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
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 PneumoniaB 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
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
Severe Acute Respiratory Syndrome- SARS
Pneumonia outbreak caused by Coronavirus in China
Rapidly spread via respiratory secretions or droplets

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. gonorrhoeae or 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.
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.