Wildlife Health Investigation and a Guide to Necropsy

Karrie Rose


1.1 Why study wildlife health?

In a global environment where approximately 75% of recently emerging and re-emerging zoonotic diseases emanate from wildlife reservoirs, there has never been more interest in wildlife health (Woolhouse 2002). Additional compelling factors driving an interest in wildlife health include public concern regarding animal welfare, zoonotic diseases and food safety issues associated with endemic and exotic disease, biodiversity protection, bioterrorism detection, climate change and its effects on animal and human health and disease, and the development of a nationally integrated biosecurity strategy (Bengis et al. 2004).

The significance of disease in wildlife populations and its impact on the conservation of biodiversity in Australia is poorly understood. Disease-causing organisms are a component of most natural ecosystems. A balance among the relationships of host, pathogen and environment most often meters the occurrence of disease. As wildlife habitats are modified through human activity and an increasing number of species are intensively managed, the possibility of disturbing these relationships increases. Wildlife health investigations are thus evolving through our increased involvement with wildlife management. The investigation of wildlife health and disease provides the opportunity to view individual species as indicators of environmental contamination, habitat degradation or climate change.

Wild animals may be subclinically infected with a variety of potential pathogens and can function as reservoirs for some disease-causing agents. Undiagnosed disease in wildlife may pose a significant risk to human health, to the agricultural industry, international trade, and to in situ and ex situ species recovery programs.

Some examples of the potential effects of wildlife disease include:

Wildlife management involving capture and animal translocation in Australia includes animal research and targeted disease surveillance, the rehabilitation and release of injured or illegally held animals, the reintroduction of species that are depleted or extinct in their natural range, the creation of safe populations of wildlife where they will not be threatened by disease, harvesting or habitat degradation, the dispersal or relocation of animals deemed pests, and the movement of feral or native animals in attempts to reduce population density to control disease or protect habitat quality.

Regardless of the circumstances that initiate your involvement in a health investigation, examining a wild animal should be viewed as an opportunity to collect as much information as possible (Woodford 2001). Collecting blood and faecal samples during restraint of an animal to allow a radio-collar to be fitted provides the opportunity to screen for blood-borne and intestinal parasites, and natural food sources. Serum samples can be tested for antibodies that may reflect exposure to potential pathogens. Some nutrient concentrations can be assessed in serum, and stored serum samples can prove invaluable in defining emerging disease syndromes.

Ultimately, the collaboration of biologists, veterinarians, researchers and diagnosticians can provide cost-effective health assessment, even if this was not the primary goal of the project.

Through our involvement with wildlife health initiatives we can attempt to maximise the success of wildlife conservation activities, contribute to successful reproductive programs and participate in the banking of rare genomic materials. Each wildlife management activity can provide animal health information that is useful as a surveillance tool to help us understand the occurrence of disease and provide information to plan disease control and eradication programs (Zepeda & Salman 2003).

Information on wildlife health from all zoological parks, universities, agriculture agencies, conservation departments and wildlife rehabilitation facilities is being systematically collated by the Australian Wildlife Health Network (AWHN 2007) to contribute to animal health information systems and national disease surveillance programs.

1.2 Health screening or surveillance

A baseline health assessment can be conducted on wild animals captured for management purposes, or it can be targeted to answer specific questions regarding the health of a population.

Common goals of a baseline health assessment in live animals could include determining:

  • physiological data (temperature, heart rate, blood pressure, respiratory rate, reproductive details etc.);
  • morphological assessment;
  • haematological and serum biochemical data and establishment of reference ranges, and identification of haemoparasites;
  • identification of ectoparasites;
  • the best method of external examination to detect evidence of disease;
  • repeated faecal examination for evidence of internal parasites;
  • bacterial fauna and potential pathogens in the upper respiratory tract, eyes, ears, lower gastrointestinal tract or lower urogenital tract;
  • analysis of genetic variability using blood, skin or oral swabs;
  • radiographic examination or skeletal analysis;
  • stomach content or scat examination for diet analysis;
  • fur or blood examination for the presence of nutrients or toxins;
  • serology to determine what organisms the animal has been exposed to in the past;
  • polymerase chain reaction (PCR), bacterial, fungal or viral culture to determine whether specific organisms are present within the animal (AAZV 2001).

An experienced wildlife veterinarian and a veterinary pathologist should be consulted during the planning phases of a health screening or surveillance study to ensure that the diagnostic testing is conducted in a humane fashion and that the laboratory findings will be rewarding.

1.3 Planning a health surveillance project

As with any endeavour, the key to successful wildlife health investigations is effective planning. Planning may be done very quickly by experienced personnel who are already well-equipped, but some wildlife health field projects may require more than a year of planning.

First, consideration should be given to seeking approval or guidance from the following groups:

The state conservation agency should be consulted before any wild animals, particularly marine mammals or migratory birds, are handled.

Projects designed to assess population health are becoming more common. Collecting samples from different populations of wildlife provides a fantastic opportunity to accumulate baseline normal data for haematology, biochemistry, parasite burdens and parameters of a general physical examination.

Baseline physiologic data determination and specific disease testing can be expensive. Collaborating with interested veterinarians and researchers can decrease the costs of investigation. However, it is important to encourage conservation agencies and recovery groups to include funding for health assessment and monitoring in their wildlife management budgets.

It can be very difficult to decide which specific disease-causing agents, toxins or nutrient concentrations to include in a health assessment. Test selection will rely on careful consideration of the species’ susceptibility to a range of agents. A thorough literature and resource search of existing health information is the basis of test selection.

The sensitivity and specificity of each potential test should be evaluated. When tests have poor sensitivity, the use of several diagnostic tests to assess exposure to and infection with a single infectious agent may be required. Often, combining several tests such as culture or PCR with serology will help to differentiate:

  • animals that may have been exposed to an infectious agent (and now have antibodies towards that agent) in the past, but are not necessarily still carrying the organism;
  • animals that are actively infected but remain healthy;
  • animals that are actively infected but have reduced function or disease;
  • animals that have not been exposed to the infectious agent and could be considered susceptible due to a lack of circulating antibodies.

Always ensure that the tests you are using have been validated for the species involved in your study. If at all possible, diagnostic tests should be thoroughly evaluated in captive wildlife prior to being used in field studies. If you are not confident that the test has been validated, speak with a pathologist or microbiologists regarding means to validate new tests through your proposed study.

Carefully consider how you will interpret your findings, both positive and negative. Identifying the presence of a potential pathogen does not necessarily indicate a clinically significant infection in the animal sampled. Negative findings do not always indicate that an individual animal is free of infection. It is also wise to contact the state chief veterinary officer in advance when you plan to test for diseases listed as notifiable.

After test selection has taken place, it can take time to find laboratories that can assist with your investigation. Canvassing laboratories for the tests that they conduct, the costs involved and the optimum method of sample collection can take several weeks for a large-scale project. Some researchers can be encouraged to test samples on a collaborative basis to reduce costs. Some large commercial laboratories offer a discount for large numbers of samples shipped in bulk, if negotiated in advance.

Creating an examination checklist to be used in the field or in the clinic when each animal is examined will ensure that all required information and samples are collected and recorded. Preparing pre-labelled specimen collection kits before the field trip will reduce the time required to process samples, reduce animal handling times and decrease the likelihood of forgetting to collect a sample.

1.4 Planning a field trip

A field trip to gather data and animal samples requires a great deal of preparation. Personnel participating in a trip must be identified and trained well in advance, as this is often required in the animal ethics committee application. Generally, at least three people are required for any venture in animal handling: 1) animal handler or anaesthetic monitor; 2) examiner and sample collector; 3) recorder. The recorder can complete the examination checklist, properly label the samples, take photographs and pass any additional equipment required during the procedure (Fig. 4.1).

Planning and preparing the equipment for fieldwork can be a mind-racking experience. Obviously, it is very disappointing to be caught without a vital piece of equipment out in the field. It is important to begin the planning early so that any unusual items can be ordered and received. An equipment list is given in Table 4.1, but if this is your first trip talk to more experienced researchers and have them check your list. All equipment should be tested prior to being packed.

When samples can’t be taken to a laboratory, it may be necessary to set up a remote lab. A variety of manual and electrical instruments can be taken into the field to assist with sample collection and analysis. Small generators can power most equipment. Centrifuges, microscopes and even serum biochemistry analysers can be transported quite readily. Gas anaesthetic machines can be small and portable.

Packing equipment into sealed plastic bins will protect the materials from water and pests. You may not be allowed onto some off-shore islands if your equipment is not in pest-proof cases.


Figure 4.1 a) Sample collection from a northern hairy-nosed wombat (Lasiorhinus krefftii) in the field. b) Cetacean necropsy set-up on a beach.

If possible, a run-through is highly recommended to ensure that all the goals can be met with the available equipment. The run-through will also ensure that personnel are comfortable with their required tasks and can function well as a team.

When planning any project, from a single necropsy in the field to a long journey, it is important to remember your own safety and comfort. Simply including a few extra tarps to erect a makeshift tent can keep you dry or shaded. Research what resources will be available on-site, and what you will have to bring.

Table 4.1 Field trip equipment checklist

Personal safety equipment

General equipment

Sample collection equipment

• Tarps and rope to create a tent to ward off rain or sun

• Good pest-proof packs for carrying equipment

• Indelible marking pen

• Insect repellent

• Cooler and ice packs

• Syringes—5, 10, 20 mL

• Sunscreen, hat, sunglasses

• Sharps disposal unit

• Needles—various gauges

• Drinking water, food

• Camera

• Butterfly catheters—various gauges

• Change of clothes

• Masking tape and packing tape

• Heparin or EDTA

• Coveralls

• Ruler

• Blood collection tubes—EDTA, heparin, oxalte and serum

• PVC apron

• Extra batteries

• Sterile plastic bottles—90 mL

• Latex gloves or dishwashing gloves

Necropsy equipment

• Sterile cryovials—2 mL

• Surgical facemasks

• Scale

• Sterile plastic bags (Whirl-pak® bags)

• Rubber boots and good walking shoes

• Necropsy worksheet

• Large ziplock bags

• Bucket, nail brush, antiseptic soap, paper towels

• Knives, sharpening stone and steel

• Aluminium foil

• Torch—hand-held and headlamp

• String and manila labels

• 1 L plastic containers filled with 10% neutral buffered formalin

• First aid kit

• Scalpel handle (# 4) and disposable blades (#24)

• 50 mL of 70–90% ethanol

• Mobile phone

• Forceps—various

• Bacterial culture swabs

• GPS unit and maps

• Scissors—various

• Dry sterile swabs

• Emergency locater beacon if on water or very remote

• Poultry shears or large bandage scissors

• Capillary tubes

Carcass collection equipment

• Bone or hacksaw and spare blades

• Glass microscope slides, cover slips and slide storage box

• Heavy-duty rubbish bags

• Hammer, chisel and vice for brain removal from large skulls

• Microscope (may require mirror as light source if no access to power)

• String

• Long-handled pruning sheers/ribcutters

• Centrifuge (manual serum separating devices are available)

• Animal sample tags and pencil or indelible pen

• Gaff hooks—useful for marine mammal necropsies

• Saline

• Wildlife incident report forms

Clean-up equipment

• 10% neutral buffered formalin

• Mortality log forms

• Tarp

• Parasite preservative

• Pencils and sharpener

• Water, scrub brush, detergent, towel

• Any special media required chlamydial culture medium, viral culture medium

• Clipboard with a clear piece of plastic to keep rain off

• Heavy-duty rubbish bags

• Methanol to fix blood films

• Faecal flotation vials and solution

• Cooler and ice bricks or liquidnitrogen dry shipper

When you finally make it to the actual field trip, take time to meet the land owners, local conservation agencies and anyone in the area who is interested in what you are doing. If these people know what you are doing and why you are doing it, the next trip will be easier to organise and you may have more help.

1.5 Sampling a wildlife population

Whenever possible, consult a veterinary epidemiologist to assist with project design prior to undertaking a wild-life health investigation. In some rare species, or those that are managed in a captive situation, it may be possible to collect samples from each animal in the population. This method of sampling is called a population census and can precisely measure the prevalence of specific diseases, characteristics or traits within the population.

Usually it is very difficult to sample the entire wildlife population, and only a small proportion of animals is examined as a study population. Prior to designing a health investigation it is important to define:

  • the population at risk or of interest;
  • the study population.

If you can only collect samples from a proportion or subset of the animals at risk or of interest, then you are sampling the population. Your study population will provide only an estimate of the prevalence of specific diseases or traits within the population. Sampling from a study population is not a precise measurement throughout the population at risk, and selection bias can be introduced (Wobeser 1994; Cameron et al. 2003).

When using a study population, it is very important to either limit your comments or inference to the population sampled, or attempt to collect a study population that accurately reflects the population at risk. Study populations can be affected by selection bias when sampling methods are not random. Ensuring that the age and sex distribution in the study group is similar to that in the entire population is important. Other factors such as ecosystem, geographic distribution and genetic variability should also be considered when identifying a study population.

Wildlife health sampling may be undertaken on a convenience basis rather than trying to select a study population that reflects the entire population. Animals are often sampled due to accessibility (they are already being handled or are the only animals found or trapped) or in a targeted program based on presenting signs that make them more likely to have the disease of interest. These sampling techniques, however, make it very difficult to make inferences regarding disease prevalence in the population as a whole. We can only comment with certainty on the prevalence of disease within the target group, rather than the entire population (i.e. the prevalence of lyssavirus infection in bats found with behavioural abnormalities).

Random sampling techniques are difficult if not impossible to apply to wildlife. The best option is to find a method that reduces bias and represents the population as closely as possible.

Many wildlife health surveillance projects are designed to detect specific disease. Determining the number of animals that need to be sampled to detect or rule out the presence of an infectious agent depends upon:

  • an estimate of the prevalence of the disease within the population;
  • the population size;
  • the accuracy of the test—sensitivity and specificity;
  • the level of certainty (confidence) in results, usually set by convention to 0.95 so that there is a 95% chance of detecting the disease (Wobeser 1994).

To determine the number of animals to test to detect a specific disease, use the following formula:


where n = sample size, P = probability of detecting at least one case of the disease if it is present in the population (usually set to 95%) and d = number of detectable cases in the population. Thus, d = population size × prevalence × sensitivity of the test. N = population size.



We want to determine if an army of 500 frogs is infected with chytrid fungus, which we suspect will have a 10% prevalence (approximately 10% of the frogs would be infected if the population had been exposed to the fungus). The diagnostic test is a real-time PCR with a sensitivity of 98%. We want to be 95% certain that we will detect the disease if it is present. Thus N = 500, P = 95%, d = 500 × .1 × 0.98 = 49


At least 28 frogs would have to be tested to determine if the population was infected with the fungus, with 95% confidence, where the prevalence is 10%. The sample size required increases with level of confidence required. It also increases as the prevalence of disease decreases and estimating the sample size for very low-prevalence diseases (<0.1%) with a high level of confidence can be difficult and very expensive. For wildlife, there may also be animal and population welfare concerns, the capacity of the diagnostic laboratory may be limiting and appropriate levels of funding and resources may simply not be available. In these instances there is often a shift from sampling to detect disease at a known level of confidence, towards determining the probability of disease freedom. These studies require targeted investigation into disease events or surveillance of high-risk individuals or populations (Salmon 2003).

1.6 Prevention of disease spread among wildlife populations

The motto of fieldwork is ‘Above all, do no harm’. It is important not to spread infectious agents to wildlife populations, domestic animals or humans during health investigations. Some infectious agents and parasites can be very hardy in the environment or adhere to clothes and equipment. Each site where wildlife is handled should be considered a quarantine site (CCWHC 1998; CCWHC 1999).

Protocols for the prevention of disease spread should be incorporated into written operating procedures and animal ethics and research application forms.

Outer clothing and equipment worn in the field should be removed, and placed into plastic bags in the field. Hands and boots should be washed and disinfected in the field. Animal-handling bags or boxes should be cleaned and disinfected between uses with different animals. All equipment and clothing should be thoroughly washed and sanitised prior to being used in another location. Once organic material has been removed from equipment, a solution of household bleach (1 part bleach to 9 parts water) is an effective disinfectant. This solution can also be used to scrub boats, vehicle tyres and work surfaces. The external surfaces of sample vials should be cleaned and disinfected in the field. Sample vials should be leak-proof, and should be double-bagged prior to submission to the laboratory. Carcasses should be individually bagged in leak-proof heavy-duty plastic bags to be submitted to the laboratory. The carcasses should be placed into plastic tubs, in case leakage does occur en route.

Carcass disposal should be undertaken with great care. Animal carcasses are difficult to burn, and can contaminate groundwater if buried improperly. Often the easiest way of managing excess carcasses is to double-bag them at the site and organise incineration by a commercial contaminated waste disposal company. If carcasses must be burned or buried, seek prior approval from the local council, state agriculture department and rural fire service.


Although the procedures and tests used to investigate disease in wildlife are similar to those used in domestic animals, the approach is dramatically different.

Veterinarians are often trained that diagnosis requires them to obtain a biopsy or collect a lump of the diseased tissue into formalin and send it to a pathologist. The pathologist will examine the tissue, make observations and interpret the lesions in comparison with a large dataset of the known diseases of that species. A sample of intestine from a dog with parvovirus usually has lesions that are characteristic of that disease, so there is generally no need to pursue viral culture. The difficulty with this approach is that we know relatively little about wildlife health and there is no definitive dataset for most non-domestic species.

Specialised diagnostic testing is often required for a definitive diagnosis of illness in wildlife. It is vital to collect appropriate samples that allow conclusions in the event of a disease outbreak in wildlife. It is also important to collect samples from healthy animals to produce baseline normal health indicators that will complete the dataset. Table 4.2 gives a list of the samples that should be collected during a routine necropsy.

Table 4.2 Routine necropsy checklist—in most cases, the following samples are sufficient

Aseptically collected samples of:





any lesion

Stored frozen pending the results of histopathology

Formalin-fixed 1 cm wide wedges of:

tonsil, axillary, inguinal, submandibular and

bronchial lymph nodes





adrenal gland




stomach, pancreas, duodenum, jejunum, ileum, large intestine and mesenteric lymph node

skeletal muscle and sciatic nerve


margin of any lesion

The collection of appropriate information is just as important as the collection of diagnostic samples. Having as much information as possible about the animal and how samples were collected will greatly improve the pathologists’ ability to interpret their findings.

Whenever possible, contact the pathologist or diagnostic laboratory before sample collection to ensure that you are collecting the appropriate materials and information to answer your questions.

2.1 Clinical signs and diseases of concern

Exotic diseases can affect wildlife. Australian fauna is distinct from domestic species and from wildlife in other parts of the world. Exotic diseases in wildlife could be displayed in unexpected ways.

If you encounter unusual or unexpected clinical signs or mortality in wildlife, contact the state veterinary laboratory or the Emergency Disease Watch Hotline 1800 675 888.

Categories of diseases with highest priority for investigation and surveillance in Australia include:

Mass mortality, behavioural abnormality, granulomas, vesicles and ulcers should trigger an investigation. If investigation of a disease syndrome in wildlife produces negative test results for relevant endemic diseases, exotic or emerging diseases should be considered.

In the face of an unusual disease event, or disease in a highly threatened species, a very detailed and thorough post mortem procedure is required. Multiple sample sets must be collected from each animal so that a wide variety of diagnostic testing can be undertaken, potentially using several different laboratories. You may be investigating a new disease. In these situations it is equally important to rule out all other possible explanations for the event as to identify the agent of concern. A complete set of samples from as many animals as possible will facilitate the investigation. Table 4.3 provides a comprehensive post mortem checklist for these situations.

2.2 Diagnostic flow

Reaching a diagnosis in wildlife involves the following:

Table 4.3 Comprehensive necropsy checklist

Identify species, sex and any physical forms of identification

External examination

Describe and photograph body condition/injuries

   check mammary glands for evidence of lactation and collect any milk present

   check the umbilicus of neonates

   examine and count the teeth

   examine the eyes, mouth and nose for any discharge

   weigh and measure the carcass

Collect samples of any wounds or discharges for bacterial culture and histopathology

Conduct a thorough internal post mortem examination. Collect samples for genetic research, bacterial and viral culture with clean instruments as soon as the internal organs are exposed

Samples needed for a very thorough post mortem examination

Bacterial culture: Minimum of two filtering organs and any lesions. Collect samples into individual sterile containers, well labelled. Store chilled and transport immediately to a laboratory.

Viral culture: Portions of lung, kidney, liver, spleen. Place in a Whirl-pak bag or other sterile container. Store chilled or frozen.

Genetics: Small samples of skin, liver and kidney placed into sterile cryotubes and stored chilled, frozen, in RNA Later® or ethanol.

Toxicology: Fat, liver, kidney and stomach content—wrap individually in aluminium foil then place in individually labelled plastic bags and store frozen.

Histopathology: Tonsil, bronchial lymph node, lung, heart, liver, spleen, adrenal gland, kidney, bladder, gonad, stomach, pancreas, duodenum, jejunum, ileum, large intestine, skeletal muscle, brain, the margin of any lesion, in 10% buffered formalin. Maximum 1 cm thickness. Many tissues may be placed in one jar as long as the volume of 10% formalin is greater than 10 times the total volume of tissues. Store at room temperature.

Serology: Blood samples collected into red top tubes. Centrifuged and serum decanted as soon as possible. Store chilled or frozen (long-term).

Parasitology: Preserve parasites in leak-proof containers in fixative (10% formalin, glacial acetic acid, or 70% ethanol). Label with animal species, identification and site of collection. Do not freeze these samples.

An impression smear of the liver or spleen stained with Diff-Quik® and examined by oil immersion microscopy to identify blood parasites.

Skeleton: Freeze the remains, or note site of burial for a museum.

May 28, 2017 | Posted by in GENERAL | Comments Off on Wildlife Health Investigation and a Guide to Necropsy
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