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Interpretation of Microbiology Reports

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Title: Interpretation of Microbiology Reports


1
Interpretation of Microbiology Reports
  • Dr. Cathal Collins

2
Objectives
  • Have some idea of laboratory processes
  • Have some idea of the relative importance of
    laboratory reports and how they should be
    interpreted

3
Workshop Format
  • First bit
  • Example to demonstrate laboratory processes
  • Middle bit
  • Examples to demonstrate how reports should be
    interpreted
  • Final bit
  • Lessons learned

4
First Bit
5
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

6
Urine microscopy
White cell
Epithelial cell
Urine microscopy counting chamber
7
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

8
Blood cultures
Blood culture machine
Blood culture bottle
9
Day 2 Laboratory
  • Blood culture flags up as positive in the blood
    culture machine

Gram stain
10
Day 2 Blood culture flags ve
Gram-positive cocci ?staph
Gram-negative bacilli
Gram-positive cocci ?strep
Yeast
11
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

12
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

13
Day 2 Laboratory
  • Good idea of what is growing on the urine agar
    plates

MacConkey NLF and LF
Chromogenic agar
14
Day 2 Laboratory
  • Urinary isolate
  • Set up biochemical identification test
  • API
  • Automated (Vitek, Phoenix etc)

API 20e
Phoenix
Vitek 2
15
Day 2 Laboratory
  • Urinary isolate
  • Set up susceptibility tests (standardised
    inoculum)
  • Disc diffusion
  • Automated (Vitek, Phoenix etc)

Disc diffusion
Vitek
E-test for MIC
16
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

17
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!

18
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
19
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df
20
(No Transcript)
21
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

22
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

23
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.

24
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.

25
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

26
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
27
Lesson Slide
  • Microscopy result early, culture result late
  • More information available in the laboratory than
    is released in the reports

28
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

29
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
30
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
31
Sputums
  • Upper respiratory tract not sterile
  • What are the significant organisms?
  • Depends on patients history

32
Sputums
  • Upper respiratory tract not sterile
  • What are the significant organisms?
  • Depends on patients history

33
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

34
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

35
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

36
Middle Bit
37
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

38
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

39
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

40
Swab of blister report
Case 2
  • Culture report
  • Staphylococcus aureus
  • S Flucloxacillin, Erythromycin
  • Pseudomonas aeruginosa
  • S Ciprofloxacin, Pip-tazobactam
  • Coagulase-negative staphylococci

41
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

42
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

43
Scenario 1
Case 3
  • Stop vancomycin!Asymptomatic bacteriuria

44
Scenario 2
Case 3
  • Same patient
  • However, new onset dysuria and frequency for 2
    days
  • No fever, no flank pain

45
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46
Stop vancomycin!Nitrofurantoin or doxycycline to
complete 7-10 days of antimicrobial treatment
Case 3
  • Scenario 2

47
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

48
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

49
Lesson Slide
  • Treat the patient, not the report!
  • A laboratory report should always be correlated
    with the clinical picture

50
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

51
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52
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?

53
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

54
Case 4
  • Both the sensitivity and specificity of HSV PCR
    are gt95 but they are not 100
  • False negative results are possible

55
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

56
Calculating PPV and NPV
57
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

58
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

59
Lesson Slide
  • Results dont always give definitive answers
  • In many ways relates to second Lesson Slide

60
Final Bit
61
Objectives
  • Have some idea of laboratory processes
  • Have some idea of the relative importance of
    laboratory reports and how they should be
    interpreted

62
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

63
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

64
Thank you
  • Any Questions?
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