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 tract is responsible for the digestion and absorption of nutrients.
• Inflammation of the stomach is called gastritis.
• Gastroenteritis is inflammation of the stomach and intestines.
• Enterocolitis is inflammation of the small and large intestines.

Gastrointestinal Tract - Introduction

• The introduction covers different parts of the gastrointestinal tract as esophagus, stomach, small intestines, large intestines, and anus.
• It details the components, showing the digestive and absorption processes.

Gastrointestinal Tract - Terms

• Diarrhea: An abnormal increase in bowel movements, ranging from loose to liquid stool.
• Dysentery: Diarrhea with cramping abdominal pain.
• Proctitis: Inflammation of the rectal mucosa, often caused by N. gonorrhoeae, C. trachomatis, or T. pallidum.

Gastrointestinal Tract - Normal Flora

• Eighty percent of the dry weight of feces consists of bacteria.
• Normal flora prevents colonization by pathogens.
• Common types include anaerobic bacilli (Bacteroides spp.), GN enteric bacilli, Enterococci, Streptococci, S. aureus, and Yeast (Candida).

Gastrointestinal Tract - Non-Inflammatory Diarrhea

• Results from bacterial toxins (enterotoxins).
• Characterized by watery, large-volume stool, and the absence of fever, blood, or pus.

Gastrointestinal Tract - Non-Inflammatory Diarrhea - Pathogens

• Vibrio cholerae: A common cause of severe watery diarrhea, also known as cholera.
• Enterotoxigenic E. coli: Bacteria that produces toxins causing diarrhea.
• Various viruses: Viruses are commonly identified causes of watery diarrhea.

Gastrointestinal Tract - Inflammatory Diarrhea

• Organisms invade the intestinal mucosa, destroying intestinal cells.
• Characterized by fever, small-volume stool, and the presence of blood and/or pus in the stool.
• Common causes include Salmonella spp, Shigella spp, Y. enterocolitica, Campylobacter spp, Enteroinvasive E. coli, and Clostridium difficile.

Gastrointestinal Tract - Enterotoxin-Mediated Diarrhea

• Caused by ingestion of food containing toxins.
• Rapid onset (within 12 hours)
• Common causes include Enterotoxigenic E. coli (ETEC), Vibrio cholerae, S. aureus, C. perfringens, and B. cereus.

Gastrointestinal Tract - Diarrheal Diseases

• Salmonella: Gastroenteritis
• Shigella: Bacillary dysentery
• Yersinia enterocolitica: Enterocolitis
• Other bacterial causes of diarrhea (e.g., Campylobacter jejuni and certain E. coli strains)

Gastrointestinal Tract - Diarrheal Diseases - Additional pathogens

• Edwardsiella tarda
• Vibrio cholerae
• Vibrio parahaemolyticus
• Plesiomonas shigelloides
• Listeria monocytogenes

Gastrointestinal Tract - Parasitic and Viral Causes

• Intestinal parasites (Giardia, Entamoeba, Cryptosporidium, Cyclospora, Microsporidia)
• Viruses (Rotavirus, adenovirus, calicivirus, astrovirus)

Gastrointestinal Tract - Other Diseases

• H. pylori: Chronic gastritis and peptic/duodenal ulcers
• C. difficile: Antibiotic-associated diarrhea, pseudomembranous colitis
• C. perfringens: Enterotoxin
• Mycobacterium avium: GI disease in AIDS patients
• E. coli (enterohemorrhagic): Hemorrhagic colitis and hemolytic uremic syndrome (HUS)

Gastrointestinal Tract - E. coli (continued)

• Enterotoxigenic, enteropathogenic (enteroadherent), and enteroaggregative: The different strains of E. coli and related diseases

Gastrointestinal Tract - Transmission Routes

• Most diarrheal diseases are transmitted via the fecal-oral route.
• Ingested food or water contaminated by feces can transmit certain types of bacteria (such as Salmonella) and their toxins (such as S. aureus).
• Direct person-to-person transmission may occur with certain pathogens (such as Shigella).
• Some pathogens can be transmitted through contact with animals.

Gastrointestinal Tract - Symptoms

• Common symptoms of gastrointestinal tract infections include nausea, vomiting, abdominal discomfort, and diarrhea.

Gastrointestinal Tract - Specimen Collection

• Collection of fecal specimens generally uses clean, wide-mouthed containers not contaminated with urine.
• Samples are commonly preserved in Cary-Blair transport media.
• Processing needs to happen within 1–2 hours after collecting samples.
• For further investigation, duodenal, colostomy, and ileostomy materials, diapers, and food might also be collected, especially in public health outbreaks.

Gastrointestinal Tract - Visual Examination

• A macroscopic examination assesses stool characteristics.
• Stool consistency (e.g., watery, formed, loose) is important along with assessing the presence of blood or mucus.
• Stool color can also be indicative of the infection process.

Gastrointestinal Tract - Microscopic Examination

• Microscopic examination of fecal specimens is used to determine the presence of white blood cells (WBCs or PMNs) to differentiate between inflammatory and non-inflammatory causes of diarrhea.
• Identifying the types of bacteria present in various samples is performed under specific microscopic magnification conditions.

Gastrointestinal Tract - Culture

• Culture is performed on various media (e.g., BAP, MAC, EMB, XLD, HE, SS, TCBS) to identify pathogens and to assess the isolate.

Gastrointestinal Tract - Media Inoculation

• Non-sterile pipettes or swabs are carefully used to inoculate the culture media.
• Media for specific pathogens would be prepared in a way suitable for the isolation of those pathogens.
• Specialized enriching broths are used to increase the detection of specific pathogens present in a sample, followed by transfer to agar media.

Gastrointestinal Tract - Media Examples

• BAP (Blood Agar Plate) detects Staph aureus and yeast overgrowth.
• MAC (MacConkey Agar) is used for differential and selective growth of E. coli.
• NLF agar is intended for use in identifying certain bacterial species.
• XLD agar screens for Salmonella and Shigella strains.

Gastrointestinal Tract - Media - MAC and Others

• MAC: A differential and selective medium.
• Hektoen Enteric Agar, Xylose-Lysine-Desoxycholate (XLD): Differential and selective media for various bacteria.
• Campy-BAP: Selective enrichment media for isolating Campylobacter.

Gastrointestinal Tract - Enrichment Media

• Enriching broths are commonly used to maintain the live condition of microorganisms, increasing the likelihood of detection or isolation.
• Selenite F broth: Intended to aid with isolation of salmonella.

Gastrointestinal Tract - Special Media

• Cefsulodin-irgasan-novobiocin (CIN) agar: Used to isolate Yersinia enterocolitica.
• Salmonella-Shigella (SS) agar: Used to target Salmonella and Shigella.
• Sorbitol MAC: Specifically developed for differentiating E. coli versus E. coli O157:H7.

Gastrointestinal Tract - Stool WBC

• Distinguishing between inflammatory and non-inflammatory conditions using WBC counts.
• Clostridium difficile is tested for using specific stool microscopy conditions.

Gastrointestinal Tract - Culture Workup

• The lab workup is tailored to the suspected pathogens and the symptoms.
• Biochemical tests might be used to narrow down the possible culprits to a limited number of pathogens.

Gastrointestinal Tract - Reporting Results

• Reporting includes pathogen identification and susceptibility testing.
• Public health officials are notified for Salmonella and Shigella detection instances.

Respiratory Tract

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

Respiratory Tract - Normal Flora (URT)

• Staphylococci (including S. aureus)
• Streptococci (including viridans, pneumococci)
• Micrococci
• Diphtheroids, Neisseria, Haemophilus, Anaerobes, Spirochetes, Candida.

Respiratory Tract - URT Infections

• Thrush, Laryngitis, Epiglottitis, Pharyngitis, Tonsillitis, Sinusitis, Otitis media, Diphtheria, and Pertussis (whooping cough) are examples of URT infections.

Respiratory Tract - Pathogens (URT)

• Respiratory viruses (influenza, parainfluenza, RSV, adenovirus, rhinovirus, coronavirus, coxsackie A, EBV, CMV)
• S. pyogenes
• β-hemolytic streptococci group C, F, and G
• Arcanobacterium haemolyticum

Respiratory Tract - Pathogens (URT) - Additional pathogens

• H. influenzae
• N. gonorrhoeae
• Corynebacterium diphtheriae
• Bordetella pertussis and parapertussis
• Yeast

Respiratory Tract - Specimen Collection (URT)

• Specimens include swabs from the posterior pharynx and tonsils, biopsies, and also use of syringes and needles for additional investigations.

Respiratory Tract - Microscopic Examination (URT)

• Gram stains are not often utilized because normal flora is abundant in the URT.
• Group A streptococcus is commonly sought via antigen testing initially.

Respiratory Tract - Throat Culture

• Throat cultures are mainly utilized to assess for group A Streptococcal infections.

Respiratory Tract - Epiglottitis

• Primarily affects 2- to 6-year-old children.
• Causative agent: H. influenzae type b (almost exclusive).
• Represents a life-threatening medical condition due to airway obstruction potential.

Respiratory Tract - Sinusitis

• Frequently follows a viral URT infection.
• Common pathogens in acute sinusitis include S. pneumoniae, H. influenzae, M. catarrhalis, group A Streptococcus, and anaerobes, S. aureus, and gram-negative rods (GNR).
• Chronic sinusitis involves persistent sinus issues; pathogens can vary and encompass a broader range including anaerobes, S. aureus (in adults), S. pneumoniae, and viridans streptococci.

Respiratory Tract - Otitis Media

• Commonly seen in children under 10.
• Usually follows viral URT infections.
• Typical agents are S. pneumoniae, H. influenzae, and other bacteria (e.g., group A strep, S. aureus, M. catarrhalis).
• The infection involves the middle ear.

Respiratory Tract - Specimen Collection (LRT)

• Specimen collection depends on the suspected infection area, and is best conducted with a method to minimize contamination with normal flora.
• Methods include expectorated sputum, induced sputum, bronchoscopy, and biopsies.

Respiratory Tract - Sputum Collection

• Non-invasive method using deep coughs into sterile containers to minimize contamination, induced by respiratory therapists by using RT assistance, chest percussions(drainage) and airway aerosols
• Invasive method is bronchoscopy, which targets the respiratory tract via the mouth or nose.
• All samples are subsequently processed, including gram stain and culture to determine quantity and type of bacteria present, and identify any pathogens.

Respiratory Tract - Gram Stain of Sputum

• Gram stain of sputum is crucial in assessing its quality—whether it is pure sputum or saliva, presence of epithelial cells indicating oropharyngeal contamination.
• A gram stain evaluation with sufficient epithelial and PMN counts helps distinguish quality, amount of bacteria and type present.
• Microscopy (100X and 10X) is used to thoroughly evaluate sputum samples.

Respiratory Tract - Routine and Anaerobic Cultures

• Routine cultures (e.g., blood agar plates, chocolate agar plates, MacConkey agar plates) are performed for the URT samples, and incubated under appropriate conditions (e.g., 35 degrees Celsius, presence of CO2).
• Specialized media is used for unusual types of pneumonia cases.
• Anaerobic culture is required for specimens that avoid the oral cavity to help reduce normal flora contamination and is used when a higher chance of pathogenic anaerobic bacteria is a possibility.

Respiratory Tract - Miscellaneous Causative Agents

• Mycobacteria (MTB)
• Legionella
• Chlamydia (C. trachomatis in neonates and C. pneumoniae in young adults)

Respiratory Tract - Emerging Viral Infections

• Avian influenza (H5N1)
• H1N1 influenza A
• SARS coronavirus (SARS-CoV)

Respiratory Tract - Bioterrorism Agents

• Bacillus anthracis (anthrax)
• Yersinia pestis (plague)
• Coxiella burnetii (Q fever)
• Francisella tularensis (tularemia)

Explore the components and functions of the gastrointestinal tract, including the esophagus, stomach, and intestines. Understand key terms related to gastrointestinal health, such as gastritis and diarrhea, as well as their implications for digestion and absorption.