Gastrointestinal tract

            The gastrointestinal tract includes the esophagus, stomach, duodenum, small intestine, and colon.

            1.   Fecal specimens

                  Submitted primarily for the detection of Campylobacter, Shigella, and Salmonella species, Clostridium difficile and in certain cases to detect Yersinia, Vibrio, and Aeromonas species and enterohemorrhagic Escherichia coli.

                  a.   General considerations

                        (1)    Fecal WBC should be ordered on liquid stools to indicate degree of inflammation.

                        (2)    Stool specimen should be mixed with transport medium to maintain viability of pathogens which may be present.

                        (3)    Do not use toilet paper to collect stool.  Toilet paper may be impregnated with barium salts, which are inhibitory for some fecal pathogens.

                        (4)    Stool specimens should not be contaminated with urine.

                  b.   Have patient obtain stool specimen by one of the following methods.

                        (1)    Pass stool directly into a sterile, wide-mouth, leakproof container and transfer to C & S Parapak vial.

                        (2)    Pass stool into a clean, dry bedpan, and transfer stool into C & S parapak vial.

            2.   Rectal swabs

                  Submitted primarily for the detection of Neisseria gonorrhoeae, Shigella  species, enterovirus, and anal carriage of Group A  or Group B strep.

                  Pass the tip of a sterile swab approximately 1 in. beyond the anal sphincter.  Carefully rotate the swab to sample the anal crypts, and withdraw the swab.  Send the swab in a swab transport or N. gonorrhoeae  transport system (Table 1) or viral transport system.

            3.   Gastric aspirates

                  The patient should fast prior to each of the following procedures.

                  a.   Gastric lavage

                        Submitted primarily for the detection of Mycobacterium tuberculosis  in patients (most frequently children) unable to produce quality sputum.  Should be performed after the patient wakes in the morning so that sputum swallowed during sleep is still in the stomach.

                        Pass a well-lubricated tube orally or nasally through to the stomach of the patient, and perform the lavage.  Before removing the tube, release the suction and clamp to prevent mucosal trauma and/or aspiration.  Transport immediately to microbiology.

                  b.   Duodenal aspiration

                        Submitted primarily for the detection of Giardia  species and larvae or Strongyloides stercoralis and Ascaris lumbricoides.

                        (1)    Pass a tube orally through to the duodenum of the patient.

                        (2)    To aspirate a sample for giardiasis, the tube should be at least in the third portion of the duodenum.

            4.   Gastric biopsies and washings

                  The patient should fast prior to each of the following procedures.

                  a.   Esophageal, stomach, duodenum specimens

                        Esophageal specimens are primarily used to detect Candida  species, cytomegalovirus (CMV), and HSV infections.  Stomach and duodenal specimens are primarily used for the detection of Helicobacter pylori.  Duodenal specimens can be used for the detection of Giardia  species and the larvae of S. stercoralis  and A. lumbricoides.

                        (1)    Pass an endoscope orally.

                        (2)    Obtain specimens through a channel in the endoscope by using one of the following procedures.

                                 (a)    Using biopsy forceps, obtain samples from the esophagus, stomach, or duodenum.

                                 (b)    Using a sheathed brush, brush suspicious areas several times to obtain adequate cellular material.

                                 (c)    Perform a wash by injecting approximately 25 to 30 ml of sterile nonbacteriostatic isotonic 0.85% NaCl through the biopsy channel onto the lesion.  Collect the specimen by aspirating the fluid through the scope into a sterile trap, which is connected to the suction tubing.  Note:  If a gastric ulcer is seen, obtain biopsy samples from the base, the surroundings gastric mucosa, and each of the four quadrants of the margin.

                  b.   Rectal biopsy

                        Submitted primarily for the detection of Entamoeba histolytica, Balantidium coli, and HSV.

                        If lesions are not evident, biopsy the posterior rectal mucosa below the peritoneal reflection (within 7 to 10 cm of the anal verge).

                  c.   Small bowel biopsy

                        Submitted primarily for the detection of Giardia, Cryptosporidium, and Microsporidium  species.

                        Biopsies of the small intestine provide the highest diagnostic yield for Microsporidia species.  Biopsies from other gastrointestinal sites (stomach, colon, rectum) have a much lower yield in comparison.  Obtain biopsy sample of lesion at surgery.

            5.   Sigmoidoscopy

                  Use in the detection of E. histolytica  and Mycobacterium  species and the diagnosis of pseudomembranous colitis associated with C. difficile  and possibly Staphylococcus aureus.

                  a.   Perform flexible or rigid sigmoidoscopy.

                  b.   Obtain endoscopic pinch biopsy samples of any lesions seen.  Additionally, aspirate liquid from the inflamed bowel with a pipette passed through the sigmoidoscope.  Transport specimens in a sterile screw-cap container.  If biopsy samples are small, add a small amount of sterile nonbacteriostatic 0.85% NaCl to prevent the specimen from drying.

 

              Table 5 - Collection considerations for gastrointestinal specimens