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)