GeneXpert assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens from a high TB endemic area of Pakistan Shakir Ullah Khan a, 1 , Hazir Rahman a, *, 1 , Sultan Ayaz b , Muhammad Qasim a , Abdul Jabbar c , Mohsin Khurshid d , Mubashir Hussain a , Niaz Muhammad a , Shoaib Ur Rehman e , Nawab Ali f a Department of Microbiology, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan b College of Animal Husbandry and Veterinary Sciences, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan c Provential TB Control Laboratory, HMC, Peshawar, Khyber Pakhtunkhwa, Pakistan d College of Allied Health Professionals, Directorate of Medical Sciences, Government College University, Faisalabad, Pakistan e Department of Biotechnology, Bannu University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan f Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, Pakistan article info Article history: Received 14 January 2016 Received in revised form 15 March 2016 Accepted 22 March 2016 Available online 23 March 2016 Keywords: Mycobacterium tuberculosis ZN microscopy MGIT culture GeneXpert assay abstract Tuberculosis is a global health problem, and its early diagnosis is the ultimate strategy for prevention and control. The current study was undertaken to evaluate conventional and molecular diagnostic assays for the detection of mycobacteria in pulmonary tuberculosis (TB) patients from Khyber Pakhtunkhwa region of Pakistan. A total of 259 clinically suspected patients of TB were processed for Zeihl Neelsen (ZN) microscopy, BACTEC MGIT liquid culture and GeneXpert assay. Among 259 samples, 28 (10.81%) were positive for acid fast bacilli (AFB) on ZN microscopy. In liquid culture, the growth of mycobacterium species was obtained in 36 (13.89%) samples while the GeneXpert assay detected Mycobacterium tuberculosis (MTB) in 49 (18.91%) samples. Detection rate of MTB was significantly high (n ¼ 49, p < 0.0095) on GeneXpert as compared to microscopy (n ¼ 28); however no significant difference (p ¼ 0.1230) was observed on GeneXpert (n ¼ 49) and culture (n ¼ 36) based detection of MTB. The strength of agreement between GeneXpert and microscopy was also poor (Kappa value < 0.114, 95% CI: 0.72 e 0.301) which support our results. MTB detection rate among female was high as compared to male TB patients while in age wise, the age group 55e64 years has almost high detection rate on mi- croscopy, culture and GeneXpert assay. Findings of the present study highlighted that GeneXpert is more efficient tool for timely diagnosis and proper TB control in high TB endemic area. © 2016 Elsevier Ltd. All rights reserved. 1. Introduction Tuberculosis (TB) is a chronic infectious disease and remains a major global health problem especially in the developing countries. The possible TB transmission from person to person is through spreading of Mycobacterium tuberculosis (MTB) into the air by an infected person. Among infectious diseases, TB is the leading cause of deaths worldwide [1,2]. Approximately one-third of the world population is currently infected with TB, and 95% of them are re- ported in underdeveloped countries. Pakistan ranks sixth among high TB burden countries in the world [3]. Early diagnosis of MTB is potential strategy to control TB. Diagnosis of TB is done by finding of consolidation in the lung apices through X-Ray. Tuberculin skin test (TST) and immune- chromatographic technique (ICT) are also used for the diagnosis of TB. In developing countries like Pakistan, Zeihl Neelsen (ZN) staining of sputum samples followed by acid fast bacilli (AFB) * Corresponding author. E-mail addresses: shakirkhattak_kk@yahoo.com (S.U. Khan), hazirrahman@ hotmail.com (H. Rahman), sultan_ayaz@yahoo.com (S. Ayaz), qasim89@gmail.com (M. Qasim), ajswati22@gmail.com (A. Jabbar), mohsin.mic@gmail.com (M. Khurshid), mubashirbangash@gmail.com (M. Hussain), microbiologist81@ gmail.com (N. Muhammad), shoaib_chem6@yahoo.com (S.U. Rehman), nawabali_ 1857@yahoo.com (N. Ali). 1 Both authors have equally contributed to this work. Contents lists available at ScienceDirect Microbial Pathogenesis journal homepage: www.elsevier.com/locate/micpath http://dx.doi.org/10.1016/j.micpath.2016.03.005 0882-4010/© 2016 Elsevier Ltd. All rights reserved. Microbial Pathogenesis 95 (2016) 82e85