Gastrointestinal Tract Overview

Gastrointestinal Tract

• The gastrointestinal tract consists of the esophagus, stomach, small intestines (duodenum, jejunum, ileum), large intestines (cecum, colon, rectum), and anus.
• Salivary glands, liver, gallbladder, and pancreas are also part of the digestive system.

Gastrointestinal Tract Infections

• Gastritis: Inflammation of the stomach.
• Gastroenteritis: Inflammation of the stomach and intestines.
• Enterocolitis: Inflammation of the small and large intestines.
• Diarrhea: Abnormal increase in bowel movements, loose to liquid stool.
• Dysentery: Diarrhea with cramping abdominal pain.
• Proctitis: Inflammation of the rectal mucosa.
• Normal Flora: 80% of dry fecal weight is bacteria; normal flora prevents pathogen colonization. Key bacterial types include anaerobic bacilli (Bacteroides spp.), Gram-negative (GN) enteric bacilli, Enterococci, Streptococci, and S. aureus. Yeast (Candida) is also present.
• Non-inflammatory Diarrhea: Caused by bacterial toxins (enterotoxins) resulting in a watery, large-volume stool; no white blood cells, blood, or mucus. Common pathogens include Vibrio cholerae, Enterotoxigenic E. coli (ETEC), and other Bacteroides spp. Viral causes also exist like Giardia lamblia, Cyclospora, and Cryptosporidium.
• Inflammatory Diarrhea: Pathogens invade intestinal mucosa; cytotoxins destroy intestinal cells. Symptoms include fever and loose, small-volume stool with white blood cells, blood, or mucus present in the stool. Common culprits include Salmonella spp., Shigella spp., Y. enterocolitica, Campylobacter spp., Enteroinvasive E. coli (EIEC), and Clostridium difficile.
• Enterotoxin-Mediated Diarrhea: Rapid onset, usually within 12 hours. Caused by toxins from food. Common pathogens include Enterotoxigenic E. coli, V. cholera, S. aureus, C. perfringens, and B. cereus.
• Diarrheal Diseases: Salmonella (gastroenteritis), Shigella (bacillary dysentery), Y. enterocolitica (enterocolitis), Campylobacter jejuni and C. coli (can resemble acute appendicitis), Edwardsiella tarda (uncommon), Vibrio cholerae (cholera), V. parahaemolyticus (milder case), Plesiomonas shigelloides, and Listeria monocytogenes (gastroenteritis).
• Intestinal Parasites and Viruses: Giardia, Entamoeba, Cryptosporidium, Cyclospora, Microsporidia, Rotavirus, adenovirus, calcivirus, astrovirus are also causes of diarrhea in humans.

Gastrointestinal Tract Diseases

- Additional bacterial and parasitic diseases may be present in the GI tract.

Gastrointestinal Specimen Collection

• Fecal Specimens: Collect 2-3 samples in clean, wide-mouth, non-sterile containers. Do not contaminate with urine. Use Cary-Blair transport medium. Process samples within 1-2 hours of collection.
• Other Specimens: Duodenal, colostomy, ileostomy materials, diapers, and food (public health lab samples) also could require collection.

Gastrointestinal Tract Visual Examination

• Macroscopic Examination: Include examination of blood, mucus, stool consistency (watery, formed, loose), and color of the stool.
• Microscopic Examination: Perform a wet mount using methyl cellulose to examine stool for white blood cells and WBC morphology. Perform Gram stain to identify types of bacteria present in the stool specimens.

Gastrointestinal Tract Culture

• Use non-sterile loops and swabs to inoculate culture media.

Gastrointestinal Tract Media

• BAP: Detects S. aureus and yeast overgrowth.
• MAC or EMB: Differential or selective media.
• NLF: Is specific media for isolating Salmonella, Shigella, Y. enterocolitica, E. tarda, Plesiomonas, Aeromonas, and Vibrio.
• XLD or HE, SS agar: Differential and selective media, looking for colourless colonies and/or black centers, indicating Salmonella and Shigella.
• Campy-BAP: Selective media looking for Campylobacter.
• Enrichment Broth: GN:, Salmonella, Shigella. Selenite F: Salmonella and some Shigella.
• Special Media: Cefsulodin-irgasan-novobiocin (CIN) agar for Y. enterocolitica (incubate aerobically); Salmonella Shigella (SS) agar for Shigella (shigella may be inhibited by MAC); sorbitol MAC for E. coli O157:H7. TCBS for Vibrio. CCFA for anaerobic Clostridium difficile.

Gastrointestinal Tract Tests

• Perform biochemical tests to identify pathogens from presumptive isolates.

Gastrointestinal Tract Reporting

• Report identification and susceptibility panels to the appropriate public health officials if pathogen is Salmonella or Shigella. Negative results may also need to be reported.

Respiratory Tract

• Upper Respiratory Tract (URT) infections involve the mouth, nose, throat, larynx (voice box), middle ear, and sinuses, and these areas contain normal flora (NF).
• Lower Respiratory Tract (LRT) infections include the trachea (windpipe), bronchi, bronchioles, and lungs and the area below the larynx is normally sterile.

Respiratory Tract Infections

• URT: Thrush, laryngitis, epiglottitis, pharyngitis, tonsillitis, sinusitis, otitis media, and diphtheria.
• LRT: Bronchitis, influenzae, pneumonia, empyema, tubercolosis.

Respiratory Tract Normal Flora

• URT: Staphylococci, CONS, S. aureus, streptococci (viridans, pneumococci), Micrococcus spp., diphtheroids, Neisseria spp., Haemophilus, anaerobes, spirochetes, and Candida spp.

Respiratory Tract Pathogens

• Respiratory Viruses: Influenza, parainfluenza, RSV, adenovirus, rhinovirus, coronavirus, coxsackie A, EBV, CMV.
• Bacteria: S. pyogenes, B-hemolytic strep group C, F and G, Arcanobacterium haemolyticum, H. influenzae, N. gonorrhoeae, Corynebacterium diphtheriae, Bordetella pertussis and parapertussis, Yeast.
• Other: Mycobacteria (MTB), Legionella, Chlamydia (C. trachomatis in neonates, C. pneumoniae in young adults),
• Bioterrorism Agents: B. anthracis, Y. pestis, Coxiella burnetii, F. tularensis.

Respiratory Tract Specimen Collection

• URT Specimens: Posterior pharynx and tonsils swabbed (usually for strep); placed in transport media; often antigen testing for group A strep first; negative testing may proceed to cultures.
• LRT Specimens (Sputum): Collected by expectoration, induced coughing, or via invasive procedures; collect in sterile screw-cap containers for transport; specimen transport and processing within two hours for culture.
• Invasive specimen collection such as bronchoscopy, bronchial washing/lavage or brushing are reserved for when a diagnosis cannot be made by a non-invasive method or when abnormal infections are suspected in chronically ill or immunocompromised patients.

Respiratory Tract Microscopy

• Gram Stain Analysis: LPF (low-power field) and HPF (high power field) review of the sputum sample, looking for quantity of PMNs and epithelial cells to determine suitability of the sample for culture.

Respiratory Tract Culture

• Routine Cultures: For sputum, tracheal aspirates, bronchial washings, bronchial brushings, and bronchial biopsies, utilizing BAP, CHOC, MAC media at 35°C in CO2, or special media for CF patients with B. cepacia, MRSA, Pseudomonas suspected.
• Anaerobic Cultures: Lung aspirates and pleural fluids.