died, but the agents detected were common in the shelter environment and were therefore not convincingly the cause of death. Moreover, it was unclear to the shelter staff whether the URI or the abscesses were related to the animals' deaths, to each other, or just coincidental findings. An unexplained increase in mortality is one of the most compelling reasons for a shelter to perform a necropsy. See Table 5.1 for a partial list of reasons to perform a necropsy, with specific attention to those significant to a shelter.
An estimated 6.5 million companion animals entered US animal shelters in 2016 according to the American Society for the Prevention of Cruelty to Animals (ASPCA 2017). Shelters are intensive housing situations where transmission, exposure, and susceptibility to infectious disease are heightened. If compared to the dairy industry, with 9 million cows in the United States in 2017 (https://www.ers.usda.gov/data‐products/dairy‐data), necropsy is not just warranted but state and federally mandated (and funded) for large animal herd health clinicians to track infectious disease. There are hundreds of clinicians and pathologists employed to perform large animal diagnostics in the US and Canada. In contrast, and despite the real and intimate interface with the human population, few states provide funding for necropsy or diagnostics of shelter animals. There is a need for more methodical scrutiny for emerging diseases, infectious diseases, and zoonoses, and necropsy is the most accurate method to collect effective diagnostic samples, assess diagnostic accuracy, and to predict disease emergence. The purpose of this chapter is to provide practical guidelines for necropsy and for collecting, storing, and shipping samples for diagnostic testing.
Table 5.1 Reasons to perform a necropsy in a shelter.
| When there is unexplained death, or deaths, in the population |
| When there is the possibility that contagious disease could affect other shelter animals (including to limit future losses) |
| When zoonoses are suspected (when contagious disease from an animal could affect human workers or visitors) |
| To evaluate the effects of treatment, especially when a new treatment is involved or if a reaction to a drug or disinfectant is suspected |
| To document the accuracy of a clinical diagnosis |
| To document a legal case (e.g. suspected poisoning or cruelty) |
| To enhance discussion of husbandry and health maintenance programs with animal shelter specialists. |
For ideal infectious disease surveillance, a board‐certified or accredited pathologist would examine all deaths at a given shelter. If that is an option, animals that die should be turned in immediately, without freezing of the carcass, for the most accurate results. However, state‐subsidized diagnostics are not an option for most shelters. Full necropsy services at state diagnostic laboratories or veterinary schools are available, and although costs vary, they can be quite high for small animals. In contrast, performing a necropsy/sampling at a shelter and testing, or at least storing samples (for possible future examination) is relatively inexpensive and both biopsy services (“necropsy in a bottle”) and microbiology services are readily available. Shelter personnel need to be trained to recognize lesions, and to perform a necropsy as part of the overall healthcare plan for their shelter population.
5.2 Why Sample Tissues at Necropsy?
Expedient pathogen identification can help minimize deaths and maximize successful outcomes from infectious illnesses. Appropriate and adequate sample collection can help with such identification and is one of the most important reasons for a shelter to perform a necropsy. See Figure 5.1.
Figure 5.1 The prosector takes a sample of lung. Samples taken for microbiological analysis (culture or PCR) should be taken first during a necropsy. Use a sterile scalpel blade or scissors to take a section, and/or use a sterile swab to sample.
Necropsy has its limitations, and necropsy findings can be inconclusive as to the actual cause of death. Some conditions are simply not characterized by lesions that can be detected either grossly or microscopically. However, it is a very useful method to rule in (or out) infectious/inflammatory vs. OTHER causes of death. It is the intention of this chapter to put clinicians in a confident position to collect samples correctly so that the best material is available for analysis and diagnosis. Samples collected at necropsy can be used for culture, cytology (impression smears), molecular diagnostics (polymerase chain reaction or PCR), serology (antibodies are generally stable in postmortem blood for serology tests), histological analyses (of target tissues or all tissues collected) or other tests.
5.3 The Necropsy
5.3.1 General Considerations
To complete an effective necropsy, specific and consistent protocols (procedure, sampling, documentation) should be followed. The optimal time to perform a necropsy is as soon as possible after the animal's death. Depending on environmental conditions, changes in tissues occur in minutes after an animal has expired. It is important, for an accurate diagnosis, to take appropriate tissue samples for culture and/or microscopic examination in a timely fashion. If a necropsy cannot be performed immediately, the animal should be placed in a cooler (for up to two days post‐death). Tissue integrity and most pathogens and toxins are stable during that time, although overgrowth of postmortem bacteria becomes a problem. For any longer time window, freezing the carcass is warranted.
Any animal that dies should be examined to the best of one's time and ability; however, a necropsy performed specifically for sample collection can be much shorter (for example, collecting gastrointestinal (GI) samples in a dog with diarrhea to confirm or exclude parvovirus). Here are a few important considerations before performing a necropsy:
1 Zoonoses: It is important to be aware that animals in the shelter may have a disease that is transmissible to humans (zoonosis) and, even more likely, a disease transmissible to other animals. The situation postmortem is no different than when the animal was alive, however, exposure to some agents is higher when a necropsy is performed (e.g. blood‐borne pathogens, anthrax, rabies, and some fecal pathogens). The necropsy should be performed in a quiet, isolated, well‐ventilated space. Precautions should be taken consistently (protective clothing, gloves, mask) during a necropsy, and any unfixed tissues should be placed in leak‐proof containers or disposed of as medical waste according to the protocols specified by the state or institution.
2 Handling cadavers: If the necropsy cannot be carried out immediately, cadavers should be stored in a refrigerator (+2 °C to +4 °C) as soon as possible after death until the necropsy can be performed. A cadaver should be frozen only if necessary; while still present in the tissue, some microbes will not be viable after freezing.
3 Euthanasia: Euthanasia policy and strategy is widely variable among shelters. The method of euthanasia should always be documented. There are both gross and histologic sequelae to any form of euthanasia, and it is important to understand whether a lesion is “real” or simply related to the method of euthanasia. For example, intra‐abdominal administration of pentobarbital can result in puncture trauma, a layer of chemically induced necrosis on the surfaces of abdominal organs, or in peri‐mortem intra‐abdominal hemorrhage (See Figure
