Diarrhea

Specimen type/volume

Collection protocol

• Bacterial culture, fecal, porcine (cultsfe) - animal age required
• Brachyspira PCR porcine panel (brpcr)
  • B. hyodysenteriae
  • B. pilisicoli
  • B. hampsonii clades I and II

• feces, small and large intestine, mesenteric lymph node
• feces, oral fluid, large intestine (colon preferred)

• Histology food (hist)
• Immunohistochemistry is available on formalin-fixed tissues for TGEV, PCV-2, Lawsonia

Formalin fixed: 

• esophagus, stomach, mesenteric lymph node, duodenum, jejunum, ileum with Peyer's patch, cecum, colon including any area with gross lesions
• remember to collect multiple sections from jejunum and ileum 

Routine tissues (filtering organs):

• kidney, liver, lung, spleen

• Fecal flotation (fflot) - optional, histology can be diagnostic for coccidia

• feces (golf ball volume)

• TGEV differentiating antibody ELISA (pcve2)

• sera from dam, surviving litter/herd mates

• Coronaviruses TGEV, PEDV, PDCoV triplex PCR (rotapcr)
• Rotavirus A, B, C PCR (rotapcr)
• PCV-1,2,3 PCR (pcv123)

• rectal swabs in virus transport medium, small intestine
• feces, small intestine

Specimen type/volume

Collection protocol

Includes testing for: (bentpnl)

• bovine coronavirus PCR/rotavirus group A and B
• sucrose wet mount
• bacterial culture

• feces-split into 3 separate sterile vials for distribution to the lab sections, if done at AHL an extra splitting charge will be applied

• Culture, food animal (cultf)-animal age required
• Mycobacterium paratuberculosis (Johne's disease) PCR (jpcr)
• E. coli, ETEC food animal - genotyping (ecolf)
• E. coli, VTEC food animal - genotyping (vtecf)

• feces, large and small intestine, mesenteric lymph node, any other tissues with visible lesions
• feces, ileum, mesenteric lymph nodes
• Feces, intestine

• Histology, food animal (hist)
• Immunohistochemistry is available on formalin-fixed tissues for BVDV, BCV, bovine rotavirus-note that BVDV IHC is NOT available for routine PI screening

• Formalin fixed: esophagus, forestomachs, abomasum, mesenteric lymph node, duodenum, jejunum, ileum with Peyer’s patch, spiral colon and cecum, including any area with gross lesions
• Also include routine tissues: e.g. filtering organs liver, kidney, spleen, lung
• Remember to collect multiple sections from jejunum and ileum

• Cryptosporidium PCR (crypto)

• feces

• Sucrose wet mount (sucwt) - Cryptosporidium 
• Fecal flotation (fflot) - coccidia, gastrointesetinal nematodes

• feces

• BCV VN (bcv)
• BVDV type 1 NADL VN (bvdn)
• BVDV type 1 Singer VN (bvds)
• BVDV type 2 NVSL VN (bvd2)

• paired sera

• BVDV PCR (bvdrt)
• For futher details of BVDV testing, see LabNote 1 - summary of bovine viral diarrhea virus (BVDV) testing at the AHL
• Rotavirus A and B PCR, Coronavirus PCR (rocopcr)

• EDTA blood for acute BVD
• serum for PI
• tissue with lesion, feces
• feces, ileum, spiral colon

Specimen type/volume

Collection protocol

• Culture, food animal (cultf) - animal age required
• Clostridium perfringens type D enterotoxemia culture and PCR genotyping (cperf)
• Mycobacterium paratuberculosis (Johne's disease) PCR (jpcr)

• feces, large and small intestine

• Histology, food animal (hist)
• Immunohistochemistry is available on formalin-fixed tissues for BVDV, BCV, bovine rotavirus - note that BVDV IHC is NOT available for routine PI screening

• Formalin fixed: esophagus, forestomachs, abomasum, mesenteric lymph node, duodenum, jejunum, ileum with Peyer’s patch, spiral colon and

• Cryptosporidium PCR (crypto)

• feces

• Sucrose wet mount (sucwt) - Cryptosporidium 
• Fecal flotation (fflot) - coccidia, gastrointestinal nematodes

• feces

• Johne's disease AGID (xjoha)

• serum

• Rotavirus A and B PCR, Coronavirus PCR (rocopcr)

• feces, ileum, spiral colon

Specimen type/volume

Collection protocol

• Bacterial culture, fecal, companion/other (cultnfe)
• C. difficile toxin ELISA (clodn)
• Bacterial culture, anaerobic, companion/other (ancun)

• feces, small and large intestine, mesenteric lymph node
• swabs are not recommended as they provide little fecal material resulting in the inability to run the toxin ELISAs
• feces or intestinal content

• Histopathology, companion/other (histcm3)
• Immunohistochemistry is available on formalin-fixed tissues for canine parvovirus, feline parvovirus (panleukopenia), canine/feline coronavirus, canine distemper virus

Formalin fixed:

• esophagus, stomach, mesenteric lymph node, duodenum, jejunum, ileum with Peyer’s patch, cecum, colon including any area with gross lesions
• remember to collect multiple sections from jejunum and ileu

Routine tissues (filtering organs):

• kidney, liver, lung, spleen

• Tritrichomonas fetus PCR (tfpcr)
• Giardia duodenalis genotyping (ggpcr)
• Toxoplasma gondii PCR (toxopcr)

• feces

• Fecal flotation (flotn)
• Tritrichomonas fetus culture (tfcf) 
• Giardia antigen ELISA (gia)

• feces

• Canine parvovirus 2 PCR (pv2mb)
• Feline parvovirus (panleukopenia PCR) (pv2mb)

• feces, small intestine

Specimen type/volume

Collection protocol

• Bacterial culture, aerobic and anaerobic (anculnm)
• Clostridium spiroforme smears
• Lawsonia intracellularis PCR (lapcn)

• ileum, cecum, feces

• Histopathology, companion/other (histcm3)

Formalin fixed:

• duodenum, jejunum, ileum, cecum, cecal appendix, proximal (sacculated) and distal colon including any area with gross lesions, stomach, mesenteric lymph node
• collect intestinal sections into small formalin containers individually labelled with the anatomic location
• remember to collect multiple sections from jejunum and ileum 
• kidney, liver, lung, spleen

• Fecal flotation (flotn) for coccidia 

• feces

Specimen type/volume

Collection protocol

Equine foal diarrhea PCR panel (fdpcrp)

• for horses <1 year of age

Includes testing for: 

• Salmonella spp.
• C. perfringens enterotoxin
• C. perfringens beta-2 toxin
• C. perfringens netF toxin
• C. difficile toxin B

• Lawsonia intracellularis
• Neorickettsia risticii
• N. findlayensis
• Rhodococcus equi
• Equine coronavirus,
• Equine rotavirus

• feces – split into 3 separate sterile vials for distribution to the lab sections, if done at AHL an extra splitting charge will be applied

Equine adult diarrhea PCR panel (adpcrp)

• for adult horses >1 year of age

Includes testing for: 

• Salmonella spp.
• C. perfringens enterotoxin
• C. difficile toxin B
• Equine coronavirus 

• Neorickettsia risticii
• N. findlayensis

• feces – split into 3 separate sterile vials for distribution to the lab sections, if done at AHL an extra splitting charge will be applied

• Equine fecal culture (cultnf1)
• C. difficile toxins A&B ELISA (clodn)

• Lawsonia intracellularis PCR (lapcn)

• feces, large & small intestine, mesenteric lymph node
• Swabs are not recommended as they do not provide enough fecal material to run the toxin ELISAs

• Histopathology (histcm3)

Formalin fixed: 

• any area with gross lesions
• collect multiple sections from jejunum and ileum
• filtering organs: kidney, liver, lung, spleen

• Potomac horse fever PCR (phfpc)

• feces, blood

• Fecal egg count - McMaster (fecm)

• feces

• Rotavirus/coronavirus PCR (rocopcr)

• feces, colon