title: Mycobacterium tuberculosis whole genome sequencing and protein structure modelling provides insights into anti-tuberculosis drug resistance.
abstract: BACKGROUND
  Combating the spread of drug resistant tuberculosis is a global health priority. Whole genome association studies are being applied to identify genetic determinants of resistance to anti-tuberculosis drugs. Protein structure and interaction modelling are used to understand the functional effects of putative mutations and provide insight into the molecular mechanisms leading to resistance.
  
  
  METHODS
  To investigate the potential utility of these approaches, we analysed the genomes of 144 Mycobacterium tuberculosis clinical isolates from The Special Programme for Research and Training in Tropical Diseases (TDR) collection sourced from 20 countries in four continents. A genome-wide approach was applied to 127 isolates to identify polymorphisms associated with minimum inhibitory concentrations for first-line anti-tuberculosis drugs. In addition, the effect of identified candidate mutations on protein stability and interactions was assessed quantitatively with well-established computational methods.
  
  
  RESULTS
  The analysis revealed that mutations in the genes rpoB (rifampicin), katG (isoniazid), inhA-promoter (isoniazid), rpsL (streptomycin) and embB (ethambutol) were responsible for the majority of resistance observed. A subset of the mutations identified in rpoB and katG were predicted to affect protein stability. Further, a strong direct correlation was observed between the minimum inhibitory concentration values and the distance of the mutated residues in the three-dimensional structures of rpoB and katG to their respective drugs binding sites.
  
  
  CONCLUSIONS
  Using the TDR resource, we demonstrate the usefulness of whole genome association and convergent evolution approaches to detect known and potentially novel mutations associated with drug resistance. Further, protein structural modelling could provide a means of predicting the impact of polymorphisms on drug efficacy in the absence of phenotypic data. These approaches could ultimately lead to novel resistance mutations to improve the design of tuberculosis control measures, such as diagnostics, and inform patient management.
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Jody
authors.initials: J
authors.lastname: Phelan
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Francesc
authors.initials: F
authors.lastname: Coll
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.|University of Cape Town Lung Institute, Lung Infection & Immunity Unit, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa.
authors.forename: Ruth
authors.initials: R
authors.lastname: McNerney
authors.affiliation: Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
authors.forename: David B
authors.initials: DB
authors.lastname: Ascher
authors.affiliation: Centro de Pesquisas René Rachou, Fundação Oswaldo Cruz, Avenida Augusto de Lima 1715, Belo Horizonte, 30190-002, Brazil.
authors.forename: Douglas E V
authors.initials: DE
authors.lastname: Pires
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Nick
authors.initials: N
authors.lastname: Furnham
authors.affiliation: Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Nele
authors.initials: N
authors.lastname: Coeck
authors.affiliation: Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.|Sydney Emerging Infections and Biosecurity Institute and School of Public Health, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.
authors.forename: Grant A
authors.initials: GA
authors.lastname: Hill-Cawthorne
authors.affiliation: Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Mridul B
authors.initials: MB
authors.lastname: Nair
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Kim
authors.initials: K
authors.lastname: Mallard
authors.affiliation: Special Programme for Research and Training in Tropical Diseases (TDR), World Health Organisation, Geneva, Switzerland.
authors.forename: Andrew
authors.initials: A
authors.lastname: Ramsay
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Susana
authors.initials: S
authors.lastname: Campino
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
authors.forename: Martin L
authors.initials: ML
authors.lastname: Hibberd
authors.affiliation: Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Arnab
authors.initials: A
authors.lastname: Pain
authors.affiliation: Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium.|Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium.
authors.forename: Leen
authors.initials: L
authors.lastname: Rigouts
authors.affiliation: Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. taane.clark@lshtm.ac.uk.|Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK. taane.clark@lshtm.ac.uk.|Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK. taane.clark@lshtm.ac.uk.
authors.forename: Taane G
authors.initials: TG
authors.lastname: Clark
mesh_terms: D000995:Antitubercular Agents / Q000627:therapeutic use; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D016680:Genome, Bacterial; D055106:Genome-Wide Association Study; D006801:Humans; D007538:Isoniazid / Q000627:therapeutic use; D008826:Microbial Sensitivity Tests; D008958:Models, Molecular; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D011487:Protein Conformation; D017422:Sequence Analysis, DNA; D018088:Tuberculosis, Multidrug-Resistant / Q000188:drug therapy / Q000235:genetics / Q000378:metabolism / Q000382:microbiology*
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D007538:Isoniazid
keywords: Association study; Convergent evolution; Drug resistance; Genomics; Protein structural modelling; Tuberculosis