Interpretation of Microbiology Reports

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Interpretation of Microbiology Reports

• Dr. Cathal Collins

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Objectives

• Have some idea of laboratory processes
• Have some idea of the relative importance of
  laboratory reports and how they should be
  interpreted

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Workshop Format

• First bit
• Example to demonstrate laboratory processes
• Middle bit
• Examples to demonstrate how reports should be
  interpreted
• Final bit
• Lessons learned

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First Bit
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Example

• Jane Doe, nursing home
• Presented to AE
• Fever, frequency, dysuria and right flank pain
• Clinical review
• Blood cultures and MSU
• Co-amoxiclav and gentamicin (both IV) started

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Urine microscopy
White cell
Epithelial cell
Urine microscopy counting chamber
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Day 1 Laboratory

• Urine microscopy is the only report that will be
  available soon after specimen arrival
• White cells (note significant pyuria gt10white
  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

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Blood cultures
Blood culture machine
Blood culture bottle
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Day 2 Laboratory

• Blood culture flags up as positive in the blood
  culture machine

Gram stain
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Day 2 Blood culture flags ve
Gram-positive cocci ?staph
Gram-negative bacilli
Gram-positive cocci ?strep
Yeast
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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

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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- dont know how much bug is in the
  drop

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Day 2 Laboratory

• Good idea of what is growing on the urine agar
  plates

MacConkey NLF and LF
Chromogenic agar
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Day 2 Laboratory

• Urinary isolate
• Set up biochemical identification test
• API
• Automated (Vitek, Phoenix etc)

API 20e
Phoenix
Vitek 2
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Day 2 Laboratory

• Urinary isolate
• Set up susceptibility tests (standardised
  inoculum)
• Disc diffusion
• Automated (Vitek, Phoenix etc)

Disc diffusion
Vitek
E-test for MIC
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Day 3 Laboratory

• Final report on urine specimen
• However, additional tests may be indicated to
  establish the resistance mechanism
• Good idea of whats in the blood cultures with
  unreliable susceptibility results for the 5 key
  anti-GNB antibiotics
• Identification of and standardised susceptibility
  testing on the blood culture isolate is performed

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Day 3 Laboratory

• The direct non-standardised susceptibility tests
  suggests that the blood culture organism may have
  reduced susceptibility to co-amoxiclav,
  pip-tazobactam, gentamicin, cefpodoxime and
  ciprofloxacin
• The urinary isolate is an Escherichia coli
• However, the standardised susceptibility pattern
  on the urinary E. coli is concerning!

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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
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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

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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
  co-amoxiclav and gentamicin and to start
  meropenem
• The infection control team are contacted and
  informed re a probable ESBL-producing isolate

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Day 4 Final Urine Report

• Microscopy
• WCC 450/mm3
• RCC 0
• No casts/crystals
• bacteria
• Culture
• gt 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.

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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.

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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

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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
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Lesson Slide

• Microscopy result early, culture result late
• More information available in the laboratory than
  is released in the reports

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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

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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

Identify all organisms growing
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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

Identify all organisms growing
Look for specific pathogens
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Sputums

• Upper respiratory tract not sterile
• What are the significant organisms?
• Depends on patients history

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Sputums

• Upper respiratory tract not sterile
• What are the significant organisms?
• Depends on patients history

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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

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Lesson Slide

• Only organisms that are considered potentially
  pathogenic are worked up from specimens from
  non-sterile sites
• Same applies to wound swabs, faecal samples etc

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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

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Middle Bit
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Case 1

• 28-year old female admitted for management of
  Crohns 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

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Urine report
Case 1

• Microscopy
• WCC 450/mm3
• RCC 0
• No casts/crystals
• bacteria
• Culture
• gt 105 cfu/ml Pure growth of Escherichia coli
• R Ampicillin, Trimethoprim
• S Co-amoxiclav, Nitrofurantoin

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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

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Swab of blister report
Case 2

• Culture report
• Staphylococcus aureus
• S Flucloxacillin, Erythromycin
• Pseudomonas aeruginosa
• S Ciprofloxacin, Pip-tazobactam
• Coagulase-negative staphylococci

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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 gt105 orgs/mL Pure growth MRSA
• R Flucloxacillin, Erythromycin
• S Nitrofurantoin, Trimethoprim, Linezolid,
  Vancomycin

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Scenario 1
Case 3

• 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

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Scenario 1
Case 3

• Stop vancomycin!Asymptomatic bacteriuria

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Scenario 2
Case 3

• Same patient
• However, new onset dysuria and frequency for 2
  days
• No fever, no flank pain

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Stop vancomycin!Nitrofurantoin or doxycycline to
complete 7-10 days of antimicrobial treatment
Case 3

• Scenario 2

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Scenario 3
Case 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

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Investigate and treat!3 sets of blood
culturesTrans-oesophageal ECHOIncrease
vancomycin dose Aim for trough levels of
15-20mg/LAdd gentamicin and rifampicin
Case 3

• Scenario 3

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Lesson Slide

• Treat the patient, not the report!
• A laboratory report should always be correlated
  with the clinical picture

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Case4

• 32 year old female, BIBA to AE
• 2 day hx of malaise, headache, fever, nausea
• Became lethargic and confused and had a focal
  seizure
• LP
• WCC 67, 98 lymphocytes
• RCC 0
• Glucose normal
• Protein slightly raised
• Gram stain no organisms seen
• Culture no growth

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Case 4

• PCR for viral pathogens (HSV 1 and 2, VZV,
  Enterovirus) negative
• Sensitivity and specificity of PCR assay for HSV
  gt95
• Patient was started on high dose IV acyclovir on
  admission for presumed HSV encephalitis

• Would you stop the acyclovir?

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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

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Case 4

• Both the sensitivity and specificity of HSV PCR
  are gt95 but they are not 100
• False negative results are possible

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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

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Calculating PPV and NPV
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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

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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

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Lesson Slide

• Results dont always give definitive answers
• In many ways relates to second Lesson Slide

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Final Bit
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Objectives

• Have some idea of laboratory processes
• Have some idea of the relative importance of
  laboratory reports and how they should be
  interpreted

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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
  non-sterile sites
• Treat the patient, not the report
• Results dont always give definitive answers

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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
  non-sterile sites
• Treat the patient, not the report
• Results dont always give definitive answers

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Thank you

• Any Questions?