Infection and Drug Resistance

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Diagnostic Yield of Oral Swab Testing by TB-LAMP

for Diagnosis of Pulmonary Tuberculosis

Yanhua Song, Yifeng Ma, Rongmei Liu, Yuanyuan Shang, Liping Ma, Fengmin
Huo, Yunxu Li, Wei Shu, Yufeng Wang, Mengqiu Gao & Yu Pang

To cite this article: Yanhua Song, Yifeng Ma, Rongmei Liu, Yuanyuan Shang, Liping Ma,
Fengmin Huo, Yunxu Li, Wei Shu, Yufeng Wang, Mengqiu Gao & Yu Pang (2021) Diagnostic Yield
of Oral Swab Testing by TB-LAMP for Diagnosis of Pulmonary Tuberculosis, Infection and Drug
Resistance, , 89-95, DOI: 10.2147/IDR.S284157

To link to this article: https://doi.org/10.2147/IDR.S284157

© 2021 Song et al.

Published online: 12 Jan 2021.

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ORIGINAL RESEARCH

Diagnostic Yield of Oral Swab Testing by TB-LAMP

for Diagnosis of Pulmonary Tuberculosis
This article was published in the following Dove Press journal:
Infection and Drug Resistance

Yanhua Song,1,* Yifeng Ma,2,* Objective: A prospective study was conducted to ascertain the accuracy of oral swab
Rongmei Liu,1,* Yuanyuan Shang,3,* specimens collected in the early morning, spot and at night for detecting pulmonary
Liping Ma,1 Fengmin Huo,3 Yunxu tuberculosis (TB).
Li,3 Wei Shu,4 Yufeng Wang,5 Methods: We prospectively enrolled patients with symptoms suggestive of pulmonary TB
Mengqiu Gao,1 Yu Pang 3 in Beijing Chest Hospital. An early morning sputum specimen was collected from each
1
Department of Tuberculosis, Beijing Chest
patient for GeneXpert MTB/RIF (Xpert) and mycobacterial culture. In addition, three oral
Hospital, Capital Medical University/Beijing swabs were collected for TB-LAMP testing.
Tuberculosis & Thoracic Tumor Research
Results: With the combined results of three oral swab specimens, the proportion of
Institute, Beijing, People’s Republic of China;
2
Clinical Laboratory, Beijing Chest Hospital, Mycobacterium tuberculosis (MTB)-positive cases achieved 40.6%, which was comparable
Capital Medical University/Beijing to results for Xpert and MGIT (P=0.603). Using Xpert plus MGIT as reference, the
Tuberculosis and Thoracic Tumor Institute,
Beijing, People’s Republic of China; sensitivity of OS-LAMP on a single specimen ranged from 32.6% on the night oral swab
3
Department of Bacteriology and to 50.0% on the morning swab. The combination of three oral swab specimens correctly
Immunology, Beijing Key Laboratory on Drug-
Resistant Tuberculosis Research, Beijing identified 38 MTB-positive cases, indicating an overall sensitivity of 82.6%, which was
Chest Hospital, Capital Medical University/ significantly higher than that of a single oral swab specimen (P<0.001, P=0.001).
Beijing Tuberculosis & Thoracic Tumor
Research Institute, Beijing, People’s Republic
Conclusion: Oral swab can be used as an alternative specimen for diagnosis of pulmonary
of China; 4Clinical Center on TB, Beijing TB using TB-LAMP. Morning oral swab exhibits the highest sensitivity, and the inclusion of
Chest Hospital, Capital Medical University/
more specimens at different time points provides compensation in diagnostic sensitivity with
Beijing Tuberculosis & Thoracic Tumor
Research Institute, Beijing, People’s Republic single oral swab.
of China; 5Department of Laboratory Quality Keywords: diagnosis, oral swab, TB-LAMP, pulmonary tuberculosis, China
Control, Innovation Alliance on Tuberculosis
Diagnosis and Treatment (Beijing), Beijing,
People’s Republic of China

*These authors contributed equally to this

work
Introduction
Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB) complex, poses a
Correspondence: Mengqiu Gao serious threat to public health, especially in developing countries.1,2 In 2018, there
Department of Tuberculosis, Beijing were an estimated 10 million cases and 1.3 million deaths from tuberculosis
Chest Hospital, Capital Medical
University/Beijing Tuberculosis & Thoracic worldwide.1 Despite increases in TB notifications, a large gap occurs between the
Tumor Research Institute, No. 9, Beiguan estimated number of incidents and the number of new cases reported (7.0 million).1
Street, Tongzhou District, Beijing 101149,
People’s Republic of China More importantly, of the TB cases notified in 2018, only 55% were bacteriologi­
Tel/Fax +86-10-8950 9322
Email gaomqwdm@aliyun.com
cally confirmed, and the remaining patients were diagnosed clinically.1 Thus,
intensified efforts are needed to improve access to early and accurate diagnosis
Yu Pang
Department of Bacteriology and that is essential for achieving the ultimate goal of TB elimination by 2035.3
Immunology, Beijing Key Laboratory on A high-quality biological specimen is of great importance for facilitating the
Drug-Resistant Tuberculosis Research,
Beijing Chest Hospital, Capital Medical diagnosis of pulmonary TB.4 Currently, the identification of active TB majorly
University/Beijing Tuberculosis & Thoracic relies on the examination of sputum specimens in individuals with symptoms
Tumor Research Institute, No. 9, Beiguan
Street, Tongzhou District, Beijing 101149, suggestive of pulmonary TB.5 However, a marked proportion of patients fail to
People’s Republic of China produce good quality sputum specimens.4,6 In the absence of quality sputum,
Tel/Fax +86-10-8950 9359
Email pangyupound@163.com multiple types of specimens have to be used as alternatives for TB diagnosis,

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Song et al Dovepress

such as induced sputum and bronchoalveolar lavage fluid Routine Laboratory Examinations
(BALF).7–9 Induced sputum testing is considered a useful Direct smear was conducted using light-emitting diode
test in the diagnosis of sputum scare patients, while its fluorescence microscopy for acid fast bacilli (AFB).15
complex procedures become a barrier to gain acceptance The positivity of smear was graded following national
from clinicians.10 BALF is another promising alternative guidelines established by the Chinese Center for
to the commonly used sputum specimen for detecting Diseases Control and Prevention. A volume of 1.0 mL
MTB in suspects.4 The higher risks of nosocomial TB of sputum was decontaminated with the N-acetyl-L-
transmission and higher costs impedes clinical applications cysteine (NALC)-NaOH method for 15 min. After
in resource-poor countries, where TB is endemic.10 neutralization with sterile PBS (pH=7.0), the decontami­
Therefore, a cheaper noninvasive method of providing nated specimen was centrifugated at 3000×g for 15 min
quality specimens would be advantageous. then each pellet was resuspended in PBS. A volume of
Oral swab testing has recently been reported to be a 0.5 mL of each suspension was inoculated into myco­
promising test in the diagnosis of bacteriologically con­ bacteria growth indicator tube (MGIT) supplemented
firmed TB patients.11,12 Compared with collection of spu­ with 0.8 mL of oleic acid-albumin-dextrose-catalase
tum specimens, oral swabbing is very easy to perform (OADC) along with PANTA. MGIT tubes were incu­
without production of aerosol. Although preliminary bated into MGIT 960 instrument. The growth of bacteria
experiments yielded encouraging results for oral swabs,12 was automatically recorded by the instrument. All posi­
the sample size was small, and the optimal sampling time tive cultures were confirmed as mycobacteria with
point was undetermined. To address these concerns, a Ziehl–Neelsen staining. The subsequent species identifi­
prospective study was conducted in the Beijing Chest cation was performed using a commercial Tibilia Rapid
Hospital to ascertain the accuracy of oral swab specimens Test (Chuangxin, Hangzhou, China).
collected in the early morning, spot and at night for detect­ For Xpert testing, 1.0 mL of sputum was digested with
2.0 mL of sample reagent. After incubation at room tempera­
ing pulmonary TB.
ture for 15 min, 2.0 mL of inactivated sputum sample was
pipetted to a Xpert MTB/RIF cartridge. The cartridge was
Materials and Methods then loaded into the GeneXpert instrument. Results were
Study Subjects automatically generated by the instrument within two hours.
We prospectively enrolled patients aged >16 years with
symptoms suggestive of pulmonary TB who were
TB-LAMP
admitted to an inpatient TB unit in Beijing Chest hospital
One milliliter of suspended swab sample was pipetted into
between November 2019 and April 2020. Patients meeting a 1.5-mL centrifugation tube followed by centrifugation at
inclusion criteria had at least one symptom of TB and 8000×g for three minutes. The supernatant was discarded,
radiological abnormalities indicative of TB.13 Symptoms and the 60 μL of pellet resuspension was used for TB-
of TB included a persistent cough of ≥2 weeks, unex­ LAMP assay as described previously. The 60 μL of resus­
plained fever for ≥2 weeks, weight loss, and night sweat. pension was transferred to a heating tube containing
Demographic and clinical information was collected from extraction solution. Then the heating tube was incubated
electronic medical record. at 90°C for five minutes for inactivation and lysis of
pathogens. Next the mixture in the heating tube was
Collection of Sputum and Oral Swabs extruded into an adsorbent tube to remove the impurity.
Early morning sputum specimen was collected from Thirty microliters of crude DNA solution was added into
each patient for GeneXpert MTB/RIF (Xpert) and myco­ the reaction tube, and then loaded into the heating block at
bacterial culture. In addition, three oral swabs were 67°C for 40 min. After amplification, the results of TB-
collected as described previously.14 Briefly, the clini­ LAMP were interpreted with the fluorescence detector.
cians firmly brushed the swab along the dorsum of the
tongue seven-to-eight times. After swabbing, the swab Statistical Analysis
was put into a 15-mL disposable tube containing 2 mL The composite reference standard of mycobacterial culture
sterile normal saline. and Xpert assay was used as the gold standard to assess

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Dovepress Song et al

the diagnostic accuracy of TB-LAMP on oral swab sam­ Table 1 Demographic and Clinical Characteristics of Individuals
ples. The chi-squared test was used to compare perfor­ with Symptoms Suggestive of Pulmonary Tuberculosis
mance among the various laboratory methods. Characteristics All Patients (n=101)
Nonparametric test was conducted to assess the difference
Median age (range), years 43.5 (17.0–88.0)
in the values of test results between two groups. A Venn Male sex, n (%) 69 (74.6)
diagram was built using an online tool available at https:// Residence
bioinfogp.cnb.csic.es/tools/venny/index.html.All statistical Resident 61 (60.4)
calculations were conducted using SPSS version 20.0 Float 40 (39.6)

(IBM Corporation, Armonk, NY, USA). Differences were Comorbidity/ies

declared significant if P-values were less than 0.05. Diabetes 16 (15.8)
Hypertension 10 (9.9)
Cardiac disease 8 (7.9)
Results Immunologic dysfunction 4 (4.0)
Participants Kidney dysfunction 4 (4.0)
A total of 103 participants with symptoms suggestive of Hepatitis 3 (3.0)
Others 2 (2.0)
pulmonary TB were recruited in this study. Of these
patients, two were excluded from the analysis as indicated
in Figure 1. Ultimately, 101 were included (74.6% were
male). The median age was 48.5 years (range: 17.0–88.0) 44.6% and 37.6%, respectively. The proportions of MTB-
(Table 1). Of the included patients 60.4% (61/101) were positive cases detected oral swab-TB-LAMP (OS-LAMP)
resident, and the most frequently observed comorbidity were 24.8% (25/101), 15.8% (16/101) and 17.8% (18/101)
was diabetes (16/101, 15.8%) (Table 1). All participants
for morning, night and spot specimens, respectively. With
in our study were HIV negative.
the combined results of three specimens, the proportion of
MTB-positive cases achieved 40.6% (41/101), which was
Diagnostic Accuracy of TB-LAMP on Oral comparable to results for Xpert and MGIT (P=0.603).
Swab Specimens The overlap between patients with a positive smear
Among 101 specimens, Xpert and MGIT methods identi­ microscopy, Xpert, MGIT, or OS-LAMP is shown in
fied 45 and 38 MTB-positive cases, for detection rates of Figure 2. Among 101 patients, there were 19 (18.8%)

Figure 1 Participant enrollment.

Abbreviation: OS, oral swab.

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93.6), which was significantly higher than that of single

oral swab specimen (P<0.001, P=0.001).

Relationship of OS-LAMP Results with

Bacterial Load
Of 45 cases with positive Xpert results, 38 had positive
OS-LAMP results. The mean Ct values of LAMP positive
group was 21.5±1.0 cycles, which was significantly lower
than that of LAMP negative group (28.9±1.0 cycles,
P=0.002). Similarly, of 38 cases with positive MGIT
results, the patients with negative OS-LAMP results
(29.2±1.9 days) had a longer time to detection of myco­
bacteria growth than the LAMP-positive group (16.8 ± 1.1
days, P<0.001) (Figure 3).
Figure 2 Venn diagram showing the distribution of 101 patients for detection of
MTB by using smear microscopy, MGIT, Xpert, and oral swab testing. Among 101
patients included, 41 were positive for MTB by oral swab testing, whereas, 45, 38,
Discussion
and 21 samples were positive by Xpert, MGIT and smear microscopy, respectively. The diagnosis of TB is hampered by lack of sputum
production or poor sample quality.16 The use of alternative
specimens is increasing in the diagnosis of this infectious
and 52 (51.5%) cases positive and negative for MTB,
disease. In this study, our data demonstrated that oral swab
respectively by all four methods. Xpert detected MTB in
can be used as an alternative specimen for diagnosis of
total 45 cases either as alone or combined with the other
pulmonary TB using TB-LAMP. In a recent study from
three methods. Of 41 cases detected by OS-LAMP, three South Africa, two oral swab per patient exhibited a com­
cases yielded negative Xpert and MGIT results, but were bined sensitivity of 92.8% relative to sputum Xpert assay
further diagnosed as confirmed laboratory TB patients by using a manual quantitative PCR targeting IS6110.11
from BALF specimens. Along with the observed high sensitivity, the specificity of
We further analyzed the performance of OS-LAMP for this assay was less than optimal due to sample
detection of MTB-positive cases using Xpert and MGIT contamination.11 We hypothesize that this difference in
results from sputum as gold standard. As summarized in sensitivity is likely because the manual PCR protocols
Table 2, a total of 46 cases exhibited positive Xpert and/or were used in the latter study that resulted in remarkedly
MGIT results. The sensitivity of OS-LAMP on a single high false positivity rate. Therefore the use of closed tube
specimen ranged from 32.6% (15/46 95%CI: 19.1–46.2) in system in our analysis may better reflect the diagnostic
night oral swab to 50.0% (23/46, 95%CI: 35.6–64.4) in yield of oral swab testing for pulmonary TB.
morning swab. The combination of three oral swab speci­ Another interesting finding of our study was the sub­
mens correctly identified 38 MTB-positive cases, indicat­ stantial lack of overlap in detection of MTB across three
ing an overall sensitivity of 82.6% (38/46, 95%CI: 71.7– samples per patient. Although the morning oral swab

Table 2 Detection of MTB with TB-LAMP from Various Oral Swab Samples
Specimen n TP FPa FN TN Sensitivity (95%CI) Specificity (95%CI) PPV (95%CI) NPV (95%CI)

Morning 101 23 2 23 53 50.0 (35.6–64.4) 96.4 (91.4–100.0) 92.0 (81.4–100.0) 69.7 (59.4–80.1)
Night 101 15 1 31 54 32.6 (19.1–46.2) 98.2 (94.7–100.0) 93.8 (81.9–100.0) 63.5 (53.3–73.8)
Spot 101 17 1 29 54 37.0 (23.0–50.9) 98.2 (94.7–100.0) 94.4 (83.9–100.0) 65.1 (54.8–75.3)
Morning + Spot 101 31 3 15 52 67.4 (53.8–80.9) 94.5 (88.5–100.0) 91.2 (81.6–100.0) 77.6 (67.6–87.6)
Night + Spot 101 28 2 15 52 60.9 (46.8–75.0) 96.4 (91.4–100.0) 93.3 (84.4–100.0) 74.6 (64.5–84.8)
Morning + Night 101 32 2 14 53 69.6 (56.3–82.9) 96.4 (91.4–100.0) 94.1 (86.2–100.0) 79.1 (69.4–88.8)
All 101 38 3 8 52 82.6 (71.7–93.6) 94.5 (88.5–100.0) 92.7 (84.7–100.0) 86.7 (78.1–95.3)
a
Note: FP is determined when Xpert and MGIT on sputum specimens are used as gold standard.
Abbreviations: TP, true positive; FP, false positive; FN, false negative; TN, true negative; PPV, positive predictive value; NPV, negative predictive value.

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Dovepress Song et al

rising out-of-pocket costs for TB patients, especially

patients in underdeveloped regions.18 Further information
is essential to inform the policy maker to formulate appro­
priate financial support strategy for incorporation OS-
LAMP into the routine diagnostic algorithm.
As expected, we found that the false negative detection
results by OS-LAMP were majorly associated with the low
bacterial load in pulmonary TB patients, such as high C(t)
values by Xpert and increased time to detection by MGIT.
Notably, three patients who were Xpert negative and
MGIT negative were identified as MTB-positive by OS-
LAMP. Further analysis on BALF demonstrated that such
patients were true TB cases. It is believed that the quality
of sputum specimen has a great impact on diagnostic
accuracy of MTB-positive TB patients. In China more
than half of the samples were of insufficient quality.19
Therefore the poor quality of sputum could be the main
reason for missed detection of tubercle bacilli. This finding
has several important implications: on the one hand, more
effort should be made to collect good quality sputum
samples that could guarantee the diagnostic accuracy; on
the other hand, this highlights that oral swab testing could
be used as an alternative to improve the detection of MTB
for patients producing poor quality sputum.
BALF is considered as a promising alternative the
commonly used sputum specimen for detecting MTB in
patients with symptoms suggestive of TB;8 however, it is
worth mentioning that invasive diagnostic procedures
Figure 3 Relationship of OS-LAMP results with bacterial load (A). Relationship of
OS-LAMP results with bacterial load by Xpert; The Xpert-generated cycle thresh­
hamper its implementation in resource-limited regions.8
old (Ct) value of Probe A was used as an indicator for bacterial load. (B) The easy-to-collect specimens are therefore a key priority
Relationship of OS-LAMP results with bacterial load by MGIT.
for diagnostic development. If these criteria are applied,
oral swab would be strongly favored over BALF for initial
exhibited the highest sensitivity, OS-LAMP missed half of investigation of pulmonary TB, as the yield of OS-LAMP
laboratory-confirmed pulmonary TB patients. In line with has been comparable to sputum Xpert.
our data, the sensitivity of a single oral swab was 43% We also acknowledged several obvious limitations to
reported by Lima et al.17 Considering that tubercle bacilli the present study. First, the major limitation was the single
or its DNA are deposited on oral surfaces, this phenom­ center recruitment of the small sample of individuals,
enon suggests that the bacterial load in an oral swab speci­ which may weaken the significance of our conclusion.
men is significantly affected by daily oral activities such as Further study is urgently needed to verify our data by
eating, drinking and oral hygiene that decrease tubercle enrollment of a large cohort of patients. Second, only
bacillus analytes on oral surface.11 The morning oral swab TB-LAMP was used to detect tubercle bacilli in oral
should be collected prior to any oral activity to improve swab samples. Additional work in needed to adapt these
detection of MTB. In addition, the inclusion of more samples for use on Xpert MTB/RIF Ultra, an automated
specimens at different times provides a practical alterna­ diagnostic platform with higher sensitivity.20 Third, as to
tive method for compensating the loss of diagnostic sensi­ the reference examinations, MGIT yielded fewer positive
tivity with a single oral swab. Despite yielding the cases compared to Xpert. This phenomenon was mainly
comparative performance as Xpert by the combination of due to the high proportion of salivary sputum that limited
three oral swab specimens, this raises concerns about the capability of MGIT culture in detecting

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Song et al Dovepress

mycobacteria.19 Fourth, the probability of true TB posi­

tives has a significant effect on the positive predictive References
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