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 section of the notes lists these elements in order, and includes an image giving a visual representation of the GI tract organs.

Gastrointestinal Tract Terms

• Gastritis: Inflammation of the stomach.
• Gastroenteritis: Inflammation of the stomach and intestines.
• Enterocolitis: Inflammation of the small and large intestines.

Gastrointestinal Tract Terms (cont.)

• Diarrhea: Abnormal increased bowel movements, often loose to liquid stool.
• Dysentery: Diarrhea with cramping abdominal pain.
• Proctitis: Inflammation of the rectal mucosa.
• Conditions causing Proctitis: N. gonorrhoeae, C. trachomatis, T. pallidum

Normal Flora

• 80% of the dry weight of feces is bacteria.
• Normal flora helps prevent colonization by pathogens.
• Key bacteria include anaerobic bacilli (Bacteroides spp.), GN enteric bacilli, Enterococci, Streptococci, S. aureus, and yeast (Candida).

Non-Inflammatory Diarrhea

• Caused by bacterial toxins (enterotoxin).
• Results in the outpouring of electrolytes and fluid, leading to watery stools.
• Individuals are not febrile.
• Stool does not contain PMN, blood, or mucus.

Non-Inflammatory Diarrhea (cont.)

• Common causes: V. cholerae, Enterotoxigenic E. coli, Bacteroides spp., Viruses, Giardia lamblia, Cyclospora, Cryptosporidium.

Inflammatory Diarrhea

• Organisms invade the intestinal mucosa.
• Cytotoxins destroy intestinal cells.
• Individuals have fever and loose, small-volume stools.
• Stool usually contains PMNs, blood, and mucus.

Inflammatory Diarrhea (cont.)

• Common causes: Salmonella spp., Shigella spp., Y. enterocolitica, Campylobacter spp., Enteroinvasive E. coli, Clostridium difficile.

Enterotoxin-Mediated Diarrhea

• Caused by ingestion of food containing toxins.
• Rapid onset (less than 12 hours).
• Common causes include Enterotoxigenic E. coli, V. cholera, S. aureus, C. perfringens, B. cereus.

Diarrheal Diseases

• Salmonella: gastroenteritis
• Shigella: bacillary dysentery
• Y. enterocolitica: enterocolitis (can resemble acute appendicitis)
• Campylobacter jejuni and C. coli
• Edwardsiella tarda (uncommon)
• Vibrio cholerae: cholera
• V. parahaemolyticus: milder case
• Plesiomonas shigelloides
• Listeria monocytogenes: gastroenteritis

Diarrheal Diseases (cont.)

• Intestinal parasites: Giardia, Entamoeba, Cryptosporidium, Cyclospora, Microsporidia
• Viruses: Rotavirus, adenovirus, calcivirus, astrovirus

Diseases (cont.)

• H. pylori: chronic gastritis, peptic and duodenal ulcers
• C. difficile: antibiotic-associated diarrhea, pseudomembranous colitis
• C. perfringens: enterotoxin
• Mycobacterium avium: GI diseases in AIDS patients
• E. coli: enterohemorrhagic (O157:H7 and others, cause hemorrhagic colitis and hemolytic uremic syndrome (HUS)), enteroinvasive (Shigella-like disease), enterotoxigenic (traveler's diarrhea), enteropathogenic (enteroadherent, usually children), enteroaggregative (traveler's diarrhea)

Specimen Collection

• For fecal specimens (2-3 samples), a clean, non-sterile, wide-mouth container without urine contamination is used with Cary-Blair transport medium.
• Process specimens within 1–2 hours of collection.
• Other specimens include duodenal, colostomy, ileostomy material, and diapers.
• Additional include food specimens collected by public health departments.

Visual Examination

• Macroscopic examination includes stool consistency (watery, formed, or loose) and color. Observation of blood and mucus is also included

Microscopic Examination

• Fecal WBC (PMN) can aid in distinguishing inflammatory from non-inflammatory diarrhea. Use methylene blue for wet mounts.
• Motility of Campylobacter can be assessed.
• Gram staining is used for identifying bacteria. Campylobacter has a seagull-wing appearance.
• GPR morphology is used to identify Clostridium.

Stool WBC

• Distinguish inflammatory diarrhea from non-inflammatory diarrhea

Culture

• Culture is not generally done for all samples, it is done based on patient history and symptoms.
• Cultures for specific specimens like Salmonella, Shigella, Campylobacter, E. coli O157:H7, and Vibrio are considered.
• Physicians should request specific culture tests.

Media Inoculation

• Non-sterile pipettes or swabs are used.
• Plates are streaked for isolation.
• Enrichment broth containing large amounts of specimen are inoculated.

Media

• BAP or EMB media detects S. aureus and yeast overgrowth.
• MAC or EMB are used for differential and selective testing.
• NLF is used to identify Salmonella, Shigella, Y. enterocolitica, E. tarda, Plesiomonas, Aeromonas, Vibrio.
• XLD or HE, SS agar is differential and selective media to identify Salmonella and Shigella (colorless colonies, +/- black center).
• Campy-BAP is a selective media used to isolate Campylobacter jejuni and C. coli.
• Enrichment broth is used (GN/Salmonella, Shigella/Selenite F/Salmonella, some Shigella).
• Special media, such as Cefsulodin-irgasan-novobiocin (CIN) agar, Salmonella Shigella (SS) agar, and Cycloserine-cefoxitin-fructose agar (CCFA), are used to identify specific organisms.

MAC

• Media is used to differentiate bacteria that ferment lactose.

Gram Stain Analysis of Sputum

• Count the number of epithelial and PMN cells per low-power field (LPF).
• A good specimen will have < 10 epithelial/LPF and >25 PMN/LPF. Reject specimens with >25 epithelial cells per LPF.
• Under oil immersion, record the quantity (rare, moderate, or many) and type of bacteria.

Acceptable Gram Stain

• Acceptable Gram Stain images are provided for comparison in the slides.

Routine Cultures

• BAP, CHOC, MAC
• Incubated at 35°C in CO2
• Other media are sometimes used for particular patient situations (e.g., cystic fibrosis)

Anaerobic Cultures

• Lung aspirates (pleural fluid) and open-lung biopsies are only cultured anaerobically if the method did not involve the oral cavity.

Work-Up

• Analysis depends on the specimen quality and type.
• Gram stain evaluation is important.

Reporting Results

• Susceptibility panel and identification results are reported.
• Public health officials are notified when Salmonella or Shigella are isolated.
• Overgrowth of S. aureus, yeast, or Ps. aeruginosa should be reported.
• Negative results report no isolation of Salmonella, Shigella, Vibrio, E. coli O157:H7, or Campylobacter.

Respiratory Tract

• Upper Respiratory Tract (URT) infections involve the oral cavity and neck (nose, mouth, throat, epiglottis, larynx)
• Contains normal flora.
• Lower respiratory tract (LRT) infections include the trachea, bronchi, bronchioles, and lung alveoli.
• Below the larynx, the tract is typically sterile.

URT Normal Flora

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

URT Infections

• Thrush, Laryngitis, Epiglottitis, Phayngitis, Tonsillitis, Sinusitis, Otitis media, Diphtheria, Pertussis (Whooping cough).

URT Pathogens

• Respiratory viruses (e.g., influenza, parainfluenza, RSV, adenovirus, rhinovirus, coronavirus, coxsackie A, EBV, CMV)
• S. pyogenes
• B-hemolytic strep group C, F and G
• Arcanobacterium haemolyticum;
• H. influenzae, N. gonorrhoeae, Corynebacterium diphtheriae, Bordetella pertussis, Parapertussis, Yeast

URT Specimen Collection

• Specimens obtained with syringes and needles, swabs, and/or biopsies.
• Diphtheria is cultured on BAP, Loeffler, tellurite media.
• Pertussis is cultured on Bordet-Gengou blood agar.
• Posterior pharynx and tonsils are swabbed, placed in transport media.

URT Microscopic Examination

• Gram stain is not typically done because it shows a lot of normal flora.

URT Culture

• Mainly for group A strep (mostly).
• Other organisms (e.g., B, C, F, G), N. gonorrhoeae, Arcanobacterium haemolyticum, and C. diphtheriae, are also possible, depending on patient needs.
• Throat cultures demonstrate specific examples.

Epiglottitis

• Common in 2–6-year-old children.
• Almost exclusively caused by H. influenzae type b (becoming rare because of vaccination).
• Can cause obstructed airways.
• Diagnosed clinically.
• Collection of samples may be hazardous.
• Blood cultures may be needed (bacteremia).

Sinusitis

• Often preceded by a viral URTI.
• Acute sinusitis agents include S. pneumoniae, H. influenzae, M. catarrhalis, group A strep, anaerobes, S. aureus, and GNR.
• Chronic sinusitis can be caused by anaerobes, S. aureus (adults) or S. pneumoniae, S. aureus, viridans streptococci (children).

Otitis Media

• Middle ear infection.
• Common in children <10 years.
• Usually follows viral URTI.
• Common agents include S. pneumoniae, H. influenzae, other bacteria (group A strep, S. aureus), M. catarrhalis, anaerobes, GNR.

Specimen Collection (Otitis Media)

• Tympanocentesis collects fluid (TF).
• Aseptically puncturing the tympanic membrane and aspirating fluid is used.
• Specimen is placed in an anaerobic transport medium.
• A swab can collect samples from ruptured eardrums.

Processing TF

• Gram stain and culture samples in both anaerobic and aerobic conditions (BAP, CHOC, MAC, anaBAP).
• Identify and perform susceptibility tests

LRT Infections

• Bronchitis/Influenzae, Pneumonia, Empyema, Pleural fluid, Tuberculosis

LRT Pathogens

• Respiratory viruses (including Influenza A and B)
• S. pneumoniae, H. influenzae, M. catarrhalis, M. pneumoniae, Chlamydia spp.
• GNR, S. aureus, Legionella spp., Anaerobes, Mycobacteria, Fungi

Community-Acquired Pneumonia

• S. pneumonia (most common, pneumococcal pneumonia)
• Mycoplasma pneumoniae, H. influenzae, M. catarrhalis

Hospital-Acquired Pneumonia

• Contaminated ventilators/inhalation therapy
• Enterobacteriaceae, K. pneumoniae, S. marcescens, S. aureus, NFGNR, P. aeruginosa, Burkholderia cepacia, CF and nosocomial S. pneumoniae, Anaerobic bacteria

Miscellaneous Causative Agents

• Mycobacteria (MTB), Legionella (immunocompromised individuals, community acquired/nosocomial), Chlamydia (C. trachomatis in neonates, C. pneumoniae in young adults).

Emerging Viral Infections

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

Bioterrorism Agents

• B. anthracis (anthrax), Y. pestis (plague), Coxiella burnetii (Q fever), F. tularensis (tularemia)

Routes of Infection

• Most are opportunistic.
• Waiting for low defenses to infect lungs.
• Inhalation of infectious aerosols.
• Hemotogenous (blood stream).
• Aspiration of oral secretions (excessive drinking, intubation).
• Sputum - easiest specimen but difficult interpretations due to contamination with normal flora.

Specimen Collection(LRT)

• Sputum - the matter ejected from the LRT through the mouth (may be contaminated with NF); Washings, brushing, biopsies, pleural fluid samples, and tracheal/bronchial aspirates; bronchial washings, brushing, biopsies.
• Specific specimens like for cystic fibrosis require specialized media like for B. cepacia, MRSA, and Pseudomonas.

Sputum: Non-invasive Collection Methods

• Expectorated Sputum, Deep Cough, Induced Sputum (methods), Assisted by RT and chest percussions
• Inhale aerosolized saline to induce cough
• Tracheostomy/endotracheal aspirates, Sucking/Suctioning secretions into tubes.

Sputum: Invasive Collection Methods

• Bronchoscopy (specimens), bronchial lavage washings, and bronchial brushings.
• Reserved for cases involving unusual infections or cases where sputum specimens cannot diagnose the condition (chronic or immunocompromised patients).

Specimen Transport and Processing (LRT)

• Sterile screw-cap cups/tubes
• Bronchial brush placement in sterile saline.
• Specimens must be cultured within two hours of collection.
• Processing includes Gram stain and culture.

Sputum Gram Stain

• May reveal the causative agent.
• Determine sputum quality, suitability for culture (e.g., distinguish between spit/sputum).
• Low-power field (LPF) (10X): determine the quantity of epithelial/normal flora/PMNs
• Oil immersion (100X): morphology, quantity.

Gram Stain Analysis of Sputum

• LPF (10X): count the number of epithelial and PMNs per LPF, classify results as <10, >10, <25, >25
• A good specimen will have < 10 epithelial and >25 PMNs per LPF.
• Reject specimens if there are more than 25 epithelial cells per LPF.
• Record the quantity of bacteria observed (rare, moderate, or many) and the type of bacteria. -Images are shown of unacceptable and acceptable gram stains