title: Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data: a pilot study.
abstract: Molecular epidemiology has transformed our knowledge of how tuberculosis (TB) is transmitted. Whole genome sequencing (WGS) has reached unprecedented levels of accuracy. However, it has increased technical requirements and costs, and analysis of data delays results. Our objective was to find a way to reconcile speed and ease of implementation with the high resolution of WGS. The targeted regional allele-specific oligonucleotide PCR (TRAP) assay presented here is based on allele-specific PCR targeting strain-specific single nucleotide polymorphisms, identified from WGS, and makes it possible to track actively transmitted Mycobacterium tuberculosis strains. A TRAP assay was optimized to track the most actively transmitted strains in a population in Almería, Southeast Spain, with high rates of TB. TRAP was transferred to the local laboratory where transmission was occurring. It performed well from cultured isolates and directly from sputa, enabling new secondary cases of infection from the actively transmitted strains to be detected. TRAP constitutes a fast, simple and low-cost tool that could modify surveillance of TB transmission. This pilot study could help to define a new model to survey TB transmission based on a decentralized multinodal network of local laboratories applying fast and low-cost TRAPs, which are developed by central reference centres, tailored to the specific demands of transmission at each local node.
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Spain; CIBER Enfermedades Respiratorias, CIBERES, Spain.
authors.forename: L
authors.initials: L
authors.lastname: Pérez-Lago
authors.affiliation: Complejo Hospitalario Torrecárdenas, Almería, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Martínez Lirola
authors.affiliation: Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Spain; CIBER Enfermedades Respiratorias, CIBERES, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Herranz
authors.affiliation: Unidad Mixta Infección y Salud, FISABIO Salud Pública-Universitat de València, 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, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Spain; CIBER Enfermedades Respiratorias, CIBERES, 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, Spain; CEI Campus Moncloa, UCM-UPM, 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; D004269:DNA, Bacterial; D016680:Genome, Bacterial; D005843:Geography; D006801:Humans; D018598:Minisatellite Repeats; D017720:Molecular Epidemiology / Q000191:economics / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D010865:Pilot Projects; D016133:Polymerase Chain Reaction / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D011159:Population Surveillance / Q000379:methods; D017422:Sequence Analysis, DNA; D013030:Spain / Q000453:epidemiology; D014376:Tuberculosis / Q000453:epidemiology* / Q000382:microbiology / Q000635:transmission*
chemical_list: D004269:DNA, Bacterial
keywords: Allele-specific PCR; TRAP; transmission; tuberculosis; whole genome sequencing