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