Chapter 13: Diagnosing Infectious Diseases PDF

Chapter 13: DIAGNOSING INFECTIOUS DISEASES FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN Accurate diagnosis of infectious diseases relies on patient history, physical examination, symptom evaluation, and proper specimen handling. This chapter focuses on clinical speci...

Chapter 13: DIAGNOSING INFECTIOUS DISEASES FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN Accurate diagnosis of infectious diseases relies on patient history, physical examination, symptom evaluation, and proper specimen handling. This chapter focuses on clinical specimens: their collection, transport, and processing. Clinical Specimens ​ Specimens like blood, urine, and feces are collected from patients to diagnose or monitor infections. ​ High-quality specimens are crucial for accurate lab results. Importance of High-Quality Specimens ​ Healthcare professionals play a vital role ​ Specimen quality directly impacts the in specimen collection and transport. accuracy of lab results. ​ High-quality specimens require: ○​ Proper specimen selection (correct type) ○​ Proper specimen collection ○​ Proper specimen transport ​ Lab P&P Manuals provide guidelines for specimen handling. Proper Selection, Collection, and Transport ​ General precautions: ○​ Select the correct specimen type. ○​ Collect specimens aseptically to minimize contamination. ○​ Collect from the site most likely Role of Healthcare Professionals to contain the pathogen. ​ Close collaboration between clinicians ○​ Collect before antimicrobial and the microbiology lab is essential. therapy begins (if possible). ​ Healthcare professionals select, collect, ○​ Collect during the acute stage of and transport specimens, and the disease. communicate findings to ○​ Collect sufficient specimen clinicians. quantity. ​ Safety precautions (Standard ○​ Use sterile containers. Precautions) must be strictly followed ○​ Transport specimens promptly during specimen handling to the lab. ○​ Protect specimens from heat, cold, and oxygen (for anaerobes). ○​ Label specimens correctly and include a completed lab requisition.  Chapter 13: DIAGNOSING INFECTIOUS DISEASES FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ○​ Handle specimens with care to ​ Urine Specimen Handling: prevent contamination. ○​ Process urine specimens within Contamination of Clinical Specimens 30 minutes of collection or refrigerate at 4°C. ​ Contamination with indigenous ○​ Refrigerated specimens should microflora can interfere with pathogen be cultured within 24 hours. identification. ○​ Failure to refrigerate can lead to ​ Proper collection techniques are bacterial overgrowth and essential to minimize contamination. inaccurate results. Types of Clinical Specimens ​ Blood: ​ Urine Culture Analysis: ○​ Blood is usually sterile within the ○​ Colony Count: body. ​ Estimates the number ○​ Bacteremia: Presence of of viable bacteria in the bacteria in the bloodstream. urine. ○​ Septicemia: Serious disease ​ Uses a calibrated loop with bacteria or their toxins in to inoculate a specific the bloodstream. volume of urine onto a ○​ Blood cultures are typically blood agar plate. collected in pairs (aerobic and ​ Counts colonies after anaerobic bottles). incubation. ○​ Aseptic technique is crucial to ​ Calculates prevent skin contamination. colony-forming units This passage describes the collection and (CFU) per milliliter of analysis of urine specimens to diagnose urinary urine. tract infections (UTIs). ​ Isolation and Identification: ​ Urine Collection: ○​ Isolates and identifies the ○​ Urine is normally sterile within specific bacterial species the bladder. causing the infection. ○​ Contamination occurs during ​ Antimicrobial Susceptibility Testing: urination due to contact with the ○​ Determines the effectiveness of distal urethra. different antibiotics against the Clean-Catch, Midstream Urine (CCMS) isolated bacteria. Collection: ​ Interpretation of Results: ​ Cleanse the urethral opening ○​ A colony count of 100,000 with soap and water. CFU/mL or higher is generally ​ Direct the initial portion of urine indicative of a UTI. into the toilet. ○​ High colony counts can also ​ Collect the midstream portion of result from specimen urine in a sterile container. contamination or improper handling. ​ Alternative Collection Methods: ○​ The presence of bacteria in urine is not always indicative of Catheterized urine collection. a UTI. ○​ Suprapubic needle aspiration ○​ Two or more bacteria per 1,000 (more invasive). microscopic fields in a Gram-stained urine smear can  Chapter 13: DIAGNOSING INFECTIOUS DISEASES FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN suggest a UTI with a high CFU ○​ Indicate the type of wound count. (e.g., dog bite, surgical site) ​ GC Cultures (Neisseria gonorrhoeae): This information provides a basic ○​ Use a sterile swab to gather a understanding of how urine specimens sample from the suspected are collected and analyzed to diagnose infection site, which could be the UTIs. urethra (for men), cervix (for women), rectum, or throat, ​ Cerebrospinal Fluid (CSF): depending on symptoms and ○​ Obtained via lumbar puncture. potential exposure; the swab is ○​ Crucial for diagnosing then placed in a specialized meningitis, encephalitis, and transport medium to preserve meningoencephalitis. the bacteria for laboratory ○​ Treated as a STAT specimen analysis. due to the severity of CNS ○​ Use Dacron or calcium alginate infections. swabs, avoid ordinary cotton ○​ Gram stain results are often swabs. reported immediately ○​ Inoculate immediately onto (preliminary report). appropriate media ○​ Important: Do not refrigerate (ThayerMartin, Martin-Lewis). CSF specimens. ○​ Incubate in a CO2 environment. ​ Sputum: ○​ Do not refrigerate GC swabs. ○​ Collected from patients with ​ Fecal Specimens: respiratory infections like ○​ Collect and process promptly to pneumonia and tuberculosis. prevent pH changes that can kill ○​ Differentiate sputum from saliva, pathogens. as saliva analysis is not ○​ Use preservatives to maintain informative. pH if immediate processing is ○​ Proper mouth hygiene is not possible. important to minimize oral flora ○​ Pathogens often overwhelm the contamination. normal gut flora in ○​ Refrigeration is generally gastrointestinal infections. acceptable for short periods. This information highlights the importance of ​ Throat Swabs: proper specimen collection and handling for ○​ Primarily for diagnosing strep accurate diagnosis of infectious diseases. throat (Streptococcus pyogenes). Pathology Department: ○​ Proper collection technique is Divided into two major divisions: crucial: swab inflamed areas or 1.​ Anatomical Pathology: Deals with tonsils, avoid touching cheeks, autopsies, tissue examinations, teeth, or gums. cytology, etc. ○​ Specify any other suspected 2.​ Clinical Pathology: Includes the CML, pathogens on the lab Clinical Chemistry, Hematology, Blood requisition. Bank, and Immunology. ​ Wound Specimens: Employs pathologists, specialized scientists, ○​ Aspirates are preferred over medical technologists (MTs), and medical swabs to minimize laboratory technicians (MLTs). contamination.  Chapter 13: DIAGNOSING INFECTIOUS DISEASES FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ​ Virology: ○​ Diagnoses viral infections. ○​ Uses techniques like immunodiagnostic tests, electron microscopy, cell culture, and molecular methods. ​ Mycobacteriology: ○​ Focuses on tuberculosis diagnosis. ○​ Uses acid-fast staining, culture, and biochemical tests. Clinical Microbiology Laboratory (CML): Responsible for diagnosing infectious diseases. Key responsibilities: ​ Process clinical specimens. ​ Isolate pathogens. ​ Identify (speciate) pathogens. ​ Perform antimicrobial susceptibility testing. Divided into sections: Bacteriology, Mycology, Parasitology, Virology, Mycobacteriology ​ Bacteriology: ○​ Isolates and identifies bacteria. ○​ Uses various techniques: Gram staining, colony morphology, biochemical tests. ​ Mycology: ○​ Isolates and identifies fungi (yeasts, molds). ○​ Uses KOH preparation, culture on Sabouraud dextrose agar, microscopic examination of tease mounts. ​ Parasitology: ○​ Diagnoses parasitic infections. ○​ Identifies parasites by observing characteristic microscopic features.  Chapter 12: HEALTHCARE EPIDEMIOLOGY FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ○​ Community-Acquired Infections: Present at Introduction to Healthcare Epidemiology admission or incubating. Definition: ○​ Iatrogenic infections: Study of health and disease in Physician-induced infections healthcare settings. (e.g., surgical site infections). Focus: Infection control and preventing healthcare-associated infections (HAIs). Frequency and Details of HAIs in the Scope: Philippines ​ Surveillance measures. ​ Risk reduction programs. Prevalence of HAIs: ​ Policy development and implementation. Pediatric Patients at Philippine General ​ Education on infection control. Hospital (2011-2014): ​ Cost–benefit assessment of prevention ​ Overall HAI prevalence: 11.37% from programs. 30,032 admissions. ​ Elimination of infection reservoirs and ​ Pediatric Intensive Care Unit (PICU): transmission pathways. 15.17%-27.81%. ​ Pediatric Wards: Goal: Protect patients, healthcare workers, and ○​ Ward 9: 9.03%-19.87%. visitors. ○​ Ward 11: 8.75%-14.76%. Importance of Microbiology in Healthcare ​ Neonatal Intensive Care Unit (NICU): 7.52%-9.44%. ​ Essential for all health-related occupations: Device-Associated Infections in ICUs (2005-2009): ○​ Hospitals, clinics, long-term care, hospice, and home care. 1.​ Ventilator-Associated Pneumonia (VAP): ​ Need for standardized procedures to ​ Adult ICUs: 16.7 per 1,000 prevent infectious diseases. ventilator-days. ​ Carelessness can lead to preventable ​ Pediatric ICUs: 12.8 per 1,000 infections. ventilator-days. ​ Neonatal ICUs: 0.44 per 1,000 ventilator-days. Importance of Microbiology in Healthcare 2.​ Central Line-Associated Bloodstream Definition: Infections acquired in healthcare Infections (CLABSI): settings. ​ Adult ICUs: 4.6 per 1,000 ​ Excludes infections present or catheter-days. incubating at hospital admission. ​ Pediatric ICUs: 8.23 per 1,000 catheter-days. ​ Neonatal ICUs: 9.6 per 1,000 Categories: catheter-days ○​ Healthcare-Associated 3.​ Catheter-Associated Urinary Tract Infections (HAIs): Develop Infections (CAUTI): within healthcare settings. ​ Adult ICUs: 4.2 per 1,000 catheter-days.  Chapter 12: HEALTHCARE EPIDEMIOLOGY FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ​ No reported cases in pediatric ​ Sufficient resources for ICUs. effective implementation. Common Pathogens: Modes of Transmission of HAIs Predominant pathogens: 1.​ Contact Transmission: ​ Gram-Positive Cocci: a.​ Direct: Person-to-person ○​ Staphylococcus aureus transfer. (including MRSA). b.​ Indirect: Via contaminated ○​ Coagulase-negative intermediate objects or persons. Staphylococci. ○​ Enterococcus spp. (including 2.​ Droplet Transmission: VRE) a.​ Respiratory droplets (>5µm) ​ Gram-Negative Bacilli: transmit infection. b.​ E.g., Sneezing or coughing. ○​ Escherichia coli ○​ Pseudomonas aeruginosa 3.​ Airborne Transmission: ○​ Enterobacter spp a.​ Airborne droplet nuclei or small ○​ Klebsiella spp. particles (≤5µm). ​ Drug sensitivities: Most Common Types of ○​ Pseudomonas species: Healthcare-Associated Infections (HAIs) Ceftazidime. ​ Urinary Tract Infections (UTIs): ○​ Klebsiella: Meropenem. ○​ ~32% of all HAIs. Challenges in Infection Control ○​ Cause ~13% of deaths ​ Nurses’ Practices in a Tertiary Hospital associated with HAIs. in Baguio City: ​ Surgical Site Infections (SSIs): ​ Good knowledge but suboptimal infection prevention practices. ○​ ~22% of all HAIs. ​ Key barriers ○​ Cause ~8% of deaths associated with HAIs ○​ Heavy workloads due to staff shortages. ​ Lower Respiratory Tract Infections (e.g., ○​ Inadequate dissemination of Pneumonia): updated guidelines. ○​ ~15% of HAIs. ○​ Discomfort with personal ○​ Cause ~36% of deaths protective equipment (PPE). associated with HAIs. ​ Conclusion: ​ Bloodstream Infections (Septicemia): ○​ HAIs remain a significant issue, ○​ ~14% of HAIs. especially in intensive care ○​ Cause ~31% of deaths settings. associated with HAIs. ○​ Addressing these issues requires: ​ Gastrointestinal Infections (C. difficile): ​ Better infection control ○​ Caused by antibiotic disruption practices. of gut flora. ​ Improved staff training.  Chapter 12: HEALTHCARE EPIDEMIOLOGY FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ○​ Symptoms: AAD, PMC ​ Isolation of infectious patients. (Antibiotic-Associated Diarrhea, ​ Use of personal protective equipment Pseudomembranous Colitis) (PPE). Patients Most Likely to Develop HAIs Infection Control Practices High-Risk Groups: ​ Medical Asepsis (Clean Technique): Reduces pathogen transmission. ​ Elderly, premature infants, newborns. ​ Women in labor, surgical, and burn ○​ Includes hand hygiene, cleaning patients. equipment, disinfection. ​ Patients with diabetes, cancer, cystic ​ Surgical Asepsis (Sterile Technique): fibrosis. Excludes all microbes. ​ Immunosuppressed individuals (organ transplants, dialysis, etc.). ○​ Used in invasive procedures (e.g., surgeries, ICU Patients: catheterizations). ​ Highest infection rates. ​ Sterilization Methods: Steam, chemical ​ HAI rates ~3x higher than general sterilant, UV light, air filtration. hospital patients. Historical Contributions to Infection Control Major Factors Contributing to HAIs Joseph Lister (1827–1912): ​ Increasing number of drug-resistant pathogens. ​ Introduced antisepsis using phenol in ​ Non-compliance with infection control surgeries. guidelines. ​ Developed sterilization techniques (e.g., ​ Growing population of steam, sterile gloves). immunocompromised patients. ​ Reduced surgical wound infections significantly. ○​ Contributing Factors: Principles of Disinfection in Healthcare ​ Overcrowding, staff shortages, lengthy Disinfection eliminates most pathogenic surgeries. microbes on inanimate objects. ​ Overuse of antibiotics and indwelling medical Key Categories of Disinfectants: devices. ​ Chemical Sterilants: Kill bacterial spores ​ Lack of training for with prolonged exposure (3–12 hours). healthcare workers. ​ High-Level Disinfectants: Eliminate all Reducing the Number of HAIs microbes except high numbers of spores. Primary Strategy: Strict compliance with ​ Intermediate-Level Disinfectants: Kill infection control guidelines. mycobacteria, bacteria, viruses, and fungi. Key Measures: ​ Low-Level Disinfectants: Effective ​ Frequent and proper handwashing: against vegetative bacteria, some fungi, and viruses in ~10 minutes. ○​ Use soap, warm water, scrub for 10–15 seconds. ○​ Dry from forearms to fingertips. ​ Proper sterilization and disinfection.  Chapter 12: HEALTHCARE EPIDEMIOLOGY FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN Spaulding System for Instrument ​ Environment: Classification ○​ Use of sterile solutions, drapes, Critical Items: and fields. ○​ Heat-sterilized surgical ​ High risk of infection; require instruments. sterilization. ​ Examples: Surgical instruments, cardiac ​ Goal: Prevent introduction of microbes catheters, implants. into sterile fields. ​ Methods: Steam sterilization, ethylene Regulations Pertaining to Healthcare oxide gas, or chemical sterilants. Epidemiology and Infection Control Semi-critical Items: OSHA Bloodborne Pathogen Standard (29 CFR ​ Contact mucous membranes or 1910.1030) non-intact skin; need high-level ​ Written Exposure Control Plan disinfection. ​ Topics Covered: ​ Examples: Respiratory therapy equipment, endoscopes. ○​ Postexposure follow-up ○​ Recordkeeping for bloodborne Noncritical Items: pathogens ​ Contact intact skin only; low-level ○​ Needlestick injuries and sharps disinfection is sufficient. handling ​ Examples: Bedpans, blood pressure ○​ Universal precautions and latex cuffs, bedside tables. allergy ○​ Bloodborne illnesses: HIV, HBV, Surgical Asepsis HCV Practices to keep objects and areas completely ○​ Labelling and signage sterile. requirements Key Differences: Standard Precautions ​ Medical Asepsis: Clean technique; ​ Combines Universal Precautions and excludes pathogens. Body Substance Isolation Precautions ​ Surgical Asepsis: Sterile technique; ​ Applies to all patients in all healthcare excludes all microbes. settings Applications: ​ Key Elements: ​ Operating rooms, labor and delivery ○​ Hand hygiene and personal areas. protective equipment (PPE) ​ Invasive procedures (e.g., blood draws, ​ Safe injection practices catheter insertions, lumbar punctures). ​ Environmental cleaning and disinfection Techniques for Surgical Asepsis ​ Handling soiled linens and sharps ​ Preparation: disposal ○​ Surgical scrubbing of hands and Hand Hygiene fingernails. ​ Most critical infection prevention method ○​ Wearing sterile masks, gloves, ​ Guidelines: caps, gowns, and shoe covers. ○​ Wash hands before and after patient contact  Chapter 12: HEALTHCARE EPIDEMIOLOGY FIRST SEMESTER I ACADEMIC YEAR 2024-2025 I PROF. JOHN LEONARD CHAN ○​ Use antimicrobial agents in Specialized Patient Environments specific scenarios ○​ Alcohol-based hand rubs for ​ Airborne Infection Isolation Rooms unsoiled hands (AIIRs): ○​ Avoid artificial nails and rings ○​ Negative pressure and HEPA during patient care filtration for airborne pathogens Personal Protective Equipment (PPE) ​ Protective Environments: ​ Components: ○​ Positive pressure rooms for ​ Gloves: Use during exposure to blood, immunocompromised patients. body fluids, or contaminated items Vaccinations for Healthcare Personnel ​ Gowns: Worn to protect skin and clothing ​ Recommended Vaccines: ​ Masks: For protection against infectious ○​ Hepatitis B, Influenza droplets or during sterile procedures ○​ Measles, Mumps, Rubella ​ Eye Protection: Goggles or face shields ○​ Varicella-Zoster for splash prevention ​ Respiratory Protection: N95 respirators Handling Food and Eating Utensils for airborne pathogens. ​ Safe Practices: Environmental Control ○​ Proper storage, preparation, ​ Routine cleaning and disinfection of and disposal of food surfaces ○​ Hand hygiene before food ​ Proper handling of soiled linens and handling patient-care equipment ○​ Routine health checks for food ​ Sharps Disposal: handlers ○​ Use rigid, puncture-resistant containers ○​ Avoid recapping or bending needles Transmission-Based Precautions ​ Used in addition to Standard Precautions Types: 1.​ Contact Precautions: For multidrug-resistant organisms, C. difficile, etc. 2.​ Droplet Precautions: For respiratory droplets >5 µm (e.g., influenza) 3.​ Airborne Precautions: For droplet nuclei ≤5 µm (e.g., tuberculosis)