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Table of Contents
ORIGINAL ARTICLE
Year : 2021  |  Volume : 9  |  Issue : 2  |  Page : 108-112

Utility of GeneXpert Mycobacterium tuberculosis/rifampicin assay in smear-negative pulmonary tuberculosis


1 Department of Respiratory Medicine, Bowring and Lady Curzon Medical College and Research Institute, Bengaluru, Karnataka, India
2 Vydehi Institute of Medical Sciences and Research Center, Bengaluru, Karnataka, India

Date of Submission14-Dec-2020
Date of Decision14-Dec-2020
Date of Acceptance24-Dec-2020
Date of Web Publication21-Apr-2021

Correspondence Address:
Dr. Javeriya Mohammadi
#18, 1st Floor, V. Nagenahalli Main Road, R T Nagar Post, Bengaluru - 560 032, Karnataka
India
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/ajim.ajim_105_20

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  Abstract 


Background: Tuberculosis (TB) remains one of the world's deadliest communicable diseases. An alarming rise in the incidence of Mycobacterium tuberculosis (MTB) has prompted the need for rapid diagnostic techniques. Despite low sensitivity in MTB detection, sputum microscopy remains the main diagnostic method, especially in resource-limited settings. Mycobacterial culture is the gold standard method for TB diagnosis; however, the use in clinical practice is limited due to longer time, biosafety requirements, and high cost. In December 2010, the World Health Organization (WHO) 1st endorsed the usage of Xpert MTB/rifampicin (RIF) assay. The WHO recommends that GeneXpert test could be used as a follow on test to microscopy, especially in smear-negative specimens. Objectives: To assess percentage of Tuberculosis cases and Multi Drug Resistant (MDR) case detection at diagnosis using Xpert MTB/RIF assay in smear-negative pulmonary cases. Materials and Methodology: Detailed relevant clinical history and examination were carried out for 105 pulmonary TB suspect patients. Sputum acid-fast bacilli smear two samples and human immunodeficiency virus status were checked under RNTCP; chest X-ray PA view was done. Smear-negative patients were subjected to bronchoscopy and bronchoalveolar lavage (BAL)/bronchial washing. BAL/Bronchial washing was tested for GeneXpert. Interpretation and Conclusion: MTB was detected in 21 (20%) samples out of 105 samples and RIF resistance was detected in 1 (1%) sample. Most common chest x-ray abnormalities were cavity (33.3%) and consolidation (33.3%). 8 cases (38.1%) among Gene xpert positives had past history of Tuberculosis. Comorbidities were found in 5 cases (23.8%) among Gene Xpert positives. The present study concludes that using standard clinical assessment for selection, five patients need to be tested to detect one case of smear-negative TB. Smear-negative patients could benefit from Xpert, particularly in areas where no culture is available.

Keywords: Acid-fast bacilli, bronchoalveolar lavage, GeneXpert, human immunodeficiency virus, multidrug resistant


How to cite this article:
Mohammadi J, Reddy GA, Haran A. Utility of GeneXpert Mycobacterium tuberculosis/rifampicin assay in smear-negative pulmonary tuberculosis. APIK J Int Med 2021;9:108-12

How to cite this URL:
Mohammadi J, Reddy GA, Haran A. Utility of GeneXpert Mycobacterium tuberculosis/rifampicin assay in smear-negative pulmonary tuberculosis. APIK J Int Med [serial online] 2021 [cited 2021 Jun 12];9:108-12. Available from: https://www.ajim.in/text.asp?2021/9/2/108/314192




  Introduction Top


Tuberculosis (TB) remains one of the world's deadliest communicable diseases. Globally in 2015, an estimated 9.6 million people developed TB and 1.1 million died from the disease.[1] An alarming rise in the global incidence of Mycobacterium tuberculosis (MTB) has prompted the need for rapid diagnostic techniques which will rapidly diagnose and treat affected patients, thereby reducing on-going transmission of disease and development of secondary resistance.[2]

Despite low sensitivity in the detection of MTB, sputum smear microscopy remains the main diagnostic method, especially in resource-limited settings. Mycobacterial culture is the gold standard method for TB diagnosis; however, the use in clinical practice is limited due to slow turnaround time, biosafety requirements, and high cost.[3]

Derivations from case burden estimates suggest that only around 70% of active TB cases are diagnosed using current strategies. The development and implementation of the Xpert assay having high sensitivity (88%)[4] and specificity (99%)[4] in detection of smear-negative TB has raised hopes of increased case detection in low- and middle-income countries.[5]

In December 2010, the World Health Organization (WHO) 1st endorsed usage of Xpert MTB/rifampicin (RIF) assay.[6] It is the only fully automated real-time DNA-based test which detects both TB bacilli and RIF resistance (rpoB gene), giving result in 2 h and thus potentially decreasing default due to delayed diagnosis.[5]

The WHO recommends that GeneXpert test could be used as a follow on test to microscopy, especially in smear-negative specimens.[7] A considerable number of articles have been written reviewing the use of GeneXpert test; generally, the views given are extremely variable. Given this scenario and limited studies available on the Indian population, there is a need to study GeneXpert utility on the Indian population.

Objectives of the study

  1. To assess percentage of Tuberculosis cases in smear negative Pulmonary cases.
  2. To assess percentage of Multi Drug Resistant (MDR) case detection at diagnosis using Xpert MTB/RIF assay.



  Materials and Methodology Top


Ethics

Ethical approval was obtained from the local institutional ethical committee.

Study design

This was a prospective observational study.

Selection and description of participants

Adult patients presenting to the respiratory medicine department in a tertiary care Centre, India, from January 2016 to June 2017 were recruited for the study.

Inclusion criteria were patients presenting with features consistent with pulmonary TB, that is, (1) one or more of the symptoms (cough >2 weeks, evening rise of fever, night sweats, loss of appetite, weight loss, breathlessness, hemoptysis, and chest pain) or (2) with abnormal chest radiograph compatible with pulmonary TB (cavitary lesions, infiltration, consolidation, and military pattern), age >18 years of age, and who have given written informed consent for the study.

Exclusion criteria were those with sputum acid-fast bacilli (AFB) smear positive and patients on current ATT and history of receiving antituberculous drug within 3 months before enrollment.

Methods of data collection followed were detailed clinical history, examination and chest X-Ray PA view was taken. Sputum AFB smear two samples were tested under RNTCP. One hundred and five patients were recruited for the study on the basis of inclusion and exclusion criteria, after obtaining written informed consent. Then, bronchoalveolar lavage (BAL)/bronchial washing sample was subjected for Gene Xpert testing in model no. GXivC2 modules, equipment name GeneXpertiv-2. Digestion/decontamination of the sample was done by N-acetyl l-cysteine/sodium hydroxide method. Human immunodeficiency virus (HIV) status was checked as per the RNTCP guidelines and parameters were analyzed.

Sample size

Assuming a prevalence of MTB as 21.32% with a precision of 8%, a sample size of 105 was calculated.

Statistical analysis

Demographic characteristics and prevalence of TB-positive cases were represented using percentages (the continuous demographic characteristics were represented using mean and standard deviation).


  Results Top


From January 2016 to June 2017, 105 smear-negative patients were tested by Xpert on BAL samples. A baseline characteristic of the patients is shown in [Table 1]. Most of the patients in my study were in the age group of 26–45 years (48.6%) and the mean age was 42.45 years. Of the 105 patients, 34 (32.4%) were female and 71 (67.6%) were male. Comorbidities were seen in 20 (19%) patients. Past history of TB was present in 35 (33.3%) patients. Chest X-ray findings are summarized in [Figure 1]. The most common chest X-ray abnormality was consolidation (25 cases), followed by cavity (21 cases).
Table 1: Baseline characteristics of 105 smear-negative cases

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Figure 1: Chest xray finding

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GeneXpert results are shown in [Figure 2]
Figure 2: Gene Xpert results

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Gene Xpert detected MTB in 21(20%) individuals and RIF resistance in 1(1%) individual. Most common chest x-ray abnormalities were cavity (33.3%) and consolidation (33.3%). 8 cases (38.1%) among Gene xpert positives had past history of Tuberculosis shown in [Table 2].
Table 2: Comparing Old PTB with Gene Xpert results

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Comorbidities were found in 5 cases (23.8%) among GeneXpert positives [Figure 3]. There was no statistical significance found between comorbidities and GeneXpert with P = 0.542 > 0.05.
Figure 3: Comorbidities among the cases

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None of the patients in my study were HIV positive.

Flow diagram of patients included in the study is shown in [Figure 4].
Figure 4: Flow diagram of patients included in the study

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  Discussion Top


Diagnosis of smear-negative cases often gets missed due to inaccessibility of molecular methods and widely use of low-sensitive methods like sputum smear microscopy.[8],[9],[10] With this background, the study was conducted to assess percentage of Tuberculosis cases and percentage of Multi Drug Resistant (MDR) case detection at diagnosis in smear negative pulmonary cases using Xpert MTB/RIF assay.

In my study among 105 samples, Gene Xpert detected MTB in 21 (20%) samples. It was found that using standard clinical assessment for selection, five patients need to be tested to detect one case of smear-negative TB which is consistent with previous studies mentioned below.

A study conducted by Shrestha et al. from February 2013 to December 2013 in Nepal on 258 patients included patients with symptoms consistent with TB and three negative sputum smears from February 2013 to December 2013. MTB was detected in 55 (21.32%) of total patients using GeneXpert on sputum samples. This study concluded that using standard clinical assessment for selection, testing five patients detected one case of smear-negative PTB.

A study was conducted by Khalil and Butt in Rawalpindi, Pakistan, between December 2012 and August 2013 on 93 cases with smear-negative or sputum scarce PTB suspects; MTB was detected in 81 (87%) samples using GeneXpert in BAL samples.[11]

Gowda, et al. conducted a prospective study in 60 smear-negative patients on BAL samples. GeneXpert detected MTB in 24 (40%) samples.[12]

From the above studies, it is clear that the yield of MTB detection is more in BAL samples than sputum using GeneXpert assay and the results can be improved by better selection of patients with a high index of suspicion for pulmonary TB.

In my study, RIF's resistance was detected in 1 (1%) sample.

A similar result was obtained with Shrestha et al. study on 258 smear-negative patients. Rifampicin resistance was detected in 2 patients (0.8%) of 55 Xpert-positive results.[5]

A study conducted by Pinyopornpanish et al. in Rawalpindi, Pakistan, on 93 cases with smear-negative or sputum scarce PTB suspects, 5 patients (5.37%) of 81 Xpert-positive cases had rifampicin resistance detected on BAL using GeneXpert.[10]

My study and the above-mentioned similar studies have detected a low percentage of MDR TB, probably because the study was performed on smear-negative cases.

In my study, cavity and consolidation were the most common abnormalities on chest X-ray among Xpert-positive groups which is consistent with a previous study conducted by Shrestha et al. in Nepal.[5] However, there was no significant correlation found between chest X-ray finding and GeneXpert result.

In my study, comorbidities were present in five cases of 21 Xpert-positive cases. Diabetes mellitus was present in four cases and steroid intake for 1 month in one case. However, there was no significant correlation found between comorbidities and GeneXpert result.

Highlighted findings were as follows:

  • Using standard clinical assessment for selection, five patients need to be tested to detect one case of smear-negative TB
  • There was no significant correlation found between the past history of TB and GeneXpert result
  • There was no significant correlation found between chest X-ray finding and GeneXpert result
  • There was no significant correlation found between comorbidities and GeneXpert result.


There are certain limitations in my study:

  • Small sample size
  • Single-center study
  • I did not use gold standard test culture for definitive diagnosis; hence, sensitivity and specificity could not be calculated
  • As the study was performed in smear-negative cases, which might have excluded MDR TB cases, this may be the reason for the low percentage of MDR TB cases.


Recommendations for further study:

  • A multicenter study on a large population is required
  • Results should be compared with gold standard LJ culture for definitive diagnosis and to calculate sensitivity and specificity
  • GeneXpert results should be cautiously interpreted, particularly when GeneXpert result shows MTB very low detected with rifampicin resistance. It should be confirmed with culture. This can be overcome by using GeneXpert Ultra which has very high sensitivity compared to GeneXpert detecting a low number of bacilli (16 bacilli/ml of sputum).



  Conclusion Top


The present study concludes that using standard clinical assessment for selection, five patients need to be tested to detect one case of smear-negative TB. The percentage of case detection using GeneXpert can be increased when applied to cases with a higher index of suspicion for TB.

Smear-negative patients could benefit from Xpert, particularly in areas where no culture is available. The test has the advantages of being inexpensive, less workforce, and gives a quick result.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.



 
  References Top

1.
WHO Global TB Report 2016. Available from: http://www.who.int/tb/publications/global_report/gtbr2016_executive_summary.pdf. [Last accessed on 2017 Apr 30].  Back to cited text no. 1
    
2.
Iram S, Zeenat A, Hussain S, Wasim Yusuf N, Aslam M. Rapid diagnosis of tuberculosis using Xpert MTB/RIF assay-Report from a developing country. Pak J Med Sci 2015;31:105-10.  Back to cited text no. 2
    
3.
Pinyopornpanish K, Chaiwarith R, Pantip C, Keawvichit R, Kanlaya W, Khamnoi P, et al. Comparison of Gene Xpert MTB/RIF assay and the conventional sputum microscopy in detecting MTB in Northern Thailand. Tuberc Res Treat 2015;2015:1-6.  Back to cited text no. 3
    
4.
WHO Policy Update. Available from: https://www.who.int/iris/bitstream/10665/112472/1/9789241506335_eng.pdf. [Last accessed on 2015 Nov 05].  Back to cited text no. 4
    
5.
Shrestha P, Arjyal A, Caws M, Prajapati KG, Karkey A, Dongal S, et al. The application of gene Xpert MTB/RIF assay for smear negative TB diagnosis as a fee paying service at a South Asian General Hospital. Tuberc Res Treat 2015;2015:1-6.  Back to cited text no. 5
    
6.
GeneXpert or Xpert TB Test | Diagnosis & Resistance Testing. Available from: https://www.tbfacts.org/xpert-tb-test/. [Last accessed on 2015 Nov 14].  Back to cited text no. 6
    
7.
World Health Organisation, Global Tuberculosis Report, WHO/HTM/TB/2013.11, World Health Organisation. Geneva, Switzerland: World Health Organisation; 2013. Available from: http://www.who.int/tb/publications/Xpert_factsheet.pdf. [Last accessed on 2015 Dec 04].  Back to cited text no. 7
    
8.
Ondimu TO, Grace MO, Samson AO, Asito SA. Comparative study of smear microscopy, GeneXpert and culture and sensitivity assays in detection of mycobacterium tuberculosis on sputum samples among tuberculosis suspected cases in Nyamira County referral hospital. Mycobacterial diseases. 2017;7.  Back to cited text no. 8
    
9.
Agrawal M, Bajaj A, Bhatia V, Dutt S. Comparative study of GeneXpert with ZN stain and culture in samples of suspected pulmonary tuberculosis. J Clin Diagn Res 2016;10:DC09-12.  Back to cited text no. 9
    
10.
Pinyopornpanish K, Chaiwarith R, Pantip C, Keawvichit R, Wongworapat K, Khamnoi P, et al. Comparison of Xpert MTB/RIF assay and the conventional sputum microscopy in detecting Mycobacterium tuberculosis in Northern Thailand. Tuberc Res Treat 2015;2015:571782.  Back to cited text no. 10
    
11.
Khalil KF, Butt T. Diagnostic yield of Bronchoalveolar Lavage gene Xpert in smear-negative and sputum-scarce pulmonary tuberculosis. J Coll Physicians Surg Pak 2015;25:115-8.  Back to cited text no. 11
    
12.
Gowda NC, Ray A, Soneja M, Khanna A, Sinha S. Evaluation of Xpert® Mycobacterium tuberculosis/rifampin in sputum-smear negative and sputum-scarce patients with pulmonary tuberculosis using bronchoalveolar lavage fluid. Lung India 2018;35:295-300.  Back to cited text no. 12
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