Animal Health and Diseases

Animal Welfare, the Five Freedoms, and Clinical Observation

Good animal husbandry means managing livestock so they remain healthy, comfortable, and productive. The Animal Health and Welfare Act 2013 provides the legal basis for animal protection in Ireland, supported by European Union directives governing pigs, calves, and poultry. Welfare standards are evaluated using the internationally recognised Five Freedoms:

• Freedom from hunger and thirst: Ready access to fresh water and a balanced diet matched to the animal's life stage and production demands.
• Freedom from discomfort: An appropriate environment, including shelter, dry bedding, and sufficient lying area (e.g. adequate cubicle space limed with hydrated lime).
• Freedom from pain, injury, and disease: Prevention through biosecurity and vaccination, rapid diagnosis, and prompt veterinary treatment.
• Freedom to express normal behaviour: Adequate space, proper social grouping with companions of their own kind, and environmental enrichment.
• Freedom from fear and distress: Calm handling facilities and stockmanship that avoid mental suffering.

Welfare failures carry severe financial penalties. For instance, overcrowded pens in finishing pigs trigger tail biting, an abnormal behavioural vice that leads to spinal infection, carcass trimming, and direct financial docking at the meat plant.

How Disease Costs the Farmer

• Lower output (liveweight gain, milk yield, lambs reared)
• Vet and medicine costs
• Discarded milk during withdrawal
• SCC milk-price penalties
• Deaths, culling and replacement costs
• Carcass or liver condemnation
• Movement restrictions (e.g. TB)
• Extra labour

A lame ewe eats less, loses condition and milk, and her lambs are sold later or lighter.

Clinical Signs: Healthy vs Sick Livestock

Daily visual checks allow stockpersons to detect illness before clinical outbreaks spread:

Microbiology of Livestock Pathogens

A pathogen is any biological organism that causes disease in a host animal. Understanding pathogen biology dictates how farmers prevent and treat livestock infections:

Bacteria

Bacteria are single-celled, prokaryotic micro-organisms that lack a membrane-bound nucleus and organelles. Their genetic material consists of a single circular chromosome, often accompanied by small circular rings of DNA called plasmids, which can carry and exchange antimicrobial resistance genes. Bacteria reproduce rapidly by binary fission, where one cell duplicates its DNA and divides into two identical daughter cells.

Under adverse environmental conditions, certain bacteria such as Clostridium chauvoei form a tough, dormant survival structure called an endospore. These endospores survive in pasture soil for many years, resisting drought, heat, and standard disinfectants, germinating only when ingested or introduced into deep wounds. Bacteria are classified by morphology:

• Coccus (round): e.g. Streptococcus uberis and Staphylococcus aureus, primary causes of bovine mastitis.
• Bacillus (rod-shaped): e.g. Escherichia coli, causing neonatal scour; Mycobacterium bovis, causing bovine tuberculosis.
• Spirillum (spiral): e.g. bacteria causing reproductive loss and infertility.

Fungi

Fungi are eukaryotic organisms with membrane-bound nuclei, mitochondria, and cell walls composed of chitin. Lacking chlorophyll, fungi cannot photosynthesise; they are heterotrophic, living as saprophytes on dead matter or as parasites on living tissue. Ringworm is caused by the fungus Trichophyton verrucosum. It forms circular, grey, crusty skin patches around the eyes and neck of young cattle. Its infectious fungal spores survive for months on timber pens and concrete, posing a significant direct infection risk to cattle and farmers (zoonosis).

Viruses

Viruses are non-cellular infectious particles consisting of a nucleic acid core (DNA or RNA) enclosed within a protein coat (capsid). They have no independent metabolism, cell walls, or protein-synthesis machinery. Because of this, they are obligate intracellular parasites that invade host cells and hijack host replication machinery. Antibiotics have no effect on viruses, because antibiotics target bacterial structures such as cell walls and bacterial ribosomes.

Infectious and Parasitic Diseases of Farm Livestock

The specification requires detailed understanding of the main infectious and parasitic diseases across ruminant (cattle, sheep) and monogastric (pig) enterprises:

The Liver Fluke Life Cycle and Parasite Control Systems

The liver fluke (Fasciola hepatica) causes major financial losses across Irish beef, dairy, and sheep farms through liver damage, poor growth rates, and slaughterhouse liver condemnations.

In the exam, draw this as a labelled circle.

How Knowledge of the Life Cycle Guides Farm Control

• Disrupting the Intermediate Host: The mud snail (Galba truncatula) needs wet, muddy ground. Suitable drainage can reduce this habitat; fencing off wet areas keeps livestock away from high-risk grazing. Without a snail host, the swimming miracidium dies within hours, breaking the cycle.
• Pasture Management: Moving vulnerable young stock away from known wet paddocks during late summer and autumn prevents animals from ingesting peak populations of encysted metacercariae.
• Targeted Flukicide Dosing: Products containing triclabendazole kill early immature, immature, and adult flukes, making them essential for autumn acute fluke risks in sheep. Many other flukicides kill only older flukes (late-immature or adult), so they are used later in the season, for example some weeks after housing.

Strategic Parasite Control in Cattle and Sheep

To prevent anthelmintic resistance, farmers must combine chemical treatments with grazing management. Send dung samples for a faecal egg count (FEC) before dosing, so you only dose when worm numbers are high. This saves money and slows wormer resistance:

Metabolic and Nutritional Disorders

Metabolic disorders are non-infectious conditions caused by acute nutritional imbalances or deficits in blood mineral concentrations during high-demand stages of production:

Notifiable Diseases, Zoonoses, and Safe Farm Practice

Notifiable Diseases

A notifiable disease is a disease of such high contagiousness, severe mortality, or extreme economic threat that anyone suspecting its presence is legally required to report it immediately. In Ireland, anyone suspecting a notifiable disease must report it without delay to a veterinary practitioner or to the Department of Agriculture, Food and the Marine (DAFM) through their local Regional Veterinary Office.

• Bovine Tuberculosis (bTB): Caused by Mycobacterium bovis. Spread by respiratory aerosols, direct contact, contaminated pastures/feed, and wildlife reservoirs (badgers, deer). Detected through annual herd testing using the Single Intradermal Comparative Tuberculin Test (SICTT). Positive reactor cattle are culled and herd movements are locked down immediately.
• Foot-and-Mouth Disease (FMD): A highly contagious aphthovirus causing painful blisters on the hooves, muzzle, and teats of cloven-hoofed animals. Can trigger severe livestock-movement and trade restrictions.
• Brucellosis: Caused by Brucella abortus; causes late-term abortion and retained afterbirth in cows. Ireland is officially brucellosis-free, making vigilance and abortion testing vital.
• Avian Influenza (Bird Flu): Highly pathogenic viral infection of poultry, transmitted by wild migratory waterfowl.
• African Swine Fever (ASF): Haemorrhagic viral fever in pigs with near 100% mortality, spread through infected meat scrap feeding (swill) or contact with wild boar.
• Other key notifiable diseases include: Bovine Spongiform Encephalopathy (BSE), Bluetongue, and Anthrax.

Bovine Viral Diarrhoea (BVD) Eradication

BVD is an economically devastating viral disease in cattle causing immunosuppression, scour, and abortion. Persistently Infected (PI) calves are formed when an uninfected cow catches the virus in early pregnancy; the developing foetus recognises the virus as 'self' and never produces antibodies. PI calves shed massive viral loads for life. Ireland's national eradication scheme mandates that every newborn calf is tissue-tag tested at birth. PI calves must be culled immediately to break the transmission cycle.

Zoonoses and Farm Safety Precautions

A zoonosis is an infectious disease that can be passed from animals to humans:

• Bovine Tuberculosis (Mycobacterium bovis): Causes chronic respiratory disease. Ingestion avoided by drinking only pasteurised milk*.
• Leptospirosis (Leptospira hardjo): Carried in cattle urine and aborted fluid; causes severe flu-like illness in humans. In contrast, Leptospira icterohaemorrhagiae* is transmitted via rat urine and causes jaundice and liver/kidney failure (Weil's disease).
• Cryptosporidiosis (Cryptosporidium parvum):* Protozoan shed in scouring calf dung; enters human drinking water or dirty hands, causing acute stomach cramps and vomiting.
• Brucellosis (Brucella abortus):* Contracted via handling aborted foetuses and fluids; causes undulant recurring fever in people.
• Orf (Parapoxvirus): Viral infection from sheep lips, entering human skin cuts and creating painful, weeping pustules.

Precautions for Farmers:

1. Wear personal protective equipment (PPE), including arm-length disposable gloves during calving, lambing, and handling afterbirth.
2. Wash hands thoroughly with antibacterial soap and cover all open cuts with waterproof bandages before eating or smoking.
3. Keep pregnant women strictly away from lambing ewes due to chlamydia and toxoplasmosis abortion risks.
4. Maintain active vermin control (baiting rats) around feed stores and calf housing.
5. Boil or pasteurise all milk intended for home consumption.

Immunity, Traceability, and Biosecurity Systems

Active vs Passive Immunity

• Active immunity: The animal's own immune system produces antibodies and memory cells following exposure to a foreign antigen. This occurs through natural recovery from infection or through vaccination (administering a dead, weakened, or partial pathogen). Active immunity takes 1–2 weeks to develop but produces long-lasting protection bolstered by booster shots.
• Passive immunity: The animal receives pre-formed, ready-made antibodies from an external source, primarily through colostrum. Protection is immediate but temporary, lasting only a few weeks until the maternal antibodies degrade.

Because the multi-layered placenta of cows, ewes, and sows completely blocks large maternal antibody proteins from passing into the foetal bloodstream during pregnancy, newborn calves, lambs, and piglets are born with zero circulating antibodies. They depend entirely on maternal colostrum.

In the first hours of life, the calf's small intestine can absorb whole, intact antibody molecules directly into the blood. This intestinal permeability declines rapidly and ceases completely by 24 hours (gut closure). Successful colostrum management follows the 3-2-1 rule:

• 3 Litres: Feed at least 3 litres of clean, high-quality colostrum (thick, antibody-rich; verified at >22% on a Brix refractometer).
• Within 2 Hours: Feed this volume within 2 hours of birth while gut absorption is at its peak.
• 1st Milking: Use colostrum exclusively from the dam's first milking, as antibody concentration drops sharply in subsequent milkings.

Farm link: Vaccinating ewes with an 8-in-1 clostridial booster 4–6 weeks prior to lambing elevates antibody concentrations in their colostrum, directly conferring passive protection to newborn lambs.

Livestock Traceability and Disease Containment

Under European and Irish law, all cattle must carry two official Department-approved ear tags and an individual animal passport. Every birth, movement, purchase, and slaughter event is logged on the national Animal Identification and Movement (AIM) database. If an outbreak of a disease like Bovine TB occurs, or an infected carcass is flagged at slaughter, veterinary inspectors instantly trace the animal's herd of origin and test every intermediate herd the animal passed through, protecting Irish export markets.

Practical On-Farm Biosecurity Protocols

1. Closed Herd Policy: Breed all replacement heifers and breeding ewes on-farm to prevent introducing subclinical diseases like BVD, Johne's, or footrot.
2. Quarantine: Isolate all purchased stock or returning show animals in a separate pen for 3–4 weeks, testing for disease before mixing with the main herd.
3. Stock-Proof Boundary Fencing: Double-fence farm boundaries with an adequate buffer gap to eliminate nose-to-nose contact with neighbouring cattle.
4. All-In, All-Out Housing: Empty, power-wash, and disinfect pig and poultry sheds thoroughly between batches to break bacterial cycles.
5. Parasite Pasture Planning: Run a leader-follower grazing system where vulnerable young calves graze clean pastures first, followed by older cattle whose developed immune systems clear remaining larvae.

Antimicrobial Resistance (AMR) and Responsible Medicine Use

Antibiotics are antimicrobial medicines that destroy or inhibit the growth of bacteria. Overuse and misuse in agriculture have accelerated the emergence of Antimicrobial Resistance (AMR), a critical threat to both animal welfare and human medicine.

Evolution of AMR via Natural Selection

The development of antibiotic resistance proceeds in five sequential steps:

1. Random Mutation: Within a large population of bacteria, a random genetic mutation spontaneously occurs in an individual bacterium, granting resistance to a specific antibiotic.
2. Antibiotic Exposure: The antibiotic is administered to the herd or flock, especially at sub-therapeutic doses or during unfinished courses.
3. Selective Advantage: The antibiotic kills the vulnerable, non-resistant bacteria, leaving the mutated resistant bacterium alive.
4. Multiplication: Relieved of competition for space and nutrients, the resistant bacterium multiplies rapidly, passing the resistance gene to all daughter cells.
5. Horizontal Gene Transfer: Resistant bacteria share their resistance genes with other bacterial strains and species via plasmid exchange. Over time, the entire bacterial population becomes resistant.

To preserve antibiotic efficacy, farmers should use alternatives to antibiotics for disease control, such as routine vaccination, high housing hygiene, culling chronic carriers, and strict biosecurity.

Responsible Medicine Use and Statutory Rules

• No Routine Blanket Antibiotic Treatments: Routine preventive antibiotic use in healthy groups of stock is prohibited under EU veterinary regulations. Antibiotics are strictly prescription-only medicines (POM).
• Selective Dry Cow Therapy (SDCT): Blanket dry cow therapy, where every cow automatically receives an intramammary antibiotic tube at drying off, is no longer permitted. Instead, farmers use selective dry cow therapy: only cows with proven infections (elevated SCC or clinical history) receive antibiotic tubes. Uninfected cows receive only an internal teat sealant to physically block the teat canal.
• Culture and Sensitivity Testing: Vets isolate the causal bacterium from milk or tissue swabs and test it in a laboratory against different antibiotic discs to identify the exact narrow-spectrum antibiotic that will work.
• Withdrawal Periods: The withdrawal period is the statutory minimum duration that must elapse between the last administration of a medicine and the slaughter of an animal for meat, or the collection of milk or eggs for human consumption. This ensures chemical residues fall below statutory Maximum Residue Limits (MRLs).
• Animal Remedies Record Book: Farmers must record every medicine purchase and administration, logging the date, animal ID, medicine name, batch number, quantity administered, prescribing vet, and the withdrawal expiry date.

Key terms

Pathogen

An organism that causes disease in a host animal, such as a bacterium, virus, fungus, or parasite.

Zoonosis

An infectious disease that can be naturally transmitted from vertebrate animals to humans (e.g. Bovine TB, Leptospirosis, Ringworm, Brucellosis).

Notifiable Disease

An animal disease of such high contagiousness, severity, or economic impact that it must, by law, be reported immediately to a vet or the Department of Agriculture, Food and the Marine (DAFM).

Antimicrobial Resistance (AMR)

The acquired evolutionary ability of bacteria to survive exposure to an antibiotic medicine that previously killed them or inhibited their growth.

Passive Immunity

Short-term disease protection acquired by an animal through receiving pre-formed maternal antibodies, primarily absorbed from colostrum.

Active Immunity

Long-lasting disease protection produced when an animal's own immune system generates antibodies and memory cells following exposure to an antigen via infection or vaccination.

Withdrawal Period

The statutory minimum time that must elapse between the final administration of a veterinary medicine and the slaughter of the animal for meat or collection of milk/eggs for food.

Somatic Cell Count (SCC)

A diagnostic count of white blood cells per millilitre of milk, used as a key indicator of udder health and subclinical mastitis.

Endospore

A tough, dormant survival structure formed inside certain bacterial cells (e.g. Clostridium chauvoei) that withstands heat, drought, and standard farm disinfectants for years.

Selective Dry Cow Therapy

The targeted farm practice of administering antibiotic tubes at drying off only to cows with confirmed bacterial infections, while treating uninfected cows with teat sealant alone.

Biosecurity

A set of practical management steps implemented to prevent the introduction of infectious diseases onto a farm and stop their spread within herds and flocks.

Intermediate Host

An organism in which a parasite's larval stages develop (for liver fluke, they also multiply asexually); the adult parasite lives and reproduces sexually only in the primary host. Example: the mud snail (Galba truncatula) in the liver fluke life cycle.