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Microbiology Nuts & Bolts
Test Yourself - Primary Care
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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Doris
• 86 year old nursing home resident
• Nursing home ask for a visit as she is becoming
increasingly confused and has developed new
urinary incontinence
• On examination she is afebrile but appears to
have some suprapubic discomfort
• A Midstream urine is taken
• The urine dipstick is positive for leucocytes and
nitrites
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What is the correct interpretation of
the urine dipstick result?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Doris has a UTI
Doris does not have a UTI
A UTI cannot be excluded
A UTI can be excluded
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Correct
• Answer: a UTI cannot be excluded
• A definition of infection is inflammation or tissue
destruction in the presence of a microorganism
• Leucocytes are the white blood cells that indicate an
inflammatory response
• The nitrites are bacterial nitrites, breakdown products
produced by bacteria
• Leucocytes and nitrites in a urine sample mean a UTI is
possible but there are other reasons why they might be
there and so they do not prove a UTI, they just mean it
cannot be ruled out
• The positive predictive value of a urine dipstick is 60%
• The negative predictive value of a urine dipstick is 97%
• A negative urine dipstick can exclude a UTI in most
patients
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Doris
• The MSU is sent to the microbiology laboratory
in a red topped boric acid container
• Doris is started on Trimethoprim for a possible
UTI as there is not other obvious focus of
infection
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Why is the MSU sent in boric acid?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
The lab analyser needs boric acid
Boric acid prevents damage to the container
The MSU should not be sent in boric acid
Boric acid stops the urine sample degrading
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Correct
• Answer: the boric acid stops the urine sample degrading
• The boric acid stops the bacteria in the sample from growing and
giving a false positive culture result
• Urine culture is a quantitative test; the lab reports the actual
number of bacteria present in a millilitre of urine
• If the bacteria are allowed to grow in the time it takes for the
sample to get to the laboratory then the number of bacteria
within the urine will be falsely high and suggest the presence of
a UTI even if the patient doesn’t actually have a UTI
• NOTE: the urine sample should not be taken directly into the
boric acid container as the dipstick cannot be done on acidified
urine, the urine should be transferred to a boric acid container
for transport to the laboratory
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Why do we take midstream urines?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
To get rid of non-sterile urethral urine
Only the upper urinary tract can be infected
To stop the container being over filled
Microbiologists like to make life difficult!
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Correct
• Answer: to get rid of non-sterile urethral urine
• The normal bacterial causes of urinary tract infections come from
the gastrointestinal tract
• These bacteria colonise the skin of the perineum and then swim
up in to the urethra
• Voiding and discarding the first part of the urine stream gets rid
of the bacteria in the urethral urine and reduces the risk of
contamination giving a false positive culture result
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Doris
• Doris initially started to improve but three days
later she became short of breath and started
coughing up thick green sputum
• On examination she had a temperature of
38.5oC and was a bit tachycardic
• She was diagnosed with pneumonia
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Which of the following is NOT a sign of
pneumonia?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Cough
Fever
Purulent sputum
Crackles on auscultation
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Correct
• Answer: crackles on auscultation
• According to the British Thoracic Society the clinical
diagnosis of pneumonia is:
– Cough PLUS 1 lower respiratory tract symptoms PLUS new focal
chest signs PLUS 1 systemic symptom
– No other explanation
– Lower respiratory tract symptoms include: shortness of breath,
purulent sputum, chest pain
– Focal chest signs include: reduced chest movement, dull percussion,
bronchial breathing, increased tactile vocal fremitus or vocal
resonance
– Systemic symptoms include: fever, sweats, shivers, aches, pains
• Crackles in the chest usually indicate heart failure,
fibrosis, chronic obstructive pulmonary disease or
pneumonitis
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Which of the following would be
appropriate empirical antibiotic(s)?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
PO
PO
PO
PO
Amoxicillin
Amoxicillin PLUS PO Clarithromycin
Cefradine
Clindamycin
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Correct
• Answer: PO Amoxicillin
• As long as Doris is not allergic to penicillin then PO Amoxicillin
will cover the common causes of mild to moderate community
acquired pneumonia (CAP)
• Alternatives in penicillin allergy are PO Clarithromycin or PO
Doxycycline
• The most common causes of mild to moderate CAP are:
– Streptococcus pneumoniae
– Haemophilus influenzae
– Viruses
• There is no need to use combination therapy
• Cefradine would work but is too broad spectrum and poses a
high risk for Clostridium difficile associated disease (CDAD)
• Clindamycin does not cover the causes and is a risk for CDAD
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Doris
• Doris is started on Amoxicillin and a sputum
sample is taken and sent to the microbiology
laboratory the next day
• Two days later Doris is feeling a bit better
• The sputum sample result is:
– Appearance: salivary
– Culture: Klebsiella pneumoniae isolated resistant to
Amoxicillin, sensitive to Co-amoxiclav, Cefradine and
Ciprofloxacin
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What is the correct interpretation of the
sputum result?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
K. pneumoniae is the cause of her CAP
The lab has contaminated the sample
K. pneumoniae is a colonising bacterium
Doris probably has cancer
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Correct
• Answer: K. pneumoniae is a colonising bacteria
• All K. pneumoniae are resistant to Amoxicillin
• When patients are given antibiotics their normal flora
changes due to the selective pressure of the antibiotic
killing off normally sensitive bacteria
• In patients who are unwell gastrointestinal bacteria are
able to colonise their upper respiratory tract replacing the
normal sensitive bacteria
• In this case Doris was correctly given Amoxicillin and this
has selected out the K. pneumoniae
• The main clue to this is the fact that the sputum sample is
salivary indicating that it is not sputum but spit and
therefore will contain bacteria from the mouth not the
lungs
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Doris
• Having been bed bound for a week with a UTI
followed by pneumonia Doris develops a
pressure sore on her sacrum
• This becomes increasingly painful and
erythematous
• She is started on PO Flucloxacillin but 2 days
later the infection appears to be worsening
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What is the likely bacterial cause for
the worsening infection?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Pseudomonas aeruginosa
Clostridium perfringens
Group A Beta-haemolytic Streptococcus
Meticillin-resistant Staphylococcus aureus
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Correct
• Answer: Meticillin-resistant Staphylococcus aureus (MRSA)
• The most common causes of skin and soft tissue infections are
Staphylococcus aureus and the Beta-haemolytic Streptococci
Groups A, C & G
• The Beta-haemolytic Streptococci are unlikely in this situation
because Doris has been on Amoxicillin and Flucloxacillin leading
up to the development of cellulitis and both of these antibiotics
are active against these bacteria
• The most likely cause is therefore a S. aureus resistant to
Flucloxacillin i.e. MRSA
• Pseudomonas aeruginosa and Clostridium perfringens are not
common causes of skin and soft tissue infections
– Pseudomonas aeruginosa commonly colonisers the warm moist
tissue of broken down areas of skin such as ulcers
– Clostridium perfringens is normally associated with soft tissue
infections following penetrating injuries
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Doris
• While waiting for the results of swabs from the
sacral sore to come back Doris was started on
PO Clindamycin
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What would have been a more
appropriate choice of antibiotic?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Erythromycin
Doxycycline
Teicoplanin
Fucidic Acid
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Correct
• Answer: Doxycycline
• Doxycycline is almost always active against MRSA in the UK and
can be taken orally
• Clindamycin is not the best choice as it is unpredictable whether
it will be active against MRSA and it is high risk for CDAD
• Erythromycin activity against MRSA is unpredictable
• Teicoplanin is active against MRSA but it is only available IV
• Fucidic Acid should never been used on it’s own either PO, IV or
topically as resistance develops very quickly, even within 24
hours!
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Doris
• Two days after starting the PO Clindamycin
Doris develops severe diarrhoea
• She is admitted to hospital where she is
diagnosed as having CDAD
• Despite appropriate treatment Doris sadly dies 2
days after being admitted to hospital
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What was the cause of her CDAD?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
PO Clindamycin
PO Flucloxacillin
Multiple courses of antibiotics
Clostridium difficile
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Correct
• Answer: Clostridium difficile
• Antibiotics predispose to CDAD but they do not cause it
• CDAD is an infection caused by the bacterium Clostridium
difficile – without the bacterium you don’t get CDAD
• The antibiotics predispose to CDAD because the bacterium is
resistant to those antibiotics and is therefore left behind or
allowed to colonise when the normal sensitive bacteria are killed
off
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Doris
• A root cause analysis is done on why Doris
developed CDAD and whether any lessons
should be learned to prevent future patients
having the same problem
• The RCAs identified where:
– Inappropriate antibiotic prescription of Clindamycin
– Poor infection control practices in the nursing home
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Which of the following are common
root causes for CDAD?
Choose A, B, C or D for the answer you feel best
fits the question
A
B
C
D
Poor hand hygiene
Inappropriate choice of antibiotics
Failure to isolate patients with diarrhoea
Prolonged courses of antibiotics
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Correct
• Answer: all of the answers are correct
• The prevention of CDAD requires:
• A multifactorial infection control approach to manage the
patients environment to reduce the risk of exposure to the
bacterium Clostridium difficile
• Good antimicrobial stewardship to ensure the patient only
ever receives the right antibiotic, at the right dose, route
and duration, for the right infection at the right time
• All healthcare professionals have a responsibility to ensure
this happens
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Doris
• The GP and the nursing home were devastated
by the findings of the root cause analysis, but
they made sure they learned from their
mistakes, and put policies and procedures in
place to prevent this happening again.
The End
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