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Microbial Aspect of Respiratory

The Spectrum of Resident Flora of Respiratory Tract
Types of Resident Microorganisms
Common Residents Oral streptococci
Neisseria spp., Branhamella or Moraxella
Corynebacteria spp
Anaerobic cocci (Veilonella)
Fusiform bacteri
Candida albicans
Streptococcus mutans
Haemophillus influenza
Occasional Residents Streptococcus pyogenes
Streptococcus pneumoniae
Neisseria meningitidis
Uncommon Residents Corynebacterium diphteriae
Klebsiella pneumoniae
Pseudomonas aeruginosa
Escherichia coli
Candida albicans
Residents in latent state in Pneumocystis jirovecii
tissues Mycobacterium tuberculosis
Cytomegalovirus (CMV)
Herpes simplex virus
Epstein-Barr virus
Major microbial Flora of the Upper Respiratory Tract
Organisms Oral cavity Nasopharynx Epiglottis, Paranasal
, Tonsil larynx sinus, Middle
Gram-positive cocci
Coagulase-negative staphylococci NF NF UP
Staphylococcus aureus CC UP UP
Pneumococci (S. pneumoniae) CC UP CP
Group A streptococci CC,CP UP CP
Groups C and G streptococci NF,CC,UP
Other streptococci NF NF,CC

Gram-positive bacilli
Diphteroids NF NF
Corynebacterium diphtheriae UC,UP UP
Arcanobacterium haemoyticum

Gram-negative coccobacilli
Haemophilus influenzae CC,UP CP CP
Other Haemophilus species NF NF

Gram-negative cocci
Neisseria meningitidis CC,UP
Neisseria gonorrhoeae UC,UP
Other neisseria spesies NF NF UP
Moraxella catarrhalis NF NF CP
Major microbial Flora of the Upper Respiratory Tract
Organisms Oral cavity Nasopharynx, Epiglottis, Paranasal
Tonsil larynx sinus, Middle
Gram-positive anaerobes
Anaerobic streptococci NF NF UP
Anaerobic diphtheroids NF NF
Actinomyces spesies NF,UP
Gram-negative bacilli
Enterobacteriaceae UC UC UP
Pseudomonas aeruginosa UC UC
Gram-negative anaerobes
Prevotella spesies NF,UP UP
Fusobacterium spesies NF,UP UP
Veilonella spesies NF
Mycobacterium tuberculosis UP UP UP UP
Borrelia spesies NF,UP NF,UP
Treponema pallidum UP UP
Candida albicans NF NF,UP
Aspergillus species UP
Mucor species UP
Major microbial Flora of the Upper Respiratory Tract
Organisms Oral cavity Nasopharynx, Epiglottis, Paranasal
Tonsil larynx sinus, Middle
Chlamydophila (Chlamydia)
Chlamydophila pneumoniae UP
Mycoplasma pneumoniae UC,UP UP UC,UP
Epstein-Barr virus CP,CC
Herpes simplex virus CC, CP UP
Influenza virus CP CP
Parainfluenza virus CP CP
Adenovirus CP,UC CP
Coxsackievirus CP CP
Rhinovirus CP CP,UC CP
Respiratory syncytial virus CP CP
Human metapenumovirus CP CP
Figure 1. A diagram showing common causes of infection and the resulting
diseases in the respiratory tract
Types of Respiratory Tract Infection
Types Microorganisms Consequences
Restricted to surface Common cold virus Local spread
Influenza virus Local (mucosal) defenses important
Streptococci in throat Adaptive (immune) response sometimes too late to
Chlamydia be important in recovery
Diphteria Short incubation period (days)
Candida albicans (thrush)

Spread through body Measles, mumps, rubella Little or no lesion at entry site
EBV, CMV Microbe spreads through body , returns to surface
Chlamydophila psittaci for final multiplication and shedding, e.g salivary
Q fever gland (mumps, EBV, CMV), respiratory tract
cryptococcosis (measles)
Adaptive immune response important in recovery
Longer incubation period (weeks)
Respiratory Invaders – Professional or Secondary
Type Requirement Examples
Professional Adhesion to normal mucosa (in Respiratory virus (influenza , rhinovirus)
invaders (infect spite of mucociliary system) Streptococcus pyogenes (throat)
healthy respiratory Streptococcus pneumoniae
tract) Mycoplasma pneumoniae
Chlamydia (psittacosis, chlamydial conjunctivitis
and pneumoniae, trachoma)
Ability to interfere with cilia Bordetella pertussis, M. pneumoniae, Strept.
pneumoniae (pneumolysin)
Ability to resist destruction in Corynebacterium diphteriae (toxin), Strept.
alveolar macrophage pneumoniae (pneumolysin)
Secondary invaders Initiation infection and damaged Staphylococcus aureus, Streptococcus pneumoniae,
(infect when host by respiratory virus (e.g pneumonia complicating influenza
defenses are influenza virus)
impaired) Local defenses impaired (e.g Staphylococcus aureus, Pseudomonas aeruginosa
cystic fibrosis),
Chronic bronchitis, local foreign H. influenzae, Streptococcus pneumoniae,
body or tumor depressed Pneumocystis jiroveci, CMV, M. tuberculosis
immune response (e.g AIDS,
neoplastic dusease)
Depressed resistance (e.g
Streptococcus pneumoniae, Staphylococcus aureus,
elderly, alcoholisms, renal or
hepatic disease)
TABEL 1. Common Agents of Respiratory Infections
Clinical Illness Bacteria Viruses Fungi Other Comment

Upper Respiratory Airway

Common cold Rare Rhinovirus Rare Rare  Common cold is caused by a multitude of
(Rhinitis, coryza) Coronavirus organisms
Parainfluenza vi.  About 90% of cases are due to viruses
RSV  Most common cause is Rhinovirus
Influenza vi.

Acute Rhinosinusitis S.pneumonia Rhinovirus Rare Rare  Virus are the most frequent cause of
H.influenzae Parainfluenza vi. acute rhinosinusitis
M.catarrhalis Adenovirus  Only ± 2% of adult and 10% of children of
Influenza vi. viral sinusitis is complicated by acute
bacterial sinusitis (ABS)
 Community-acquired ABS: S. pneumoniae
and ntHI.
 Hospital-acquired ABS : more likely gram-
 ABS usually self limited (75 % resolving
without treatment).
 However, untreated ABS are at risk of
intracranial and orbital complications as
well as chronic sinus disease.
 Maximum medicamentosa therapy: a.b +
sinus irigation + topical steroid
TABEL 1. Common Agents of Respiratory Infections
Clinical Bacteria Viruses Fungi Other Comment
Upper Respiratory Airway
Chronic Anaerobic strept . Aspergillus Certain  Usually polymicrobial infection
Rhinosinusitis Prevotella spp. Mucor parasite  Anaerobic organisms account 51%
(CRS) S. aureus Rhizopus spp s
Candida  S.aureus has been cultured as many as
Enteric Gram-
negative bacilli.
Pseudomonas  Aspergillus, Mucor, Rhizopus spp produce
Alternaria invasive CRS
Nocardia  Hypersensitivity reaction to airborne
Legionella fungi contribute to some case CRS
Atypical  In immunocompromized : Candida,
mycobacteria. Alternaria, Nocardia, Legionella, and
atypical mycobact, also parasites.

Otitis Externa S.epidermidis Rare Rare  Skin flora are major e/ agents
(OE) S.aureus  A diffuse acute OE (Swimmer's ear) may
Diphtheroids be caused by P. aeruginosa, along with
P.acnes other skin flora
P.aeruginosa  Malignant OE (severe necrotizing) usually
caused by P. aeruginosa.
TABEL 1. Common Agents of Respiratory Infections

Clinical Bacteria Viruses Fung Comment

Illness i
Upper Respiratory Airway
Otitis Media S. pneumoniae Respiratory Rare  Usually polymicrobial infection.
H.influenzae viruses  M. pneumoniae (rare) has been reported to cause
M.catarrhalis hemorrhagic bullous myringitis.
 Respiratory viruses may play a role but this remains
Pharyngitis S.pyogenes See table 4 C.albi  90% in adults and 60–75% of sore throats in children
(Sore throat) Group C and G cans are caused by viruses.
and Tonsilitis streptococci  GAS-pharyngitis accounts for 25-40% cases in
N.Gonorrhoea children and 10-25% in adults.
Meningococci  Antibiotic is justified only in patient with GAS-
H.influenzae pharyngitis and have not proved effective in
C.diphteriae management of non-streptococcal pharyngitis.
 Delaying th/of strep throat, increases the chances of
M.hominis (type 1)
potentially severe post-streptococcal complications.,
Mixed anaerobs included ARF, AGN, and local or systemic septic.
 Post streptococcal AGN is rarely the consequence of
GAS-pharyngitis. No evidence that a.b might prevent
the occurrence of AGN.
 The efficacy of a.b in cases of GAS-pharyngitis is rapid
disappearance of symptoms, the eradication or
decreased dissemination of GAS, and the prevention
of ARF demonstrated by penicillin G.
TABEL 1. Common Agents of Respiratory Infections
Clinical Bacteria Viruses Fung Other Comment
Illness i
Respiratory Airway
Epiglotitis H.influenzae type b Rare Rare Rare  H.influenzae type b is the most common
(Hib) cause, particularly in children age 2 to 5.
 Some cases of epiglotitis in adults may be of
viral origin
 A viral URTI may precede infection with H
influenzae in episodes of epiglottitis
 Once H influenzae type b infection starts,
bacteremia is usually present.
 H.influenzae type b is isolated from the
blood or epiglottis therefore a blood culture
should always be performed.
Tracheolaryng H.influenzae type b Parainfluenza Rare Rare  Parainfluenza v. are most common causes.
itis (Croup) S.pyogenes v  More serious bacterial infections.
C.diphtheriae Adenoviruses  A history of preceding cold-like symptoms
M.pneumoniae Influenza v is typical of laryngotracheitis.
Enteroviruses  Sputum or pharyngeal swabs cultures may
be used to isolate pathogens.
 Serologic studies to various viruses are
helpful for retrospective diagnosis.
Parainfluenza Virus
• Parainfluenza viruses are important viral
pathogens causing upper and lower
respiratory infections in adults and children.
• These viruses are a member of family
Paramyxoviridae which include:Parainfluenza
virus (PIV types 1,2,3,4), Mumps virus, Sendai
virus [mice], Morbillivirus (Measles virus), and
Pneumovirus (Respiratory Syncytial Virus/RSV)
The Cell Structure and Viral
• Relatively large viruses of about 150-300 nm
in diameter
• A spherical or pleomorphic shape
• RNA is negative sense, unsegmented and
single stranded (ss)
• nucleocapsid core has helical RNA tightly
associated with Nucleoprotein (NP), and also
Phosphoprotein (P) and Large protein (L).
These are enveloped viruses with a host-derived lipid-
bilayer, associated with two virus-specific

• Hemagglutinin-Neuraminidase (HN
• Fusion protein (F). It promotes the fusion of host and
viral cell membranes which is an initial step in
• Matrix (M) protein, located just within the envelope,
is hydrophobic.
Viral Replication
• RSV is a member of family Paramyxoviridae,
genus Pneumovirus. Infection of cells results in
syncytium formation.
The Cell Structure

These are spherical or pleomorphic enveloped

viruses (100-350 nm) with single-stranded,
negative sense linear RNA. The envelope has 2
• F - fusion protein, is important for fusion of
viral particles to target cells and fusing
infected cells to neighboring cells to form
• G - which is highly glycosylated, is important
for viral attachment to host cells
Pathogenesis and Viral Replication

• Virus attaches (via G protein) to cells of

respiratory tract. Infected cells undergo
necrosis, also syncytia form through fusion.
Cell to cell transfer of virus leads to spread
from upper to lower respiratory tract. Smaller
airways (bronchioles) become plugged with
debris and mucin; bronchoconstriction also
occurs. The host immune response also
induces some of the pathological changes
• Haemophilus influenzae is a small, nonmotile
Gram-negative bacterium in the family
• Gram-negative coccobacilli
• It is present in the nasopharynx of
approximately 75 percent of healthy children
and adult
Virulence Factors and Clinical
Relevance of H. influenza
• H. influenzae causes ear infections (otitis
media) and sinusitis in children and is
associated with respiratory tract infections
(pneumonia) in infants, children and adults
• In infants and young children (under 5 years of
age), H. influenzae type b (Hib) causes
bacteremia and acute bacterial meningitis
• Occasionally, it causes epiglottitis (obstructive
laryngitis), cellulitis, osteomyelitis, and joint