title: Rifampicin resistance mutations in the 81 bp RRDR of rpoB gene in Mycobacterium tuberculosis clinical isolates using Xpert MTB/RIF in Khyber Pakhtunkhwa, Pakistan: a retrospective study.
abstract: Multi-drug resistant tuberculosis (MDR-TB) is a major public health problem especially in developing countries. World Health Organization (WHO) recommends use of Xpert MTB/RIF assay to simultaneously detecting Mycobacterium tuberculosis (MTB) and rifampicin (RIF) resistance. The primary objective of this study was to determine the frequency of MDR-TB in patients suspected to have drug resistance in Khyber Pakhtunkhwa. The frequency of probes for various rpoB gene mutations using Xpert MTB/RIF assay within 81 bp RRDR (Rifampicin Resistance Determining Region) was the secondary objective.
  
  
  
  A total of 2391 specimens, received at Programmatic Management of Drug Resistant TB (PMDT) Unit, Lady Reading Hospital (LRH) Peshawar, Pakistan, between October 2011 and December 2014, were analyzed by Xpert MTB/RIF test. MTB positive with rifampicin resistance were further analyzed to first line anti-mycobacterial drug susceptibility testing (DST) using middle brook 7H10 medium. The data was analyzed using statistical software; SPSS version 18.
  
  
  
  Out of 2391 specimens, 1408 (59 %) were found positive for MTB and among them, 408 (29 %) showed rifampicin-resistance with four different rpoB gene mutations within 81 bp RRDR. The frequency of various probes among RIF-resistant isolates was observed as: probe E, in 314 out of 408 isolates; B, 44 out of 408; A, 5 out of 408; D, 34 out of 408; and probe C was observed among 6 out of 408 RIF-resistant isolates. The probe A&B and E&D mutation combination was found in only 1 isolate in each case, while B&D mutation combination was detected among 3 out of 408 RIF-resistant isolates.
  
  
  
  Hence, it is concluded from our study on a selected population, 29 % of patients had MDR-TB. Probe E related mutations (also known as codon 531and 533) were the most common rpoB genetic mutation [314 (77 %)], acknowledged by Xpert MTB/RIF assay. Least mutation was detected within the sequence 511 (1.2 %).
authors: Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan. irfan_btn@hotmail.com.|Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan. irfan_btn@hotmail.com.
authors: Irfan
authors: I
authors: Ullah
authors: Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
authors: Aamer Ali
authors: AA
authors: Shah
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Anila
authors: A
authors: Basit
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Mazhar
authors: M
authors: Ali
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Afsar
authors: A
authors: Khan
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Ubaid
authors: U
authors: Ullah
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Muhammad
authors: M
authors: Ihtesham
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Sumaira
authors: S
authors: Mehreen
authors: Department of Biotechnology and Microbiology, Sarhad University of Science and Information technology Peshawar, Peshawar, Pakistan.
authors: Anita
authors: A
authors: Mughal
authors: Programmatic Management of Drug resistant TB Pulmonology, Lady Reading Hospital Peshawar, Peshawar, Pakistan.
authors: Arshad
authors: A
authors: Javaid
mesh_terms: D000293:Adolescent; D000328:Adult; D001426:Bacterial Proteins / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics*; D005260:Female; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000187:drug effects* / Q000235:genetics* / Q000302:isolation & purification; D010154:Pakistan; D012189:Retrospective Studies; D012293:Rifampin / Q000494:pharmacology* / Q000627:therapeutic use; D018088:Tuberculosis, Multidrug-Resistant / Q000382:microbiology; D055815:Young Adult
chemical_list: D001426:Bacterial Proteins; C505805:rpoB protein, Mycobacterium tuberculosis; D012321:DNA-Directed RNA Polymerases; D012293:Rifampin
keywords: MDR-TB; RNA polymerase B gene; RRDR; Xpert MTB/RIF