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

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.

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

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

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)

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

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

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

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

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

Anatomy of RT Lower RT Trachea Bronchi Lungs, alveoli

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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.

Community-Acquired Pneumonia

Community-Acquired Pneumonia B A

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.

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

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

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

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

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

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

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/

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

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

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

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

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.