Professional Documents
Culture Documents
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Respiratory Hypertension Gastrointestinal Diabetes Depression
Infections Disorders
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From the Host perspective ……………
9
From the agents perspective………………..
• Microbes that engage in mutual or commensal associations = normal
(resident) flora, indigenous flora, microbiota
• Pathogenicity - the ability of a microbe to cause disease
– True pathogens – capable of causing disease in healthy persons
with normal immune defenses (Influenza virus, plague bacillus,
malarial protozoan, N. gonorrhoeae, S. typhi, GAS, V. cholera,
pathogenic E.coli)
– Opportunistic pathogens – cause disease when the host’s
defenses are compromised or when they grow in part of the body
that is not natural to them (Pseudomonas sp., S.aureus, Candida
albicans, most of normal flora)
• The Virulence factor - structure or characteristic that contributes to
the ability of a microbe to cause disease
• Severity of the disease depends on the virulence factor
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The Spectrum of Resident Flora of Respiratory Tract
Types of Resident Microorganisms
Common Residents Oral streptococci*
Neisseria spp., Branhamella or Moraxella
Corynebacteria spp*
Bacteroides
Anaerobic cocci (Veilonella)
Fusiform bacteria**
Candida albicans**
Streptococcus mutans
Haemophillus influenza
Occasional Residents Streptococcus pyogenes
Streptococcus pneumoniae
Neisseria meningitidis
Uncommon Residents Corynebacterium diphteriae
Klebsiella pneumoniae
Pseudomonas
Escherichia coli
C.albicans
Residents in latent state in tissues Pneumocystis jiroveci
Mycobactium tuberculosis
Cytomegalovirus (CMV)
Herpes simplex virus
Epstein-Barr virus
Major microbial Flora of the Upper Respiratory Tract
Organisms Oral cavity Nasopharynx, Epiglottis, Paranasal sinus,
Tonsil larynx Middle ear
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 spesies 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 sinus,
Tonsil larynx Middle ear
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
Mycobacterium tuberculosis UP UP UP UP
Spirochetes
Borrelia spesies NF,UP NF,UP
Treponema pallidum UP UP
Fungi
Candida albicans NF NF,UP
Aspergillus spesies UP
Mucor spesies UP
Major microbial Flora of the Upper Respiratory Tract
Organisms Oral cavity Nasopharynx, Epiglottis, Paranasal sinus,
Tonsil larynx Middle ear
Chlamydophila (Chlamydia)
Chlamydophila pneumoniae UP
Mycoplasma
Mycoplasma pneumoniae UC,UP UP UC,UP
Viruses
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
Upper Respiratory Tract infection URTI
Pathology changes
Symptoms resolve
2 5 7 14 30
TABEL 1. Common Agents of Respiratory Infections
Clinical Illness Bacteria Viruses Fungi Other Comment
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.
Tracheolaryngi H.influenzae type b Parainfluenza v Rare Rare Parainfluenza v. are most common causes.
tis (Croup) S.pyogenes (GABHS) RSV More serious bacterial infections.
C.diphtheriae Adenoviruses
M.pneumoniae Influenza v A history of preceding cold-like symptoms is
Enteroviruses typical of laryngotracheitis.
Sputum or pharyngeal swabs cultures may be
used to isolate pathogens.
Serologic studies to various viruses are helpful
for retrospective diagnosis.
COMMON COLD
Grade A
Professional concensus
Symptomatic treatment Symptomatic treatment +
follow up
In case of secondary
bacterial complication
Abnormal persistence or worsening of symptoms under
symptomatic treatment
Re-assessment
TABEL 2. Some Infectious Agents that Cause the Common Cold
The bacteria listed in Table 2 cause over 70% of the infections of the paranasal sinuses.
TABLE 4. Some Viral Causes of Pharyngitis
Symptomatic treatment
Positive Culture Negative
S. pyogenes (Group A) (Family Streptococcaceae)
General characteristics
- Occurs in single, pairs, or chained Gram (+) coccus
- Facultative anaerobe, attaches to epithelial surface via the
lipoteichoic acid portion of pili
Attributes of pathogenesis
- M protein
- Hyaluronic acid capsule (promotes invasiveness)
- Erythrogenic toxin (causes rash)
- Hemolysins : streptolysin S & O
- Other enzyme :
- Streptokinase (enhances tissue penetration)
- Hyaluronidase (solubilises tissue ground substance)
Lower Respiratory Tract infection URTI
Pneumonia
• A major killer in both developed and developing
countries
• Accounts for more deaths than other infectious
diseases
• Mortality rates vary but can be as high as 25%
• A major cause of death in children in developing
countries
• Microbiological criteria are specific for predicting the
cause of pneumonia
Classification of pneumonia
• Community-acquired
• Hospital-acquired
• Aspiration and anaerobic
• Pneumonia in immunocompromised
• AIDS-related
• Geographically restricted
• Recurrent
MICROBIOLOGICAL CAUSES (%) OF COMMUNITY ACQUIRED
PNEUMONIA FROM HOSPITAL BASED STUDIES (N=3,000)
• Non-invasive:
– Blood count, urea, albumin, LFT’s, sputum gram,
chest X-ray, CT scan
– Culture of sputum, blood, pleural fluid
– Serology: pneumococcal, Legionella antigen
• Invasive: induced sputum, bronchoscopy,
open lung biopsy
Streptococcus pneumoniae
General characteristics
• Part of normal flora oropharynx in 40-70% human
• Gram (+), α-hemolytic, lancet-shaped diplococcus
• Possesses a group-specific carbohydrate
• Possesses a type-specific polysaccharide capsule, >>80
different antigenic type, differentiated by swelling of the
capsule test
• Should be DD/ from non pathogenic S. viridans, by optochin,
bile solubility test, inulin test
Attributes of pathogenesis
• is attributed to the antiphagocytic capacity of the capsule
• Little evidence exist for production of toxin
Clinical Disease
1. Identification
a. Based on clinical presentation and serology
b. Culture on PPLO agar, “fried egg” appearance
c. Giemsa stain : small pleomorphic bacteria
d. DNA probes
2. Clinical specimen
a. Acute - Convalescent sera : CFT & cold agglutination
reaction
b. Nasopharyngeal secretion
Control
1. Treatment : tetracycline or erythromycin
2. Prevention, re-infection are common
Legionella pneumophila
General characteristics
– poorly stained, Gram negative rod, longer filament
– staining Dieterle’s silver stain
– facultative, intracellular organism
– has high density of cellular branched fatty acid
– catalase (+), most strain are weakly oxidase (+)
– hydrolyzes hippurate
– stream bacterium that contaminates air-conditioning
cooling tower
– frequently harbored by bacteria
Classification
– classified in new family and genus aquatic organisms
– major causative agent of legionaire’s disease
Attributes of pathogenesis
– grows intracellularly and fail to activate the alternate
C pathway
– produces cytotoxin, β-lactamase, endotoxin
Clinical Disease
– Pneumonia (legionaire’s disease)
– Pontiac’s fever
VIRUSES THAT CAUSE COMMUNTIY
ACQUIRED PNEUMONIA
INFLUENZA VIRUS
influenza virus A
influenza virus B,
much lesser extent influenza virus C
Influenza virus Genom
P1 81-94kD Polymerase RNA2
P2 RNA3
P3 RNA1
Na 60kD Neuraminidase RNA6
NP 53kD Nucleoprotein RNA5
H1 58kD Hemaglutinin1 RNA4
H2 28kD Hemaglutinin2 RNA7
MP 25kD Matrix protein
NS1 23kD Non structural RNA8
NS2 11kD
Type A :
– Human, avian, mammals (horse, seal, pig)
– Sub-type
– Epidemic and pandemic
– Mutation:
Antigenic drift
Antigenic shift
TYPE B:
– Only human, no animal reservoir
– No sub-type
– Only epidemic
– So far no shifts have been recorded
Type C:
– much lesser extent influenza virus C
Viral proteins
The internal antigens
M1 and NP proteins are the type-specific proteins (type-
specific antigens)
used to determine whether a particular virus is A, B or C
The external antigens
HA and NA show more variation and are the subtype and
strain-specific antigens
Haemagglutinin (H 1-15)
Neuraminidase (N 1-9)
used to determine the particular strain of influenza A
responsible for an outbreak
HA involved in attachment and membrane fusion in
the endosome of the infected cell
Antigenic drift
– Antigenic drift is due to mutation
– Antibodies to the HA protein are the most
important in protection, although those to NA also
play a role
– Both proteins undergo antigenic drift (i.e.
accumulate mutations) and after a few years may
have accumulated sufficient changes that an
individual immune to the original strain is not
immune to the drifted one
– Antigenic drift results in sporadic outbreaks and
limited epidemics
Antigenic shift
– Antigenic shift is due to reassortment
– In the case of influenza A, antigenic shift
periodically occurs
– Apparently "new" HA and/or NA are found in the
circulating viral strains.
– There is little immunity (particularly if both proteins
change, or if new HA is present) and an
epidemic/pandemic is seen
Pandemic influenza H1N1
• An acute respiratory illness
• Sudden onset of: fever (>38oC), headache,
cough, sore throat, muscle aches, pneumonia
• Transmitted by respiratory droplets from
coughing, sneezing, and from “infected”
surfaces.
Underlying diseases with an increased risk
of severe influenza
• Chronic lung, liver, CNS, conditions,
• Immunosuppression
• Diabetes mellitus
• Asthma
• Age <5 years or >65 years
• Severely obese (BMI 40 or more)
• Pregnancy
• haemoglobinopathies
Preventing the spread of pandemic (swine)
influenza
• Wash hands with soap and water
• Avoid unnecessary contact with cases
• Avoid touching eyes, nose , mouth
• Cover mouth and nose with tissue
• Patients admitted to hospital who have a confirmed
diagnosis will be nursed in a negative pressure room
• HCW’s wear protective clothing
Treatment and prevention of pandemic
influenza H1N1
• Oseltamivir treatment of severe cases
• Can also be considered as antiviral prophylaxis
in selected high risk patients
• Should be used prudently because of risk of
drug resistance
• Vaccine about to be issued, will include
provision for health care workers
OTHER VIRAL CAUSES