Evaluation of Xpert MTB/RIF Assay for the Rapid Identification of TB and Rifampin Resistance in HIV...
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Transcript of Evaluation of Xpert MTB/RIF Assay for the Rapid Identification of TB and Rifampin Resistance in HIV...
Evaluation of Xpert MTB/RIF Assay for the Rapid
Identification of TB and Rifampin Resistance in HIV Infected & HIV
uninfected Pulmonary TB suspects: ACTG 5295/TBTC 34
AF Luetkemeyer, C Firnhaber, MA Kendall, X Wu, D Benator, GH Mazurek, B Metchock, P Johnson, S Swindells, I Sanne, DV Havlir, B Grinsztejn, D Alland, on behalf of the ACTG A5295/TBTC 34 Study teams
Disclosures
• Instruments, cartridges and research grant support from Cepheid
• Funding from NIH AIDS Clinical Trials Group (ACTG) and the CDC Tuberculosis Trials Consortium (TBTC)
Background• GeneXpert MTB/RIF: automated real
time PCR that diagnoses M. tuberculosis & identifies rifampin resistance in < 2 hours
• Performance in high TB prevalence settings well characterized– Sensitivity of 1 Xpert: AFB+ 98-99% , AFB-
~60-70%– Specificity: 98-99%
• Limited data for use in lower TB prevalence regions and in HIV coinfection
Study Aims • Determine sensitivity and specificity of
Xpert MTB/RIF assay overall and by AFB smear status
• Evaluate Xpert performance by:– low TB prevalence (US) vs. higher TB
prevalence (Brazil and South Africa)– HIV-infected vs. HIV-uninfected
• Evaluate by Xpert performance for RIF resistance detection
• Performance in setting of non-tuberculosis mycobacterial growth
Study population
• Pulmonary TB suspects– AFB+ sputum within 7 days of entry, or– Clinical suspicion of TB as evidenced by
decision to send sputum for AFB smear/culture in addition to cough, fever, night sweats, or weight loss
• TB treatment < 48 hours• Regions by TB prevalence
– Low prevalence (US: target enrollment ≥ 70%)
– Higher prevalence (Brazil & South Africa)
• HIV-infected and uninfected– All participants underwent HIV testing
Methods• 2 sputum samples for Xpert MTB/RIF testing (G4
cartridges) – Method of sputum collection (induced or expectorated) and
processing (unprocessed or sedimented) prior to Xpert testing determined by local standard of care and not assigned by study
– Xpert conducted within 7 days of sputum collection• Xpert testing at 2 central labs in US (Emory, UCSF)
and at 1 lab in Rio de Janeiro, Brazil and 1 in Johannesburg, South Africa– All labs participated in external Xpert Quality Assurance
program• Xpert results compared to 2 sputum specimens, each
evaluated with AFB smear, liquid and solid mycobacterial culture
• Rifampin resistance by proportions method on Middlebrook agar
• rpoB sequencing conducted on a specimen from each participant with ≥1 culture with TB growth
Results
• 720 of 994 participants had results for 2 AFB smears, 2 liquid and solid media mycobacterial cultures, and 2 Xpert available at time of analysis
Median Age (Q1,Q3) 46.5 (454/720)
Male 63%
Site of enrollment• US: 71% • South Africa: 19%• Brazil: 10%
HIV+
48% (343/720)• US 41% (211/512)• South Africa 79% (107/139)• Brazil 34% (25/72)
Median CD4+ cells/mm3 for 330 HIV+ participants
(Q1,Q3)157 (44,369)
Results≥ 1 culture TB+ 15 % (109/720 )
• US: 53% (58/109) • South Africa: 40% (44/109) • Brazil: 6% (7/109)
AFB+ 63% (69/109)
HIV+ 39% (42/109)
Rifampin susceptibility (agar proportions
method)
• Rifampin resistant 2.8% (3/109) • Rifampin sensitive 91.7% (100/109) • Contaminated or no growth on DST media
5.5% (6/109)
Non Tuberculosis Mycobacterial(NTM)
Growth
9.3% (67/720)• M. avium complex (MAC): 67% (45) US (45), S. Africa (0), Brazil (0)• M. kansasii: 6% (4) US (3), S. Africa (0), Brazil (1)• Other NTM: 27% (18) US (11), S. Africa (3), Brazil (4)
Sensitivity of 1 Xpert
• No significant impact of region on sensitivity in AFB-/TB culture+
Sensitivity (95% CI)
Xpert +/ TB culture +
Overall 85.8% (78.0%, 91.2%)
91/106
AFB+/TB culture +
100% (94.6%, 100%)
67/67
AFB-/TB culture +
61.5% (45.9%, 75.1%)
24/39
Specificity of 1 Xpert
Specificity (95% CI)
Xpert - / TB culture -
All Participants 98.8% (97.6%, 99.4%)
591/598
AFB+ 100% (51.0%, 100 %)
4/4
AFB- 98.8% (97.6%, 99.4%)
587/594
US only 99.3% (98.0%, 99.8%)
441/444
AFB+ 100% (51%, 100%)
4/4
AFB- 99.3% (98.0%, 99.8%)
437/440
• No significant impact of region on specificity
Xpert Performance in HIV infection
• HIV status did not significantly impact sensitivity or specificity
HIV+ Sensitivity (95% CI)
Specificity (95% CI)
AFB+ 100% (84.5,% 100%)
100% (20.7%, 100%)
AFB- 57.9% (36.3%,76.9%)
98.3% (96.1% , 99.3%)
HIV-
AFB+ 100% (92.3%, 100%)
100% (43.9%, 100%)
AFB- 65.0% (43.3%, 81.9%)
99.3% (97.6,% 99.8%)
Xpert in setting of NonTuberculosis Mycobacteria(NTM) Growth
n Xpert TB positive
AFB+/Non tuberculosis
Mycobacterial Culture +
3(all MAC) 0/3
AFB-/Non tuberculosis
Mycobacterial Culture +
641/64
(this specimen with MAC growth)
Discordance between Xpert & Culture
• All discordance occurred in AFB smear negative specimens
• 10 with Xpert TB+/ TB Culture negative:
n 1st Xpert 2nd Xpert TB culture
4 positive positive negative
3 positive negative negative
2 negative positive negative
1 failure positive negative
Xpert TB Negative /TB culture +
• Of the 15 with 1st Xpert TB negative, 2nd Xpert was TB+ in 3 out of 15 – 20% incremental yield of 2nd Xpert test
• In AFB-/TB culture+: – Sensitivity of 2 Xperts: 69.2% (27/39)– Sensitivity of 1 Xpert: 61.5% (24/39)
Rifampin susceptibility
• 3 Rifampin resistant specimens by culture-based DST: Xpert detected 3 out of 3
• Specificity: 98.8% (81/82)• One participant: Xpert RIF resistant /
Culture RIF sensitive– 2 Xpert tests: 1 RIF resistant, 1 RIF
sensitive– rpoB sequencing: wild type
• NPV: 100%• PPV: 75% (n=4)
Conclusions
• Excellent performance for detection of TB including in low prevalence settings – Sensitivity AFB+100%, AFB- 61.5%– Specificity 98.9% overall, 99.3% in low prevalence
• Performance not significantly impacted by region nor HIV status
• Xpert detected 3 of 3 specimens rifampin resistant specimens by culture
• Data support use of Xpert MTB/RIF in low prevalence settings and in HIV infection
Acknowledgements• Study participants• Support from NIH, CDC, & Cepheid • ACTG 5295 Team• Tuberculosis Trials Consortium (TBTC) S34
Team• CDC Tuberculosis Lab• Participating ACTG & TBTC sites & site
investigatorsACTG TBTC
603 UCLA 11101 WITS 31475 VCU 22 Denver 62 Houston
701 UCSD
12101 FIOCRUZ 31477 UMDNJ 40 South Texas 63 San Antonio
801 UCSF 30329 Columbia 31472 Henry Ford
53 Washington VA
70 Vanderbilt
1201 USC 31468 Bronx Lebanon
31473 Houston
54 Duke UCSF TBTC
5802 Emory
7804 Cornell