Microbiology of Respiratory

Infection
 Respiratory Infections

Infections of throat and pharynx

Infections of middle ear and sinuses
Infections of trachea and bronchi
Infections of the lungs
 Infections of throat and
pharynx

Sore throat
Diphtheria
Candida/thrush
Vincents angina
 Infections of throat and
pharynx

Diagnosis:
Well taken throat swab
SORE THROAT
 Sore throat

VAST MAJORITY (OVER TWO

THIRDS) - VIRAL
DO NOT NEED ANTIBIOTICS
 Bacterial sore throat
The most common BACTERIAL cause is
Streptococcus pyogenes (also known as
Group A streptococci)

Clinical: Acute follicular tonsillitis

Treatment:Penicillin
Streptococcus pyogenes
 Streptococcal sore throat

Acute complications:
Peritonsillar abscess (quinsy)
Sinusitis/ otitis media
Scarlet fever
QUINSY (PERITONSILLAR
ABSCESS)
 Streptococcal sore throat

Late complications
Rheumatic fever
3 weeks post sore throat
fever, arthritis and pancarditis

Glomerulonephritis
1-3weeks post sore throat
haematuria, albuminuria and oedema
 Diphtheria
Corynebacterium diphtheriae

Clinical: Severe sore throat with a grey

white membrane across the pharynx. The
organism produces a potent exotoxin which
is cardiotoxic and neurotoxic.
DIPHTHERIA
DIPHTHERIA
 Diphtheria

Epidemiology : Rare, but increased in certain parts

of the world eg Russia

Treatment: Antitoxin and Supportive and

Penicillin/erythromycin
 Candida/Thrush
Candida albicans

Clinical: White patches on red, raw mucous

membranes in throat/ mouth

Cause: endogenous

Treatment: Nystatin
ORAL THRUSH
 Vincents angina
Mixture of organisms (Borrelia vincenti and
Fusobacterium sp.)

Clinical:Foul smelling mouth and throat

ulcers

Treatment: penicillin
VINCENTS ANGINA
 Respiratory Infections

Infections of throat and pharynx

Infections of middle ear and sinuses
Infections of trachea and bronchi
Infections of the lungs
EAR
OTITIS MEDIA
 Infections of middle ear and
sinuses
Often viral with bacterial secondary
infection
Most common bacteria: Haemophilus
influenzae, Streptococcus pneumoniae and
Streptococcus pyogenes.
Treat: Amoxycillin
 Respiratory Infections

Infections of throat and pharynx

Infections of middle ear and sinuses
Infections of trachea and bronchi
Infections of the lungs
 Infections of trachea and
bronchi

Acute epiglottitis
Acute exacerbations of COPD
Cystic fibrosis
Pertussis (whooping cough)
 Acute epiglottitis

Haemophilus influenzae
Clinical: severe croup in children aged 2-7
years, may progress to respiratory
obstruction and death.
EPIGLOTTITIS
EPIGLOTTITIS
 Acute epiglottitis

Microbiology of Haemophilus influenzae

Habitat - upper respiratory tract
Microscopy- small gram negative bacillus
Culture - Chocolate agar -small translucent
colonies
Identify - X and V test; H influenzae requires
both factors X and V to grow.
Haemophilus influenzae
 Acute epiglottitis

Diagnosis: blood culture (?throat swab)

Treatment: ITU and ceftriaxone

 COPD

Acute exacerbations of COPD.

Exacerbations of this chronic condition are
often associated with bacterial infection.
 Acute exacerbations of COPD

Often follow viral infection, or fall in

atmospheric temperature with increase in
humidity (often in winter)
Clinical: Patients present with increased
breathlessness. The volume and purulence
of sputum is increased.
Acute exacerbations of COPD
The most common organisms associated
are:
Haemophilus influenzae
Streptococcus pneumoniae
Moraxella catarrhalis
NB All three organisms are present in
normal upper respiratory tract flora.
 Acute exacerbations of COPD
Treatment:
Give antibiotics if sputum purulence. If no sputum
purulence then antibiotics not needed unless consolidation
on CXR or signs of pneumonia.
1ST LINE Amoxicillin 500mg tds 2ND LINE
Doxycycline 200mg on day 1 then 100mg daily (5 days)

With time becomes increasingly difficult to treat, due to

acquisition of more resistant organisms.
 Cystic fibrosis

Inherited defect
leads to abnormally viscid mucus which blocks
tubular structures in many different organs
including the lungs.
 Cystic fibrosis
Chronic respiratory infection is a major
problem.
Causal bacteria:
Staphylococcus aureus and Haemophilus
influenzae
Pseudomonas aeruginosa
Burkholderia cepacia
 Pertussis (whooping cough)
Bordetella pertussis
Clinical: Acute tracheobronchitis
cold like symptoms for two weeks
paroxysmal coughing (2 weeks)
repeated
violent exhalations with severe inspiratory
whoop, vomiting common
residual cough for month or more
 Pertussis (whooping cough)
Diagnosis:
pernasal swab (charcoal blood agar/ Bordet-Gengou
medium)
serology
clinical ( by the stage of paroxysmal coughing
organism numbers much reduced)
Treatment: most effective in the first 10 days of
illness, also reduces spread to susceptible contacts
Vaccination
Pernasal swab
 Respiratory Infections

Infections of throat and pharynx

Infections of middle ear and sinuses
Infections of trachea and bronchi
Infections of the lungs
 Infections of the lungs

Community acquired pneumonia

Nosocomial pneumonia
Legionnaires disease
Pneumocysitis carinii pneumonia (PCP)
Fungal chest infection
Tuberculosis
 Community acquired
pneumonia

Clinical: cough, sputum production,

dyspnoea, fever.
Chest x-ray with infiltrates.
Acquired in the community
 Community acquired
pneumonia

Causative organisms:
Streptococcus pneumoniae 70%
Atypicals/viruses 20%
Staphylococcus aureus 4%
Other bacteria 1%
Haemophilus influenzae 5%
 Community acquired
pneumonia
Streptococcus pneumoniae
Microbiology:
Microscopy - gram positive cocci
Culture - Alpha haemolytic colonies, typically
draughtsmen ie with sunken centre.
Identify - Optochin sensitive

Treatment - generally penicillin sensitive

Streptococcus pneumoniae
Lobar pneumonia
 Community acquired
pneumonia
Atypicals - old term for pneumonias not
attributable to any of the common bacterial
causes of pneumonia.
Refer to Dr McIntyres talk
 Community acquired
pneumonia

Treatment , follow the Tayside Critical Care

Pathway for the Management of
Community-Acquired Pneumonia
 CURB65 SCORE
3 OR MORE
(SEVERE)

ANTIBIOTICS: SEVERE
ALL SHOULD INITIALLY RECEIVE:
IV CO-AMOXICLAV 1.2g x3/day PLUS IV
CLARITHROMYCIN 500mg x2/day or PO
DOXYCYCLINE 100mg x2/day
(PENICILLIN ALLERGY:
IV Levofloxacin 500mg2/day)
Step down to oral doxycycline 100mg x 2/day in
all patients
ALL SHOULD HAVE: Paired serology, throat
swab/gargle for virology PCR, urinary legionella
antigen tests
Treat for at least 10 days (IV/oral)
 Nosocomial pneumonia
= hospital acquired pneumonia
Predisposing factors:
Intubation
Intensive care unit
Antibiotics
Surgery
Immunosuppression
 Nosocomial pneumonia
Organisms -60% gram negative organisms :
includes Pseudomonas aeruginosa, and Coliforms
(such as E.coli, Klebsiella sp)
If aspiration pneumonia anaerobes may be involved
Treatment
Severe IV Amoxicillin + Metronidazole + Gentamicin
Step down to Coamoxiclav PO 7-10 days total
Non severe Amoxicillin + Metronidazole for 7 days
 Legionnaires disease
Legionella pneumophila
Clinical:
flu like illness which may progress to a severe
pneumonia, with mental confusion, acute renal
failure and GI symptoms.
Epidemiology
often associated with travel, usually associated
with water.
 Legionnaires disease

Diagnosis: Legionella urinary antigen/

Serology
Treatment:
Erythromycin/clarythromycin
Fluoroquinolones
 Pneumocysitis carinii
pneumonia (PCP)
A cause of pneumonia in patients with
AIDS
Diagnosis: Bronchioalvelar lavage (BAL)
or induced sputum and identification of
cysts.
Treatment: Cotrimoxazole, pentamidine.
 Fungal chest infection

Aspergillus fumigatus
Clinical: Causes severe pneumonia/systemic
infection in the severely immunocompromised.
Or aspergilloma
Diagnosis : Culture
Treatment : iv Amphotereicin B
ASPERGILLOMA
 TUBERCULOSIS
Mycobacterium tuberculosis
Acid Alcohol Fast Bacilli
Bread crumb like growth on special
medium, after prolonged (up to 3 months)
incubation
Acid and Alcohol Fast Bacilli
(AAFB)
Growing Tuberculosis
 Tuberculosis

For more detailed information see Dr

Winters Lecture
Infections in lungs

General diagnostic points

 Infections of the lungs -
Diagnosis

Isolation of causal pathogen

Sputum NB Quality of sputum sample
important
Blood culture (organism in blood of one third
of patients with pneumonia)
 Infections of the lungs -
Diagnosis
Detection of bacterial antigen
eg Legionella urinary antigen
Direct immunofluorescence for PCP
Serology
eg Legionella serology
 Immunisation
UK guidance is summarised in a document
called The Green Book available online
at:
http://www.dh.gov.uk/PolicyAndGuidance/Hea
lthAndSocialCareTopics/GreenBook/fs/en
 Pneumococcal immunisation
Pneumococcal polysaccharide vaccine
covers 23 different capsule types
Efficacy 50-70% reduction of bacteremia risk
Pneumococcal conjugate vaccine covers 7
different capsular types common
childhood strains
Efficacy 97% protection
 Pneumococcal immunisation
Indications
All those aged 65 years and over
Childhood immunisation schedule
Risk groups
No spleen
Various chronic diseases including COPD
Immunosuppressed
Patients with CSF shunts
 Hib
Invasive Haemophilus infection caused
most commonly by Type b capsular strains
(Hib).
Conjugate vaccine offered to all children
less than 1, and all asplenic individuals
Highly effective
 Pertussis immunisation
Acellular vaccine 5 purified pertussis
components
Given as part of the childhood
immunisation schedule
Immunisation for Tuberculosis
Live attenuated strain of Mycobacterium
bovis
UK efficacy of 70% in protecting against
TB
Risk based approach to identify those who
receive the vaccine
 Community acquired
pneumonia

Causative organisms:
Streptococcus pneumoniae 70%
Atypicals/viruses 20%
Staphylococcus aureus 4%
Other bacteria 1%
Haemophilus influenzae 5%