Introduction: Cepheid Xpert MTB/RIF Assay

Transcription

1 Introduction: Cepheid Xpert MTB/RIF Assay Kathleen G. Beavis, MD, Director, Microbiology and Immunology Laboratories, University of Chicago Medicine, Chicago, IL Michael F. Iademarco. MD, MPH, CAPT USPHS, Chief, Laboratory Branch, Division of Tuberculosis Elimination, NCHHSTP, CDC, Atlanta, GA David Warshauer. Ph.D. D(ABMM), Deputy Director, Communicable Diseases, Wisconsin State Laboratory of Hygiene, Madison, WI. 1

2 Faculty Disclosure The Association of Public Health Laboratories adheres to established standards regarding industry support of continuing education for healthcare professionals. The following disclosures of personal financial relationships with commercial interests within the last 12 months as relative to this presentation have been made by the speaker(s): Kathleen G. Beavis, MD Michael F. Iademarco. MD, MPH, CAPT USPHS David Warshauer. Ph.D. D(ABMM) Nothing to disclose Nothing to disclose Nothing to disclose 2 2

3 Introduction: Cepheid Xpert MTB/RIF Assay David Warshauer, PhD Chief Bacteriologist and Deputy Director, Communicable Disease Division Wisconsin State Laboratory of Hygiene Laboratory Impact of the Cepheid Xpert MTB/RIF Assay Webinar October 21, 2013 from Madison, WI 3

4 4 Cepheid Xpert MTB/RIF Assay Automated commercial system for identification of M. tuberculosis complex and detection of rifampin resistance Decontamination, digestion, DNA extraction, amplification, and detection in single, sealed cartridge Integrated positive control assures that a negative result is not due to NAA inhibitors in the specimen Results in ~2 hours Minimal hands on manipulation- technically simple 4

5 Cepheid Xpert MTB/RIF Assay Target: rpob gene Nested PCR and molecular beacon technology Same segment of the rpob gene is used for detection of both M. tb complex and rifampin resistance PCR amplifies a small region relevant for rifampin resistance; uses 5 probes to assess for mutations 5

6 M. Tb Complex PCR for All aidsmap.com 6

7 finddiadnostics.org 7

8 MTB/RIF Assay design 8 The MTB assay target is the 81 bp region (RRDR) of the rpob gene. Molecular Beacon Target Hybrid Example of Rif-Sensitive Profile 5 probes are positive SPC Each probe is labeled with a different fluorophore, permitting simultaneous detection of the presence of wild type. Courtesy Ken Jost, Texas SPHL 8

9 Review of existing CDC guidance of use of NAA testing in light of Xpert MTB/RIF availability Michael F. Iademarco, M.D., M.P.H. Captain, U.S. Public Health Service Division of Tuberculosis Elimination, U.S. CDC Laboratory Impact of the Cepheid Xpert MTB/RIF Assay Webinar October 21, 2013 from Atlanta, GA 9

10 CDC draft MMWR Provides interim guidance, based on existing recommendations o Xpert MTB/RIF* is an NAA test for MTBC plus RMP ** resistance o 2009 Use of nucleic acid amplification tests o 2005 Preventing Transmission of TB in Health-Care Settings Focuses on three areas o Diagnosis of MTBC o Need for confirmatory testing with suspected drug resistance o Potential role of Xpert MTB/RIF and NAA testing in infection control *Xpert MTB/RIF is by Cepheid NAA test is nucleic acid amplification test MTBC is Mycobacterium tuberculosis complex **RMP is rifampin 10

11 NAA tests and diagnostic delay Diagnostic delay was a significant factor in 27 outbreaks in which CDC assisted, * In 2009, public health laboratories performed NAA testing for MTBC for 14% of persons suspected of TB nationally CDC issued cautious guidelines in 1996 and 2000, due to limited evidence of programmatic effectiveness CDC updated NAA test guidance in 2009 *Mitruka K, et al. Emerg Infect Dis 2011; 17(3): CDC. Unpublished data 11

12 NAA testing should be performed on at least one respiratory specimen from each patient with signs and symptoms of pulmonary TB for whom a diagnosis of TB is being considered but has not yet been established, and for whom the test result would alter case management or TB control activities. 12

13 Recent Study* of NAA testing Retrospective cohort of 2140 reported patients with suspected TB, from four states, Compared 43% evaluated by MTD to those with no MTD Significant health systems benefits o Diagnostic accuracy improved, and delay reduced o Reduced respiratory isolation, CT exams, bronchoscopy, biopsy, unnecessary treatment, and contact investigations o Cost savings for patients with HIV infection, homelessness, and substance abuse *Marks SM, et al; CID 2013;57: MTD is M. tuberculosis direct nucleic acid amplification test by GenProbe 13

14 Point #1: Diagnosis of MTBC Health care institutions and enterprises and public health programs should promote algorithms that reduce diagnostic delay Use NAA test, preferably on the first specimen NAA testing does not replace need for mycobacteriological testing o AFB smear microscopy o Culture o Drug susceptibility testing 14

15 Point #2: Confirm Xpert MTB/RIF RMP resistance positive results Sensitivity is 95% and specificity, is 99% Yet, because the U.S. prevalence of RMP resistance is about 1.8%, the PPV* of a test positive is less than 50% Therefore, report the result and secure confirmatory testing o o o o DNA sequencing: rpob, inha, and katg (for both RMP and INH, i.e., MDR) Avoiding delay, perform molecular testing for first-line and second-line drugs in cases suspected of MDR TB CDC s Molecular Detection of Drug Resistance service at TBLAB@CDC.GOV Also prompt growth-based DST MMWR will contain suggested minimal reporting language Goal is effective second line regimen for MDR TB *PPV is positive predictive value 15

16 Point #3: Infection control (1) In current guidelines, airborne infection isolation precautions can be discontinued for patients suspected of pulmonary TB* when o Contagious TB is considered unlikely; and either o Another diagnosis is made that explains clinical syndrome, or o Three sputum smears, collected at 8 to 24 hour intervals, one should be early-morning, are AFB smear negative Focus on NPV for contagiousness *Pulmonary TB to include here disease of the lung, airway, or larynx AFB is acid-fast bacilli NPV is negative predictive value 16

17 Point #3: Infection control (2) Logically because sensitivity and specificity of NAA for MTBC is greater than AFB microscopy, then any one NAA test could substitute for a sputum smear Given NTM is more common than TB, NAA results negative for MTBC but with sputum smear results positive for AFB more likely represents NTM disease MMWR will provide some tabular guidance on how to deal with mixed AFB smear, NAA, and Xpert results Studies are needed to examine how many NAA tests provide sufficient NPV for contagiousness 17

18 Point #3: Infection control (3) Not to be confused with patients with TB; discontinuation of airborne precautions o On standard therapy o Clinical response o Three sputum smears are AFB negative 18

19 Summary TB is increasingly an uncommon condition, and drug resistant disease is rare in the United States Therefore, prompt consultation with public health departments and other highly specialized experts is essential NAA testing and Xpert MTB/RIF offer an opportunity to reduce systems delay, thereby decreasing transmission Prompt access to other mycobacteriological testing, such as AFB-smear microscopy, culture, and drug susceptibility testing, are still needed 19

20 References (1) CDC. Guidelines for Preventing the Transmission of Mycobacterium tuberculosis in Health-Care Settings, 2005; MMWR 2005;54(No. RR-17) CDC. Updated Guidelines for the Use of Nucleic Acid Amplification Tests in the Diagnosis of Tuberculosis; MMWR 2009;58:7-10 Report of an Expert Consultation on the Uses of Nucleic Acid Amplification Tests for the Diagnosis of Tuberculosis, Atlanta, ing/moldstreport.pdf, accessed July 4,

21 References (2) Marks SM, et al; The Health-System Benefits and Costeffectiveness of Using Mycobacterium Tuberculosis Direct Nucleic Acid Amplification Testing to Diagnose Tuberculosis Disease in the United States; CID 2013;57: CDC s DTBE mycobacteriology laboratory services, including the Molecular Detection of Drug Resistance Service, accessed September 30, 2013 Davis JL, et al; The clinical and public health impact of automated nucleic acid testing for TB evaluation in San Francisco. ATS International Conference. Denver, Colorado; p. A

22 TABLE 1. Result Interpretation and Proposed Laboratory Report Language for Xpert MTB/RIF Assay a GeneXpert Instrument System Generated Result b MTB d DETECTED, Rif Resistance DETECTED MTB DETECTED, Rif Resistance NOT DETECTED MTB DETECTED, Rif Resistance INDETERMINATE MTB NOT DETECTED Xpert MTB/RIF Assay Result Interpretation MTB target is detected within the sample. A mutation e in the rpob gene has been detected. MTB target is detected within the sample. A mutation in the rpob gene has not been detected. MTB target is detected within the sample. A mutation in the rpob gene could not be determined due to insufficient signal detection. MTB target is not detected within the sample. Minimum Laboratory Report c MTBC detected. A mutation in rpob gene has been detected, indicating possible rifampin resistance. Confirmatory testing should follow f. MTBC detected. No rpob gene mutations detected; probably rifampin susceptible. MTBC detected; presence of rpob gene mutations cannot be accurately determined. MTBC not detected. 22

23 TABLE 2. Use of SS and NAA testing for infection control in health-care settings for patients with suspected TB Results of combinations of SS* and NAA testing, on a total of at least three specimens, each collected 8 to 24 hours apart, with one being an early morning specimen SS results NAA test results All SS are negative At least one SS is positive At least one is positive At least one is positive If SS not available All SS are negative All SS are negative All NAA tests are negative for the detection of MTBC All NAA tests are negative for the detection of MTBC At least one NAA test is positive for the detection of MTBC At least one Xpert MTB/RIF assay is positive for the detection of MTBC and RMP resistance At least one NAA test is positive for the detection of MTBC At least one NAA test is positive for the detection of MTBC At least one Xpert MTB/RIF assay is positive for the detection of MTBC and RMP resistance Decisional analysis DRAFT TABLE In combination with other requirements (3) supports discontinuation of AII precautions. Consistent with presence of NTM; pulmonary or laryngeal TB is unlikely but cannot be excluded, pending culture results and other clinical determinants. Decision to discontinue AII precautions based on evaluation of all clinical information and potential risk for transmission. Consistent with pulmonary or laryngeal TB; supports continuation of AII precautions until recommended criteria are met (3). Consistent with suspected pulmonary or laryngeal MDR TB; Xpert MTB/RIF assay RMP resistance result should be confirmed by rapid DNA sequencing and be accompanied by first and second line growth-based DST; if RMP resistance is confirmed, some infection-control practitioners may choose AII precautions during the entire hospitalization or until culture conversion is documented (3). Consistent with pulmonary or laryngeal TB; SS needed to contribute to infection control decision making. Consistent with pulmonary TB but less contagious than if SS positive; may support discontinuation of AII precautions if other criteria for discontinuing AII precautions are met (e.g., patient has received a sufficient duration of effective TB treatment) or patient is housed in setting where risk of transmission is low and treatment is started promptly. Consistent with suspected pulmonary MDR TB and low bacillary load; the Xpert MTB/RIF assay RMP resistance result should be confirmed by rapid DNA sequencing and first and second line growth-based DST; if confirmed as RMP resistant, some infection-control practitioners may choose AII precautions during the entire hospitalization, or until culture conversion is documented (3). 23

24 Cepheid Xpert MTB/RIF Assay: The Public Health Laboratory Perspective David Warshauer, PhD, D(ABMM) Chief Bacteriologist and Deputy Director, Communicable Disease Division Wisconsin State Laboratory of Hygiene Laboratory Impact of the Cepheid Xpert MTB/RIF Assay Webinar October 21, 2013 from Madison, WI 24

25 Education Role of the Public Health Laboratory o Clinical laboratories o Clinicians o Infection Control o Public Health o TB Controllers Assure test availability o Provide NAA testing in-house o Arrange for referral to another laboratory 25

26 Educational Objectives Increase awareness of the availability of the Xpert MTB/RIF for the laboratory diagnosis of Mtb infection and detection of rifampin resistance Describe o Appropriate specimen types o Testing algorithms that incorporate Xpert MTB/RIF, AFB smear, culture, and molecular and phenotypic DST o Xpert MTB/RIF results interpretation o Reporting language o Additional testing that may be needed 26

27 Increasing Awareness of the availability of NAA Testing Use of NAAT by US Public Health Laboratories in ,425 suspect TB patients 92,877 not tested 88% 12,548 tested 12% 5,855 from Florida Starks et al CDC 2008 NAR2010 P 77 27

28 Use of Xpert MTB/RIF NAAT is a supplemental test o Does not replace AFB smear and culture o Smear needed for interpretation o Culture still the Gold Standard for TB diagnosis In a low TB prevalence population, most smear positive specimens will be NTMs Predictive value of rifampin resistance with Xpert MTB/RIF will be low in the U.S. population 28 28

29 First Respiratory Specimen Smear Positive Smear Negative NAAT NAAT Positive: Presumed TB, Pending culture results Negative Use clinical judgment to determine whether to begin therapy while awaiting culture results and determine if additional diagnostic testing is needed. Consider testing another specimen (not to exceed a total of two). If a second specimen is smear positive, NAAT negative. the patient is presumed to have an infection with non-tuberculous mycobacteria, pending culture results, Inhibitors Detected: Test result is of no diagnostic help. Consider testing second specimen (not to exceed a total of two). Positive Use clinical judgment to determine whether to begin therapy while awaiting culture results and determine if additional diagnostic testing is needed. Consider testing another specimen (not to exceed a total of two). NAAT Positive: A patient can be presumed to have tuberculosis, pending culture results, if two specimens are NAA positive. Negative Use clinical judgment to determine whether to begin therapy while awaiting results of culture and other diagnostic tests. Currently available NAA tests are not sufficiently sensitive to exclude the diagnosis of TB in AFB smear negative patients suspected of having TB.

30 Communication of Xpert MTB/RIF Results Report results as soon as available o Optimally with the AFB smear result Treat positive results as a critical value o Report positive NAA results ASAP to public health and TB controllers in addition to health care provider and infection control 30

31 APHL Guidance Document 31

32 Cepheid Xpert MTB/RIF Assay: The Clinical Laboratory Perspective Kathleen G. Beavis, MD Director, Microbiology and Immunology Laboratories University of Chicago Medicine Laboratory Impact of the Cepheid Xpert MTB/RIF Assay Webinar October 21, 2013 from Chicago, IL 32

33 Laboratory Considerations Safety Workflow Verification Quality Control Proficiency Testing Future Considerations 33

34 Safety Specimen preparation o Viable organisms o Use of biosafety cabinet 34

35 Workflow Specimen quantity One TB/RIF test TB/RIF with repeat Sputum sediment 0.5 ml 1ml Raw sputum 1mL 2 ml Additional workflow depends on TB services offered in the laboratory o Smear only o Smear and Culture 35

36 Verification MTB and RIF MIC Validation/Verification Study Phase II There is documentation that the laboratory has performed a validation/verification study prior to reporting patient results. Note: Specimens must include positive and negative patient samples 36

37 Quality Control Internal controls suffice if all of the following are met: o For qualitative tests, the test system includes an electronic/procedural /built-in internal control run daily o Unmodified FDA-cleared or approved system o Laboratory has performed studies showing adequacy of limiting daily QC o External QC run per new lot, shipment, software upgrade, and the more frequent of every 30 days or per PI 37

38 Proficiency Testing Wisconsin State Laboratory of Hygiene currently offers two options 2 mailings with either 3 or 5 challenges CAP is finalizing their offerings for

39 Future Considerations Can Xpert MTB/RIF save a patient with positive smears from antituberculous drugs? Can Xpert MTB/RIF be used instead of a smear? Can Xpert MTB/RIF be used at point-of-care? 39

40 For Additional Information on FDA approved/market authorized TB NAATs: Cepheid Romain Prieur Sr.Director, Critical Infectious Disease, Cepheid Kaoru Otaki Marketing Manager, Critical Infectious Disease, Cepheid Hologic Gen-Probe Peter Kelly Director of National Accounts