Upper and Lower RT Infections

1. Upper and Lower RT Infections MLAB 2434 – Microbiology Keri Brophy-Martinez

2. Concepts:Normal Respiratory Flora • Exists in symbiotic relationship with host • Normal flora also produces bacteriocins, which are toxic to other bacteria • Keeps host system primed for invasion by pathogenic microbes.

3. Concepts:Normal Respiratory Flora • In absence of disease, presence of normal flora is called “colonization” • Colonizers prevent proliferation and invasion by pathogenic bacteria through competition for nutrients and receptor sites

4. Concepts:Normal Respiratory Flora • Patients receiving broad-spectrum antibiotics, hospitalized, or with chronic illnesses may have altered normal flora • Microbiologists must be able to determine whether the organism is a colonizer or a disease causer

5. Concepts: Immune Status of Host • Age as a risk factor • infants and elderly more susceptible • Immunocompromised • Opportunistic infections • Reduced clearance of secretions • Immature anatomical development (e.g., eustachian tube) • Reduced function of respiratory cilia after viral infection • Obstruction by foreign body(e.g., aspirated foods) • Disease that alters RT anatomy (tumors) • Alterations in viscosity of mucus (e.g., cystic fibrosis) • Infection-induced airway obstruction • (e.g., epiglottitis)

6. Concepts • Seasonal and Community Trends in Infections • Fall/winter: viral • Year round: mycoplasma • Empiric Antimicrobial Therapy • Treating patient prior to getting culture results

7. Concepts • Always consider the following: • Source of specimen • Patient’s age • Immunologic status of host • Clinical setting of the patient

8. Specimen Collection, Transport and Handling • Specimen Types • Sputum- specimen resulting from a deep cough, often contaminated with oropharyngeal flora • Bronchial washing/brushing- collected through bronchoscope, minimizes contamination with upper respiratory flora • Needle or open biopsy of lung- minimizes contamination with upper respiratory flora • Throat swab- swab areas with pus or that are red and swollen, avoid tongue, cheeks and roof of mouth • Nasopharyngeal swab- using a calgiswab, insert through nostril into nasopharynx hold for several seconds before withdrawal

9. Specimen Collection, Transport and Handling • Transport and Handling • Place specimens in a sterile container with a tight fitting lid, get to lab asap • Refrigerate specimens for up to 24 hours if a delay in processing occurs • Specimens submitted for anaerobic analysis should be processed asap

10. Anatomy of RT • Upper RT • Nasal cavity (sinuses) • Nasopharynx • Oropharynx • Epiglottis • Larynx

11. Anatomy of RT • Lower RT • Trachea • Bronchi • Lungs, alveoli

13. Function of RT • Perform respiration: exchange of CO2 and O2 • Deliver air from outside body to the alveoli where gas exchange occurs • Components within RT defend against invaders

14. Barriers to Infection • Nasal hairs • Filters air • Cilliary cells • Clears particulates and secretes antimicrobial substances • Coughing • Expels particulate matter • Normal flora • Prevents colonization • Phagocytes/Inflammatory cells • Ingest organisms • Tracheobronchial tree secretes immunoglobulins

15. URT Infections:Pharyngitis • Most common bacterial cause • S. pyogenes (Group A) • Viruses • Occurs in winter and early spring • Unusual pathogens • N. gonorrhoeae • C. diphtheriae

16. URT Infections:Pharyngitis • Specimen Collection • Collect two swabs • Target tonsillar exudate • Laboratory diagnosis • Rapid strep screening • Culture with A disk or PYR positive • Gram stain from throats NOT helpful

17. URT Infections:Sinusitis • Causes • Bacterial pathogens • S. pneumoniae and H. influenzae • Less common isolates: S. pyogenes, M. catarrhalis, S. aureus • Viruses: most frequent cause • Respiratory allergies • Obstruction • Occurs in winter and spring • Symptoms • Purulent nasal discharge • Pain in face, headache

18. URT Infections:Sinusitis • Laboratory diagnosis • Nasal secretions, sputums are not reliable culture sources • Best culture material is from sinus puncture and aspirates • Gram stain, culture media (aerobic and anaerobic) • X-rays and CT scans are reliable indicators of infection

19. URT Infections:Sinusitis • Treatment – since specimens are difficult to obtain, most sinus infections are treated with antibiotics known to be effective against the most common pathogens (empiric treatment) • Complications • Spread of infection to adjacent sites • Anaerobic infection

20. URT Infections:Otitis media • Middle ear infection • Seen mostly in pre-school age children due to crowded conditions in day care and immature eustachian tube • Causes • Bacterial pathogens • S. pneumoniae and H. influenzae • Less common isolates: S. pyogenes, M. catarrhalis, S. aureus

21. URT Infections:Otitis media • Laboratory diagnosis • Specimens not normally cultured • If ordered a gram stain, and aerobic plates inoculated

22. URT Infections:Otitis Media • Treatment – usually empiric • High- dose amoxicillin • Complications • Damage to ear drum and possible hearing loss • Infection spread to adjacent area

23. URT Infections:Epiglottitis • Infection causes the epiglottis to swell which is a serious condition due to potential airway obstruction • Very painful swallowing • Seen in preschool-age children

24. URT Infections:Epiglottitis • Causes • Bacterial pathogen • H. influenzae type B • Laboratory diagnosis • Direct smear and culture with swab • Treatment: vaccine

25. URT Infections:Pertussis • Respiratory illness with severe “whooping” cough • Mostly seen in infants and young children • Highly transmissible • Causes • Bacterial pathogens • Bordetella pertussis • Bordetella parapertussis • Complications: pneumonia, seizures

26. URT Infections:Pertussis • Laboratory diagnosis • Nasopharyngeal swabs( calcium alginate) for FA direct staining and culture • Bordet-Gengou/Regen Lowe selective media • Treatment: vaccine

27. LRT Infections • Bypass the mechanical and nonspecific barriers of URT • Acquired by: • Inhalation of aerosols • Aspiration of oral or gastric contents • Spread of infection

28. LRT Infections:Bronchitis & Bronchiolitis • Causes • Viruses • RSV- respiratory syncytial virus • Bacterial • Mycoplasma pneumoniae • Chlamydia pneumoniae • Bortedella pertussis

29. LRT Infections:Bronchitis & Bronchiolitis • Peaks in winter months • Cough and fever; cough is productive later in illness • X-rays do NOT show radiographic findings • Laboratory diagnosis • Gram stain • Culture

30. LRT:Pneumonia • Causes • Bacterial • Viral • Chemical irritants • Categories • Community-acquired • Nosocomial • Aspiration • Chronic

31. LRT Infections:Community-Acquired Pneumonia • Children • Most common pathogens • Usually due to viral pathogens that cause RTI in winter months • RSV, Parainfluenza virus • Adenovirus, Mycoplasma pneumoniae • Less common • S. pneumoniae, H. influenzae, • Grp B. Strep (neonates)

32. LRT Infections:Community-Acquired Pneumonia • Adults • Most common pathogens • Usually due to bacterial infection • S. pneumoniae • M. pneumoniae (“walking” pneumonia) • Less common pathogens • H. influenzae • Gram negative rods • S. aureus • Legionella sp.

33. Community-Acquired Pneumonia

34. Community-Acquired Pneumonia B A

35. LRT Infections:Nosocomial pneumoniae • Onset occurs 48 hours or longer after hospital admission • Result of compromise of barriers and colonization with pathogens • Sub-category • VAP- ventilator-associated pneumonia • Common pathogens • G N Rods (60%) – Klebsiella, Enterobacter, Escherichia, Serratia, and Pseudomonas sp. • G P Organisms (16%) • Anaerobes, Legionella sp.

36. LRT Infections:Aspiration Pneumonia • Aspiration of oropharyngeal or gastric contents into LRT • Affects both adults and children • Common pathogens – mixed anaerobes and aerobes

37. LRT Infections:Chronic Pneumonia • Chronic Pneumonia • Mycobacterium • Fungi • Immunocompromised • Aspergillus • Cryptococcus • Immunocompetent • Hisptoplasma capsulatum, Blastomyces dermatitidis, and Coccidioides immitis

38. LRT Infections:Empyema • Localized extension of a lung infection between lung and chest wall • Common pathogens • S. aureus • S. pneumoniae • S. pyogenes • G N Rods

39. Influenza A & B • Seen in winter months • Symptoms include fever, fatigue and myalgias • Two types of virus • A: Involved in annual outbreaks or epidemics • B: Outbreaks every 2-4 years • Subtypes undergo antigenic drift • Amino acid substitution allows virus to evade host immunity • Drifts cause outbreaks

40. Influenza Testing:Why is it done? • Identification of influenza strains • Identification of outbreaks • Clinical decision making

41. Influenza:How is Testing Done? • Laboratory Diagnosis • Detection of virus in throat swabs, nasal washes, sputum, and BAL’s • Viral culture • Immunofluorescence, PCR, EIA • Rapid tests • Treatment • Annual vaccine • Uses surveillance data to identify dominant strains

42. Emerging Viral RT Infections • Avian Influenza- H5N1 • “Bird flu” • Acquired from birds • http://www.cdc.gov/flu/avian/ • Severe Acute Respiratory Syndrome- SARS • Pneumonia outbreak caused by Coronavirus in China • Rapidly spread via respiratory secretions or droplets • http://www.cdc.gov/niosh/topics/SARS/

43. Emerging Viral RT Infections • Novel H1N1 Influenza • “swine flu” • Influenza A virus

44. Respiratory Tract Infections in the Immunocompromised • Occurs due to impairment of host defense mechanisms • Chemotherapeutic protocals for malignancy • Organ & bone marrow transplants • Autoimmune & congenital immune disorders • HIV/ AIDS

45. Respiratory Tract Infections in the Immunocompromised • Pulmonary infection most common presenting factor • Common pathogens • S. aureus • S. pneumoniae • H. influenzae • Mycobacterium spp. • Fungus • CMV

46. Normal Flora • Upper Respiratory Tract • Coagulase negative Staphylococcus species • Streptococcus species viridans group • Neisseria species, other than N. gonorrhoeaeor N. meningitidis • Enterococcus and Non-Enterococcus • Diptheroids • Yeast, in rare amounts • Enteric gram negative rods, in rare amounts • Haemophilus species, in rare amounts • Staphylococcus aureus, in rare amounts • Anaerobic organisms • Lower Respiratory Tract • Normally sterile

47. References • Appold, K. (2010, February). A Mid-Winter Check-Up on H1N1. Advance/Laboratory. • http://www.cdc.gov/index.htm • http://www.thefreedictionary.com/epiglottis • Mahon, C. R., Lehman, D. C., & Manuselis, G. (2011). Textbook of Diagnostic Microbiology (4th ed.). Maryland Heights, MO: Saunders. • Penno, K. (2007, October). The Flu and You. ADVANCE for Medical Laboratory Professionals.