Gastrointestinal Tract Overview

Gastrointestinal Tract

• The gastrointestinal tract includes the esophagus, stomach, small intestines (duodenum, jejunum, ileum), large intestines (cecum, colon, rectum), and anus.
• The introduction of the gastrointestinal tract describes different parts of the system and mentions related terms.
• Inflammation of the stomach is gastritis.
• Inflammation of the stomach and intestines is gastroenteritis.
• Inflammation of the small and large intestines is enterocolitis.
• Diarrhea is an abnormal increase in bowel movements, often loose to liquid stool.
• Dysentery is diarrhea with cramping abdominal pain.
• Inflammation of the rectal mucosa is proctitis.
• 80% of the dry weight of feces is bacteria.
• Normal flora prevents colonization of pathogens.
• Normal flora in feces includes anaerobic bacilli (Bacteroides spp.), GN enteric bacilli, Enterococci, Streptococci, S. aureus, and Yeast (Candida).
• Non-inflammatory diarrhea results from bacterial toxins or enterotoxins, causing water and electrolyte imbalance.
• Watery, large-volume stool is characteristic of non-inflammatory diarrhea. There is no blood, mucus, or PMN (polymorphonuclear leukocytes).
• Types of non-inflammatory diarrhea include: V. cholerae, Enterotoxigenic E. coli, Bacteroides spp., Viruses (Giardia lamblia, Cyclospora, Cryptosporidium).
• Inflammatory diarrhea involves organisms invading the intestinal mucosa, destroying intestinal cells (cytotoxins).
• Characteristic signs of inflammatory diarrhea include fever, loose, small-volume stool, and fecal specimens containing PMN, blood, and mucus.
• Agents associated with inflammatory diarrhea include Salmonella spp., Shigella spp., Y. enterocolitica, Campylobacter spp., Enteroinvasive E. coli, and Clostridium difficile.
• Enterotoxin-mediated diarrhea involves ingesting food containing toxins (e.g., Enterotoxigenic E. coli, V. cholera, S. aureus, C. perfringens, B. cereus).
• Symptoms of diarrhea may include nausea, vomiting, and abdominal discomfort.
• Specimen collection for diarrheal diseases involves collecting 2-3 fecal samples in clean, non-sterile, wide-mouth containers.
• Collection of other specimens may include duodenal, colostomy, and ileostomy material, as well as diapers.
• Food samples may be collected in certain circumstances, such as Salmonella peanut butter outbreaks.
• Diarrhea diseases may include Salmonella (gastroenteritis), Shigella (bacillary dysentery), Y. enterocolitica, and Campylobacter spp. (enterocolitis).
• Other diarrheal diseases also include Edwardsiella tarda, Vibrio cholerae, V. parahaemolyticus, Plesiomonas shigelloides, and Listeria monocytogenes.
• Intestinal parasites, including Giardia, Entamoeba, Cryptosporidium, Cyclospora, and Microsporidia, may also cause diarrhea diseases.
• Diseases to consider may include H. pylori (chronic gastritis, peptic, and duodenal ulcers), C. difficile (antibiotic-associated diarrhea, pseudomembranous colitis), C. perfringens (enterotoxin), and Mycobacterium avium (GI diseases in AIDS patients).
• E.coli may cause enterohemorrhagic (e.g., E. coli O157:H7), enteroinvasive, and other types
• Specimen collection includes 2–3 fecal samples, non-sterile wide mouth container; avoid urine contamination; transport medium is Cary-Blair; process specimens within 1–2 hours of collection.
• Visual examination includes macroscopic observation of blood, mucus, stool consistency (watery, formed, and loose), and color.
• Microscopic examination includes fecal WBC (PMN), methylene blue wet mount, motility, Gram stain of morphology, identifying Campylobacter, curved GNR (Vibrio), and GPR (Clostridium).
• The presence of stool WBC distinguishes inflammatory from non-inflammatory cases.
• Culture involves looking for Salmonella, Shigella, Campylobacter, E. coli O157:H7, and Vibrio.
• Media used in culture include BAP, MAC, EMB, NLF, XLD, and HE.
• Inoculation uses non-sterile pipettes or swabs.
• Incubation conditions depend on the microorganism in question (35C in ambient air, 42°C with microaerobic conditions, or CO2).
• Work up of bacteria includes examining plates and using biochemical tests.
• Reporting involves identification and susceptibility panel results.
• Public health officials are notified for Salmonella and Shigella.
• Overgrowth of S. aureus, yeast, and Ps. aeruginosa should be reported.
• Negative results indicate no Salmonella, Shigella, Vibrio, E. coli O157:H7, or Campylobacter isolated.

Respiratory Tract

• Upper Respiratory Tract (URT) infections involve the oral cavity, nose, mouth, throat, epiglottis, and larynx; has normal flora.
• Lower Respiratory Tract (LRT) infections involve the trachea, bronchi, bronchioles, and lung alveoli; normally sterile.
• URT normal flora includes Staphylococci, Streptococcus viridans, pneumococci, Micrococcus spp., diphtheroids, Neisseria spp., Haemophilus, anaerobes, spirochetes, and Candida spp.
• URT infections can include thrush, Laryngitis, epiglottitis, pharyngitis, sinusitis, otitis media, tonsillitis, and diphtheria.
• URT pathogens can include respiratory viruses (influenza, parainfluenza, RSV, adenovirus, rhinovirus, coronavirus, coxsackie A, EBV, and CMV), S. pyogenes, B-hemolytic strep group C, F, and G, and Arcanobacterium haemolyticum.
• Other pathogens include H. influenzae, N. gonorrhoeae, Corynebacterium diphtheriae, Bordatella pertussis, and parapertussis.
• Specimens for URT infections can include swabs, syringues and needles, and biopsies, depending on the area of infection (eg, throat, nasal cavity, or sputum).
• Specimen collection involves swabbing the posterior pharynx and tonsils and using transport media.
• Most specimens in labs need antigen testing for group A strep; if negative, confirmation cultures may be performed.
• Microscopic examination is less helpful.
• Culture is primarily for group A strep, and other agents upon request (B, C, F, G groups, N. gonorrhoeae, Arcanobacterium haemolyticum, and C. diphtheriae).
• Throat cultures primarily identify group A strep.
• Epiglottitis is mainly observed in 2–6-year-olds with H. influenzae, type b (almost exclusive), and is life-threatening.
• Sinusitis is preceded by URTIs, with acute sinusitis caused by S. pneumoniae, H. influenzae, and other organisms (M. catarrhalis, group A strep, anaerobes, and GNR). Chronic sinusitis can involve anaerobes, S. aureus in adults, and S. pneumoniae/streptococci in children.
• Specimens are collected through aspiration or opening of the sinus (sinus ostium) or other means, using anaerobic transport medium.
• Samples are processed for gram stain and cultured for aerobic and anaerobic bacteria.
• For otitis media, tympanocentesis fluid is a specimen collected, and it's processed aerobically or anaerobically.
• Lower Respiratory Tract (LRT) organisms include S. pneumoniae (community-acquired pneumonia), H. influenzae, M. catarrhalis, M. pneumoniae, Chlamydia spp., Gram-negative rods (GNR), S. aureus, anaerobes, Legionella, and Mycobacteria spp. (e.g. Mycobacteria Tuberculosis (MTB)).
• Specimens can include sputum, tracheal or bronchial aspirates, or biopsies; sputum specimens may be contaminated with normal flora.
• Bronchoscopy samples allow direct collection from the bronchi/lung or lavage.
• Processing involves gram stain and culture.
• Anaerobic cultures are performed in certain circumstances. Specific tests and cultures may be used based on infection type (e.g., sorbitol MacConkey agar to identify E. coli O157:H7)