Latin American and Caribbean Workshop on Targeted Next-Generation Sequencing for Resistant Mycobacterium tuberculosis

Panama, July 12th, 2024.  The Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP) and the Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES) organized the Latin American and Caribbean Workshop on Targeted Next-Generation Sequencing for Resistant Mycobacterium tuberculosis.  This workshop occurred from July 8th to 12th at INDICASAT AIP facilities in the City of Knowledge, Republic of Panama.

Tuberculosis is a preventable and curable disease caused by the bacteria Mycobacterium tuberculosis.  According to the Global Tuberculosis Report 2023, 7.5 million people were newly diagnosed with TB in 2022, the highest number since the World Health Organization (WHO) began global monitoring of the disease in 1995.  In addition, it is estimated that 410,000 patients developed tuberculosis with some form of drug resistance, but less than half started the corresponding treatment[1].  It is therefore necessary to expand access to drug resistance testing and get more patients on treatment as soon as possible.

Targeted next-generation sequencing (NGS) technology merges targeted gene amplification with next-generation sequencing technology.  This allows the detection of drug resistance in a single test.  Recently, the WHO published the 1) Consolidated Guidelines and 2) Operational Manual on Tuberculosis: Module 3 on rapid diagnosis of tuberculosis[2]^,[3], which provides recommendations for using targeted NGS.  The guidelines recommend using NGS in patients with bacteriologically confirmed tuberculosis and bacteriologically confirmed resistant tuberculosis, except under certain conditions.  Deeplex® Myc-TB, from Illumina, is a massive sequencing-based test that allows the identification, genotyping, and prediction of antibiotic resistance at the species level in strains of the Mycobacterium tuberculosiscomplex.  For this reason, the early implementation of NGS in Latin American and Caribbean countries is essential.

The objective of the theoretical and practical workshop was to train laboratorians and scientists from Latin America and the Caribbean in the use and application of the methods and platform for determining Mycobacterium tuberculosisresistance point mutations.  In addition, participants could learn about regional experiences and current applications for public health and research development.

The workshop was inaugurated last Monday, July 8^th, with welcoming remarks by Dr. Ricardo Lleonart, Acting Director of INDICASAT AIP; Dr. Rosalba González, Director of Research and Technological Development of ICGES; Eng. Milagro Mainieri, Director of Research and Development (R&D) of the Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT); Dr. Ernesto Montoro, Coordinator of Tuberculosis Laboratories of the Pan American Health Organization (PAHO); and Dr. Carlos Gartner, Coordinator of the National Tuberculosis Program of the Caja de Seguro Social (CSS).

Throughout five days, participants from Ecuador, Panama, Guatemala, Peru, and Bolivia had the opportunity to participate in theoretical and practical sessions.

Professional speakers from reference laboratories and scientific research laboratories in Latin America presented the theoretical sessions:

• Ernesto Montoro of PAHO, USA, who presented the update on tuberculosis laboratory diagnosis.
• Nazir Ismail, South Africa, who presented WHO recommendations for the use of targeted next-generation sequencing (NGS).
• Andrea Cabbibe, Italy, presented the implementation of NGS for resistance detection in tuberculosis.
• Dilcia Sambrano, MSc of INDICASAT, Panama, presented on safety and biosafety in the biotechnology and genomics laboratory.
• Fermín Acosta and Priya Patel, BS of INDICASAT, Panama, who presented on DNA extraction.
• Federico Lorenzo of Instituto Malbran, Argentina, who shared the use of whole genome sequencing in tuberculosis: Experience with Illumina.
• Monserrath Rodríguez, of Illumina, USA, who presented the Deeplex® Myc-TB.
• Deborah Pérez. BS of BioLab, Panama, who presented the Deeplex® Myc-TB workflow and best practices.
• Gloribel Vergara, MSc, of BioLab, Panama, presented Illumina sequencing technology and the importance of quality control.
• Ethel Salazar, of Illumina, USA, presented on MiSeq equipment preparation and analysis of Deeplex® Myc-TB results.
• Luis Narváez, México, who shared the experiences of implementation of Deeplex® Myc-TB in Mexico and its application in clinical cases of drug-resistant tuberculosis.
• Fermín Acosta of INDICASAT-AIP, Panama, shared the experience of whole genome sequencing to characterize the M. tuberculosis Beijing lineage in Panama.
• Samantha Rosas, MSc, del ICGES, Panama, shared about the tuberculosis laboratory network in Panama and the integration of molecular tools.
• Christophe Sola, Universidad Paris-Saclay, France, shared about the TB-Annotator tool, a scalable web application that allows in-depth analysis of very large datasets of publicly available Mycobacterium tuberculosiscomplex genomes.

In the hands-on sessions, participants had the opportunity to develop skills in performing Illumina´s Deeplex® Myc-TB targeted NGS tests, such as:

• Mycobacterium tuberculosis DNA extraction
• DNA enrichment
• DNA quality verification
• Sample preparation for targeted NGS
• Verifying the quality of simples for targeted NGS
• Preparing and performing the targeted NGS run
• Data collection and analysis
• Data interpretation

Among the workshop activities, attendees also visited BioLab Internacional’s facilities, representatives of Illumina in Panama, and the Miraflores Locks of the Panama Canal.

To end the tuberculosis epidemic by 2030, it is necessary to translate the commitments made at the 2023 United Nations High-Level Meeting on Tuberculosis into action, such as fostering and strengthening tuberculosis research by creating enabling environments among Member States^1,[4]. These activities allow countries to exchange experiences and best practices and gain knowledge of new technologies. Working together as a region, we will ensure no one is left behind in the fight against tuberculosis.

This activity was supported by Illumina, Biolab Internacional, City of Knowledge, Secretaría Nacional de Ciencia, Tecnología e Innovación (SENACYT), and the Sistema Nacional de Investigación (SNI) of Panama.

About INDICASAT-AIP:  Association of public interest with the mission to establish itself as a platform for Panama’s scientific and technological advancement, contributing to the training of human resources of excellence in research – development applied to the different priority disciplines for the advancement of the country.  Learn more at https://indicasat.org.pa/.

For more information, please contact:

Amador Goodridge

Researcher and member of the organizing committee

Instituto de Investigaciones Científicas y Servicios

de Alta Tecnología (INDICASAT AIP)

Email:  agoodridge@indicasat.org.pa

Phone. 517-0722

[1] Global tuberculosis report 2023. Geneva: World Health Organization; 2023. License: CC BY-NC-SA 3.0 IGO.  https://www.who.int/publications/i/item/9789240083851

[2] WHO consolidated guidelines on tuberculosis. Module 3: diagnosis – rapid diagnostics for tuberculosis detection, third edition. Geneva: World Health Organization; 2024. License: CC BY-NC-SA 3.0 IGO. https://www.who.int/publications/i/item/9789240089488

[3] WHO operational handbook on tuberculosis. Module 3: diagnosis – rapid diagnostics for tuberculosis

detection, third edition. Geneva: World Health Organization; 2024. License: CC BY-NC-SA 3.0 IGO. https://www.who.int/publications/i/item/9789240089501

[4] Resolución A/RES/78/5 – Declaración política de la reunión de alto nivel sobre la lucha contra la tuberculosis.  Nueva York:  Organización de las Naciones Unidas; 2023.  https://daccess-ods.un.org/access.nsf/Get?OpenAgent&DS=A/RES/78/5&Lang=S