Upper and Lower RT
Infections
MLAB 2434 – Microbiology
Keri Brophy-Martinez
Concepts:
Normal Respiratory Flora
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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
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
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
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Age as a risk factor

infants and elderly more susceptible

(e.g., epiglottitis)
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
Concepts

Seasonal and Community Trends in
Infections
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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
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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

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
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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
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
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
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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
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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
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Treatment – usually empiric
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High- dose amoxicillin
Complications
Damage to ear drum and possible
hearing loss
 Infection spread to adjacent area

URT Infections:
Epiglottitis
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
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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
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Causes

Bacterial pathogen
• H. influenzae type B

Laboratory diagnosis
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Direct smear and culture with swab
Treatment: vaccine
URT Infections:
Pertussis
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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
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
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
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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
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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
A
B
LRT Infections:
Nosocomial pneumoniae
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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

Chronic Pneumonia
 Mycobacterium
 Fungi
• Immunocompromised
• Aspergillus
• Cryptococcus
• Immunocompetent
• Hisptoplasma capsulatum,
Blastomyces dermatitidis, and
Coccidioides immitis
LRT Infections:
Empyema
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Localized extension of a lung infection
between lung and chest wall
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Common pathogens
S. aureus
 S. pneumoniae
 S. pyogenes
 G N Rods
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Influenza A & B
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Seen in winter months
Symptoms include fever, fatigue and
myalgias
Two types of virus
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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?
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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
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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
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Pulmonary infection most common
presenting factor
Common pathogens
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S. aureus
S. pneumoniae
H. influenzae
Mycobacterium spp.
Fungus
CMV
Normal Flora

o
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
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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.