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)
Male
Site of enrollment
HIV+
Median CD4+ cells/mm3 for 330
HIV+ participants (Q1,Q3)
46.5 (454/720)
63%
• US: 71%
• South Africa: 19%
• Brazil: 10%
48% (343/720)
• US 41% (211/512)
• South Africa 79% (107/139)
• Brazil 34% (25/72)
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)
Non Tuberculosis
Mycobacterial(NTM)
Growth
• Rifampin resistant 2.8% (3/109)
• Rifampin sensitive 91.7% (100/109)
• Contaminated or no growth on DST media 5.5%
(6/109)
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
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
• No significant impact of region on sensitivity in
AFB-/TB culture+
Specificity of 1 Xpert
Specificity (95% CI)
All Participants
Xpert - / TB culture -
98.8% (97.6%, 99.4%)
591/598
AFB+
100% (51.0%, 100 %)
4/4
AFB-
98.8% (97.6%, 99.4%)
587/594
99.3% (98.0%, 99.8%)
441/444
AFB+
100% (51%, 100%)
4/4
AFB-
99.3% (98.0%, 99.8%)
437/440
US only
• No significant impact of region on specificity
Xpert Performance in HIV infection
HIV+
AFB+
AFB-
Sensitivity (95% CI)
Specificity (95% CI)
100% (84.5,% 100%) 100% (20.7%, 100%)
57.9% (36.3%,76.9%) 98.3% (96.1% , 99.3%)
AFB+
AFB-
100% (92.3%, 100%) 100% (43.9%, 100%)
65.0% (43.3%, 81.9%) 99.3% (97.6,% 99.8%)
HIV-
• HIV status did not significantly impact
sensitivity or specificity
Xpert in setting of NonTuberculosis
Mycobacteria(NTM) Growth
AFB+/Non
tuberculosis
Mycobacterial
Culture +
AFB-/Non
tuberculosis
Mycobacterial
Culture +
n
Xpert TB positive
3
(all MAC)
0/3
64
1/64
(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 investigators
ACTG
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