title: Alternate efflux pump mechanism may contribute to drug resistance in extensively drug-resistant isolates of Mycobacterium tuberculosis.
abstract: BACKGROUND
  Extensively drug-resistant tuberculosis (XDR-TB) has emerged as one of the biggest threats to public health and TB control programs worldwide. XDR-TB is caused by Mycobacterium tuberculosis (MTB) strains resistant to rifampin and isoniazid, as well as to a fluoroquinolone and to at least one injectable aminoglycoside. Drug resistance in MTB has primarily been associated with single nucleotide polymorphisms (SNPs) in particular genes. However, it has also been shown that efflux pumps may play a role in resistance of MTB. Upregulation of drug efflux pumps can decrease the intracellular concentration of drugs and reduce their efficacy.
  
  
  METHODS
  Whole genome sequencing was performed on 32 XDR-TB clinical isolates. Sequence data were used to investigate SNPs in efflux pump genes as compared with the H37Rv reference genome.
  
  
  RESULTS
  Of the XDR MTB strains, eight (21.62%) were wild type for rpsL, rrs (500 region), and gidB genes, but had non-synonymous (ns) SNPs (aspartic acid to histidine) in the drrA efflux pump gene at position 3273138. Three of eight (37.5%) XDR MTB strains, wild type for rpsL, rrs (500 region), gidB, and gyrB genes were phenotypically streptomycin sensitive and five (62.5%) XDR MTB strains were streptomycin resistant, while all XDR MTB strains, wild type for rpsL, rrs, gidB, and gyrB genes were resistant to fluoroquinolone (ofloxacin) and ethambutol. In addition, three XDR MTB strains wild type for rpsL, rrs, gidB, and drrA genes showed nsSNPs (isoleucine to valine) in the major facilitator superfamily, Rv1634 efflux pump gene at position 1839306.
  
  
  CONCLUSIONS
  Our data show an nsSNP in the drrA efflux pump gene that may result in upregulation of drug efflux mechanisms in MTB strains. It is therefore imperative to understand the mechanism of efflux and its role in drug resistance, which will enable the identification of new drug targets and development of new drug regimens to counteract the drug efflux mechanism of MTB.
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Akbar
authors.initials: A
authors.lastname: Kanji
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Rumina
authors.initials: R
authors.lastname: Hasan
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Ambreen
authors.initials: A
authors.lastname: Zaver
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Asho
authors.initials: A
authors.lastname: Ali
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Kehkashan
authors.initials: K
authors.lastname: Imtiaz
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Mussarat
authors.initials: M
authors.lastname: Ashraf
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
authors.affiliation: Lung Infection and Immunity Unit, Division of Pulmonology, Department of Medicine, University of Cape Town, and UCT Lung Institute, Cape Town, South Africa.
authors.forename: Ruth
authors.initials: R
authors.lastname: McNerney
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan.
authors.forename: Samreen
authors.initials: S
authors.lastname: Shafiq
authors.affiliation: Department of Pathology and Laboratory Medicine, The Aga Khan University, Stadium Road, Karachi 74800, Pakistan. Electronic address: zahra.hasan@aku.edu.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Hasan
keywords: Efflux pumps; MTB; XDR