title: A novel strategy based on genomics and specific PCR reveals how a multidrug-resistant Mycobacterium tuberculosis strain became prevalent in Equatorial Guinea 15 years after its emergence.
abstract: OBJECTIVE
  Molecular epidemiology techniques in tuberculosis (TB) can identify high-risk strains that are actively transmitted. We aimed to implement a novel strategy to optimize the identification and control of multidrug-resistant (MDR) TB in a specific population.
  
  
  METHODS
  We developed a strain-specific PCR tailored from whole genome sequencing (WGS) data to track a specific MDR prevalent strain in Equatorial Guinea (EG-MDR).
  
  
  RESULTS
  The PCR was applied prospectively on remnants of GeneXpert reaction mixtures owing to the lack of culture facilities in Equatorial Guinea. In 147 (93%) of 158 cases, we were able to differentiate between infection by the EG-MDR strain or by any other strain and found that 44% of all rifampicin-resistant TB cases were infected by EG-MDR. We also analysed 93 isolates obtained from Equatorial Guinea 15 years ago, before MDR-TB had become the problem it is today. We found that two of the scarce historical MDR cases were infected by EG-MDR. WGS revealed low variability-six single nucleotide polymorphisms acquired by this strain over 15 years-likely because of the lack in the country of a specific program to treat MDR-TB.
  
  
  CONCLUSIONS
  Our novel strategy, which integrated WGS analysis and strain-specific PCRs, represents a low-cost, rapid and transferable strategy that allowed a prospective efficient survey and fast historical analysis of MDR-TB in a population.
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain.
authors.forename: L
authors.initials: L
authors.lastname: Pérez-Lago
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
authors.forename: S
authors.initials: S
authors.lastname: Izco
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Herranz
authors.affiliation: Servei de Microbiologia, Hospital Clinic-CDB, Barcelona, Spain; IS Global, Barcelona, Spain.
authors.forename: G
authors.initials: G
authors.lastname: Tudó
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Carcelén
authors.affiliation: Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Spain.
authors.forename: I
authors.initials: I
authors.lastname: Comas
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
authors.forename: O
authors.initials: O
authors.lastname: Sierra
authors.affiliation: Servei de Microbiologia, Hospital Clinic-CDB, Barcelona, Spain; IS Global, Barcelona, Spain.
authors.forename: J
authors.initials: J
authors.lastname: González-Martín
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain.
authors.forename: M J
authors.initials: MJ
authors.lastname: Ruiz-Serrano
authors.affiliation: Programa Nacional TB y Lepra, Malabo, Equatorial Guinea.
authors.forename: J
authors.initials: J
authors.lastname: Eyene
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain.
authors.forename: E
authors.initials: E
authors.lastname: Bouza
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain. Electronic address: dgviedma2@gmail.com.
authors.forename: D
authors.initials: D
authors.lastname: García de Viedma
mesh_terms: D000483:Alleles; D000995:Antitubercular Agents / Q000494:pharmacology; D024881:Drug Resistance, Bacterial / Q000187:drug effects; D016703:Equatorial Guinea / Q000453:epidemiology; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D006801:Humans; D008826:Microbial Sensitivity Tests; D018598:Minisatellite Repeats; D058885:Multilocus Sequence Typing; D009169:Mycobacterium tuberculosis / Q000187:drug effects / Q000235:genetics*; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D015995:Prevalence; D018088:Tuberculosis, Multidrug-Resistant / Q000453:epidemiology* / Q000382:microbiology*
chemical_list: D000995:Antitubercular Agents
keywords: Emergence; Equatorial Guinea; MDR; Screening; Tuberculosis