Interpretation of
Microbiology Reports
Dr. Cathal Collins
Objectives
• Have some idea of laboratory processes
• Have some idea of the relative importance of
laboratory reports and how they should be interpreted
Workshop Format
• First bit:
– Example to demonstrate laboratory processes
• Middle bit
– Examples to demonstrate how reports should be interpreted
• Final bit
– Lessons learned
First Bit
Example
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•
Jane Doe, nursing home
Presented to A&E
Fever, frequency, dysuria and right flank pain
Clinical review
Blood cultures and MSU
Co-amoxiclav and gentamicin (both IV) started
Urine microscopy
White cell
Epithelial cell
Urine microscopy counting chamber
Day 1 Laboratory
• Urine microscopy is the only report that will be
available soon after specimen arrival
–
–
–
–
–
White cells (note significant pyuria >10white cells/mm3)
Red cells
Epithelial cells
Casts/crystals
Bacteria (present or not)
• Appropriate agar plates are inoculated in attempt to
culture pathogens for identification and
susceptibilities
Blood cultures
Blood culture bottle
Blood culture machine
Day 2 Laboratory
• Blood culture flags up as positive in the blood culture
machine
Gram stain
Day 2: Blood culture flags +ve
Gram-positive cocci ?staph
Gram-negative bacilli
Gram-positive cocci ?strep
Yeast
Gram stain and Organisms
• Gram-positive cocci
– Staphylococcus spp
– Streptococcus spp
– Enterococcus spp
• Gram-positive bacilli
– Listeria monocytogenes
– Clostridium spp
– Bacillus spp
• Gram-negative cocci
– Neisseria spp
– Moraxella catarrhalis
• Gram-negative coccobacilli
– Haemophilus spp
– Acinetobacter spp
– Bordetella pertussis
• Gram-negative bacilli
–
–
–
–
–
–
Escherichia coli
Klebsiella spp
Proteus spp
Enterobacter spp
Serratia spp
Pseudomonas spp
Day 2 Laboratory
• Gram stain of blood: interim report issued and
communicated with advice
• Appropriate agar plates are inoculated
– Direct susceptibility testing using 5 or 6 key antibiotics:
e.g. co-amoxiclav, pip-tazobactam, gentamicin,
ciprofloxacin, cefpodoxime
– Not standardised- a drop of blood is lawned onto an agar
plate- don’t know how much bug is in the drop
Day 2 Laboratory
• Good idea of what is
growing on the urine agar
plates
MacConkey NLF and LF
Chromogenic agar
Day 2 Laboratory
• Urinary isolate:
– Set up biochemical
identification test
• API
• Automated (Vitek,
Phoenix etc)
API 20e
Phoenix
Vitek 2
Day 2 Laboratory
• Urinary isolate:
– Set up susceptibility tests
(standardised inoculum)
• Disc diffusion
• Automated (Vitek,
Phoenix etc)
Disc diffusion
Vitek
E-test for MIC
Day 3 Laboratory
• Final report on urine specimen
• However, additional tests may be indicated to
establish the resistance mechanism
• Good idea of what’s in the blood cultures with
unreliable susceptibility results for the 5 key antiGNB antibiotics
• Identification of and standardised susceptibility
testing on the blood culture isolate is performed
Day 3 Laboratory
• The direct non-standardised susceptibility tests
suggests that the blood culture organism may have
reduced susceptibility to co-amoxiclav, piptazobactam, gentamicin, cefpodoxime and
ciprofloxacin
• The urinary isolate is an Escherichia coli
• However, the standardised susceptibility pattern on
the urinary E. coli is concerning!
Susceptibility pattern of urinary E. coli
Antibiotic
Susceptibility
Ampicillin
R
Co-amoxiclav
I
Cephradine
R
Cefuroxime
R
Cefotaxime
I
Ceftazidime
S
Cefepime
I
Cefoxitin
S
Pip-tazobactam
I
Meropenem
S
Ciprofloxacin
R
Nitrofurantoin
S
Co-trimoxazole
R
Amikacin
S
Gentamicin
R
http://www.bsac.org.uk/_db/_documents/Chapter_11.pdf
Day 3 Laboratory
• The susceptibility pattern is highly suggestive that the
organism is an extended-spectrum beta-lactamase
(ESBL) producer
• Confirmatory ESBL tests set up on both urinary and
blood culture isolate:
– Looking for differences in susceptibility between a 3rd/4th gen
cephalosporin with and without a beta-lactamase inhibitor
Meanwhile…
• The patient has not improved clinically, remaining ill
with a persistent fever and rising inflammatory
markers
• The clinical team are advised to stop the coamoxiclav and gentamicin and to start meropenem
• The infection control team are contacted and
informed re a probable ESBL-producing isolate
Day 4: Final Urine Report
• Microscopy:
–
–
–
–
WCC 450/mm3
RCC 0
No casts/crystals
++ bacteria
• Culture:
– > 105 cfu/mL Pure growth of E. coli
– S: Meropenem
– R: Ampicillin, Ciprofloxacin, Gentamicin
• Comment:
– Similar isolate to that in blood. This isolate is an ESBL producer.
Infection control precautions in a healthcare setting are indicated.
Please contact the clinical microbiology team if any concerns.
Day 4: Final Blood Culture Report
• Gram:
– Gram-negative bacillus both bottles at 12 hours
• Culture:
– Escherichia coli
– S: Meropenem
– R: Ampicillin, Ciprofloxacin, Gentamicin
• Comment
– Significance as discussed. Similar isolate to that in urine.
This isolate is an ESBL producer. Infection control
precautions in a healthcare setting are indicated. Please
contact the clinical microbiology team if any concerns.
Antimicrobial stewardship
“Prioritization of tested antimicrobials and selective reporting
of susceptibility profiles (e.g., not routinely reporting
susceptibility of S. aureus to rifampin to prevent inadvertent
monotherapy with rifampin) can aid in the prudent use of
antimicrobials and direct appropriate therapy based on local
guidelines”
Antimicrobial stewardship
“…there is an association between antibiotic susceptibility
reporting from microbiology laboratories and antibiotic
prescribing for the treatment of urinary tract infections.”
Ciprofloxacin and risk of resistant organisms e.g. C. difficile
Lesson Slide
• Microscopy result early, culture result late
• More information available in the laboratory than is
released in the reports
Sterile v Non-sterile Site
• Sterile
These sites normally do not
contain any bacteria so any
bacteria found there are
significant
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Urine
Blood
CSF
Bile
Fluids: Pleural, peritoneal,
synovial, pericardial,
amniotic, bursa, CAPD
– Deep tissue samples?
• Non-sterile
These sites are open to the
external environment and
normally contain bacteria
(normal flora, colonisers)
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–
Throat swabs
Skin swabs
Wound swabs
Ear swabs
Nasal swabs
Sputum samples
Nail clippings
Faeces
Sterile v Non-sterile Site
• Sterile
These sites normally do not
contain any bacteria so any
bacteria found there are
significant
–
–
–
–
–
Urine
Blood
CSF
Bile
Fluids: Pleural, peritoneal,
synovial, pericardial,
amniotic, bursa, CAPD
– Deep tissue samples?
• Non-sterile
These sites are open to the
external environment and
normally contain bacteria
(normal flora, colonisers)
–
–
–
–
–
–
–
–
Throat swabs
Skin swabs
Wound swabs
Ear swabs
Nasal swabs
Sputum samples
Nail clippings
Faeces
Sterile v Non-sterile Site
• Sterile
These sites normally do not
contain any bacteria so any
bacteria found there are
significant
–
–
–
–
–
Urine
Blood
CSF
Bile
Fluids: Pleural, peritoneal,
synovial, pericardial,
amniotic, bursa, CAPD
– Deep tissue samples?
• Non-sterile
These sites are open to the
external environment and
normally contain bacteria
(normal flora, colonisers)
–
–
–
–
–
–
–
–
Throat swabs
Skin swabs
Wound swabs
Ear swabs
Nasal swabs
Sputum samples
Nail clippings
Faeces
Sputums
• Upper respiratory tract
not sterile
• What are the significant
organisms?
– Depends on patient’s
history
Sputums
• Upper respiratory tract
not sterile
• What are the significant
organisms?
– Depends on patient’s
history
Sputums
• Bronchitis, chest infection, COPD, pneumonia:
– H. influenzae, S. pneumoniae, S. aureus, M. catarrhalis,
other organisms in pure growth may be significant
• Bronchiectasis, cystic fibrosis, immunocompromised,
ICU:
– As above
– Enterobacteriaceae, Pseudomonads, fungi
• Cystic fibrosis
– All the above
– B. cepacia complex
Lesson Slide
• Only organisms that are considered potentially
pathogenic are worked up from specimens from nonsterile sites
– Same applies to wound swabs, faecal samples etc
CSFs
• Initial microscopy including Gram stain performed
urgently on sample when it arrives in the lab and the
results are communicated immediately
• Culture plates are examined daily but may not get a
definitive result for a number of days
• Many reasons for no growth in a patient with
bacterial meningitis
– Antibiotics before sample was taken
– Delicate organism
– Fastidious organism
Middle Bit
Case 1
• 28-year old female admitted for management of
Crohn’s disease exacerbation
• Day 3 of admission
• Dysuria, frequency and suprapubic pain for one day
prior to admission
• No fever or flank pain on admission
• Commenced on ciprofloxacin 500mg BD PO by
team; now day 3
Case 1
Urine report
• Microscopy:
– WCC 450/mm3
– RCC 0
– No casts/crystals
– ++ bacteria
• Culture:
– > 105 cfu/ml Pure growth of Escherichia coli
– R: Ampicillin, Trimethoprim
– S: Co-amoxiclav, Nitrofurantoin
Case 2
• 37-year old male
• Admitted with cellulitis of left lower limb
surrounding left ankle and extending proximally
• Was ice-skating 5 days previously- healing blister on
left ankle
• No past medical history of note
• On flucloxacillin 500mg QDS IV and
benzylpenicillin 600mg QDS IV
Case 2
Swab of blister report
• Culture report:
– Staphylococcus aureus
• S: Flucloxacillin, Erythromycin
– Pseudomonas aeruginosa
• S: Ciprofloxacin, Pip-tazobactam
– Coagulase-negative staphylococci
Case 3
• 66-year old male
• On vancomycin 500mg BD IV day 2 because of the
urine report below; trough level today 7.5mg/L
• Mid-stream urine sent to the laboratory 4 days earlier
– Report:
• White cell count 20/mm3
• No red cells
• No casts
• Culture: >105 orgs/mL Pure growth MRSA
– R: Flucloxacillin, Erythromycin
– S: Nitrofurantoin, Trimethoprim, Linezolid, Vancomycin
Case 3
Scenario 1
• Admitted as an emergency 25 days previously with a
perforated bowel
• Required a laparotomy and a course of antibiotics
(amoxicillin, gentamicin, metronidazole)
• Was admitted to ICU (central line etc), now on the
wards
• Finished course of antibiotics over 2 weeks earlier
• MRSA screen persistently positive (nose and groin)
• Urinary catheter removed 4 days previously
• Was always afebrile and well with no urinary or
systemic symptoms
Case 3
Scenario 1
Stop vancomycin!
Asymptomatic bacteriuria
Case 3
Scenario 2
• Same patient
• However, new onset dysuria and frequency for 2 days
• No fever, no flank pain
Case 3
Scenario 2
Stop vancomycin!
Nitrofurantoin or doxycycline to complete 7-10 days
of antimicrobial treatment
Case 3
Scenario 3
• Same patient
• No urinary symptoms
• However, fever for the last 10 days not settling
despite empiric pip-tazobactam (which was stopped
that morning)
• Complains of dyspnoea, chest pain
• New systolic murmur on auscultation
Case 3
Scenario 3
Investigate and treat!
3 sets of blood cultures
Trans-oesophageal ECHO
Increase vancomycin dose
Aim for trough levels of 15-20mg/L
Add gentamicin and rifampicin
Lesson Slide
• Treat the patient, not the report!
– A laboratory report should always be correlated with the
clinical picture
Case4
• 32 year old female, BIBA to A&E
• 2 day hx of malaise, headache, fever, nausea
• Became lethargic and confused and had a focal
seizure
• LP:
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–
–
–
–
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WCC 67, 98% lymphocytes
RCC 0
Glucose normal
Protein slightly raised
Gram stain: no organisms seen
Culture: no growth
Case 4
• PCR for viral pathogens (HSV 1 and 2, VZV,
Enterovirus) negative
• Sensitivity and specificity of PCR assay for HSV
>95%
• Patient was started on high dose IV acyclovir on
admission for presumed HSV encephalitis
• Would you stop the acyclovir?
Sensitivity and Specificity of a Test
• Sensitivity
– The proportion of people with the disease that the test
correctly classifies as having the disease
• Specificity
– The proportion of people without the disease that the test
correctly classifies as not having the disease
Case 4
• Both the sensitivity and specificity of HSV PCR are
>95% but they are not 100%
• False negative results are possible
PPV and NPV of a Test
• Positive predictive value
– The probability of a disease being present assuming a
positive result is obtained (true positives/ test positives)
– The post-test probability of being infected after a positive
test result
• Negative predictive value
– The probability of not having a disease assuming a negative
result is obtained (true negatives/ test negatives)
– The post-test probability of being uninfected after a
negative test result
Calculating PPV and NPV
Case 4
• Pre-test probability of HSV disease approx 60%
• Worst case scenario: sensitivity and specificity of test
95%
• NPV 93%
• Post-test probability of HSV disease with a negative
HSV PCR approx 7%
• Acyclovir should be continued
Case 4
• If patient did not have confusion or focal neurological
findings, the pre-test probability of HSV disease
would be approx 5%
• The post-test probability of HSV disease with a
negative HSV PCR result now would be approx 0.3%
• Acyclovir can be stopped
Lesson Slide
• Results don’t always give definitive answers
– In many ways relates to second Lesson Slide
Final Bit
Objectives
• Have some idea of laboratory processes
• Have some idea of the relative importance of
laboratory reports and how they should be interpreted
Lessons
• Microscopy result early, culture result late
• More information available in the lab than is released
in the reports
• Only organisms that are considered potentially
pathogenic are worked up from specimens from nonsterile sites
• Treat the patient, not the report
• Results don’t always give definitive answers
Lessons
• Microscopy result early, culture result late
• More information available in the lab than is released
in the reports
• Only organisms that are considered potentially
pathogenic are worked up from specimens from nonsterile sites
• Treat the patient, not the report
• Results don’t always give definitive answers
Thank you
Any Questions?