The Open Microbiology Journal

ISSN: 1874-2858 ― Volume 13, 2019

Diagnosis of Pulmonary Tuberculosis in Resource Limited Setting of Rawalpindi

Fatima Zahra, Aamer Ikram, Gohar Zaman, Luqman Satti, Farida Lalani, Maria Khan*
Department of Microbiology, Armed Forces Institute of Pathology, National University of Medical Sciences, Rawalpindi, Pakistan



Tuberculosis is an infectious disease with a high prevalence of about 9 million cases occurring annually. Ziehl Neelsen microscopy is the most widely used technique to detect Acid Fast Bacilli, but it is less sensitive. However, fluorescent microscopy is more helpful with simple diagnostic criteria. Gene Xpert® MTB/RIF assay is a rapid molecular assay that enables diagnosis of Tuberculosis with simultaneous detection of rifampicin resistance. Owing to this fact, we aimed at evaluating the diagnostic accuracy of Ziehl Neelsen microscopy, fluorescent microscopy and Xpert MTB/RIF keeping MTB culture (Mycobacterial Growth Indicator Tube) as a gold standard for the diagnosis of tuberculosis.


This study was carried out at a tertiary care hospital of Rawalpindi in the year 2016. Patients aged 18 to 70 years irrespective of gender with suspected TB based on history, clinical and radiological examination were included in the study. Respiratory clinical specimens including sputum, Broncho-Alveolar Lavage (BAL), and endobronchial washings were collected. Specimens were processed by MGIT (MTB culture), ZN microscopy, fluorescent microscopy and Gene Xpert MTB/RIF assay.


A total of 352 respiratory specimens were tested among which 160 (45%) samples were positive by culture. Out of culture positive samples, 158 samples (98.7%) were GeneXpert TB positive while 2 were negative. While only 49 (30.6%) were positive on ZN microscopy and 89 (55%) were positive on fluorescent microscopy. Out of the culture negative samples, 2 were positive with ZN microscopy, one was positive with fluorescent microscopy and 3 were positive on Gene Xpert. Sensitivity, specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV) and diagnostic accuracy of ZN Smear microscopy was 39%, 99.5%, 96%, 63% and 14.5% respectively. Sensitivity, specificity, PPV, NPV and diagnostic accuracy of fluorescent smear microscopy was 55% and 99.5%, 98%, 72% and 79% respectively. Sensitivity, specificity, PPV, NPV and diagnostic accuracy of Gene XPERT was 98% and 99%, 98%, 99% and 98% respectively.


In countries like Pakistan where Tuberculosis is endemic, the diagnostic accuracy with highest sensitivity and specificity was Gene Xpert Polymerase Chain Reaction (PCR) MTB/RIF assay which can help in well-timed diagnosis of the disease.

Keywords: Pulmonary Tuberculosis, Fluorescent microscopy, Gene Xpert, Auramine phenol stain, WHO report, Positive predictive value.

Article Information

Identifiers and Pagination:

Year: 2018
Volume: 12
First Page: 376
Last Page: 380
Publisher Id: TOMICROJ-12-376
DOI: 10.2174/1874285801812010376

Article History:

Received Date: 30/8/2018
Revision Received Date: 10/11/2018
Acceptance Date: 11/11/2018
Electronic publication date: 30/11/2018
Collection year: 2018

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© 2018 Zahra et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: ( This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Microbiology, Armed Forces Institute of Pathology, National University of Medical Sciences, Rawalpindi, Pakistan; Tel: 0092-3319111986; E-mail:


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