ORIGINAL ARTICLE Year : 2021  |  Volume : 70  |  Issue : 1  |  Page : 31-37

Study of diagnostic role of GeneXpert test in patients with pulmonary tuberculosis at El-Mahalla Chest Hospital

Hisham E.S Abd El Aaty, Maha Y El-Hefnawy, Fatma S Khalaf
Department of Chest Disease and Tuberculosis, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt

Date of Submission27-Jun-2019Date of Decision09-Jul-2019Date of Acceptance12-Sep-2019Date of Web Publication26-Mar-2021

Correspondence Address:
MBBS Fatma S Khalaf
Department of Chest Disease and Tuberculosis, Faculty of Medicine, Menoufia University, Shibin El Kom, 31951
Egypt

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ejcdt.ejcdt_135_19

Background Tuberculosis (TB) is a serious health problem in middle-income and low-income countries and needs rapid diagnosis and treatment. Xpert MTB/RIF assay provides early results by simultaneous detection of Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance.
Aim To evaluate the performance of GeneXpert MTB/RIF technique in diagnosing patients with pulmonary TB at El-Mahalla Chest Hospital, Egypt.
Patients and methods Data of pulmonary TB were retrospectively analyzed between February 2017 and February 2018 from patient files and included laboratory results regarding Ziehl–Neelsen (ZN) smear microscopy, GeneXpert assay, and culture. Patients were divided into group I, having confirmed TB, where MTB was detected, and group II, having unconfirmed and unlikely TB, where MTB was not detected.
Results A total of 150 patients were recruited. Overall, 80% were males, and the median age was 45.2±15.1 years. Positivity of ZN smear for TB bacilli was 61.1%, positivity of GeneXpert MTB was 65.9%, and culture positivity was 67.3%. GeneXpert sensitivity and negative predictive value were 96 and 96%, respectively, and were found to be higher when compared with ZN smear with 89 and 90%, respectively. Specificity of both techniques was 100%. Previous history of TB was an independent predictor for GeneXpert positivity, whereas both previous history of TB and positive sputum smear were independent predictors of RIF resistance.
Conclusion GeneXpert has a higher diagnostic value compared with ZN smear, providing a faster diagnosis for pulmonary TB than culture, and it can detect RIF resistance.

Keywords: GeneXpert, pulmonary tuberculosis, rifampicin resistance, Ziehl–Neelsen smear

How to cite this article:
Abd El Aaty HE, El-Hefnawy MY, Khalaf FS. Study of diagnostic role of GeneXpert test in patients with pulmonary tuberculosis at El-Mahalla Chest Hospital. Egypt J Chest Dis Tuberc 2021;70:31-7
How to cite this URL:
Abd El Aaty HE, El-Hefnawy MY, Khalaf FS. Study of diagnostic role of GeneXpert test in patients with pulmonary tuberculosis at El-Mahalla Chest Hospital. Egypt J Chest Dis Tuberc [serial online] 2021 [cited 2021 Dec 5];70:31-7. Available from: http://www.ejcdt.eg.net/text.asp?2021/70/1/31/312130   Introduction 

Tuberculosis (TB) is considered one of the top most 10 causes of death worldwide [1],[2], and most of TB cases occur in low-income and middle-income countries, for example, Egypt [3],[4]. Emergence of drug-resistant TB, including multidrug resistant and extensively drug resistant, increase in morbidity and mortality, and continuing the transmission of disease could be the result of lack of the ability to promptly diagnose and treat the affected cases [3],[5]. The general nonspecific symptoms and radiological manifestations of TB make its diagnosis a difficult healthcare problem [6]. The gold standard for diagnosis of TB is the conventional culture, but it takes long time and may provide result between 2 and 8 weeks [7]. Despite smear microscopy being a cheap and quick method for detection of acid-fast bacilli, it has low sensitivity [8]. Prompt diagnosis and detection of rifampicin (RIF) resistance is needed for TB control, as transmission and development of multidrug resistant TB are critical health problems [9].

The GeneXpert MTB/RIF assay utilizes a reverse transcriptase PCR to identify the TB-specific rpoB gene [10]. Mutation of the rpoB is correlated with resistance to RIF [10]. GeneXpert MTB/RIF assay was recommended for use by WHO in middle-income and low-income countries for rapid diagnosis of TB in 2010 [11]. This test can provide rapid and simultaneous detection of Mycobacterial tuberculosis (MTB) and RIF resistance in less than 2 h [12]. Although there are many GeneXpert evaluation studies, the information is still limited in size and geographic representation [13]. El-Mahalla Chest Hospital is a tertiary Egyptian chest hospital in western delta region that services most of the patients from this region, mainly two governorates, Gharbia, and Kafr El-Shiek. Approximately 100 new confirmed TB cases are registered annually, according to hospital archives. In year 2016, 84% of these new cases were pulmonary TB, and 16% were extrapulmonary TB. El-Mahalla Chest Hospital started using GeneXpert assay for diagnosis of TB and RIF resistance by the end of year 2016 [14]. Hence, the objective of this study was to evaluate the performance of GeneXpert MTB/RIF technique in diagnosing patient with pulmonary TB at El-Mahalla Chest Hospital, Egypt, to help better planning of national TB control protocols.

  Patients and methods 

This was a retrospective study where clinical and laboratory data of patients presented to the TB clinic at El-Mahalla Chest Hospital between February 2017 and February 2018 were obtained from hospital archives. An ethical approval from Menoufia University Hospital Ethics Committee was obtained before the study.

Inclusion criteria for the study were as follows: (a) patients with clinical symptoms suggestive of pulmonary TB including cough for more than 2 weeks, persistent low-grade fever, loss of weight, and hemoptysis; (b) abnormal chest radiographic findings; and (c) availability of Ziehl–Neelsen (ZN), culture, and sputum GeneXpert results. Exclusion criteria were as follows: (a) patients with symptoms of extrapulmonary TB or any chest disease other than pulmonary TB and (b) patients with incomplete data.

Clinical data included age, sex, residence, special habits, clinical symptoms, comorbidities, history of previous TB, and chest radiographic results. Laboratory data included sputum acid-fast bacilli smear, culture, and GeneXpert results.

GeneXpert version 5 (Cepheid, Sunnyvale, California, USA) test was used at El-Mahalla Chest Hospital, and patients were divided into two groups based on the results of their clinical, radiological, and laboratory investigations: group I (confirmed TB) included patients in whom MTB was detected, that is, sputum is positive by smear microscopy, culture, or Xpert MTB/RIF, and group II included patients in whom MTB was not detected and include (a) unconfirmed TB, where bacteriological confirmation was not obtained, along with at least two of the following: symptoms/signs suggestive of TB, chest radiograph consistent with TB, close TB exposure or immunologic evidence of MTB infection, and positive response to TB treatment, and (b) unlikely TB, where bacteriological confirmation was not obtained and criteria for ‘unconfirmed TB’ were not met [15],[16].

Statistical analysis

Data were collected, tabulated, and statistically analyzed using a personal computer with statistical package of the social sciences (SPSS) version 22 (IBM corporation; Armonk, New York, United State), where the following statistics were applied: (a) descriptive statistics, for example, number, percentage, arithmetic mean, which was used as a measure of central tendency, and SD, which was used as a measure of dispersion, and (b) analytic statistics, for example, χ2-test was used to find association between two or more qualitative variables, Fischer exact test was used for 2×2 tables when expected cell count of more than 25% of cases was less than 5, and Mann–Whitney test was used for comparison between two groups having quantitative variables with independent nonparametric data. Sensitivity, specificity, negative predictive value, and positive predictive value, of GeneXpert assay and ZN smear were calculated, and 95% confidence interval (CI) was determined. Binary logistic regression analyses for factors associated with positivity of GeneXpert and RIF resistance were done using odds ratio (OR) and 95% CI. P values less than 0.05 were considered as statistically significant.

  Results 

In this study, the total number of studied patients were 150 patients divided into two groups: group I included 99 (66%) patients in whom MTB was detected, and group II included 51 (34%) patients, in whom MTB was not detected.

The mean±SD age of all studied patients was 45.2±15.1 years. Male patients were 120 (80%), and 101 (67.3%) were from rural areas. According to special habits, they were divided into nonsmoker [32 (21.3%)], ex-smoker [10 (6.7%)], cigarette smoker [107 (71.3%)], goza smoker [10 (6.7%)], and addicts [13 (8.7%)]. Common symptoms were cough in 136 (90%), fever in 82 (54.7%), and weight loss in 61 (40.7%). Overall, 28 (18.7%) of the studied patients had history of previous TB. Associated comorbid diseases were diabetes mellitus in 19 (12.7%), hypertension in 25 (16.6%), and COPD in 60 (40%). Chest radiographic findings were divided into normal [four (2.7%)], patch [97 (64.7%)], cavity [36 (24%)], nodule [11 (7.3%)], micronodule [three (2%)], and others [25 (16.7%)] ([Table 1]).

As shown in [Table 2], among 58 smear-negative patients, seven were found to be positive for MTB by GeneXpert distributed as follows: one in whom MTB detected was very low, 4 in whom MTB detected was low, and two in whom MTB detected was medium. A total of four ZN smear-positive (scanty) patients were detected by GeneXpert and distributed as follows: one in whom MTB detected was very low, two in whom MTB detected was low, and one in whom MTB detected was medium). Moreover, 31 ZN smear-positive + patients were detected by GeneXpert and distributed as follows: 16 in whom MTB detected was low, 10 in whom MTB detected was medium, and five in whom MTB detected was high. Overall, 30 ZN smear-positive ++ patients were detected by GeneXpert and distributed as follows: one in whom MTB detected was low, 20 in whom MTB detected was medium, and nine in whom MTB detected was high. A total of 27 ZN smear-positive +++ patients were detected by GeneXpert and distributed as follows: three in whom MTB detected was medium, and 24 in whom MTB detected was high. A total of 150 patients detected by GeneXpert were distributed as follows: 51 negative, two in whom MTB very low, 23 in which MTB low, 36 in which MTB detected medium, and 38 in whom MTB detected was high.

Table 2 Distribution and findings of Ziehl–Neelsen smear and GeneXpert

Click here to view

As shown in [Table 3], among the 150 studied patients, 101 (67.3%) represented group I (confirmed TB). Of them, 92 (61.3%) were smear, GeneXpert, and culture positive; seven (4.7%) were smear negative and GeneXpert and culture positive; and two (1.3%) were smear and GeneXpert negative but culture positive. Of the 150 patients, 49 (32.7%) represented group II (unconfirmed and unlikely TB). Of them, one (0.7%) was unconfirmed TB and 48 (32%) were unlikely TB, who were distributed as follows: old TB in 19 (12.7%), bronchogenic carcinoma in nine (6%), pneumonia in eight (5.3%), lung abscess in six (4%), bronchitis in two (1.3%), metastatic lung cancer in two (1.3%), and diffuse parenchymal lung disease in two (1.3%).

As shown in [Table 4], RIF resistance represented 10%, and there was complete matching between culture and GeneXpert results.

As shown in [Table 5], GeneXpert MTB/RIF positivity was significantly associated with previous history of TB (OR=4.5; 95% CI: 2.10–7.5; P=0.01), so previous history of TB was a significant independent predictor of GeneXpert positivity.

As shown in [Table 6], RIF resistance was significantly associated with previous history of TB (OR=3.29; 95% CI: 2.5–11.2; P=0.02) and positive sputum smear (OR=1.99; 95% CI: 1.5–8.3; P=0.001), so previous history of TB and positive sputum smear were significant independent predictors of RIF resistance. On the contrary, other variables were nonsignificant predictors of RIF resistance.

As shown in [Table 7], GeneXpert MTB/RIF sensitivity, positive predictive value, and negative predictive value were found to be higher when compared with smear. On the contrary, specificity was found to be the same for both GeneXpert and ZN smear.

  Discussion 

In this study, smear positivity was found to be 61.1% and GeneXpert positivity for MTB was found to be 65.9% ([Table 2]). This result matches with the result of Munir et al. [4], where positivity for smear and GeneXpert was found to be 67.5 and 77.4%, respectively. Positivity for Smear and GeneXpert was higher in the research of Darwish and Abd Elwadood [17], where smear positivity represented 77.5% and GeneXpert positivity represented 82.5%, and they explained this by the selected cases were strongly suspected by clinical parameters of having pulmonary TB from Abbassia Chest Hospital. As well as positivity was higher in the research of Ann et al. [18], where positivity was 78.5 and 100% for smear and GeneXpert, respectively, and they explained this by the selected case included higher percentage of people living with HIV and retreatment cases compared with our study. However, lower positivity was reported in the research of Ondimu et al. [19], which represented 7.1 and 26.69% for smear and GeneXpert, respectively, and they explained this that 18.32% of patients with definite TB were HIV positive whose sputum has a very low bacillary load.

In this study, most studied patients (67.3%) fulfilled the criteria of confirmed TB group, and they were distributed as follows: smear, GeneXpert, and culture positive by 61.3%, smear negative and GeneXpert and culture positive by 4.7%, and smear and GeneXpert negative but culture positive by 1.3% ([Table 3]). These results match the results of Munir et al. [4], where confirmed TB represented 77.4%, and they explained this owing to the inclusion of highly suspicious cases. On the contrary, these results mismatch with the results of Moussa et al. [9], where confirmed TB represented 32.5%, and they explained this by the use of fluoroquinolone as drug therapy before diagnosis of TB, resulting in delayed diagnosis owing to its strong bactericidal effect against MTB [20].

In this study, unconfirmed TB (smear, GeneXpert, and culture negative) represented 0.7% of patients ([Table 3]). This result mismatches with the result of Moussa et al. [9], where unconfirmed TB represented 59.1%, and they explained this by the use of positive tuberculin skin test and history of contact in selection criteria for studied patients, which were not involved in our study.

In this study, smear-negative pulmonary TB represented 7.8% (7.1 and 0.7% for confirmed and unconfirmed TB groups, respectively). In this study, unlikely TB group represented 32% of patients (smear, GeneXpert, and culture negative), and their final diagnoses were old TB (12.7%), infectious diseases (pneumonia is the most common 5.3%, lung abscess 4%, and bronchitis 1.3%), and noninfectious diseases (bronchogenic carcinoma is the most common in 6%, metastatic lung cancer in 1.3%, and diffuse parenchymal lung diseases in 1.3%) ([Table 3]). This result matches with the result of Reechaipichitkul et al. [21], where unlikely TB group represented 49.6% of cases, and the most common final diagnoses were old TB (11.9%), pneumonia (7.3%), and bronchogenic carcinoma (4%), and they explained this by that all the selected cases with signs and symptoms of TB had negative sputum acid-fast bacilli smear results. However, this result mismatches with result of Moussa et al. [9], where unlikely TB group represented 6.8%.

In this study, RIF resistance was recorded in 6.7% of studied patients, whereas RIF-sensitive patients represented 93.3%, and there was a significant difference between the two groups (IV). This result matches with the result of Rasaki et al. [22], where RIF resistance was recorded in 7.2% of patients with TB, and they explained this by that RIF resistance serves as a surrogate marker for the detection of MDR-TB, as 90% of RIF isolates are also isoniazid resistant [23]. History of previously treated TB, sputum acid-fast bacilli smear 3+, and presence of lung cavities upon chest radiograph are risk factors for development of drug resistance [24],[25]. Barroso et al. [26] stated in their research that smoking is considered a risk factor for development of MDR-TB. This result mismatches with result of Guenaoui et al. [27], where RIF resistance was recorded in 42% of patients with TB, and they explained this by that selected studied patients were clinically suspected MDR-TB cases (retreatment failure, retreatment cases sputum positive at 4 months, contact of known MDR-TB case, and sputum positive retreatment case at diagnosis).

In this study, history of previous TB was the only significant independent predictor of GeneXpert positivity (OR=4.5; 95% CI: 2.10–7.5; P=0.01) ([Table 5]). This result matches with the result of Mulu et al. [28], where previous history of TB was a significant independent predictor of GeneXpert positivity, and they explained this by failure of previous treatment to eliminate bacteria from host, and could be owing to development of primary or secondary drug resistant, and ongoing transmission of TB. However, the study of Ejetab et al. [29] demonstrated that productive age was the significant independent predictor of GeneXpert MTB/RIF positivity, and they explained this by higher movability and contact with infected cases, which accelerate the development of TB infection.

In this study, positive sputum smear (OR=1.99; 95% CI: 1.5–8.3; P=0.001) and previous history of TB (OR=3.29; 95% CI: 2.5–11.2; P=0.02) were the significant independent predictors of RIF resistance ([Table 6]). This result matches with the result of Bulabula et al. [30], where positive sputum smear was a significant independent predictor of RIF resistance, and they explained this by inadequate treatment within short period of time owing to high bacterial load, leading to increased TB transmission as a result of presence of persistently sputum smear-positive individual in community through compensatory mutation of TB strains [31]. Mulu et al. [28] demonstrated the same result, and they explained this that RIF resistance has been developed as a result of inappropriate way of treatment taking, leading to bacterial mutation and resistant development, and contact with drug resistant TB [32]. These results mismatch with the results of Stosic et al. [33], where default from treatment was significant independent predictor for drug resistance, and they explained this by using of disease-specific factors (TB treatment interruptions) as variable involved in the study, which were not present in our study, and they stated default from treatment increase probability of acquired drug resistance where patient do not adhere to treatment, remain infectious, and increase risk of TB recurrence.

In this study, GeneXpert sensitivity and specificity for detection of MTB were found to be 96 and 100%, respectively, when compared with culture as gold standard for diagnosis of TB ([Table 7]). These results match with the results of Darwish and Abd Elwadood [17], where GeneXpert sensitivity and specificity were 79.14 and 100%, respectively. Contrary to this, lower GeneXpert sensitivity and specificity were reported in the research of Laskar et al. [34], which represented 87.64 and 75%, respectively.

In this study, ZN smear sensitivity and specificity were found to be 89 and 100%, respectively, when compared with culture ([Table 7]). These results match with the results of Moussa et al. [9], where sensitivity and specificity of ZN smear represented 86.43 and 99.66%, respectively. Contrary to this, a lower ZN smear sensitivity was reported in the research of Ondimu et al. [19], which represented 26.4%.

In this study, there was a complete matching between culture and GeneXpert regarding positivity and detection of RIF resistance. This matches with the result of Darwish and Abd Elwadood [17].

  Conclusion 

GeneXpert MTB/RIF assay is a useful test for early diagnosis of pulmonary TB (smear positive and smear negative pulmonary TB) with higher level of positivity as compared with ZN smear microscopy. Rapid diagnosis of drug-resistant TB can be achieved by GeneXpert assay. Previous history of TB and history of smoking were significant predictors for GeneXpert positivity, whereas previous history of TB and positive sputum smear were significant predictors for RIF resistance.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.

 

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  [Table 1], [Table 2], [Table 3], [Table 4], [Table 5], [Table 6], [Table 7]