Gastrointestinal Tract Quiz

Gastrointestinal Tract

• The gastrointestinal tract includes the esophagus, stomach, small intestines (duodenum, jejunum, ileum), large intestines (cecum, colon, rectum), and anus.
• The introduction section describes the different parts of the gastrointestinal tract.
• Diagrams of the gastrointestinal tract show the relationship and location of each part, including organs like the liver, gallbladder, and pancreas.
• Common terms used to describe inflammation include gastritis (stomach inflammation), gastroenteritis (inflammation of stomach and intestines), and enterocolitis (inflammation of small and large intestines).
• Diarrhea is an abnormal increase in bowel movement, loose to liquid stool.
• Dysentery is diarrhea with cramping abdominal pain.
• Proctitis is inflammation of the rectal mucosa.
• Specific microbes causing Proctitis include N. gonorrhoeae, C. trachomatis, T. pallidum.
• Normal flora is 80% of the dry weight of feces is bacteria.
• Normal flora prevents colonization of pathogens.
• Examples of normal flora include anaerobic bacilli (Bacteroides spp.), GN enteric bacilli, Enterococci, Streptococci, S. aureus, and Yeast (Candida).

Non-Inflammatory Diarrhea

• Bacterial toxins or enterotoxins cause non-inflammatory diarrhea,
• This results in electrolyte and fluid loss, and leads to watery stools.
• Patients with non-inflammatory diarrhea do not have a fever
• Stool does not contain white blood cells (PMNs), blood or mucus.
• Examples of microbes associated with this type of diarrhea are V. cholerae, Enterotoxigenic E. coli, and Bacteroides spp.
• Viruses (Giardia lamblia, Cyclospora, Cryptosporidium) can also cause non-inflammatory diarrhea.

Inflammatory Diarrhea

• Organisms invade the intestinal mucosa.
• Cytotoxins destroy intestinal cells
• Patients with inflammatory diarrhea experience fever and loose, small-volume stools.
• Stool samples show white blood cells (PMNs), blood, and mucus.
• Microbes associated with this type of diarrhea include Salmonella spp., Shigella spp., Y. enterocolitica, Campylobacter spp., Enteroinvasive E. coli, and Clostridium difficile.

Enterotoxin-Mediated Diarrhea

• Ingestion of food containing toxins results in rapid onset diarrhea (<12 hours)
• Microbes associated with this type of diarrhea include Enterotoxigenic E. coli, V. cholera, S. aureus, C. perfringens, and B. cereus.

Diarrheal Diseases

• Some bacteria cause diarrhea including Salmonella, Shigella, Y. enterocolitica,Campylobacter jejuni, and C. coli.
• Other microbes like Edwardsiella tarda, Vibrio cholera, V. parahaemolyticus, Plesiomonas shigelloides, and Listeria monocytogenes.
• Intestinal parasites (Giardia, Entamoeba, Cryptosporidium, Cyclospora, Microsporidia) can also cause diarrhea.

Diseases

• H. pylori causes chronic gastritis, peptic and duodenal ulcers.
• C. difficile leads to antibiotic-associated diarrhea and pseudomembranous colitis.
• C. perfringens causes enterotoxin.
• Mycobacterium avium causes GI diseases in AIDS patients.
• E. coli enterohemorrhagic causes hemorrhagic colitis and hemolytic uremic syndrome.
• E. coli enteroinvasive causes Shiga-like disease.
• E. coli (cont.) is associated with enterotoxigenic (traveler's diarrhea), enteropathogenic (enteroadherent, usually children), and enteroaggregative (traveler's diarrhea) types.

Specimen Collection (Gastrointestinal)

• Fecal specimens should be collected in a clean, non-sterile, wide-mouth container.
• Use 2-3 samples to ensure a good analysis.
• Avoid urine contamination.
• Transport medium— Cary-Blair medium— should be used to transport the specimen.
• Specimens should be processed within 1-2 hours of collection.
• Collect other specimens, such as duodenal, colostomy, or ileostomy material and diapers.

Visual Examination of Gastrointestinal Specimens

• Observe macroscopic features—blood, mucus, consistency (watery, formed, loose), and color.

Microscopic Examination of Gastrointestinal Specimens

• Use fecal WBC (PMN) examination to distinguish inflammatory from non-inflammatory conditions.
• Use methylene blue and make a wet mount.
• Use gram stain and morphology to look Campylobacter (which has a darting motility), vibrio (curved GNR), and Clostridium (GPR).

Culture

• A wide range of microbes, like Salmonella, Shigella, Campylobacter, E. coli O157:H7, and Vibrio may be present.
• Physician input can help in selecting specific culture conditions.

Media Inoculation

• Non sterile pipette or swab is used to inoculate culture media.
• Plates are streaked for isolation, and enrichment broth containing large amounts of specimen is inoculated.

Various Media Used

• BAP: detects S. aureus and yeast overgrowth
• MAC or EMB: differential and selective for various microbes.
• NLF (Salmonella, Shigella, Y. enterocolitica, E. tarda, Plesiomonas, Aeromonas, Vibrio)

MAC Media

• It helps in identifying microbes based on their ability to ferment lactose.

Other Media

• XLD or HE, SS agar are differential and selective, helping identify Salmonella and Shigella (colorless colonies, +/- black center).
• Campy-BAP, a selective media, helps isolate C. jejuni and C. coli.
• Enrichment broth (GN: Salmonella, Shigella; Selenite F: Salmonella and some Shigella)
• Special media (Cefsulodin-irgasan-novobiocin, Salmonella Shigella, Sorbitol MAC, and TCBS)

Respiratory Tract

• The upper respiratory tract (URT) includes the oral cavity and neck (nose, mouth, throat, epiglottis, larynx).
• The lower respiratory tract (LRT) includes the trachea, bronchi, bronchioles, and lung alveoli.
• The lower respiratory tract below the larynx is usually sterile

URT Normal Flora

• Includes Staphylococci (CONS, S. aureus), Streptococci (viridans, pneumococci), Micrococcus spp., and Candida spp.
• Also includes Diphtheroids, Neisseria spp., Haemophilus, Anaerobes, and Spirochetes.

Infections of the URT

• Include thrush, laryngitis, epiglottitis, pharyngitis, tonsillitis, sinusitis, otitis media, diphtheria, and pertussis.

LRT Pathogens (Viruses)

• Includes Influenza, parainfluenza, RSV, adenovirus, rhinovirus, coronavirus, coxsackie A, EBV, and CMV.
• Also includes S. pyogenes, B-hemolytic strep group C, F, and G, and Arcanobacterium haemolyticum.

LRT Pathogens (Bacteria)

• Includes H. influenzae, and parainfluenzae, N. gonorrhoeae, Corynebacterium diphtheriae, Bordetella pertussis, and parapertussis, and along with Yeast.
• Also includes GNR, S. aureus, Legionella spp., Anaerobes, Mycobacteria, and Fungi

Community Acquired Pneumonia

• S. pneumo (most common), Mycoplasma pneumoniae, H. influenzae, and M. catarrhalis.

Hospital Acquired Pneumonia

• Includes Enterobacteriaceae, K. pneumoniae, S. marcescens, S. aureus, NFGNR, P. aeruginosa, Burkholderia cepacia, CF, S. pneumoniae bacteria, and anaerobic bacteria

Miscellaneous Causative Agents

• Includes Mycobacteria (MTB), Legionella, Chlamydia (C. trachomatis, C. pneumoniae).

Emerging Viral Infections of Respiratory Tract

• Avian influenza-H5N1, H1N1 influenza A, SARS coronavirus.

Bioterrorism Agents

• Includes B. anthracis, Y. pestis, Coxiella burnetii, and F. tularensis.

Routes of Infection

• Most respiratory pathogens enter via aerosol inhalation
• Routes include hematogenously (blood stream) and aspiration of oral secretions.
• Sputum is an easy specimen to collect, but cultures can be difficult to interpret.

Specimen Collection and Respiratory Infections

• URT collects specimens (swab or syringe/needle biopsy), placed in transport media, usually using posterior pharynx swab for strep test in media for collection and use of antigens.
• LRT specimens (sputum, washings, brushings, biopsies) using a sterile screw-cap cup and saline solution to prepare specimens.
• Specimens should be cultured within two hours.

Sputa

• Samples need to be processed and evaluated for quality.
• Low-power field (LPF) and high-power field (HPF) evaluation for epithelial, PMN, etc...
• Unacceptable LPF/HPF are evaluated.

Routine Cultures and Anaerobic Cultures

• BAP, CHOC, MAC, and special media for cystic fibrosis cases (B. cepacia, MRSA, and Pseudomonas) for respiratory isolates.
• Specimens like lung aspirates (pleural fluid) and open lung biopsies undergo anaerobic culturing process if necessary to bypass oral cavity.
• Work-up procedures are performed based on specimen quality indicators.

Otitis Media

• Middle ear infection, typically occurring after a viral URTI, and caused by microbes like S. pneumoniae, H. influenzae, others (A strep, S. aureus, M. catarrhalis, anaerobes, and GNR).
• Specimens (tympanocentesis fluid) are collected and placed in anaerobic transport media or via swabs when eardrum ruptures..
• Culture processing typically involves gram stain and aerobic/anaerobic culture use of BAP, CHOC, MAC, etc

Test your knowledge on the functions and disorders of the gastrointestinal tract. This quiz covers nutrient absorption, types of diarrhea, and the role of intestinal flora. Challenge yourself with questions on gastritis and inflammatory conditions.