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Microbiology Nuts & Bolts
Test Yourself Session 1
Begin here
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The patient in this test yourself case is
entirely fictitious, however it is based
on many clinical scenarios the author
has come in to contact with during his
medical career. Any similarity to a real
case is entirely coincidental.
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Steven
• 67 year old smoker
• Presents with fever & cough 1 week
• On examination
– Temperature 38.5 oC
– Decreased air-entry at the right base
• No recent travel abroad
• No pets
• Works as a salesman
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What will be the most help in exploring
the immediate differential diagnosis in
this patient?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
FBC,
FBC,
FBC,
FBC,
CRP,
CRP,
CRP,
CRP,
Sputum culture, Chest X-ray
U&Es, Sputum microscopy, Chest X-ray
U&Es, Urine dipstick, Chest X-ray
U&Es, LFTs, Urine MC&S, Chest X-ray
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Correct
• Answer: FBC, CRP, U&Es, Urine dipstick, Chest X-ray
• FBC
– Total white cell count and differential gives information about
the likelihood of infection and the possible aetiological agents
e.g. ↑ WBC with a neutrophilia indicates likely bacterial cause
– Platelets are an acute phase reactant, going up in infection
and inflammation
• U&Es
– Knowledge of renal function is essential to prescribe safely
– Urea can be used to help assess severity of CAP
• CRP
– Rises in bacterial infection
• Urine dipstick
– Absence of leucocytes and bacterial nitrites has
approximately 97% negative predictive value for UTI
• Chest X-ray
– Part of the British Thoracic Society criteria for CAP in hospital
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Steven
• Bloods
– WBC 22 x 109/L
– CRP 313
– U&Es – Urea 9, Creat 133
• Urine
– Dipstick ++ leucs, ++
nitrites
• Chest X-ray
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What is the most likely diagnosis?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
UTI
Community Acquired Pneumonia
UTI + Upper Respiratory Tract Infection
UTI + Community Acquired Pneumonia
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Correct
• Answer: Community Acquired Pneumonia (CAP)
• The White blood cells and CRP suggest an acute bacterial
infection
• Even though the urine is consistent with a diagnosis of UTI the
positive predictive value of this test is poor (approximately 60%)
and so it does not diagnose a UTI
• The Chest X-ray shows right basal consolidation and so the
diagnosis is CAP
• Note: dual pathology is rare and so it is unlikely for the patient
to have both CAP and a UTI
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Steven
• On the basis of the Chest X-ray appearances
Steven is re-examined to look for signs of
pneumonia
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Which of the following is NOT usually a
clinical sign Community Acquired
Pneumonia?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Crackles in the chest
Dullness to percussion
Increased vocal resonance
Reduced chest expansion
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Correct
• Answer: Crackles in the chest
• The clinical findings consistent with consolidation in the chest
are:
– Observation: decreased chest movement
– Palpation: decreased chest expansion, decreased tactile vocal
fremitus
– Percussion: dullness
– Auscultation: increased breath sounds with bronchial
breathing
• Crackles are usually sign of heart failure or fibrosis rather than
consolidation
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Steven
• Further investigations ordered
– Sputum culture
– Blood cultures
– Urine for Legionella antigen (Ag)
• Repeat clinical examination to look for signs of
pneumonia
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Which of these sputum appearances is
consistent with a diagnosis of
Community Acquired Pneumonia?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Mucoid
Purulent
Salivary
Mucopurulent
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Correct
• Answer: Purulent
• The appearance of sputum can help in distinguishing infection
from upper respiratory tract contamination when looking at
sputum culture results:
– Salivary
• Spit not phlegm, risk of contamination
– Mucoid
• Upper respiratory tract specimen, no evidence of
inflammation, therefore culture result likely to represent
contamination not infection
– Purulent
• Indicates inflammation and therefore is consistent with a
deep sample from an infect chest
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Steven
• Observations deteriorate
–
–
–
–
–
SaO2 92% on air
Temperature 39.5 oC
H.R. 110bpm, B.P. 115/60
Respiratory rate 32/min
Starts having rigors
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What antibiotics should the patient be
started on?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
IV
IV
IV
IV
Piptazobactam + Gentamicin
Piptazobactam + Clindamycin
Co-amoxiclav + Clarithromycin
Teicoplanin + Levofloxacin
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Correct
• Answer: IV Co-amoxiclav + Clarithromycin
• Most hospitals use a combination of a beta-lactam and a
macrolide antibiotic for severe CAP
• Piptazobactam is unnecessarily broad spectrum for CAP
• Gentamicin does not penetrate into the chest very well and has
no action against non-culturable bacteria”
• Whilst Clindamycin is often considered with the macrolides it is
actually a lincosamide and has a different spectrum of activity. It
has no action against non-culturable bacteria
• Teicoplanin + Levofloxacin are often used for severe CAP in
patients who are allergic to beta-lactams however this patient
has no evidence of this and therefore he would be exposed to
nephrotoxic and high risk CDAD antibiotics unnecessarily
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Steven
• Diagnosed with Community Acquired Pneumonia
• Starts IV Co-amoxiclav and Clarithromycin as
CURB-65 score =4
–
–
–
–
–
Confusion
Urea >7mmol/L
Respiratory Rate >30/min
BP >90systolic or <60 diastolic
Age >65 years
X




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Which of the following is NOT usually
a cause of Community Acquired
Pneumonia?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Legionella pneumophila
Streptococcus pneumoniae
Pseudomonas aeruginosa
Staphylococcus aureus
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Correct
• Answer: Pseudomonas aeruginosa
• The common causes of CAP are:
– Staphylococcus aureus
– Streptococcus pneumoniae
– Haemophilus influenzae
– Mycoplasma pneumonia
– Legionella pneumophila (especially if travelled)
– Chlamydia pneumoniae
– Viral e.g. Influenza, Parainfluenza, Respiratory Syncytial
Virus, Adenovirus
• Pseudomonas aeruginosa is more common if the patient has a
pre-existing lung condition such as Chronic Obstructive
Pulmonary Disease (COPD)
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Steven
• Next day
• Bloods
– WBC 27 x 109/L
– CRP 375
– U&Es – Urea 10, Creat 125
• Urine
– Microscopy >100 WBC, no epithelial cells
– Culture = No growth
• Blood Culture
– Gram-positive coccus
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How would you manage the patient
now?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Change IV Co-amoxiclav to IV Piptazobactam
Change the IV Clarithromycin to IV Levofloxacin
Stop current antibiotics and start IV Meropenem
Persist with Co-amoxiclav and Clarithromycin
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Correct
• Answer: Persist with Co-amoxiclav and Clarithromycin
• There is no reason to suspect that this patient has anything
other than one of the normal causes of CAP
• It is most likely that he needs more time to respond to the
prescribed treatment or that he might need more respiratory
support e.g. oxygen or non-invasive ventilation
• In particular, dropping the macrolide antibiotic would be a
mistake as this means that unculturable bacteria are no longer
covered
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Steven
• Steven continued on Co-amoxiclav and
Clarithromycin
• Next day he felt a little better
• Temperature was settling
• Bloods
– WBC 19 x 109/L
– CRP 198
– U&Es – Urea 12, Creat 150
• Blood Culture
– Coagulase negative staphylococcus
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Steven
• Results were followed up at 48 hours
• Urine – No growth
• Blood cultures – Coagulase negative
Staphylococcus
• Sputum – Streptococcus pneumoniae
• Urine – Positive for Legionella Ag
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What is the most likely diagnosis?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Legionella pneumophila pneumonia
Streptococcus pneumoniae pneumonia
Aspiration pneumonia
Staphylococcal endocarditis
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Correct
• Answer: Legionella pneumophila pneumonia
• The urinary antigen test for Legionella pneumophila is very good
– Sensitivity 95%
– Specificity 95%
– The main drawbacks are
• It only detects Serogroup 1 (there are 14 in total)
however in reality almost all infections are Serogroup 1
• It can cross react with Campylobacter sp. infection
• Growth of Streptococcus pneumoniae in the sputum can occur in
the absence of pneumonia as this organism is part of the normal
respiratory flora in healthy individuals as well as those with CAP
• The presence of a Coagulase negative Staphylococcus is the
result of contamination of the blood culture at the time it was
taken, usually due to poor aseptic technique
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Steven
• Steven was diagnosed as having Legionella
pneumophila pneumonia
• The case was notified to the health Protection
Unit who under took further investigations for
the source of infection.
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What is the treatment of Legionella
pneumophila pneumonia?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
IV Meropenem for 3 weeks
Oral Co-amoxiclav for 3 weeks
Oral Clarithromycin for 3 weeks
Oral Levofloxacin for 3 weeks
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Correct
• Answer: Oral Levofloxacin for 3 weeks
• Levofloxacin is superior to Clarithromycin for the treatment of
Legionella pneumophila reducing the mortality rate from
approximately 10% to 0.5%
• Levofloxacin has very good oral bioavailability and so if the
patient is showing signs of improvement it is rarely necessary to
give it by the IV route
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Steven
• Steven was converted to oral Levofloxacin and
continued for a 3 week course of treatment.
• He made a full recovery
• The source of his Legionella pneumophila was
never discovered
The End
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