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Transcript
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 • • • • • • 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 – – – – – 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 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: – – – – – – 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?
