title: Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda.
abstract: Understanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.
authors.affiliation: Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands. Electronic address: willyssengooba@gmail.com.
authors.forename: Willy
authors.initials: W
authors.lastname: Ssengooba
authors.affiliation: Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium.
authors.forename: Conor J
authors.initials: CJ
authors.lastname: Meehan
authors.affiliation: National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda.
authors.forename: Deus
authors.initials: D
authors.lastname: Lukoye
authors.affiliation: National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda.
authors.forename: George William
authors.initials: GW
authors.lastname: Kasule
authors.affiliation: National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda.
authors.forename: Kenneth
authors.initials: K
authors.lastname: Musisi
authors.affiliation: Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda.
authors.forename: Moses L
authors.initials: ML
authors.lastname: Joloba
authors.affiliation: Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; KNCV Tuberculosis Foundation, The Hague, The Netherlands.
authors.forename: Frank G
authors.initials: FG
authors.lastname: Cobelens
authors.affiliation: Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Division of Infectious Diseases, New York University, New York, NY, USA.
authors.forename: Bouke C
authors.initials: BC
authors.lastname: de Jong
mesh_terms: D000328:Adult; D000995:Antitubercular Agents / Q000494:pharmacology*; D001426:Bacterial Proteins / Q000235:genetics; D005260:Female; D016680:Genome, Bacterial; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D009154:Mutation; D009169:Mycobacterium tuberculosis / Q000145:classification / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D011718:Pyrazinamide / Q000494:pharmacology; D012293:Rifampin / Q000494:pharmacology; D017422:Sequence Analysis, DNA / Q000379:methods*; D018088:Tuberculosis, Multidrug-Resistant / Q000382:microbiology*; D014454:Uganda; D055815:Young Adult
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D011718:Pyrazinamide; D012293:Rifampin
keywords: Complement; Drug resistance surveys; Tuberculosis; Whole genome sequencing