Download RT Infections II

Microbiology: Lower Respiratory Tract Infections
BASICS:

Age is a key determinant for pneumonia:
o Children: viruses are primary causes; bacteria cause secondary infections
o Adult: depends on a variety of risk factos

Adult pneumonia may be CA or HA/Nosocomial:
o CA Risks: alcohol abuse, occupational exposure, underlying condition
o HA Risks: immunocompromise and mechanical ventilation

Atypical pneumonias are caused by a pathogen other than S.pneumo: also defined as primary pneumonia that did
NOT involve an initiating viral infection
BACTERIA CAUSING LOWER RESPIRATORY TRACT INFECTIONS:

Streptococcus pneumoniae (Pneumococcus):
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Polysccharide capsule (90 serotypes): primary virulence factor

Prevents complement deposition (C3b)

Prevents phagocytosis by alveolar macrophages

Facilitates evasion of lung surfactant

Abs to capsule confer host immunity
o Pneumolysin: sulfhydryl activated cytolysin (hemolysin)

Damages membranes (related to SLO); subunits oligomerize in cell membrane to form a pore

Cholesterol is cell membrane receptor

Acts on several cell types (pulmonary epithelium, PMNs and monocytes)

Role in Pathognesis:
 Evasion of the immune response and clearance from nasopharynx
 May permit spread to bloodstream from alveoli (bacteremia)
 Cell-bound form activates complement, contributes to inflammation
o Cell Wall TA and Peptidoglycan:

Gram (+) Shock: strong inflammatory response (similar to LPS in G negative); inflammation
elicits fever and lung damage (bloody sputum)
 Activate alternate complement pathway
 Production of IL-1 and TNF alpha
Etiology:
o Exclusively a human pathogen: many asymptomatic carriers (transient carriage also possible)
o Transmission: person to person (droplet spread)
o Recurrent pneumococcal pneumonia: is a presenting manifestation of AIDS
o Most common cause of acute bacterial pneumonia in any age group
Pathogenesis:
o Establishment of Organism in Lower Respiratory Tract:

Aspiration of pneumococci from middle respiratory tract

Compromised cough reflex permits entry into lower respiratory tract
 Common Causes: stroke, alcoholism, drugs, anesthesia, viral infection

Alveolar Abs usually clear pneumococci from lower respiratory tract
o Acute Pneumonia: infection of lung parenchyma

Cough: with productive sputum (purulent material from alveoli)

Inflammatory Response:
 Complement components increase vascular permeability (fluid accumulates)
 Disrupted gas exchange (suffocation)
o Secondary Complications:

Bacteremia: due to inflammatory response and damage to endothelial cells

Acute Purulent Meningitis: bacteremia may lead to meningitis
 Pneumococci adhere to vascular endothelium in CNS and cause cell death
 Pneumococci breach BBB/BCB to enter CSF
Clinical ID:
o Sputum Gram Stain: important diagnostic tool, but issues

Major Problem: contamination with flora from oropharynx
 Sputum is MONOMICROBIC and contains PMNs
 Contaminating saliva is POLYMICROBIC and has squamous epithelial cells
o
o
o
o
Characteristics:

G(+) lancet shaped diplococcic

Alpha-hemolytic

No Lancefield grouping
Biochemical Tests:

Capsular serotyping

Quelling reaction (anti-capsule Abs)

Optochin (P disk) sensitive

Bile soluble (distinguish from viridians strep)
Blood Culture:

Detects bacteremia and confirms sputum sample

Latex agglutination used to detect circulating pneumococcal Abs
Radiology: shows bronchopneumonia that can consolidate to lobar pneumonia

Haemophilus influenzae:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Polysaccharide capsule

Anti-phagocytic

Subject to Ag variation

Hib most virulent (capsular serotype B)
Etiology:
o Normal Flora: commonly in upper respiratory tract

Humans can be carriers of both encapsulated and non-encapsulated (non-typable) strains
o Transmission: person to person (droplet)
o Peak Age Group: 2-5 years old
Pathogenesis:
o Pneumonia: can be caused by both encapsulated and non-encapsulated strains

Encapsulated: similar disease to pneumococcal pneumonia
 Hib pneumonia: increased virulence with a higher incidence of positive blood
cultures (less common than non-typable because lower colonization rates)

Non-Encapsulated: less virulent
 Predisposing Factors of Nontypable Pneumonia:
o Chronic bronchitis
o Emphysema
o Obstructive pulmonary disease
o Acute Epiglotittitis: can also be caused by H.influenzae
Clinical ID:
o Sample Collection:

Sputum and blood cultures (positive in 10-15% of patients; higher with Hib pneumonia)
o Cultures:

G(-) coccobacilli

Fastidious (requires X and V blood factors for growth)

Legionella pneumophilia:
Etiology:
o Parasite of freshwater and soil protozoa: Acanthomoeba, Naeglaria

Found in reservoirs for ameba/bacteria (cooling towers, AC systems, plumbing, hospital
respiratory equipment); routine disinfection of cooling systems used as prevention

Existence inside ameba provides survival advantage
 More resistant to disinfectants
 Can survive over winter inside cyst of ameba
 May be capable of living outside of ameba in biofilms
o Transmission: inhalation (but NO person-to-person spread)
Pathogenesis:
o Acute Pneumonia:

Generally low virulence in humans: most people have Abs because of it ubiquity in nature

Contributors to pathogenesis: nosocomial infections, immunocompromise, smoking,
excessive alcohol use, old age
o
-
Syndromes Caused:

Legionnaire’s Disease: severe pneumonia with a 2-10 day incubation period (high mortality
rate, especially in immunocompromise)

Pontiac Fever: nonpneumonic (no pneumonia) febrile illness with a 1-2 day incubation
period (self-limiting); may be immune response to inhalation of dead/low virulence strains

Disseminated Disease: very rare; usually presents with pneumonia after a long incubation
period (days-weeks)
o Disease Process:

Inhaled organism has tropism for lung alveoli and bronchioles (forms microabsecesses)

Has a surface protein that binds C3 (enhances its own phagocytosis)
 “Coiling” phagocytosis
 Uptake may also occur without opsonization (bacteria-induced phagocytosis)

Survives in monocytes/macrophages as intracellular parasite

Once in the cell, expresses 30 new proteins that:
 Prevent phagolysosome fusion and acidification of the endocytotic vesicle
 Induce accumulation of ribosomes and mitochondria around phagosome
 Facilitate scavenging of iron from transferrin

Multiplication of Legionella is normally inhibited in an activated macrophage
Clinical ID:
o Urine EIA test for soluble Ag
o Normal staining and culture techniques not useful:

Does not Gram stain well:
 May be visualized with simple stains devoid of decolorization or silver impregnation
 Appears thin, pleomorphic G(-) rod with filamentous forms also seen

Growth media:
 Requires amino acids L-cysteine, and ferric ions
 Also needs to be on buffered medium (pH restrictions)
 Slow growth (2-5 days)
o PCR: used by reference lab for identification (most human infections caused by Philadelphia strain)
o Microscopic exam of tissue required: since Gram stain not useful

Legionella should be suspected in cases of severe progressive pneumonia with no known
etiologic agent

Organism is rarely found in sputum
 Need to collect lung aspirate, transtracheal aspirate, or lung biopsy

Identification based on antigenic structure and DNA homology tests
 Indirect immunofluorescence of serum (rise in Ab titer to Legionella)
 Difficult to assess due to high exposure rates in population
o Serological Diagnosis (Summary Chart): immunofluorescence

Acinetobacter spp.
Etiology:
o Environment: lives in soil, water and on the skin of healthy people (especially healthcare workers); can
survive on dry surfaces for up to 20 days
o Antibiotic resistant: innately resistant to man classes of antibiotics
o Frequent cause of nosocomial infections
Pathogenesis: causes pneumonia and serious blood/wound infections in immunocompromised patients
Clinical ID: G(-) coccobacillus (resembles Haemophilus)

Mycoplasma pneumoniae:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Adhesin: binds sialic acid containing glycolupids or glycoproteins on bronchial epithelial cells
o Hydrogen peroxide: damages tissue
o Superoxide: damages tissue
o Autoantibodies may be generated during infection: homology between host cell and mycoplasma
membrane glycolipids; reactive to lymphocytes, smooth muscle, brain, lung tissue
Etiology:
o Common age group: teenagers
o
-
-
Transmission: droplet spread (very low infectious dose); common in closed communities

Organism shed both before and long after onset of symptoms
Pathogenesis:
o Walking Pneumonia: less severe than other bacterial pneumonias
o Disease Process:

Colonization of bronchial epithelium interferes with ciliary action

Inflammation and exudate are the primary contributors to pathogenesis
o Second Infection Site: non-purulent otitis media
o Sequelae:

Immunopathology due to cross-reactive Abs

Possible complications:
 Hemolytic anemia
 Aseptic meningitis
 Pancreatitis
Clinical ID:
o Culture:

No organism in sputum

Organism grows too slow to culture (require cholesterol for growth)

No Gram stain (no cell wall)

Difficult to detect microscopically
o Structure:

Lack cell wall (no Gram stain or treatment with B-lactams); bound by triple membrane
containing sterols
o Serodiagnosis: can be used to detect circulating Ags or complement-fixing Ab

Ab to M.pneumoniae is diagnostic (disease has a long IP so patient presents with high titers)
o DNA hybdrization or PCR: also being developed for detection
o Serological Diagnosis (Summary Chart): complement fixation or IgM titers (ELISA)

Chlamydia pneumoniae:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Life Cycle:

Elementary Body: infectious stage that carries adhesin for receptor binding (attaches and
induces endocytosis into columnar epithelial cells)

Reticulate Body: replicates once in cell; metabolically active (uses host ATP)
 Eventually reorganize and release infectious EB from the cell
Etiology:
o Humans are only host: ~50% of adults seropositive, but reinfection still occurs
o Causes:

Pharyngitis

Bronchitis

Atypical Pneumonia (Walking Pneumonia): in school children and young adults
Pathogenesis:
o Clinical picture resembles M.pneumoniae
Clinical ID:
o Morphology/Growth:

G(-) outer membrane, but no cell wall (cannot Gram stain or treat with B-lactams)

Coccobacillus

Inclusions are glycogen (-)
o Detection:

Direct immunofluorescent staining of outer membrane proteins

DNA or RNA detection using probes and PCR

Inclusions do not contain glycogen
o Serological Diagnosis (Summary Chart): immunofluorescence or ELISA

Staphylococcus aureus:
Etiology/Pathogenesis:
o Acute pneumonia: secondary to some other insult to the lung (ie. influenza)
o
o
-

Empyema: purulent infection of pleural space (gains access by contiguous spread from infected lung)
Lung Abscess: complication of acute or chronic pneumonia (may be caused by aspiration of oral or
gastric contents)
Clinical ID:
o Samples: sputum, lung abscess aspirate, blood culture (disseminated infection)

G(+) cocci in clusters

Catalase (+)

Coagulase (+)
o Antibiotic susceptibilities required
o Radiology: used to diagnose lung absecesses
Mycobacterium tuberculosis:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Mycolic Acid (Cord Factor): long chain fatty acid

Resistance to drying and disinfectants

Promotes hypersensitivity granuloma

Promotes inflammatory response (TNF) and damage to lung tissue
o Lipoarabinomamman: cell wall glycolipid

Suppresses T cell proliferation

Prevents macrophage activation
o Sulfolipids (Polyanionic Lipids): inhibits macrophage phagosome-lysosome fusion
o Catalase: degrades hydrogen peroxide
o Ammonia Production: prevents acidification in phagolysosome
Etiology:
o Pathogenic Mycobacteria spp.:

M.tuberculosis: primary cause of TB

M.bovis: from infected milk; has been eradicated through pasteurization (rare cause of TB)

M.africanum: causes TB in Africa

M.avium complex (avium and intracellulare): opportunistic pathogens causing TB-like
disease; cause disseminated disease in AIDS patients

M.leprae: causes leprosy (degenerative disease of skin and nerves; rare in US)
o US Infection Points:

Incidence is significant amongst AIDS patients and immigrants

Outbreaks often occur in closed communities (nursing homes, shelters, prisons)

~1% are multi-drug resistant
o Types of TB:

Primary Infection: unapparent in 95% of cases
 Gohn (Primary) Complex: lung granuloma (due to DTH reaction) and enlarged LNs

Progressive Primary TB: occurs in ~5% of cases of primary TB (infection does not resolve)
 Disseminates: bloodborne or miliary TB

Reactivation TB: low percentage of cases (risk increases with age, alcoholism, diabetes,
decreased immune function)
 Common Site: apex of lung (highest oxygen tension- aerobic organism)

Disseminated TB: either due to progressive primary TB or reactivation TB
 Occurs through lymph or erosion of necrotic tubercle in lung
 Results in infection of liver, spleen, kidney, bone or meninges
o Tuberculin Skin Test:

Inject a purified protein derivative (PPD): autolyzed bacteria containing protein, lipid,
polysaccharide and nucleic acid injected under the skin and reaction read in 48-72 hours

DTH Reaction to PPD: local induration and erythema is positive reaction (seen 6 weeks after
primary infection)

Positive DTH Reaction Significance:
 Coincides with tubercle (hypersensitivity granuloma) formation
 Indicates exposure (to M.tuberculosis or cross-reactive species), but not necessarily
active disease (only 5% of skin test positive cases progress to active disease)
 BCG vaccination renders test invalid (will always be positive)

Negative DTH Reaction Significance:
 No exposure to organisms



-
-

In prehypersensitivity stage (within 6 weeks of exposure)
Loss of sensitivity (disappearance of Ag from primary complex)
Anergy due to immunocompromise (poor prognosis if test was previously positive)
Pathogenesis:
o Transmission: aerosol inhalation, enters the lungs (primary focus)
o Engulfed by alveolar macrophages: carried to LN
o Resists innate defenses: PMNs, inactivated macrophages, lysozyme
o Humoral response is weak (IgM): no effective complement-mediated killing
o Cell-Mediated response:

Helper and cytotoxic T cells activate alveolar macrophages to ingest organisms

Activated macrophages prevent replication of organism; if there is an inadequate response,
the organism can replicate in the macrophage phagosome

Slow replication (part of pathogenesis)

Cytokine response to organism causes systemic TB symptoms (weight loss, fever)
o Containment of pathogen in tubercle (microscopic granuloma):

Made of multinucleated giant cells, activated macrophages and lymphocytes

Can become necrotic and caseous (cheesy)

Fibroblasts and collagen accumulate at lesion

Tissue destruction causes chronic productive cough and blood-stained sputum
o Potential fates of tubercle:

Become fibrotic/calcified with dead bacteria (shows up on chest X-ray)

Can remain dormant for years (source of reactivation)

Necrotic tubercles may erode into blood vessels (causing disseminated/miliary TB)
o DTH reaction confers long-lived memory and protection from re-infection:

Loss of prior DTH is a bad prognostic indication of rapidly progressing disease (see above)

Basis of tuberculin skin test
Clinical ID:
o Specimen collection: sputum, biopsy (sometimes), blood (if miliary TB)
o Staining: provides diagnosis BEFORE bacteria grows (slow growing)

Acid Fast Stain (Ziehl-Neelsen)

Chemotherapy monitored by periodic examination for AFB counts
o Cultivation:

Very slow growth: decontamination of sputum (4% NaOH) to inhibit faster growing bacteria;
appearance of visible colonies may take 2 weeks (24 hour doubling time)

Special media: Lownstein Jensen (LJ) agar or Middlebrook agar
o Rapid ID:

rRNA and DNA probes

PCR to detect common insertion sequence

Growth in 14C-palmitic acid (catabolized to CO2 which is therefore labeled and measured)
o Drug susceptibilities: done in reference labs
o Extensively drug-resistance TB (XDR TB): rare type of multidrug-resistant TB (MDR TB)

Resistant to first line and second line drugs
Pseudomonas aeruginosa:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Adhesins:

Protein pilus adhesin (binding to asialoGM1)

Non-pilus adhesin (binding to mucus)
o Alginate: polysaccharide capsule for biofilm formation

Permits colonization of lung and evasion of the host immune response

Regulated in response to environmental signals
o Elastase: protease that degrades lung elastin (tissue damage)
o Exotoxin A: similar structure/activity to diphtheria toxin (ADP ribosylation of elongation factor 2)
o Multiple resistance to antimicrobials and disinfectants:

Mutation leads to loss of porin and decreased entry of antimicrobials

Alteration of LPS to form that does not bind antibiotics
-
-
Etiology: common environmental isolate that can cause nosocomial infections (waterborne)
Pathogenesis:
o Conditions causes:

Acute pneumonia

Empyema

Abscesses
o Infections in Cystic Fibrosis:

CF Lung: increased mucus secretion due to defect in CFTR (causes decreased sialylation of
surface glycolipids)

Increased susceptibility to infection by Pseudomonas: because of increase in asialoGM1

Resistance to phagocytosis: Pseudomonas infecting CF lung phenotypically switch to mucoid
form
 Alignate gel + excess mucus in CF = physical barrier to phagocytosis
 In addition, anti-pseudomonas Abs may be defective in CF patients

Resistance to antimicrobials: alginate gel + excess mucus in CF = physical barrier to drugs
 Primary infection in younger age group by S.aureus; colonizing Pseudomonas
strains develop resistance to anti-staphylococcal drugs used to treat it

Lung tissue damage: persistent colonization and elastase release by pathogen results in
tissue damage and inflammation (recruited PMNs also release protease that contributes)

Infection rarely spreads beyond lungs in patients with CF
Clinical ID:
o G(-) rods in sputum
o Aerobic (OF Dextrose tubes demonstrate aerobic growth)
o Oxidase (+)
FUNGI CAUSING LOWER RESPIRATORY TRACT INFECTIONS:

Aspergillus spp.:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o NO DIMORPHIC GROWTH PHASE
o Infectious conidia: germinate to mold form
o Hyphae: bind fibrinogen and complement components
o (Alflatoxin: produced by A.flavus growing on peanuts- potent carcinogen)
Etiology:
o Basics: common environmental mold that is an emerging etiologic agent of nosocomial pneumonia
o Predisposing Factors:

Asthma

Chronic bronchitis

TB

Immunosuppression (opportunistic infection)
o Requirements for infection:

Frequent inhalation of infectious conidia

Inhalation of fungal elements (spores) or colonization (allergic aspergillosis/Farmer’s lung)
o May colonize respiratory tract:

May lead to tissue invasion by hypae

Principal host defense is pulmonary PMN killing of invasive hyphae
Pathogenesis:
o Infections Cause:

Acute Pneumonia

Lung Abscesses
Clinical ID:
o Lung aspiration, bronchial lavage, or biopsy:

Mold form: grows rapidly and is easily identified

Structure: typical septate hyphae with conidia (spore)
o Radiology: visible fungus ball can form in pulmonary cavity

Histoplasma capsulatum:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Dimporphic Growth Phase: mold in environment that produces infectious conidia; pathogenic yeast in
tissue
Etiology:
o Environmental source: associated with bird and bat droppings
o Transmission: inhalation of conidia (exposure is common, but disease is rare); no person to person
transmission
Pathogenesis:
o Primary infection site: pulmonary
o Causes a chronic pneumonia: grows inside macrophages and produces a granuloma similar to TB; may
disseminate to infect organs of the reticuloendothelial system
o Immune response: T cell activation of macrophages to prevent intracellular growth (long term
immunity to re-infection)
Clinical ID:
o Samples:

Radiograph: granulomas resembling TB

Blood or biopsy required: sputum not useful

If disseminated infection: biopsy of liver, spleen, and LN

Isolation of yeast cells: in bone marrow
o Cultural isolation/histological identification (firm diagnosis):

Grows slowly on BAP and Sabouraud agar

Fungus appears dimorphic (yeast and mold forms)

Mold form produces tuberculate macroconidia (finger-like projections carrying spores)
o Seroological Tests:

There is widespread exposure and cross-reactivity to other pathogens

DTH skin reaction to mycelial Ag used for epidemiological analyses

Complement fixing Ab test for yeast and mycelial Ags predicts prognosis
o Immunodiffusion test
o DNA probe

Blastomyces dermatitidis:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Similar to Histoplasma: dimorphic growth phase
o Difference: yeast cells exist extracellularly, not in macrophages
Etiology:
o Geographic distribution: similar to Histoplasma (middle and SE US)
o More common in males: probably due to occupational exposure
Pathogenesis:
o Conidia inhaled from soil: results in pulmonary infection with yeast cells
o PMN infiltration: and formation of granuloma, leading to chronic pneumonia

May mimic pulmonary tumor or TB
o May disseminate:

Chronic infection of skin and bone most common
 May even disseminate in subclinical infections
 Necrosis and fibrosis at infected area can lead to disfigurement

Dissemination to UG tract also possible
o Immune response:

T cell mediated response and cytokine-activated macrophages

Large yeast cells can resist oxidative and non-oxidative killing mechanisms
Clinical ID:
o Biopsy:

Large yeast cells with broad buds

Grows slowly on mycological media (~4 weeks)
o Serodiagnosis: hampered by cross-reactivity with other fungi
o No skin test

Coccidioides immitis:
Virulence Factors (Relevant to Lower Respiratory Tract Infections):
o Dimorphic growth phase

Mold: produces infectious arthroconidia

Spherule: invasive tissue form that produces reproductive endospores
Etiology:
o Geographical: Southwestern US (Valley Fever)
Pathogenesis:
o Usually mild disease: Valley fever is acute pulmonary infection with cough, chest pain, and myalgia
o May become chronic pneumonia: occurs with decreased T cell response (AIDS, chemo)
o May disseminate: to skin, bone, joints and meninges (very rare)
o Disease Process:

Arthroconidia inhaled and converts to spherule

PMNs and macrophages respond
 Arthroconidia phagocytosed
 Spherule grows too large for phagocytosis

Release of endospores from spherules induces a strong inflammatory response
 Endospores phagocytosed
 Intracellular forms can prevent phagolysosome fusion and survive

Inflammatory response results in granuloma formation (15% cavitate)
o Immune Response:

Cell mediated (PMN, T Cell) immunity to arhtoconidia or endospores

Chronic or progressive infection can result in T cell anergy
 Spherules burst and pathogen load is so heavy it induces anergy)
Clinical ID:
o Best: detection of characteristic spherules in histologic sections
o Detection of complement fixing Abs indicates prognosis:

Low titers: primary pulmonary disease with good CMI response

High titers: disseminated disease and T cell anergy
o Skin test detects DTH, but is of limited value: due to common exposure

Positive: 1-4 weeks after onset and positive for life (indicates immunity to reinfection)

Negative: may be performing too soon after exposure or disease has progressed to anergy
o Immunodiffusion
o DNA probe

Pneumocystis (carinii) jirovecii:
Etiology:
o Very common infection of generally low virulence
Pathogenesis:
o Causes PCP in immunocompromised hosts:

Premature infants

Patients undergoing chemotherapy

Organ transplant patients on immunosuppressants

AIDS (primary predisposing factor)
o Presenting Manifestation of AIDS:

Most common opportunistic infection in AIDS

Prophylaxis and HAART has reduced incidence

Occurs due to loss of T cell function (risk increases when T cell count below 200)
o Acute Pneumonia/Lethal Pneumonitis:

Progressive, diffuse pneumonia after:
 Corticosteroid use and leukemia
 AIDS onset (insidious onset; lesions outside of lung may also be seen)

Concurrent infections common (bacterial, fungal, parasitic, viral)

Alveoli become filled with desquamated cells, organisms, monocytes and fluid (foamy
appearance)
Clinical ID:
o Classification:

Classified as a protozoan based on morphology and drug susceptibility
o
o
o
o

Classified as a fungus based on rRNA sequence homology with other fungi
Sample Collection:

Sputum induced with hypertonic saline (only usefully in AIDS patients because of larger
number of organisms)

Brochoalveolar lavage and transbronchial biopsies more helpful
Histological (Definitive):

Extracellular cysts and trophs seen

Latent infections characterized by scattered cysts in contact with alveolar cells
PCR
Based on Symptoms:

Mild or low grade fever

Typical signs of pneumonia absent (cough is non-productive)

Progressive dyspnea and tachypnea

Cyanosis and hypoxia

Death by asphyxiation