estb_state Abattoir / boning room establishment number allocated by local (state) authorities

Tag_table_idLot_key_id Used internally by NLISOrig_pic_id Original PIC when the kill_key was generatedLot_key End kill_key of a group of kill key

CarcaseID

CarcaseRowID Primary keyKill_key Foreign Key linked to CarcaseHeaderId_type Tag ID type (1=NLISID, 2=RFID, 3= PIC)Delivery_type The delivery mechanism for an ID deviceId_location The location of the IDTag_id NLISID or RFID or PIC as uploaded by the Processor

CarcaseBodyInfo

CarcaseBodyInfoID Primary keyKill_key Foreign Key linked to CarcaseHeaderCarcsex The sex characteristics of a carcaseCarcdent Number of teeth, either molar or incisor, of a carcaseKill_type A code representing an abattoir’s internal kill classification codeMscl_score Muscle score as per AUSMEAT Meat Language1

Q_est_act Denotes if a transmitted value is an actual or estimated valueSf_colour The fat colour as measured on the slaughter floorFat_mm Fat depth measured in mmFat_score Fat depth expressed as a scoreQ_fatsite_est_act Denotes if a transmitted value is actual value or estimatedFat_site Site at which a fat measurement was takenTrim Standard trim codes and weight adjustment criteriaSkinned Is the carcase skinnedBreed_mix Breed mix (parentage) of an animalBreed_level At what level is the breed being describedDays_on_feed The number of days on feed at a feedlotLive_weight On-the-hoof weight in kilogramsQual_lw_est_act Denotes if a transmitted value is actual value or estimatedAvg_total Defines if a value is total (=T) or average (=A)Hours_off_feed Number of hours since the animal last had access to feedHours_off_water Number of hours since the animal last had access to waterHGP_free Is the carcase free of hormonal growth promotantsResidue_free Is the carcase free of residues contaminationPred_yield Predicated percentage yield of saleable meatActual_yield Actual percentage yield of saleable meat

Free_textA general comment area (can be used for transferring information which is too complex / variable to codify)

CarcaseSideInfo

CarcaseSideInfoID Primary keyKill_key Foreign Key linked to CarcaseHeaderCarc_side The carcase side the record relates to (L= let, R= right, B= body)Carc_ctg Carcase CategoryBruise Carcase bruisingCondemn Condemnation status for the carcaseCondemn_area Which part of the carcase was condemnedDamage A code representing some type of damage to the carcaseGrade A code representing an abattoir’s internal gradeSpec_ref A private specification reference codeHSCW Individual weight of a carcase/side in hot standard carcase

weight (HSCW) kilogramsCold_weight Individual weight of a Carcase/Side in Cold Weight kilogramsTrim_weight Individual weight of a Carcase/Side in Trimmed Weight

kilogramsWeight_score AUS-MEAT defined weight scores based upon HSCW

CarcaseValue CarcaseValueID Primary keyKill_key Foreign key linked to CarcaseHeader


ATTACHMENT A


QualCarcUnit The carcase unit (side) to which a particular attribute appliesValue Value of the itemQualAvgTotal Defines if a value is a total (=T) or average (=A)QualValType The type of monetary value information being transmittedRate The rate used to arrive at a valueQualRateType The type of rate used to arrive at a value

CarcaseMeasurements

CarcaseMeasurementsID Primary keyKill_key Foreign Key linked to CarcaseHeaderQualCarcUnit The carcase unit (side) to which a particular attribute appliesCAMethod Chiller assessment measurement methodVIAMethod Video image analysis methodCAOperator A coded reference to the person taking chiller assessment

measurementsMeas_DateCAFatColour Chiller assessment fat colourQualCAMeastypeFatColourCAMeatColouring Chiller assessment meat colourQualCAMeastypeMeatColourCAMarbling Chiller assessment marblingQualCAMeastypeMarblingCATendertec Tendertec readingChiller Assessment textureCAEMA Chiller assessment eye muscle area (in mm2)QualCAMeastypeCAEMACAFatDepth Chiller assessment fat depth QualCAMeastypeFatDepthQualFatSite Site at which a fat measurement was takenCAFatPercent Percentage of fat as determined in chiller assessment/ video

image analysis equipmentCAGrade Carcase grade allocated during chiller assessmentCAWeight Chiller Assessment weight of carcase/side assessedQualCarcUnitCAWeightQualWeightType The type of weight measuredCAAssessor Accreditation reference number for a Chiller AssessorCADamage Chiller assessed carcase damage codepH pH levelBreedMix Breed mix (parentage) of an animalQualBreedLevel At what level is the breed being describedCAVIASpare1 Spare field transmitted from video image analysis equipmentCAVIASpare2 Spare field transmitted from video image analysis equipmentCAVIASpare3 Spare field transmitted from video image analysis equipment

ManualKillUpload

ManualKillUploadID Primary keyUpldID Manual Kill Upload IDKillDate Date the animal was slaughteredEstabNo Abattoir or boning room establishment number as allocated by

AQIS or StateLot A code allocated to group animals/carcases to bring them into a

single commercial transaction groupBodyNo An internal reference number for the animalChainNo A code which uniquely identifies a slaughter chain in works

which have more than one chain per speciesOperator A code used to identify an operator. An operator code often

identifies an 'owner'NLIS_ID NLIS identifier- printed on ear tags or paired with bolusesRFID The right most 16 characters are provided; 4th character is a

spacePicNRF PIC that consigned the animal


ATTACHMENT A1 Aus-meat Ltd, 2011

Appendix 3: Sheep and goat (mob-based) NLIS data schema (as per NLIS, 2016)


Report: NLIS database surveillance

Appendix 4: Sheep and goat data fields (as per NLIS, 2016)


NVDNumber

UpldID The upload ID that created the movement recordNVDSerialNumber The serial number of the movement documentTransferDate The date the movement occurredFromPICID The PIC ID of the property the animals were fromNumberHead The number of animals in the mobSaleyardPICID The PIC ID of the saleyardNVDID Primary key. Unique identifier of a movementSpecies The species of the animals movedComment

BreedOnVendorPICAnswerThe answer to question 3 of the National Vendor Declaration (NVD) – which is, were the animals bred by the vendor?

BreedOnVendorPICTimeSincePurchase

If the animals were not bred on the vendor’s PIC, the amount of time they spent on the PIC (A = Less than 2 months; B = 2 to 6 months; C = 6 to 12 months; D = more than 12 months)

NVDAgentAgentUID User ID of the Selling Agent recorded on the Saleyard movementNVDID Foreign key link to NVDNumberNVDAgentID Primary key

NVDToPIC

ToPICID The PIC ID of the destination propertyTotalHead The number of animals moved to the ToPICIDNVDToPICID Primary keyNVDID Foreign key link to NVDNumber

NVDOtherFromPICNVDID Foreign key link to NVDNumberNVDOtherFromPICID Primary keyOtherFromPIC Other From PIC

NVDPostBreeder

PICID PIC IDSerialNo Serial Number of the Post-breeder tagNVDID Foreign key link to NVDNumberNVDPostBreederID Primary key

MobBasedKill

KillRowID Primary KeyProcessorPICID PIC ID of the ProcessorMobKillDate The date the mob was killedNumberOfHead Number of head killed

SourceTypeWhether the animals came from a saleyard or were direct consigned (“Saleyard” or “Direct”). For direct consigned animals, a movement will be created by the system

Species The species of animal killed (sheep or goat)FromPICID From PIC ID

RollbackUpldIDUpload ID of the rollback if the kill has been rolled back. If this is non-blank, then the kill should be excluded from reports

NVDID Foreign key link to NVDNumber
