Upper and Lower RT Infections MLAB 2434 – Microbiology Keri Brophy-Martinez
Jan 14, 2016
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 specimenPatient’s ageImmunologic status of hostClinical 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 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)NasopharynxOropharynxEpiglottisLarynx
Anatomy of RT
Lower RTTracheaBronchiLungs, 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. gonorrhoeaeC. 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)
ComplicationsSpread of infection to adjacent
sitesAnaerobic 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
CausesBacterial pathogens
• S. pneumoniae and H. influenzae• Less common isolates: S. pyogenes, M.
catarrhalis, S. aureus
URT Infections:Otitis media Laboratory diagnosis
Specimens not normally culturedIf 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 diagnosisDirect 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 aerosolsAspiration of oral or gastric
contentsSpread 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 stainCulture
LRT:Pneumonia Causes
BacterialViralChemical irritants
CategoriesCommunity-acquiredNosocomialAspirationChronic
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 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
MycobacteriumFungi
•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 pathogensS. aureusS. pneumoniaeS. pyogenesG 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 mechanismsChemotherapeutic protocals for
malignancyOrgan & bone marrow transplantsAutoimmune & congenital
immune disordersHIV/ 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 organismso 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.