OPEN
SUBJECT AREAS:
TUBERCULOSIS
LABORATORY TECHNIQUES
AND PROCEDURES
Received
9 May 2014
Accepted
16 June 2014
Published
11 July 2014
Determinants of PCR performance (Xpert
MTB/RIF), including bacterial load and
inhibition, for TB diagnosis using
specimens from different body
compartments
Grant Theron1, Jonny Peter1, Greg Calligaro1, Richard Meldau1, Colleen Hanrahan2, Hoosain Khalfey1,
Brian Matinyenya1, Tapuwa Muchinga1, Liezel Smith1, Shaheen Pandie3, Laura Lenders1, Vinod Patel4,
Bongani M. Mayosi3 & Keertan Dheda1,5
1
Correspondence and
requests for materials
should be addressed to
K.D. (Keertan.dheda@
Lung Infection and Immunity Unit, Division of Pulmonology & UCT Lung Institute, Department of Medicine, University of Cape Town,
Cape Town, South Africa, 2Johns Hopkins Bloomberg School of Public Health, Department of Epidemiology, Baltimore, MD, USA,
3
Division of Cardiology, Department of Medicine, Groote Schuur Hospital and University of Cape Town, South Africa, 4Department
of Neurology, University of KwaZulu Natal, South Africa, 5Institute of Infectious Diseases and Molecular Medicine, University of
Cape Town, Cape Town, South Africa.
uct.ac.za)
The determinants of Xpert MTB/RIF sensitivity, a widely used PCR test for the diagnosis of tuberculosis
(TB) are poorly understood. We compared culture time-to-positivity (TTP; a surrogate of bacterial load),
MTB/RIF TB-specific and internal positive control (IPC)-specific CT values, and clinical characteristics in
patients with suspected TB who provided expectorated (n 5 438) or induced sputum (n 5 128), tracheal
aspirates (n 5 71), bronchoalveolar lavage fluid (n 5 152), pleural fluid (n 5 76), cerebral spinal fluid (CSF;
n 5 152), pericardial fluid (n 5 131), or urine (n 5 173) specimens. Median bacterial load (TTP in days) was
the strongest associate of MTB/RIF positivity in each fluid. TTP correlated with CT values in pulmonary
specimens but not extrapulmonary specimens (Spearman’s coefficient 0.5043 versus 0.1437; p 5 0.030).
Inhibition affected a greater proportion of pulmonary specimens than extrapulmonary specimens (IPC CT
. 34: 6% (47/731) versus 1% (4/381; p , 0.0001). Pulmonary specimens had greater load than
extrapulmonary specimens [TTPs (interquartile range) of 11 (7–16) versus 22 (18–33.5) days; p , 0.0001].
HIV-infection was associated with a decreased likelihood of MTB/RIF-positivity in pulmonary specimens
but an increased likelihood in extrapulmonary specimens. Mycobacterial load, which displays significant
variation across different body compartments, is the main determinant of MTB/RIF-positivity rather than
PCR inhibition. MTB/RIF CT is a poor surrogate of load in extrapulmonary specimens.
T
uberculosis (TB) is a leading cause of morbidity and mortality, and accurate and rapid diagnostic tests for TB
are key to limiting the spread of the epidemic1,2. In settings with a high HIV prevalence, up to a third of
individuals with pulmonary TB may be unable to provide a specimen for testing3. Individuals infected with
HIV are at an increased risk of developing extrapulmonary TB [which can represent 15–50% of the total TB
incidence in HIV prevalent settings4,5. Due to the paucibacillary but disseminated nature of extrapulmonary TB,
and the difficulties associated with specimen acquisition in patients who are sputum scarce, many patients are
often difficult to diagnose using conventional techniques and are at risk of increased mortality6.
Xpert MTB/RIF (Cepheid, USA) is an automated real-time PCR system that simultaneously detects TB and
resistance to rifampicin. The test has excellent accuracy when performed on sputum7 and is endorsed by the
World Health Organisation (WHO)8,9 and the USA Federal Drug Administration10 for this purpose. In addition
to containing PCR reagents and TB-specific primers, each MTB/RIF cartridge contains a set quantity of Bacillus
globigii spores and a primer pair specific for the DNA in these spores11. If the amplification of this internal positive
control fails, or occurs after 38 cycles, the test result is designated invalid12.
SCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
1
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Information regarding Xpert MTB/RIF’s performance on nonsputum specimens is emerging5,13–26; however, it is not extensive,
nor sufficiently validated in HIV-prevalent settings. MTB/RIF has
thus been granted a conditional recommendation for the diagnosis of
extrapulmonary TB by the WHO, however, the overall body of evidence has been cited as weak9. Furthermore, countries which are presently implementing it for the diagnosis of pulmonary TB, such as
South Africa, do not currently permit its routine use on extrapulmonary specimens.
While the relationship between sputum bacillary load (measured
using smear microscopy, culture, and MTB/RIF) has been previously
characterised27–31, little is known about the comparative variation in
mycobacillary load in fluids from different sites in the body, despite
the high burden of extrapulmonary and increased risk of poor outcomes in these patients32,33. This is critical for informing the development and application of new tests for extrapulmonary TB (where, in
some cases, a biomarker-based approach might be optimal).
Furthermore, there is no information regarding how the performance of MTB/RIF is influenced by constituents of extrapulmonary
specimens or any associated clinical factors. This is important,
because salts, proteins or cellular debris are commonly found in
non-sputum specimens and can be enriched after specimen processing (e.g., after centrifugation). These can interfere with the amplification enzyme and thereby inhibit the PCR, leading to inaccurate
or unreliable results.
In this study, we first compared mycobacterial load in different
fluids from different cohorts of patients with TB recruited from
similar settings in South Africa (over 1000 patients overall). We
identified clinical factors, including HIV co-infection and CD4
count, and specimen characteristics that may modulate liquid culture
time-to-positivity (TTP) and MTB/RIF quantitative information
[cycle threshold (CT) values] in these fluids. We evaluated the degree
of MTB/RIF PCR inhibition in each fluid, and how this modified the
relationship between MTB/RIF and culture results.
Methods
Study information. We have performed a series of studies at the University of Cape
Town and the University of KwaZulu-Natal that assessed the accuracy of MTB/RIF
for the diagnosis of TB in different body fluids. These were performed in independent
cohorts of patients who were clinically suspected of having pulmonary or
extrapulmonary TB. Comparative data from these studies for the following specimens
types are presented here: expectorated sputum from patients with suspected
pulmonary TB attending primary care TB clinics in Cape Town, South African34,35;
induced sputum from sputum-scarce or smear-negative patients attending primary
care TB clinics in Cape Town36; tracheal aspirates from mechanically-ventilated
patients in the intensive care unit of a tertiary level hospital (Groote Schuur Hospital)
in Cape Town (#NCT01530568); bronchoalveolar lavage fluid (BALF) from sputumscarce or smear-negative patients attending the respiratory clinic at the same
hospital23; pleural fluid from patients with suspected pleural TB attending the same
respiratory clinic; cerebral spinal fluid (CSF) from patients with suspected TB
meningitis from Inkosi Albert Luthuli Central Hospital in Durban, South Africa37,38;
pericardial fluid from patients suspected of TB pericarditis from four district- and one
tertiary-level hospital in South Africa39; and urine from patients suspected of TB who
are hospitalised in Groote Schuur Hospital20. Patients on anti-TB treatment longer
than 48 hours were excluded from the analyses. Only patients with paired liquid
culture and MTB/RIF results (i.e., from either the same specimen or specimens
collected at the same time) were included.
Ethics statement. Each sub-study was approved by the University of Cape Town or
University of Kwa-Zulu Natal research ethics committees, all patients provided
written informed consent for participation and the use of their data, and each substudy was conducted in accordance with the relevant approvals.
Smear microscopy, liquid culture and Xpert MTB/RIF. When MTB/RIF was
performed on sputum, a paired specimen was NALC-NaOH decontaminated, and
the sediment used for concentrated fluorescent smear microscopy and liquid culture
using the BACTEC MGIT 960 system (BD Diagnostics, USA) performed at a qualityassured accredited reference laboratory. For studies involving other specimen types
(induced sputum, tracheal aspirates, BALF, pleural fluid, CSF, pericardial fluid, and
urine), the same specimen used for MTB/RIF testing was used for smear microscopy
and liquid culture after decontamination. A ,10 ml volume of urine20 was first
centrifuged and resuspended in 1 ml phosphate buffered saline prior to processing
for MTB/RIF. As our study objectives are to compare bacterial load and MTB/RIF-
SCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
inhibition in different fluids, which would be confounded by different methods of
specimen concentration, all other specimens (other than urine) were processed raw
and centrifuged, and a volume of 1 ml used. The recommended 2-fold volume of
sample buffer was thereafter added and the MTB/RIF procedure started40.
Statistical analyses. Statistical analyses were performed using Graphpad Prism
(version 6.0; GraphPad Software, USA, www.graphpad.com), the VassarStats online
statistical package (www.vassarstats.net/index.html), and STATA SE (version 12;
StataCorp, USA). P-values less than ,0.05 were considered significant. A backward
elimination strategy was used for multivariate analyses of culture TTP, MTB/RIF
Mycobacterium tuberculosis-specific CT values, and MTB/RIF inhibition. Variables
with p-values ,0.100 in univariate analyses were included in the final multivariate
model. Fisher’s exact test with mid-P correction was used for comparisons between
proportions. The Mann-Whitney test to compare medians. Fisher’s z transformation
was used to compare differences in Spearman’s correlation coefficient between TTPs
and CT values. For some within-specimen type comparisons of TTP and CT values,
there were too few HIV-infected culture-positive patients (n # 5) for meaningful
comparisons.
Results
Patient characteristics and accuracy of MTB/RIF in different
specimen types. Demographic and clinical characteristics are
shown in Table 1 for each cohort. The expectorated sputum,
induced sputum, tracheal aspirate, BALF, pleural fluid, CSF,
pericardial fluid, and urine cohorts had 428, 128, 71, 152, 76, 152,
131, and 173 patients, respectively. The sensitivity and specificity of
MTB/RIF for the detection of TB in each specimen type and using
liquid culture as a reference standard has been described elsewhere20,23,34,35,41,38 (these studies also examined the impact of centrifugation on MTB/RIF performance), but is also shown in
Table 2. The sensitivity of MTB/RIF in pulmonary specimens
compared to extrapulmonary specimens was 82% (141/172) versus
50% (48/97; p , 0.0001) and the specificity was 96% (595/617) versus
86% (225/262; p , 0.0001). In contrast, the sensitivity of smear
microscopy in pulmonary and extrapulmonary specimens was 60%
(73/122) and 2% (2/96), respectively.
Culture time-to-positivity in different types of specimens. Overall.
Liquid culture TTP was the shortest in expectorated sputum
compared to culture-positive specimens of other types (indicating
greater bacillary load; ANOVA p , 0.0001), and in pulmonary specimens was shorter than in extrapulmonary specimens [11 (7–16) vs.
22 (18–33.5); p , 0.0001] (Figure 1A and B; Table 2).
Differences in TTP in Xpert MTB/RIF-positive and –negative specimens. Scatter plots of TTP in MTB/RIF-positive and –negative culture specimens of different types are shown in Figure 2. MTB/
RIF-positive, culture-positive expectorated sputum and induced sputum both had a shorter TTP compared to those that were MTB/RIFnegative [7 (6–11) vs. 18 days (12–26; p , 0.0001) for expectorated
sputum, and 10 (7–13) vs. 18 days (15–24; p 5 0.0081) for induced
sputum] but not for the other specimen types tested.
Differences in TTP according to HIV status. Median TTPs (IQR)
amongst culture-positive patients were shorter for expectorated sputum and induced sputum in HIV-uninfected compared to -infected
patients [7.5 (6–12) vs. 11.50 (7–15.75) days for expectorated sputum
(p 5 0.0339); 9 (6.5–12.5) vs. 15.50 (9.75–19.5) days for induced
sputum (p 5 0.0352)]. When data were pooled, patients that were
HIV-uninfected had a similar TTP to those that were HIV-infected
[9 (7, 14.25) vs. 13 (7, 18.5) days for pulmonary specimens (p 5
0.0726); 25 (18.5, 31.5) vs. 21 (18, 35) days for extrapulmonary specimens (p . 0.9999)].
Differences in TTP according to CD4 count. HIV-infected patients
with a CD4 count #200 cells/ml had a longer median TTP versus
those with a CD4 count .200 cells/ml for expectorated sputum [14
(10.25, 20.00) vs. 8 (6, 12) days (p 5 0.0027)] and CSF [26 (21, 36) vs.
18.5 (18, 20.25) days (p 5 0.0110)], but not for induced sputum [24
(17.5, 36.5) vs. 16.5 (12.75, 24.5) days (p 5 0.1071)] or pericardial
fluid [21 (15, 27) vs. 24 (17.5, 36.5) days (p 5 0.4755)]. When data
2
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Table 1 | Demographic and clinical characteristics of the different cohorts. Only significant p-values for comparisons between expectorated sputum and other specimen types are shown. Pvalues for pulmonary specimens and extrapulmonary specimens are for comparisons between the two groups. For protein concentration, only significant p-values for comparisons versus pleural
fluid are shown. *Two patients in the urine group were missing age information. {The following number of patients in each group were of unknown smoking status: 12 in the expectorated sputum
group, 6 in the tracheal aspirate group, 10 in the BALF group, and 5 in the pleural fluid group. {The following number of patients in each group refused HIV testing or had missing data: 31 in the
expectorated sputum group, 3 in the induced sputum group, 11 in the tracheal aspirate group, 26 in the BALF group, 23 in the pleural fluid group, and 6 in the pericardial fluid group. 1HIVinfection was an eligibility criterion for the parent study of this cohort. **The following number of patients infected with HIV in each group were missing CD4 count information: 6 in the
expectorated sputum group, 1 in the induced sputum group, 1 in the tracheal aspirate group, 1 in the BALF group, 9 in the CSF group, 4 in the pericardial fluid group, and 9 in the urine group.
{{
The following number of patients in each group were missing information about their previous TB: 10 in the expectorated sputum group, 4 in the tracheal aspirate group, 6 in the BALF group, 7
in the pleural fluid group, and 4 in the pericardial fluid group. Abbreviations: BALF, bronchoalveolar lavage fluid; CSF, cerebral spinal fluid; IQR, interquartile range; ND, not done
Specimen type
Expectorated
sputum
(n 5 438)
Demographic characteristics
Median age in years
39 (30–49)
(IQR)*
Male gender (%)
298 (67)
Tobacco smoker (%){
258 (61)
Median CD4 count
215 (127–360)
(cells/ml) (IQR) if HIVinfected**
173 (40)
Previous TB (%){{
Tracheal
aspirates
(n 5 71)
39 (30–59)
36 (27–49)
63 (49)
p , 0.0001
52 (41)
p , 0.0001
41 (58)
21 (32)
p , 0.0001
47 (38)
25 (42)
250
(148–373)
49 (38)
BALF
(n 5 152)
Pleural fluid
(n 5 76)
CSF
(n 5 152)
46 (33–55) 55 (38–65) 32 (26–37)
p 5 0.002 p , 0.0001 p , 0.0001
82 (54)
45 (58)
57 (38)
p 5 0.002
p , 0.0001
41 (29)
19 (27)
NR
p , 0.0001 p , 0.0001
Pericardial fluid
(n 5 131)
35 (29–42)
82 (63)
NR
Urine
(n 5 173)
Pulmonary
specimens
(n 5 789)
35 (29–40) 39 (31–50)
p , 0.01
69 (40)
61 (481/789)
p , 0.0001
35 (20)
49 (372/761)
p , 0.0001
35 (28–42)
p , 0.0001
48 (253/532)
p , 0.0001
22 (54/244)
p , 0.0001
N/A1
80 (403/503)
p , 0.0001
120 (58–231)
p , 0.0001
159
(58–379)
23 (18)
9 (17)
131 (86)
90 (72)
p 5 0.004 p 5 0.030 p , 0.0001
p , 0.0001
243
102 (68–
138 (60–247) 141 (82–256)
(80–451)
271)
p 5 0.008
84 (45–197) 211 (122–376)
p , 0.0001
24 (36)
50 (34)
62 (47)
9 (13)
41 (27)
p , 0.0001 p 5 0.003
40 (31)
Extra-pulmonary
specimens
(n 5 532)
32 (223/718)
38 (296/769)
29 (152/521)
p 5 0.0006
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Clinical characteristics
128 (31)
HIV-infected (%){
Induced
sputum
(n 5 128)
SCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
Table 2 | Culture time-to-positivity, Xpert MTB/RIF accuracy and cycle threshold values in different fluids. Only significant p-values for comparisons between expectorated sputum and other
specimen types are shown. P-values for pulmonary specimens and extrapulmonary specimens are for comparisons between the two groups. *No patients had culture-positive urine. {Sensitivity
and specificity calculations used liquid culture from either the same or a paired specimen of the same type as a reference standard. 196 patients in the expectorated sputum group and all of the
patients in the tracheal aspirate group did not have a smear microscopy result, as this test was not part of the original trial designs. 1 patient in the BALF group was missing a smear microscopy
result. Abbreviations: BALF, bronchoalveolar lavage fluid; CSF, cerebral spinal fluid; IQR, interquartile range; CT values, cycle threshold values; IPC, internal positive control
Specimen type
Expectorated
sputum
(n 5 438)
Liquid culture
Percentage
25 (109/438)
culture-positive
Time-to-positivity
8 (6–13)
(days)
Smear microscopy
Sensitivity{ (%)
69 (49/71)
Specificity{ (%)
99 (170/171)
Xpert MTB/RIF
Sensitivity{ (%)
83 (90/109)
Median CT values
(IQR)
Median IPC CT
values (IQR)
Tracheal
aspirates
(n 5 71)
BALF
(n 5 152)
Pleural fluid
(n 5 76)
CSF
(n 5 152)
Pericardial fluid
(n 5 131)
20 (25/128)
p 5 0.2100
13 (8–18)
p 5 0.0251
15 (11/71)
p 5 0.0837
13 (8–21)
p 5 0.0489
18 (27/152)
p 5 0.0724
16 (13–23)
p , 0.0001
21 (16/76) 23 (35/152)
p 5 0.4721 p 5 0.6456
28 (20–34) 21 (18–33)
p , 0.0001 p , 0.0001
36 (9/25)
p 5 0.0037
100 (103/103)
p 5 0.4368
ND
58 (15/26)
p 5 0.2972
99 (124/125)
p 5 0.8234
0 (0/15)
3 (1/35)
2 (1/46) p ,
p , 0.0001 p , 0.0001
0.0001
100 (59/59) 100 (117/117) 100 (85/85)
p 5 0.5561 p 5 0.4073
p 5 0.4799
93 (25/27)
p 5 0.1969
96 (120/125)
p 5 0.7347
27.1 (19.2–
30.0)
p 5 0.3440
25.55 (24.70–
26.93) p 5
0.0060
31 (5/16)
46 (16/35)
p , 0.0001 p , 0.0001
90 (54/60) 94 (110/117)
p 5 0.0204 p 5 0.2128
31.0 (25.2– 30.8 (24.1–
33.1) p 5
34.3) p 5
0.0007)
0.0016
27.6 (26.2– 27.15 (26.38–
29.4) p ,
27.98) p 5
0.3502
0.0001
ND
64 (16/25)
91 (10/11)
p 5 0.0394
p 5 0.4793
97 (318/329)
96 (99/103)
97 (58/60)
p 5 0.7939
p 5 0.9968
22.4 (18.1–28.4) 24.4 (21.3–27.6) p 27.9 (21.2–
5 0.3570
31.1) p 5
0.2293
26.2 (25–28)
28.1 (26.83–
28.2 (27.1–
29.10) p ,
28.85) p 5
0.0001
0.0156
35 (46/131)
p 5 0.0210
22 (15–32)
p , 0.0001
Urine
(n 5 173)
Pulmonary
specimens
(n 5 789)
0
22 (172/789)
N/A*
11 (7–16)
N/A*
60 (73/122)
100 (173/173) 99 (397/399)
p 5 0.3138
59 (27/46)
N/A*
p 5 0.0016
72 (61/85)
82 (141/173)
p , 0.0001
p , 0.0001
28.6 (26.1–31.2) 29.5 (26.5–
p , 0.0001
32.6) p ,
0.0001
28.20 (27.10–
26.50 (25.15–
27.6)
28.85) p 5
p 5 0.6801
0.0567
82 (141/172)
96 (595/617)
23.4
(18.5–28.4)
26.50 (25.10–
28.20)
Extra-pulmonary
specimens
(n 5 532)
18 (97/532)
p 5 0.1144
22 (18–33.5)
p , 0.0001
2 (2/96)
p , 0.0001
100 (434/434)
p 5 0.1398
50 (48/97)
p , 0.0001
86 (225/262)
p , 0.0001
29.4
(26.4–32.2)
p , 0.0001
26.60
(25.60–28.10)
p 5 0.2033
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Specificity{ (%)
Induced sputum
(n 5 128)
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Figure 1 | Comparison of culture days-to-positivity (A and B) and Xpert MTB/RIF CT values (C and D) in different fluids, and in pulmonary specimens
versus extrapulmonary specimens. Asterisks indicate specimen types with significantly lower bacterial load than expectorated sputum or pulmonary
specimens. Abbreviations: BALF, bronchoalveolar lavage fluid; CSF, cerebral spinal fluid. No urine specimens were culture-positive.
from HIV-infected patients were pooled, patients with a CD4 count
#200 cells/ml had a longer median TTP compared to those with a
CD4 count .200 cells/ml for pulmonary specimens [15 (11.25, 20)
vs. 9.5 (6, 14.5) days (p 5 0.0052)], but not for extrapulmonary
specimens [22 (19, 35) vs. 20 (18, 24) days (p 5 0.2241)].
greater load) (IQR) were compared across fluids, those from pleural fluid, CSF, pericardial fluid, and urine were greater than expectrated sputum (Figure 1C and D; Table 2). CT values in pulmonary
specimens were lower than in extrapulmonary specimens [23.4
(18.5–28.4) vs. 29.4 (26.4–32.2); p , 0.0001].
Correlates of time-to-positivity. Multivariable linear regression analyses of culture-positive patients showed the following clinical and
demographic factors to be associated with increased TTP: younger
age (p 5 0.035) and HIV-infection (p 5 0.047) for induced sputum
(Table S2), previous TB (p 5 0.022) for tracheal aspirates (Table S3).
No significant associations were found for the other fluids or pooled
pulmonary data after multivariable adjustments were performed (see
supplement).
Differences in CT values according to HIV status. Median CT values
(IQR) amongst MTB/RIF-positive patients were similar in HIV-uninfected patients versus -infected patients for expectorated sputum
[21.37 (17.71–26.71) vs. 25.09 (18.60–31.08; p 5 0.1027)] or induced
sputum [24.41 (21.87–29.11) vs. 23.34 (18.37–26.77; p 5 0.5363)],
and no differences were detected when pooled pulmonary or extrapulmonary data were used [23.43 (18.02–28.33) vs. 24.40 (19.05–
30.85) for pulmonary specimens (p 5 0.3698); 30.75 (27.65–32.88)
vs. 29.00 (26.50–32.04) for extrapulmonary specimens (p 5 0.3921)].
Xpert MTB/RIF-generated cycle threshold values in different
types of specimens. Overall. When median MTB/RIF-generated
cycle threshold values (CT values; a smaller CT value indicates
SCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
Differences in CT values according to CD4 count. HIV-infected
patients with a CD4 count #200 cells/ml had higher CT values versus
5
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Figure 2 | Scatter plots of days-to-positivity in different types of liquid culture-positive specimens obtained from separate patient cohorts. Each circle
represents an individual specimen. Solid circles indicate specimens which were Xpert MTB/RIF-positive, whereas empty circles indicate Xpert MTB/RIFnegative specimens. Comparisons below each graph are between median (IQR) TTPs for Xpert-MTB/RIF-positive vs. –negative specimens for that fluid.
*Only one MTB/RIF-negative, culture-positive tracheal aspirate specimen was present; {Fluids from the lung include expectorated sputum, induced
sputum, tracheal aspirates, and bronchoalveolar lavage fluid; {Fluids from elsewhere in the body include pleural fluid, cerebral spinal fluid, and pericardial
fluid. No patients had culture-positive urine.
those with a CD4 count .200 cells/ml for expectorated sputum
[29.81 (24.75, 31.95) vs. 20.60 (17.74, 27.30; p 5 0.0125)], but not
for pericardial fluid [29.15 (26.58, 31.53) vs. 28.10 (25.23, 30.68; p 5
0.6390)] or urine [29.53 (26.18, 32.0) vs. 31.01 (28.58, 34.12; p 5
0.1532)]. Patients with a CD4 count #200 cells/ml had higher median CT values compared to those with a CD4 count .200 cells/ml for
pulmonary specimens [28.68 (21.57, 32.25) vs. 20.70 (17.74, 26.36; p
5 0.0119)] but not for extrapulmonary specimens [29.47 (26.41,
32.01) vs. 29.51 (25.99, 33.19; p 5 0.8033)].
Correlates of MTB/RIF-positivity. Multivariable logistic regression
analyses showed MTB/RIF-positivity to be associated (p # 0.100)
with TTP for expectorated sputum (p , 0.001; Table S1), induced
sputum (p 5 0.078; Table S2), BALF (p 5 0.082; Table S4), and CSF
(p 5 0.029; Table S6), whereas for pericardial fluid HIV-infection
was the only significant associate (p 5 0.010; Table S8). Patients who
are male or had previously had TB were less likely to have MTB/RIFpositive urine (p-values of 0.051 and 0.054, respectively; Table S10).
When pooled pulmonary data were examined, patients who were
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HIV-infected (p 5 0.059) and had a longer TTP (p , 0.001) were
less likely to be MTB/RIF-positive (Table S5). Extrapulmonary specimens with a longer TTP (p 5 0.003) were also less likely to be MTB/
RIF-positive and HIV-infection (p 5 0.013) was associated with an
increased likelihood of MTB/RIF-positivity (Table S9).
Comparative PCR inhibition in different specimen types. Overall.
Scatter plots of IPC CT values (smaller IPC CT values indicate less
inhibition) are shown in Figure 3. Internal control CT values for
expectorated sputum differed to those for induced sputum,
tracheal aspirates, BALF, pleural fluid, and CSF, and were similar
for pulmonary specimens and extrapulmonary specimens. The
proportion of MTB/RIF results with an IPC CT value .34, which
have been shown to be due to inhibition in sputum30, for
expectorated sputum, induced sputum, tracheal aspirates, BALF,
pleural fluid, CSF, pericardial fluid, and urine were 9% (39/433),
5% (6/128; p-value compared to expectorated sputum of 0.1140),
3% (2/68; p 5 0.0898), 3% (2/76; p 5 0.0596), 1% (1/131; p 5
0.0013), and 1% (1/142; p 5 0.0007), respectively. Collectively, the
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Figure 3 | Scatter plots of Xpert MTB/RIF internal positive control (IPC) cycle threshold values in different types of culture-positive specimens
obtained from separate patient cohorts. Each circle represents an individual specimen. Solid circles indicate patients who were Xpert MTB/RIF-positive,
whereas empty circles indicate Xpert MTB/RIF-negative specimens. Comparisons are between median (IQR) IPC CTs for Xpert-MTB/RIF-positive vs. –
negative specimens. *Only one MTB/RIF-negative, culture-positive tracheal aspirate specimen and one MTB/RIF-negative, culture-positive BALF
specimen were present; {Pulmonary specimens include expectorated sputum, induced sputum and bronchoalveolar lavage fluid; {Extrapulmonary
specimens include tracheal aspirates, pleural fluid, cerebral spinal fluid, and pericardial fluid. No patients had culture-positive urine.
proportion of MTB/RIF results with an internal control CT value
.34 for pulmonary specimens and extrapulmonary specimens was
6% (47/731) and 1% (4/381; p , 0.0001), respectively. Median (IQR)
IPC CT values were similar for comparisons between MTB/RIFpositive and –negative culture-positive specimens of each type,
except for CSF [27.80 (27.10–28.70) vs. 27.10 (26.5–27.15); p 5
0.0236]. MTB/RIF-negative, culture-positive pulmonary specimens
and extrapulmonary specimens had median IPC CT values of 28.45
(27.10, 31.15) and 27.30 (26.05, 28.20), respectively (p 5 0.0048).
Correlates of inhibition. When multivariable linear regression analyses were performed (p # 0.100), female gender was associated with
decreased internal control CT values for expectorated sputum (p 5
0.007; Table S1), HIV infection for CSF (p 5 0.078; Table S6), older
age for pericardial fluid (p 5 0.089; Table S8), and reduced protein
concentration in urine (p 5 0.072; Table S10). There was no assoSCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
ciation between MTB/RIF positivity and internal control CT value for
each of the other fluids tested (see supplement), however, when
pulmonary data and extrapulmonary data were pooled, female gender (p 5 0.008) and younger age (p 5 0.076) were respectively
associated with less inhibition (Table S4 and S9) for each specimen
type respectively.
Correlation between time-to-positivity and cycle threshold values
in different specimen types. When the strength of the correlation
between culture TTPs and CT values, which may be modulated by
PCR inhibition, were compared, similar Spearman correlation
coefficients (p-value vs. expectorated sputum) of 0.501, 0.623 (p 5
0.5252), 0.100 (p 5 0.5287), 20.051 (p 5 0.5287), and 0.199 (p 5
0.1211) for expectorated sputum, induced sputum, pleural fluid,
CSF, and pericardial fluid, respectively were obtained. When data
for pulmonary specimens were pooled (Figure 4), TTPs and CT
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Figure 4 | Correlation between liquid culture time-to-positivity and
Xpert MTB/RIF cycle threshold values in (A) pulmonary specimens and
(B) extrapulmonary specimens.
values were correlated (Spearman coefficients of 0.5043; p , 0.0001),
however, there was no significant correlation amongst extrapulmonary specimens (Spearman coefficient of 0.1437; p 5 0.4032),
and the correlation observed amongst pulmonary specimens was
stronger (p 5 0.030). CT values correlated less strongly with low or
high levels of bacterial load, rather than due to any intrinsic
properties of extrapulmonary specimens. For example, although
CT values and TTP exhibited a significant correlation overall for
pulmonary specimens, this was not present amongst specimens
with a TTP in the bottom (Spearman coefficient of 0.1805; p 5
0.1535) or top tertile (Spearman coefficient of 0.0899; p 5 0.5139),
but was amongst those in the middle tertile (Spearman coefficient of
0.3758; p 5 0.0017).
Discussion
This study is the first to compare mycobacterial load using culture
TTP, MTB/RIF-generated CT values, and MTB/RIF inhibition in
specimens from different body compartments. Briefly, our key findings are: (i) compared to expectorated sputum, MTB/RIF is inhibited
more in induced sputum, tracheal aspirates, and BALF, but less in
pleural fluid; (ii) ‘‘false-negative’’ MTB/RIF results (MTB/RIF-negative, culture-positive) from CSF displayed a greater inhibition compared to ‘‘true-positive’’ results, and pulmonary specimens inhibited
MTB/RIF more than extrapulmonary specimens; (iii) CT values correlate with TTP in pulmonary specimens but not in extrapulmonary
specimens, suggesting the assay to be unsuitable for estimation of
mycobacterial load amongst patients with extrapulmonary TB;
SCIENTIFIC REPORTS | 4 : 5658 | DOI: 10.1038/srep05658
(iv) TTP is the strongest correlate of MTB/RIF-positivity in both
pulmonary specimens and extrapulmonary specimens, even after
adjusting for inhibition; and (v) extrapulmonary specimens are more
paucibacillary than pulmonary specimens and, of the pulmonary
specimens, expectorated sputum had the highest bacillary load.
We found pulmonary specimens to have a greater proportion of
MTB/RIF results with evidence of inhibition [IPC CT value .3430]
compared to extrapulmonary specimens. It is likely that this is driven
by the viscous nature of sputum which, even after the addition of
sample buffer, may not be completed homogenised and thus still
interefere with the reaciton. Importantly, the inhibitory effect caused
by the viscous nature of some sputum specimens is likely offset by the
thick mucous within it, which has been shown to contain over 30fold more bacilli than the watery component, and thus the overall
sensitivity remains good30.
In our study, we found ‘‘false-negative’’ MTB/RIF results to display more inhibition on CSF than those that are ‘‘true-positive’’,
suggesting that this fluid contains material that interferes significantly with the PCR and thus may be a cause of false-negative results.
This is the first description of MTB/RIF inhibition in extrapulmonary specimens. Interestingly, we have shown in a separate study41
that, if a 3 ml volume of CSF is centrifuged, the pellet washed, and
resuspended in buffer prior to testing, the sensitivity of MTB/RIF
improves by almost 40%. In addition to concentrating the bacilli in
the specimen, this centrifugation and resuspension step likely also
removes PCR inhibitors. Such an approach should be considered for
other fluids that inhbit PCR-based tests. The other types of extrapulmonary specimens analysed did not display evidence of significant inhibition.
Several studies have detailed the performance of MTB/RIF on
extrapulmonary specimens and pulmonary specimens other than
sputum5,13–26,42, however, there is little comparative data on how
bacilliary load in these differents fluids vary. We found extrapulmonary specimens to have less bacillary load than pulmonary specimens
and, in our mulitvariate analyses, bacterial load was the chief determinant of MTB/RIF positivity in both pulmonary specimens and
extrapulmonary specimens, rather than inhibition, or any other of
the clinical and demographic characterstics examined.
In pulmonary specimens, HIV-infection was associated with a
decreased likelihood of a positive MTB/RIF result, however, in extrapulmonary specimens, HIV-infection was associated with an
increased likelihood of MTB/RIF-posivity. This is reflective of the
lower bacillary load seen in the lungs of HIV-coninfected patients
with pulmonary TB (due to the lower frequency of caviation in these
patients) compared to those who are HIV-uninfected. In contrast,
patients who are HIV-infected displayed a higher TB bacillary load in
specimens from extrapulmonary sites than those who were HIVuninfected, and thus those who are HIV-infected are more likely to
be MTB/RIF-positive for EPTB. Although EPTB is more frequent in
HIV-infected patients, their extrapulmonary bacillary load is lower
than HIV-infected patients with pulmonary TB. This means that
EPTB specimens with a concetration of bacilli below the limit of
detection of MTB/RIF will occur more frequently, and that patients
with suspected TB who have a negative MTB/RIF result should still
be investigated further. A further rammification of the low load seen
in extrapulmonary specimens is that in fluids such as pleural fluid or
pericardial fluid a biomarker-based approach using a molecule such
as interferon-c might be superior43 to a nucleic acid amplication
assay. Thus, MTB/RIF is not necessarily a ‘‘one size fits all’’, although
it does universally outperform microscopy (the only alternative rapid
test in some settings)7.
As has been documented by others23,28,30,34,44,45, we found MTB/
RIF-generated CT values to correlate significantly with culture timeto-positivity in pulmonary specimens. Such a conclusion is important because, for pulmonary TB, sputum bacillary load at diagnosis is
one of the strongest baseline predictors of long-term outcome46–49,
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and could thus be used for the prognostication of patients. We now
show there is no correlation with bacterial load in extrapulmonary
specimens, and that this appears to be as a result of the CT valuesTTP correlation deteriorating at low levels of bacterial load. While a
direct association between baseline MTB/RIF CT values and clinic
outcome has not yet been demonstrated, it appears that MTB/RIF
would not be useful for such a purpose amongst patients with extrapulmonary TB, or for a meaningful estimation of disease severity as
approximated by bacterial load.
This study has limitations. Although this is the first study to report
on MTB/RIF inhibition in fluids other than sputum, we did not
capture data on specimen-specific factors such as viscosity, appearance, or salt concentration, which may interefere with MTB/RIF.
Although shown to be useful by us and other25,41,42, we did not assess
bacterial load and inhibition in centrifuged specimens (other than
urine), as these data were not available for all the specimen types
included in this study and, when it were, different specimen volumes
were used for concentration. Our analyses were also restricted in
some instances by the comparatively small number of culture-positive specimens, especially after stratification by MTB/RIF- and/or
HIV-status and specimen type; however, the size of the cohort in
each of these parent studies is mostly in excess of that reported
elsewhere7. While we28,31 and others30 have described how MTB/
RIF can be used to predict smear-positivty in sputum, we were unable
to replicate such an analysis here, due to the small number of nonsputum specimens that were smear-positive. Our specimens of different types were stored for different durations, and this may have
influenced some differences, however, recent work has demonstrated
that MTB/RIF accuracy is not significantly affected by storage duration7,18, suggesting this effect, if any, to be minimal.
In summary, this study has demonstrated that low mycobacillary
load in extrapulmonary specimens is, rather than inhibition, primarily responsible for the diminished sensitivity of MTB/RIF in these
specimens compared to those from the pulmonary system. While
‘‘false-negative’’ CSF displayed more inhibition than ‘‘true-positive’’
specimens, pulmonary specimens displayed the most inhibition
overall, suggesting that MTB/RIF quantitative information might
not be useful in a significant minority of patients with suspected
pulmonary TB. Furthermore, the quantitative information generated
by MTB/RIF from extrapulmonary specimens does not correlate
with bacterial load, and is unlikely to be useful. Future studies on
the exact clinical and specimen-specific determinants of MTB/RIF
inhibition are important, as well additional specimen preparation
steps that may reduce inhibition, especially if MTB/RIF quantitative
information will used for patient management.
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Author contributions
Conception and design: G.T., J.P., K.D.; Analysis and interpretation: G.T., J.P., G.C., R.M.,
C.H., H.K., B.M., T.M., L.S., S.P., L.L., V.P., B.M., K.D. Drafting the manuscript for
important intellectual content: G.T., J.P., G.C., R.M., C.H., H.K., B.M., T.M., L.S., S.P., L.L.,
V.P., B.M., K.D.
Additional information
Supplementary information accompanies this paper at http://www.nature.com/
scientificreports
Competing financial interests: Keertan Dheda is an editor for Sci Reports.
How to cite this article: Theron, G. et al. Determinants of PCR performance (Xpert MTB/
RIF), including bacterial load and inhibition, for TB diagnosis using specimens from
different body compartments. Sci. Rep. 4, 5658; DOI:10.1038/srep05658 (2014).
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