Evaluation of whole genome sequencing for diagnosis of drug resistant tuberculosis in patients of Sao Paulo State

• Grant number: 20/12585-7
• Support Opportunities: Research Grants - Research in Public Policies
• Duration: April 01, 2022 - March 31, 2024
• Field of knowledge: Health Sciences - Collective Health - Public Health
• Principal Investigator: Lucilaine Ferrazoli
• Grantee: Lucilaine Ferrazoli
• Host Institution: Instituto Adolfo Lutz (IAL). Coordenadoria de Controle de Doenças (CCD). Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
• Associated researchers: Ana Marcia de Sá Guimarães ; Angela Pires Brandao ; Cláudia Regina Gonçalves ; Claudio Tavares Sacchi ; Denise Arakaki-Sanchez ; Erica Chimara Silva ; Juliana Failde Gallo ; Juliana Maíra Watanabe Pinhata ; Maria Josefa Penon Rujula ; Rosangela Siqueira de Oliveira ; Sidney Bombarda ; Suely Fukasava
• Associated research grant: 17/50333-7 - Institutional research development plan of the Instituto Adolfo Lutz (PDIp), AP.PDIP
• Associated scholarship(s): 22/05493-4 - Evaluation of whole genome sequencing for diagnosis of resistant tuberculosis in patients of São Paulo state, BP.TT

Abstract

Tuberculosis (TB) remains an important public health problem. Of great concern is the increase in number of drug-resistant TB and the reduced therapeutic option for its treatment. In Brazil, in 2018, 1,119 patients with TB resistant to rifampicin (TBRR) or to rifampicin and isoniazid (TBMR) were notified. Of the total number of cases reported as TBRR/MR, only 141 (12.6%) were tested for second-line drugs. Drug susceptibility testing (DST) can be done using phenotypic and/or molecular tests. Phenotypic DST techniques are laborious and their time to a final result is long, while molecular tests detect a reduced number of mutations associated with drug-resistance. Whole Genome Sequencing (WGS) has proven to be a powerful tool for determining resistance to drugs of the Mycobacterium tuberculosis complex (MTBC). The aim of this study will be to evaluate WGS using the Ion Torrent S5 platform to detect resistance to drugs used to treat drug-resistant TB, to develop a pipeline for mutation analysis and a reporting form. MTBC isolates received at the Adolfo Lutz Institute, from TBRR/MR patients from the state of São Paulo, will be prospectively analyzed during one year. The isolates will be submitted to WGS by the Ion Torrent platform and to phenotypic DST by MGIT960. For genomic analysis, contigs will be subjected to drug-resistance detection on the PhyResSE online platform. To accommodate the need to detect resistance to the drugs not included in this platform, a pipeline for detection of resistance to first and second line drugs will be developed. A model of report will be prepared to release the results. For each drug, sensitivity, specificity and positive and negative predictive values of WGS will be calculated considering phenotypic DST as the gold standard. (AU)