1 Microbiology:Screening for bacterial or fungal organisms of significance can be performed on feces, small intestinal contents, or a combination of both. Be aware that antibiotic therapy can skew or prevent the culture of many bacteria. Any pre‐mortem therapy should be noted in the submission form and on the necropsy report. Feces can be collected in any number of different sterile or clean containers, including bags, urine cups, or tubes. If feces are submitted, it should be specified on the request that significant enteric organisms (such as Salmonella, Clostridia, and Campylobacter) are of concern. Culture results need to be correlated with histologic findings; Clostridia, for example, can be cultured from normal intestines, so histologic correlates or toxin testing has to be performed concurrently with culture. Salmonella, although always significant for herd health and zoonotic reasons, can be shed asymptomatically in cats and dogs. Be aware also that so‐called “commensal” (usually non‐pathogenic) organisms can become virulent (e.g. some strains of E. coli). Diagnosis in these cases would require a combination of histologic and microbiologic results or specialized microbiologic analysis. Specimens destined for culture should be transported and processed as soon as possible; delays of more than 48 hours are undesirable. If processing is delayed, refrigeration is preferable to storage at ambient temperature; freezing will kill many types of bacteria (see adjunct diagnostics).Figure 5.6 The intestines, extending from the gastroesophageal junction (arrowhead) to the distal colon (asterisk) have been removed. In the case of GI disease (or for any complete necropsy) the ileo‐ceco‐colic junction (bracketed by arrows) is one of the important sections for submission.Figure 5.7 The ileo‐ceco‐colic junction is pictured. The intestine can be opened along a sagittal plane for greater penetration of the formalin fixative.

      2 Molecular diagnostics:Detection and characterization of pathogenic organisms increasingly rely on DNA or RNA amplification techniques (PCR). These samples need to be taken early in the postmortem from tissue minimally manipulated, but the tissue can be frozen immediately and used at a future date if warranted. DNA or RNA from the infectious agent will degrade at rates dependent on time, environmental factors (temperature, pH) and the organism itself. Ideally, samples from affected organs are fresh or fresh/frozen for molecular analysis. Most diagnostic laboratories or veterinary schools can offer guidance and a list of possible tests, the preferred or potentially useful tissue samples, and the preferred method of shipment. Whole blood (e.g. heart blood) or highly vascularized tissues (spleen, liver, lung) are reliable sources for circulating infectious agents (bacteria, viruses, or hemoparasites).

      1 Toxicology:It is best to contact a toxicology laboratory, state laboratory, and/or a poison control center such as the ASPCA (http://www.aspca.org/apcc) for guidance. The appropriate sample for analysis is dependent on the type of toxin, among other variables. In the case of GI illness, source (food) and stomach contents should be saved. For heavy metal analysis, samples of liver and kidney should be collected, placed in separate plastic bags, and frozen until submitted. If a toxin is suspected but unknown, a necropsy should be performed and, in addition to histologic samples, liver, kidney, fat, stomach contents, and muscle samples should be frozen until submitted.

      2 Serology:Serodiagnostic tests are tests performed on serum or plasma to detect either the presence of antibodies to a particular pathogen or the presence of circulating antigens from the pathogen itself. Both of these types of tests can be performed postmortem on serum obtained from a pooled blood source (e.g. heart, major veins). The significance of the result should be considered before this particular technique is used; few tests are validated for postmortem serum. Nonetheless, a positive titer is generally considered significant. See Chapter 4 for more details on serologic testing.

      1 Establishing cause:Tissues for histology: Necropsy with histology can confirm the presence of parvovirus and would be important in ruling out parvovirus during an investigation of an unusual outbreak of GI disease. Acute cases of parvovirus are nearly pathognomonic by histologic analysis and chronic (historic) cases can also be detected by a pathologist; the architecture of the small intestine is not restored to normal for two to three weeks post‐infection.Other tests: In dogs, although the parvovirus antigen tests on feces are highly sensitive during viral shedding in the early stages of infection, these peak viral titers are brief and occur at the same time as, or prior to, the onset of clinical signs (Greene 2011). Subsequent viral shedding is known to fluctuate, and if the fecal antigen test is performed late after infection, virus in feces may be undetected. Testing of nearby, recently exposed animals is warranted, and in an animal that has died, feces should be retested at the time of necropsy with fecal material collected from pooled segments of the lower intestine (duodenum, jejunum, and colon). Numerous cases of dogs or cats have been seen whose feces were negative one to two days prior to death and submitted for evaluation of “non‐parvoviral diarrhea.” These same animals were often positive by fecal antigen tests at the time of necropsy and in these cases, there was concurrent histologic confirmation of parvoviral disease to establish etiology.

      1 Unusual presentation: