Upper and Lower RT Infections

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Upper and Lower RT Infections

• MLAB 2434 Microbiology
• Keri Brophy-Martinez

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ConceptsNormal 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.

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ConceptsNormal 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

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ConceptsNormal 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

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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)

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Concepts

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

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Concepts

• Always consider the following
• Source of specimen
• Patients age
• Immunologic status of host
• Clinical setting of the patient

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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

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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

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Anatomy of RT

• Upper RT
• Nasal cavity (sinuses)
• Nasopharynx
• Oropharynx
• Epiglottis
• Larynx

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Anatomy of RT

• Lower RT
• Trachea
• Bronchi
• Lungs, alveoli

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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

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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

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URT InfectionsPharyngitis

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

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URT InfectionsPharyngitis

• 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

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URT InfectionsSinusitis

• 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

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URT InfectionsSinusitis

• 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

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URT InfectionsSinusitis

• 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

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URT InfectionsOtitis 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

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URT InfectionsOtitis media

• Laboratory diagnosis
• Specimens not normally cultured
• If ordered a gram stain, and aerobic plates
  inoculated

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URT InfectionsOtitis Media

• Treatment usually empiric
• High- dose amoxicillin
• Complications
• Damage to ear drum and possible hearing loss
• Infection spread to adjacent area

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URT InfectionsEpiglottitis

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

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URT InfectionsEpiglottitis

• Causes
• Bacterial pathogen
• H. influenzae type B
• Laboratory diagnosis
• Direct smear and culture with swab
• Treatment vaccine

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URT InfectionsPertussis

• 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

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URT InfectionsPertussis

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

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LRT Infections

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

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LRT InfectionsBronchitis Bronchiolitis

• Causes
• Viruses
• RSV- respiratory syncytial virus
• Bacterial
• Mycoplasma pneumoniae
• Chlamydia pneumoniae
• Bortedella pertussis

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LRT InfectionsBronchitis 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

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LRTPneumonia

• Causes
• Bacterial
• Viral
• Chemical irritants
• Categories
• Community-acquired
• Nosocomial
• Aspiration
• Chronic

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LRT InfectionsCommunity-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)

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LRT InfectionsCommunity-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.

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Community-Acquired Pneumonia
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Community-Acquired Pneumonia
B
A
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LRT InfectionsNosocomial 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.

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LRT InfectionsAspiration Pneumonia

• Aspiration of oropharyngeal or gastric contents
  into LRT
• Affects both adults and children
• Common pathogens mixed anaerobes and aerobes

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LRT InfectionsChronic Pneumonia

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

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LRT InfectionsEmpyema

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

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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

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Influenza TestingWhy is it done?

• Identification of influenza strains
• Identification of outbreaks
• Clinical decision making

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InfluenzaHow is Testing Done?

• Laboratory Diagnosis
• Detection of virus in throat swabs, nasal washes,
  sputum, and BALs
• Viral culture
• Immunofluorescence, PCR, EIA
• Rapid tests
• Treatment
• Annual vaccine
• Uses surveillance data to identify dominant
  strains

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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/

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Emerging Viral RT Infections

• Novel H1N1 Influenza
• swine flu
• Influenza A virus

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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

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Respiratory Tract Infections in the
Immunocompromised

• Pulmonary infection most common presenting factor
• Common pathogens
• S. aureus
• S. pneumoniae
• H. influenzae
• Mycobacterium spp.
• Fungus
• CMV

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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

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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.