EPID 525 Lecture 1 General Lab Issues UMHS Pathology Anatomic Clinical Surgical Pathology Autopsy Cytopathology Immunohistochemistry Blood Bank Hematology Chemistry Cytogenetics Molecular Microbiology • Role of the clinical microbiology laboratory • Diagnostic functions – Direct examination of the specimen – Grow/cultivate/DETECT organisms present – Analyze cultivated/DETECTED organisms • Communication of findings – present info in such a way as to avoid or minimize confusion – add interpretive comments where appropriate – provide educational updates • Expedited result reporting – • computerized through laboratory information systems Review various sources of technical guidelines – – – – Manual of Clinical Microbiology Clinical Microbiology Procedures Handbook Clinical Laboratory Standards Institute College of American Pathologists • Specimen collection and handling – Collection techniques • laboratory provides instructions • collect during acute phase, prior to administration of antibiotics • prepare site to minimize contamination with normal flora • sputum vs. saliva http://www.pathology.med.umich.edu/handbook/ • Specimen preservation, storage, labeling, requisition – transport to the lab ASAP • • • – oxygen anaerobes temperature Neisseria pH Shigella use preservatives, or anticoagulants if delays • Specimen rejection – – – – – – mislabeled/unlabeled improper transport temp. or container/medium quantity not sufficient (QNS) leaking delay in transport (> 2 hrs unpreserved) inappropriately received in fixative, or received dried up – MUST COMMUNICATE WITH CARE TEAM • Specimen processing – Direct microscopic examination • • • • can assess specimen quality (e.g. sputum) can assess inflammation (e.g. WBCs) compare direct smear with culture different stains: – Gram stain: bacteria, WBC, RBC, epithelial cells – Fungi: KOH or calcofluor white (fluorescent) – AFB: Kinyoun, Ziehl-Neelsen, or auraminerhodamine (fluorescent) • Specimen processing – Selection of culture media • nutritive: support the growth of wide range of (most) organisms • differential: allow for distinguishing between organisms because of different growth characteristics • selective: support the growth of one group of organisms but not another because of the addition of inhibitors (antibiotics, dyes, alcohol) • Specimen processing – Specimen preparation • homogenization (tissue) • concentration (CSF) • decontamination (respiratory) – Inoculation of solid media • quantitative cultures • streaking for isolation – Nucleic acid extraction/detection Laboratory Safety • Sterilization and Disinfection – Methods of sterilization: all forms of microbial life (including spores) are killed • physical methods: – – – – – • incineration: flame moist heat: autoclave; 121ºC, 15 psi dry heat: 160-180ºC filtration: 0.2 μm gamma irradiation: microwaves, X-rays chemical method: – ethylene oxide: gas for heat sensitive material • Sterilization and Disinfection – Methods of disinfection: only pathogenic microorganisms are destroyed • physical methods: – – – • boiling: 100ºC, 15 min pasteurization: 63ºC, 30 min or 72ºC, 15 sec UV light chemical methods: – – alcohol, bleach, phenol impacted by organism load, concentration, environmental conditions • Biosafety & Exposure Control Plan – – – Employee education and orientation Disposal of hazardous waste Standard precautions • • • • – No eating, drinking, smoking, applying cosmetics Treat every specimen as if it is HIV+ Wash hands Avoid needlesticks, sharps exposures Engineering controls • • • Biological safety cabinets (BSC) Personal protective equipment (PPE) Post-exposure control • Classification of Biologic Agents – Biosafety level 1 agents: no potential to cause disease in healthy people • – Standard precautions Biosafety level 2 agents: most common agents of infectious diseases • Standard precautions, limit access to lab, special training and supervision, BSCs for aerosols • Classification of Biologic Agents – Biosafety level 3 agents: unusual pathogens not routinely encountered. • • – Biosafety level 4 agents: rarely encountered hemorrhagic fever viruses and arboviruses • • Mycobacterium tuberculosis, mould forms of dimorphic fungi, Francisella, Brucella TRANSMITTED BY AEROSOL BSL 2, plus engineering controls, additional PPE BSL 3, plus special containment and PPE Mailing Biohazardous Materials • Regulated by the International Air Transport Association (IATA) – Dangerous goods regulations CLIA • Clinical Laboratory Improvement Act of 1988 • Resulted from public and Congressional concerns about the quality of clinical laboratory testing in the U.S. • Basic set of guidelines to apply to all labs, regardless of size, complexity, or location. • Implementation and development of working guideline was assigned to HCFA (Health Care Finance Agency), now known as CMS (Center for Medicare and Medicaid Services). Labs exempted from CLIA 88 • • • • • Labs accredited by state agencies (NY, WA) Law enforcement agencies Forensic testing and SAMSHA accredited labs Patient self-testing Research testing of human samples when there is no report of patient specific results. • VA system CLIA • The intent of CLIA is to promote the development, implementation, delivery, monitoring, and improvement of high quality laboratory services. CLIA Original consisted of 4 sets of rules describing: Laboratory standards Personnel standards Quality control requirements Test complexity model Quality assessment of the complete testing process Application process and user fees Enforcement procedures Approval of accreditation programs Total Testing Process Pre Analytic Analytic Post-Analytic Physician order Patient preparation Specimen acquisition Specimen handling Sample transport Sample prep Analyzer setup Test calibration Quality Control Sample analysis Test report Transmittal of report Receipt of report Review of test results Action on test results Quality Assurance Program designed to monitor and evaluate the ongoing and overall quality of the total testing process (preanalytic, analytic, and postanalytic) Quality Control Activities designed to monitor and evaluate the performance of instruments and reagents used in the testing process Is a component of a QA program Quality Assurance activities Patient test management assessment - specimen collection, labeling, transport - test requisition - specimen rejection - test report format and reporting systems Quality control assessment - calibrations and controls - patient data ranges - reporting errors Quality Assurance activities (cont.) Proficiency testing assessment - regulated and unregulated analytes Comparison of test results - different assays or instruments used for same test - accuracy and reproducibility Quality Assurance activities (cont.) Relationship of patient info. to test results - results consistent with patient info. - age, sex, diagnosis, other results Personnel assessment - education; competency Quality Assurance activities (cont.) Communications and complaint investigations - communications log QA review with staff - review during regular meetings Quality Assurance activities (cont.) QA records - retention for 2 years Verification of methods - accuracy, precision - analytical sensitivity and specificity - reportable range - reference range(s) (normal values) Quality Assurance activities (cont.) Quality monitors - TAT - smear/culture correlation - contamination rates Assessment of compliance College of American Pathologists (CAP) - Profession pathology organization - Been granted “deemed status” by CMS - Groups of peers conduct bi-annual site inspections - Publish checklists for laboratories to document compliance The next driver of changes? • Maryland General Hospital in Baltimore – Over a period of 14 months, the lab reported almost 500 HIV and hepatitis serologies when quality control was out. – Lab and hospital passed CAP and JCAHO inspections during this time period. • Result “Unannounced” inspections How do we assess the performance of our tests? Verification • Background • CLIA requirement to check (verify) the manufacturer’s performance specifications provided in package insert – – Assures that the test is performing as intended by the manufacturer » Your testing personnel » Your patient population » Your laboratory setting One time process performed prior to implementation Verification • Accuracy • Are your test results correct? – Assures that the test is performing as intended by the manufacturer » Use QC materials, PT materials, or previously tested patient specimens Verification • Precision • Can you obtain the same test result time after time? – – Same samples on same/different days (reproducible) Tested by different lab personnel (operator variance) Verification • Reportable Range • How high and how low can test values be and still be accurate (qualitative)? – • Choose samples with known values at high and low end of range claimed by manufacturer What is the range where the test is linear (quantitative)? – Test samples across the range Verification • Reference ranges/intervals (normal values) • Do the reference ranges provided by the test system’s manufacturer fit your patient population? – – Start with manufacturer’s suggested ranges Use published ranges » Can vary based on type of patient » May need to adjust over time » Normal patients should be within range, abnormal patients should be outside range Verification • Number of samples to test • Depends on the test system and laboratory testing volume – – • • FDA-approved: 20 positive and negatives Non-FDA approved: 50 positive and negatives The number used for each part of the verification will vary Laboratory director must review and approve results before reporting patient results Sensitivity • The probability of a positive test result given the presence of disease • How good is the test at detecting infection in those who have the disease? • A sensitive test will rarely miss people who have the disease (few false negatives). Specificity • The probability of a negative test result given the absence of disease. • How good is the test at calling uninfected people negative? • A specific test will rarely misclassify people without the disease as infected (few false positives). Sensitivity and Specificity DISEASE Present Absent True False Positive Positive Positive (TP) (FP) TEST False True Negative Negative Negative (FN) (TN) Sensitivity = TP/TP+FN Specificity = TN/TN+FP Predictive Value • The probability of the presence or absence of disease given the results of a test – PVP is the probability of disease in a patient with a positive test result. – PVN is the probability of not having disease when the test result is negative. Predictive Value DISEASE Present Absent True False Positive Positive Positive (TP) (FP) TEST False True Negative Negative Negative (FN) (TN) Predictive Value Positive (PVP) = TP/TP+FP Predictive Value Negative (PVN) =TN/TN+FN Predictive Value • How predictive is this test result for this particular patient? • Determined by the sensitivity and specificity of the test, and the prevalence rate of disease in the population being tested. Prevalence Rate Number of cases of illness existing at a given time divided by the population at risk Anatomy of an epidemic: W eeks fro m Peak 14 12 10 8 6 4 2 0 -2 -4 -6 -8 18 16 14 12 10 8 6 4 2 0 -10 P ercen t of Cases first case - transition - peak - last case Hypothetical Influenza Test Performance Prevalence = 20.0% Disease + - + 380 64 - 20 1536 Test Sensitivity = 380/400 = 95.0% Specificity = 1536/1600 = 96.0% Predictive Value Positive (PVP) = 380/444 = 85.6% Predictive Value Negative (PVN) = 1536/1556 = 98.7% Hypothetical Influenza Test Performance Prevalence = 1.0% Disease Test + - + 19 80 - 1 1900 Sensitivity = 19/20 = 95.0% Specificity = 1900/1980 = 96.0% Predictive Value Positive (PVP) = 19/99 = 19.2% Predictive Value Negative (PVN) = 1900/1901 = 99.9% 100% 80% 60% 40% 20% 0% 2% 4% 6% 8% 10 % 12 % 14 % 16 % 18 % 0% 20 % Predictive Value Positive Predictive Value Positive Dependence on Sensitivity, Specificity and Prevalence Prevalence Sens/Spec: 80/80 90/90 95/95 99/99 Predictive Values of Hypothetical Test Based on Wisconsin & National Prevalence Surrogates, 1999/2000 & 2000/2001 110.0% 100.0% 90.0% 80.0% 70.0% 60.0% 50.0% 40.0% 30.0% PVN PVP State (Wisconsin) Data 20.0% 10.0% 0.0% 110.0% 100.0% 90.0% 80.0% 70.0% 60.0% 50.0% National (CDC) Data 40.0% 30.0% 20.0% 10.0% 0.0% • The PVP varies widely throughout the year. • The PVN displays much less variability through the year Infection Control • Incidence of Nosocomial Infections – Function of IC is to prevent hospitalacquired (nosocomial) infections • • – Historically, handwashing was found to prevent nosocomial infections These infections add days to patient stays and increase morbidity and mortality Tracked by National Nosocomial Infections Surveillance (NNIS) by the CDC • Types of Nosocomial Infections – – – – • Urinary tract infections: indwelling catheters Lung infections: intubation or ventilator Surgical site infections Bloodstream infections: indwelling devices Emergence of Antibiotic-Resistant Organisms – – – – – – MRSA: Methicillin resistant Staphylococcus aureus VRE: Vancomycin resistant Enterococcus VISA: Vancomycin intermediate Staphylococcus aureus VRSA: Vancomycin resistant Staphylococcus aureus ESBL: Extended spectrum beta lactamase producing enteric gram negative bacilli Toxigenic Clostridium difficile • Hospital Infection Control Programs – Establish programs to prevent the spread of microorganisms Standard precautions for all patients Transmission-based precautions for selected patients – – • • TABLE 5-1 Role of the Microbiology Laboratory – – Provide data to IC regarding positive cultures Work with IC to report infections of public health importance Characterizing Strains Involved in an Outbreak – • • • Antibiograms Serotyping Molecular typing