Experts on Xpert: A laboratorian and a clinician discuss interpretation of Xpert MTB/RIF Results

Transcription

1 Experts on Xpert: A laboratorian and a clinician discuss interpretation of Xpert MTB/RIF Results Pennan Barry, MD, MPH Grace Lin, MS September 6, 08 Curry International Tuberculosis Center Learning Objectives By the end of the training, participants will be able to: describe the principles behind the Xpert MTB/RIF test identify circumstances that should trigger additional testing or where false identification of MTB/RIF resistance should be suspected identify probes that most frequently detect mutations conferring RIF resistance and silent mutations not conferring RIF resistance identify situations where additional Xpert testing is not indicated Xpert interpretatiom-curry Center-9/6/8 September 6, 08

2 None Disclosures Xpert interpretatiom-curry Center-9/6/8 3 Agenda Intro: Not an introduction to Xpert use Not about release from respiratory isolation What is Xpert and how does it work? Case discussions: Illustrate nuances of Xpert interpretation (focus on RIF resistance result) When to ask for more info or more testing When not to test more Xpert interpretatiom-curry Center-9/6/8 4 September 6, 08

3 Xpert MTB/RIF assay Great tool for TB detection FDA Approved Shortens time significantly Testing time. hr; Easy to perform Real-Time PCR molecular beacon probes rpob gene (core region, codons 07-33) Xpert Clinical Report Xpert interpretatiom-curry Center-9/6/8 6 September 6, 08 3

4 Hidden Info: Report on Xpert computer Xpert interpretatiom-curry Center-9/6/8 7 Methodology: Realtime PCR Realtime PCR = PCR + probes PCR = Polymerase Chain Reaction Generates copies of specific segments of DNA DNA copies double with each PCR cycle Probes report whether specific sequence is present Probes bind to amplicons; generate signals with each PCR cycle PCR cycles Xpert interpretatiom-curry Center-9/6/8 8 September 6, 08 4

5 PCR Cycles 9 Molecular Beacon probe (Hairpin structure head & two arms) Head (functional part, MTBC sequence, ~0 nt) Two arms (-7 nt) Fluorophore Quencher At rest stage, two arms bind together forming a stem. Fluorophore is quenched. No signals are produced. 0 September 6, 08

6 Fluorescence produced by probe binding Experts on Xpert: A Laboratorian and a Clinician Discuss Interpretation of Xpert MTB/RIF Results Mutation Detection with Molecular Beacons (Head containing wildtype SQ) Mutant Sequence Wildtype Sequence MB resting MB head does not bind to mutant SQ. Arms remain closed. No signals produced. MB in action! MB head binds to wildtype SQ. Arms open. Fluorophore away from quencher. Signals produced. Ct: Threshold Cycle at which signal crosses threshold Low DNA in the specimen High Ct 0 Sample (Wildtype) Ct=8 Threshold PCR Cycle September 6, 08 6

7 Fluorescence produced by probe binding Fluorescence produced by probe binding Experts on Xpert: A Laboratorian and a Clinician Discuss Interpretation of Xpert MTB/RIF Results 0 Ct: Threshold Cycle at which signal crosses threshold Low DNA in the specimen High Ct Sample (Wildtype) Ct=8 Ct= Sample (Wildtype) Threshold PCR Cycle 3 Ct: Threshold Cycle at which signal crosses threshold Low DNA in the specimen High Ct 0 Ct=8 Sample (Wildtype) Ct= Sample (Wildtype) 0 Threshold Sample PCR Cycle 4 September 6, 08 7

8 No signals: 3 possibilities Mutation(s) present MTBC DNA insufficient or not present Smear-negatives (if < ~0 colonies/ml) Unable to generate enough DNA copies Smear positive but not MTBC Inhibitory substance Inhibit amplification Xpert has internal control (SPC) to detect this Signals in SPC indicate no inhibitory substance in specimen Xpert interpretatiom-curry Center-9/6/8 Critical Rules for Interpretation (Set by the Xpert software) MTBC detected at least probes are positive RIF-R detected If highest and lowest Ct differs by more than 4 (Δ Ct max > 4) See more rules in package insert 6 September 6, 08 8

9 Typical Xpert results (Examples showing Xpert s rules work as intended -- No nuance!) 7 Ct End-pt MTBC: Not detected No probe has signal SPC has signal. If no signal, test is invalid. 8 September 6, 08 9

10 Ct Ct End-pt End-pt MTBC detected probes up RIF-S No mutation Δ Ct max < 4 ( =.) 9 Ct End-pt MTBC detected 4 probes up RIF-R detected Probe E no signals Δ Ct max > 4: 4.8-0=4.8 Most common MDR mutation: S3L, detected by probe E 0 September 6, 08 0

11 September 6, 08 Xpert Probes: Coverage of rpob Codon # Most common mutation confers resistance (3 TTG) Ask your lab which probe resulted in the RIF-R result Can Xpert differentiate M. tuberculosis (MTB) from M. tuberculosis complex (MTBC)? Xpert interpretatiom-curry Center-9/6/8

12 M. tuberculosis Complex M. tuberculosis M. bovis M. africanum M. caprae M. pinnipedii M. microti M. mungi, M. orygis, M. canettii, M. suricattae (proposed) All cause tuberculosis Xpert interpretatiom-curry Center-9/6/8 3 MTB / MTB Complex? Species in the MTB complex have same rpob core region sequence Xpert can only identify MTBC, not MTB species. MTBC is the correct term. Xpert results for M. tuberculosis and M. bovis indistinguishable 4 September 6, 08

13 Complications encountered in the real world TB clinic Apply your new knowledge of the hidden info on the Xpert computer Xpert interpretatiom-curry Center-9/6/8 The problems Silent mutations Xpert software does not know they are silent Interprets as RIF-R Smear-negatives (low MTBC DNA) May falsely detect RIF-R May falsely identify NTM as MTBC [rare] Dead bugs Xpert finds DNA; cannot distinguish between alive and dead organisms Xpert interpretatiom-curry Center-9/6/8 6 September 6, 08 3

14 Case 70 yo man born in Mexico Cough, wt loss, night sweats x months CXR shows left upper lobe infiltrate Sputum is smear positive Xpert is ordered Xpert interpretatiom-curry Center-9/6/8 7 Ct Ct End-pt MTBC detected 4 probes up RIF-R detected Probe B (no signals) Caution: Most common Silent mutation in probe B 8 September 6, 08 4

15 Xpert Probes: Coverage of rpob Codon # Most common silent mutation (4 TTT) Ask your lab which probe resulted in the RIF-R result 9 Big surprise! ~0% of all the mutations detected in the rpob core region are Silent! (In California and other low MDR areas) Most common is 4TTT Mutations detectable by probe B: 70% is this silent mutation Disputed mutation: 6TAC, 6TTC, RIF-R mutations: 6GTC, 3AAA, GAA, etc. Pennan, how to deal with probe B mutations? Xpert interpretatiom-curry Center-9/6/8 30 September 6, 08

16 Number and Proportion MDR-TB by Country/Region of Origin, CA 0 0 Country/Region No. % Former Soviet Republics. Laos 6. Burma 3.4 India 3. Guatemala 3.0 Korea (N&S) 7.9 Peru.6 Ethiopia.0 Philippines 7.7 Vietnam 3.4 China (incl Taiwan) 7. United States Cambodia 0.7 Mexico 0.6 Countries with >3 cases tested for MDR 3 Number and Proportion MDR-TB by Country/Region of Origin, CA 0 0 Country/Region No. % PPV (99% spec) PPV (98% spec) Former Soviet Republics. 93% 87% Laos 6. 84% 7% Burma % 63% India 3. 7% 60% Guatemala 3.0 7% 60% Korea (N&S) % 9% Peru.6 7% 6% Ethiopia.0 66% 0% Philippines 7.7 6% 4% Vietnam 3.4 7% 40% China (incl Taiwan) 7. 4% 37% United States % 8% Cambodia % % Mexico % % Countries with >3 cases tested for MDR 3 September 6, 08 6

17 MDR-TB Cases by Country/Region of Origin and Years in the US, CA 0 0 Country/Region Total MDR TB cases years in US No. (%) > years in US No. (%) All Countries* (excl U.S.) (3.7) 7 (.) Vietnam* 3 9 (7.9) 3 (0.4) China* (incl Taiwan) 7 (8.8) (0.4) Philippines* 7 8 (4.0) 9 (.4) * Difference is statistically significant 33 Order Xpert or PSQ for Patients with MDR Risk! MDR risks: Prior TB treatment Contact to patient with drug resistant TB Non-U.S.-born from country with increased MDR risk ( % MDR among TB cases in California) Arriver to U.S. within years HIV positive Among 4 smear positive MDR cases with MDR risk, 0 did not get Xpert or PSQ on sputum (California, 0-06) Lowenthal, NTCA/CTCA poster September 6, 08 7

18 Probe B Interpretation Interpret in clinical context Are there risks for DR TB? Is there a pressing need to start treatment immediately? In this case: born in Mexico, no prior treatment, not a contact probably silent Pyrosequencing: 4TTT (Silent mutation) 3 Testing smear-negative samples 36 September 6, 08 8

19 Case 30s yo F cough x 4 weeks No prior TB treatment Born in country with low MDR prevalence; no travel Household contact to pan-s case year prior Xpert interpretatiom-curry Center-9/6/8 37 MTBC Detected RIF-R detected High Cts ΔCt = = September 6, 08 9

20 MTBC Detected RIF-R not detected High Cts ΔCt = =.9 39 Case Treated with RIPE Clinically improved after week Pyrosequencing: no amplification DSTs: PanS Xpert interpretatiom-curry Center-9/6/8 40 September 6, 08 0

21 Xpert MTB/RIF Performance on Smear Negative Sputum Compared with Culture, U.S. patients Sensitivity Specificity Xpert Xperts 9.3% (6/7) 7.4% (0/8) 99.% Should we always test two samples? Luetkemeyer Clin Infect Dis 06 4 Case 3 0 yo man born in Mexico, in U.S. for 0 yrs 6 weeks of cough, night sweats CXR RUL nodular infiltrate No MDR contact, no prior treatment All smears are negative Xpert pending Order testing samples to increase sensitivity!? 4 September 6, 08

22 Sample # Sample # MTBC not detected MTBC detected Rif Resistance not detected Conflicting results! Shall I worry false positivity? Ask lab to test another specimen!? Xpert interpretatiom-curry Center-9/6/8 43 Sample 3 Sample 4 MTBC detected Rif resistance indeterminate MTBC detected Rif resistance detected Sample #3 results were indeterminate. Order another test!! Sample #4 results were RIF-R. Hit the jackpot! 4 tests 4 different results! 44 September 6, 08

23 Problems with testing smear-negatives MTBC DNA Low, very low or not present Xpert s detection limit is about 0 CFU/mL Xpert results less reproducible, because: Reduced amplification: generate fewer amplicons PCR efficacy varies between runs Reduced probe binding: generate less signals Probe s binding efficacy varies more among probes Increased Δ Ct max: Increased false RIF-R detection Xpert interpretatiom-curry Center-9/6/8 4 Follow-up actions MTBC not detected Does not rule out MTBC. Consider second Xpert Wait for culture results. MTBC detected Rifampin resistance not detected Most reliable MTBC detected Rifampin resistance detected Need to be confirmed by sequencing. MTBC detected Rifampin resistance indeterminate [not discussed today] Likely happens when testing smear-negatives. If this is a first test, test nd specimen. If this is a nd test. Wait for culture results. Xpert interpretatiom-curry Center-9/6/8 46 September 6, 08 3

24 Two probes positive = MTBC? This is a dangerous rule! Especially when the sample is smear-negative Two probes pos = 3 or more mutations Very RARE to have 3 mutations within 8 bp Out of 374 tested, samples had 3 mutations (MDL data) None detected by 3 probes! One detected by probes (A & B) One detected by probe (D) Xpert interpretatiom-curry Center-9/6/8 47 When should NTM be suspected? Smear-negative Only two probes are positive. Xpert reports MTBC and RIF-R detected. Smear-positive Multiple Xperts: MTBC not detected Xpert interpretatiom-curry Center-9/6/8 48 September 6, 08 4

25 Can we use Xpert for detection of relapses? Xpert interpretatiom-curry Center-9/6/8 49 Case 4 70 yo man from China years ago treated for cavitary TB with RIPE cured Presents to ED with days of SOB, no fever, night sweats or weight loss (weight gain) CXR with bilateral pleural effusions Smear neg, Xpert positive, RIF-R (Probe A) No sequence detected by PSQ Culture grew a rapid grower DNA of the isolate from years ago, showed rpob CCG (detectable by probe A) Kelly et al Am J Resp Crit Care Med 04 0 September 6, 08

26 Case 4 History concerning for MDR Clinical presentation atypical for TB, more compatible with CHF Treated for weeks then stopped All cultures negative, including mos later Negative cultures and same rpob mutation as prior --> dead bugs? Kelly et al Am J Resp Crit Care Med 04 Xpert positivity on treatment Insert figure from publication 7% Weeks after treatment initiation Friedrich, Lancet Respir Med 03; : September 6, 08 6

27 Don t get Xpert after treatment start or in previously treated patients Xpert cannot determine alive vs dead Xpert can remain positive for years after curative treatment Package insert recommends against Xpert in anyone treated for >3 days If you order it, only helpful if different RIF result from prior (e.g., a previously pan-s case has a probe E RIF-R result) 3 Summary Points Order Xpert! If results surprise you, talk to your lab! Ask for probe and Ct info Interpret in clinical context How likely is it that this patient has TB and DR-TB? MDR risk factors? Prior treatment, contact to MDR case, born in country with high MDR prevalence? Can you wait for culture results? Get rpob sequencing for all RIF-R specimens If smear negative (Ct > 8), wait for culture Xpert interpretatiom-curry Center-9/6/8 4 September 6, 08 7

28 Ed Desmond Phil Lowenthal Neha Shah MDR Service Microbial Disease Lab Acknowledgments Leslie Phil Pennan Henry Lowenthal Barry Jenny Flood Neha Shah Gayle Schack (Ret) Lisa True Kristen Christy Pak Wendorf (Ret) Not pictured: Shereen Katrak Wendy Cheung Stephen Yu Grace Lin Terry Weber Lucy Pham Zachraias Zachraias Kitty Reiher Amelia Alonis Thank You! Xpert interpretatiom-curry Center-9/6/8 6 September 6, 08 8

29 Resources California Microbial Diseases Lab PSQ: Screening.pdf Curry/CDPH MDR TB Survival Guide Lab Chapter: laboratory CDC TB Lab: NTCA/APHL Consensus Statement on Xpert for release from isolation: Khan academy PCR unit: Xpert MTB/RIF Package Insert: files/f6a0c86cd73ce46ba39c4a3eabc4-3a9ca7ef6b9b88dc736ea437f4eb3a-xpert-mtbrif-english-packageinsert Rev-C.pdf 7 rpob Facts Most common mutation conferring RIF-R rpob 3TTG detectable by Probe E nd most common mutation conferring RIF-R rpob 6TAC & 6GAC detectable by probe D Most common silent mutation rpob 4TTT detectable by probe B (>0% of all mutations) Disputed mutations are not common, but are detectable But you would not know unless sequenced. Not common to have mutations, very rare to have 3 mutations. Even more rare to have 3 mutations detected by 3 probes. 8 September 6, 08 9

30 rpob codon numbering change Historically rpob codons numbered with E. coli All other loci numbered according to M. tuberculosis Change to M. tuberculosis numbering to align with whole genome sequencing data Good news: just subtract MDL has started using MTBC numbering (As of 8//8) Codon conversion info provided in comment Xpert interpretatiom-curry Center-9/6/8 9 Xpert Ultra WHO recommends the use of Ultra. specific targets for detection of MTBC IS60 & IS08 Increased sensitivity for MTBC detection 66% (G4) vs 79% (Ultra) Added a step to analyze melting temperature for identification of specific mutations. 4 sloppy MB probes for detecting rpob mutations. F4F Silent mutation is not detected. Great news! 60 September 6, 08 30