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.