Receipt within 1 day of specimen collection. Report AFB b smear result within 1 day from receipt of specimen

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1 Recommendation Promote rapid delivery of specimens to the laboratory Use fluorescent acid-fast staining and promptly transmit results by phone, FAX, or electronically Identify growth as acid-fast and use rapid methods to identify and report isolates as MTBC c as soon as possible Determine the susceptibilities of initial MTBC isolates to first- line drugs in a rapid culture system and report results promptly Benchmark Receipt within 1 day of specimen collection Report AFB b smear result within 1 day from receipt of specimen Report identification results within days from receipt of specimen Report susceptibilities to first-line drugs within 17 days of MTBC identification from culture Performance Target a 67% of specimens received within 1 day 92% of specimens with AFB smear result reported within 1 day of receipt 74% of MTBC isolates identified from initial diagnostic specimens reported as MTBC within 21 days of receipt 69% of rifampin results reported for initial diagnostic specimens within 17 days of MTBC identification from culture Healthy People Reduce the average time for a laboratory to confirm and report tuberculosis cases using NAAT d Report NAAT within 2 days from receipt of specimen 77% of MTBC cases that are later culture confirmed diagnosed using NAAT (or other direct detection method) within 2 days of receipt a Performance targets represent the median percent of diagnostic specimens meeting benchmark turnaround time (TAT) as calculated from a multicenter evaluation, with the exception of NAAT. TAT benchmarks and target for NAAT are defined within Healthy People b AFB Acid-fast bacilli c MTBC Mycobacterium tuberculosis complex d NAAT Nucleic Acid Amplification Test

2 LABORATORY GLOSSARY The following definitions should be used for the purposes of this program. These terms are used in the program announcement. 1. Calendar day: successive days, not working days. This includes days that the laboratory is not open for business (weekends, holidays). 2. Clinical specimen: sample derived directly from a patient (e.g., sputum, CSF) that is submitted to the laboratory for testing. These are also known as primary or raw specimens 3. Individual patient: unique person 4. Isolate: organism obtained by processing and culturing a clinical specimen. This would include, for example, a positive MGIT or other broth tube, or an LJ slant or 7-H-11 plate with visible growth. 5. Initial diagnostic specimen: first clinical specimen received in your laboratory from an individual patient, that has a positive result (identification or drug susceptibility test). This does not include follow-up specimens. This should include clinical specimens referred to another laboratory for testing 6. Initial M. tuberculosis complex isolate: first M. tuberculosis complex (MTBC) isolate recovered from an individual patient. For example, if 2 sputum specimens were submitted on Patient A, one on 9/10 and one on 9/12, and the first M. tuberculosis isolate identified was from the specimen submitted on 9/12, then this would be the initial isolate, even if M. tuberculosis grows from the 9/10 specimen. 7. Jurisdiction: state, city, or county covered by the cooperative agreement program. 8. NAAT: nucleic acid amplification test for the detection of M. tuberculosis complex performed directly on a clinical specimen, e.g. real-time PCR, GenProbe MTD, Cepheid GeneXpert MTB/RIF 9. Direct, or rapid detection test: test for the detection of M. tuberculosis complex performed directly on a clinical specimen (e.g. NAAT, direct HPLC). This does not include species identification tests performed on isolates, such as ACCUPROBE 10. Reference isolate, referred isolate: organism obtained by processing and culturing a clinical specimen in another laboratory that is referred to your laboratory for testing. This includes isolates referred on solid and in liquid media. See Isolate, above. 11. Sediment, Referred sediment: concentrated or processed specimen or centrifuged sediment from a patient, that is sent from another laboratory 12. First-Line Drugs: isoniazid, ethambutol, rifampin, and pyrazinamide. 13. Growth-based DST: Drug susceptibility test that is phenotypic, or growth-based, e.g. MGIT DST or agar-proportion DST. 14. IGRA: Interferon gamma-release assay to detect latent TB infection, performed on blood specimens, e.g. Quantiferon-Gold-in- Tube, T-Spot.TB.

3 For all TAT indicators: TO CALCULATE TURNAROUND TIMES (TAT) All indicators should be measured in calendar days, not working days and should include weekends and holidays, e.g. a specimen that arrives at the laboratory on a Friday afternoon and is processed with the smear read and the result reported on the following Monday would have a TAT of three days. For all indicators (except the Healthy People 2020 indicator), percent can be determined by the following formula (using specimen receipt in one calendar day for 2017 as an example) Number of specimens received in one calendar day All specimens received in laboratory in 2017 x 100 Receipt of Specimens in the laboratory: This indicator should measure the time (in calendar days) it takes for a clinical specimen to reach the laboratory from time of collection to time of delivery to the laboratory building itself (not the TB section). Weekends and holidays should be included. Calculate the percent reaching the lab within 1, 2, and 3 calendar days. This calculation should be cumulative, i.e., the percent within 3 days includes the percent within 1 and 2 days. Smear results: This indicator should measure the time (in calendar days) it takes for a clinical specimen to have a smear result reported from the time of specimen receipt in the laboratory. Calculate the percent of specimens having smear results reported within 1, 2, and 3 calendar days. This calculation should also be cumulative. ID of MTBC within 21 days: This indicator should measure the time (in calendar days) it takes for an initial diagnostic specimen 1 to be identified as MTB complex (from a culture of the specimen) from the time of specimen receipt in the laboratory. This does not include identification of referred isolates, nor does it pertain to direct detection of MTBC from clinical specimens such as NAA testing. To calculate, determine the number of identifications of MTB complex from initial diagnostic specimens (the denominator), and of those, the number that were identified within 21 days of specimen receipt (the numerator). DST of MTBC within 17 days of identification: This indicator should measure the time (in calendar days) it takes to report the rifampin result (from a culture of MTBC from an initial diagnostic specimen 1 ) after ID of MTBC (see above). This indicator does not include DSTs performed on referred isolates or by molecular testing. To calculate this indicator, determine the number of DSTs performed from initial diagnostic patient specimens (the denominator), and of those, the number that were reported within 17 days of the date of ID of MTBC (the numerator). For laboratories using the DST Reference Center or another reference laboratory, TAT for DST should be calculated in the same manner as above from ID of MTBC in your laboratory to report of rifampin result by your laboratory. Challenges experienced with referral and those encountered internally should be documented. 1 P age

4 Healthy People (HP) Reduce the average time for a laboratory to confirm and report tuberculosis cases using NAA testing: The HP2020 indicator measures number of individuals positive for TB by culture that were detected by a positive NAA test within 48 hours of specimen receipt. First, identify number of individual patients for whom a clinical specimen was processed for smear and culture (workload indicator 2). Of these, determine number of individual patients for whom at least one culture was positive for MTBC (workload indicator 2a). Then, of these individuals positive for MTBC by culture, determine how many of these were initially positive by NAA testing of a clinical specimen in your laboratory (workload indicator 2b). Finally, the HP2020 indicator is of these (2b), how many were reported within 48 hours of specimen receipt. This number should be a subset of 2b, which is a subset of 2a, which is a subset of 2. Although a number is requested for the HP2020 indicator for the Cooperative Agreement data, a percentage can be calculated for use within the laboratory to aid in establishing local laboratory goals and assessing strategies and activities and to compare to HP2020 national goals. To calculate a percentage, divide the HP2020 number (numerator) by number of individual patients for whom at least one culture was positive for MTBC (2a) (denominator). Data checking common errors: For specimen receipt and for smear results, the percent within 3 calendar days should be greater than the percent within 1 and 2 calendar days, and the percent within 2 calendar days should be greater than the percent within 1 calendar day. If the percent within 1 calendar day for receipt of specimens and for smear result is reported as 100%, please double check to make sure you are using calendar days, not working days in your calculations. Laboratories that are not open on weekends or holidays are unlikely to truly meet these indicators 100% of the time in one calendar day. For the Healthy People 2020 indicator, the number indicated (patients with positive NAAT within 48 hours) should not exceed the number of patients tested by NAAT on line 2b of the Workload Data Collection Form. This should be reported as a number, not a percentage. Indicator/Benchmark National Targets: % within recommended time 2016 National averages: % within recommended time Receipt of specimens within 1 day 67% 50% City Labs 80% State Labs 46% Receipt of specimens within 2 days City Labs 88% State Labs 66% Receipt of specimens within 3 days City Labs 95% State Labs 78% Smear results within 1 day of specimen receipt 92% 90% ID of MTBC within 21 days of specimen receipt 74% 73% DST results within 17 days of ID of MTBC 69% 63% HP2020 goal 77% 52% 1 Initial diagnostic specimen: first clinical specimen received in your laboratory from an individual patient that has a positive result (identification or drug susceptibility test). This does not include follow-up specimens. This should include clinical specimens referred to another laboratory for testing. 2 P age

5 Tuberculosis Elimination Cooperative Agreement Checklist Laboratory Upgrade Component 1. An organizational chart of the laboratory 2. One designated laboratory point of contact with associated contact information 3. A brief description of methods used in the laboratory Description of work flow within the laboratory 4. Element 1 Ensure availability of high-quality and prompt core laboratory services Laboratory workload and turnaround time (TAT) data for 2017 and 2018 (Jan-June) in tabular form (see the Workload Data Template for specific items to include) A narrative on laboratory activities related to each of the TAT recommendations including Annual, internal measurable goals for improving TAT Description of measurable goals for each laboratory-specific benchmark for coming year Description of specific strategies and activities for achieving the stated goals Explanation of potential obstacles to meeting outcomes Update of past year s achievement of previously stated goals/outcomes 5. Element 2* Promote continual advancement of laboratory efficiency and quality assurance through use of local data Update of past year s achievement of previously stated strategies/activities (goals/outcomes) Description of measurable goals/outcomes appropriate for your laboratory volume and services for upcoming calendar year Description of specific strategies and activities for achieving the outcomes Evaluation plan for strategies/activities and progress towards outcomes 6. Element 3* Collaborate with partners (e.g., healthcare providers, TB Control, and laboratory network) to ensure optimal use of laboratory services and timely flow of information Update of past year s achievement of previously stated strategies/activities (goals/outcomes) Description of measurable goals/outcomes appropriate for your laboratory volume and services for upcoming calendar year Description of specific strategies and activities for achieving the outcomes Evaluation plan for strategies/activities and progress towards outcomes 7. Budget A line-item budget reflecting anticipated funding level categorized as follows: Salaries and wages, Fringe benefits, Consultant costs, Equipment, Supplies, Travel, Other Categories, Total Direct Costs, Total Indirect Costs, and Contractual Costs. Justification/description required for each category Each line item should include the number anticipated and per unit cost Requests for personnel support should include the position title and the name of the individual (or if the position is vacant) *A true needs budget is not required (can be submitted if available) for the laboratory for the annual performance report this year. *Laboratory volume considerations for Elements 2 and 3: 2,000 clinical specimens each year should provide at least one measurable outcome for Elements 2 and 3 2,001-6,000 clinical specimens each year should provide at least two measurable outcomes for Elements 2 and 3 >6,000 clinical specimens each year should provide at least three measurable outcomes for Elements 2 and 3

6 2018 TB Cooperative Agreement Data Template Workload Data Collection Form Description of the laboratory workload (from your jurisdiction only) 1. Total number of clinical specimens (e.g. sputum, CSF, biopsy) processed for smear and culture. Do not include isolates referred from another laboratory. 2. Number of individual patients for whom a clinical specimen was processed for smear and culture. 2a. Of these, report the number of individual patients for whom at least one culture was positive for M. tuberculosis complex (MTBC). 2b. Of these individuals positive for MTBC by culture, how many were initially positive by nucleic acid amplification testing (NAAT) of a clinical specimen in your laboratory? Note: This number should not include specimens referred for NAAT only (i.e., no culture performed in your laboratory). (Allows assessment of Healthy People 2020 goal) 3. Number of individual patients for whom a reference isolate was received to rule out or confirm the identification of MTBC. This should not include known nontuberculous mycobacteria. 3a. Of these, report the number of individual patients for whom at least one reference isolate identified as MTBC. 4. Number of individual patients for whom growth based MTBC first-line DST was performed (either in-house or, if testing not done in-house, isolates referred to another laboratory for first-line DST). Note: If growth-based DST results were unavailable for a patient (e.g., due to contamination, no growth, or alternative testing algorithm) and molecular drug resistance testing was performed, the molecular results can be reported for the per patient DST workload component. Please do not double count for patients who have both growth-based and molecular results available. 5. Number of individual patients for whom a clinical specimen or processed referred sediment was tested directly with a NAAT. (This includes testing performed in-house and referred testing.) This does not refer to rapid species identification tests performed on isolates (e.g., ACCUPROBE). 5a. Of these, report the number of individual patients for whom a NAAT result was positive for MTBC. Note: For labs that accept referred specimens or sediments for NAAT-only, this number may be higher than data reported for 2b above. 6. Number of individual patients for whom the laboratory referred an isolate of MTBC for genotyping. 7. If applicable, provide the total number of interferon gamma release assays (IGRA) performed by your public health laboratory

7 2018 TB Cooperative Agreement Data Template Turnaround Time Data Collection Form Description of turnaround times (TAT) for initial diagnostic specimens Promote rapid delivery of clinical specimens to the laboratory. (Benchmark: Specimens should be received in the laboratory within 1 day of specimen collection) Report cumulative percent of specimens received within 1, 2, and 3 calendar days. % of specimens received within 1 calendar day CY2017 % of specimens received within 2 calendar days CY2017 % of specimens received within 3 calendar days CY2017 Use fluorescent acid-fast staining and promptly transmit results by phone, FAX, or electronically. (Benchmark: Report acid-fast microscopy results within 1 day of specimen receipt.) Report cumulative percent of acid-fast smear results reported within 1, 2, and 3 calendar days. % of smear results reported within 1 calendar day CY2017 % of smear results reported within 2 calendar days CY2017 % of smear results reported within 3 calendar days CY2017 Identify growth as acid-fast and use rapid methods to identify isolates from specimens as M. tuberculosis complex (MTBC) as soon as possible and report result promptly (Benchmark: ID within 21 calendar days from receipt of clinical specimen) Report percent MTBC identified from initial diagnostic specimens (e.g., sputum, CSF, etc.) identified within 21 calendar days. % of MTBC identified within 21 calendar days CY2017 CY 2018 (to date) Determine the susceptibilities (DST) of initial MTBC isolates to first-line drugs in a rapid culture system and report results promptly. (Benchmark: DST within 17 calendar days from ID of MTBC) Report the percent of rifampin DST results reported for MTBC isolates from initial diagnostic specimens within 17 days of ID of MTBC. % of rifampin DST results reported within 17 calendar days of ID of MTBC : CY2017 CY 2018 (to date) Healthy People Reduce the average time for a laboratory to confirm and report tuberculosis cases using NAAT. Healthy People 2020 goal is 2 days from receipt of clinical specimen for 77% of cases that are later culture confirmed. Of those identified as MTBC by culture, report the number of individual patients for whom a laboratory report of MTBC (i.e., positive NAAT or other positive direct detection method) was provided within 48 hours of clinical specimen receipt. CY2017 CY 2018 (to date)