Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights

Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights | medRxiv Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights Charlotte Genestet , Quentin Testard , Genna Ben-Hassen , Claire Bardel , Maxime Vallée , Chloé Bourg , Olivier Bahuaud , Brune Joannard , Caroline Tatai , Sophie Barabotti , Florence Ader , Cédric Dananché , Elisabeth Hodille , Oana Dumitrescu doi: https://doi.org/10.64898/2026.03.16.26348245 Charlotte Genestet 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 2 Laboratoire de bactériologie, Hospices Civils de Lyon, Institut des Agents Infectieux , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site For correspondence: charlotte.genestet{at}gmail.com Quentin Testard 3 NGS-HCL Platform, Bioinformatics Group, Hospices Civils de Lyon , Bron, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Genna Ben-Hassen 3 NGS-HCL Platform, Bioinformatics Group, Hospices Civils de Lyon , Bron, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Claire Bardel 3 NGS-HCL Platform, Bioinformatics Group, Hospices Civils de Lyon , Bron, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Maxime Vallée 3 NGS-HCL Platform, Bioinformatics Group, Hospices Civils de Lyon , Bron, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Chloé Bourg 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 2 Laboratoire de bactériologie, Hospices Civils de Lyon, Institut des Agents Infectieux , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Olivier Bahuaud 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 4 Hospices Civils de Lyon, Service des Maladies Infectieuses et Tropicales , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Brune Joannard 2 Laboratoire de bactériologie, Hospices Civils de Lyon, Institut des Agents Infectieux , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Caroline Tatai 5 Centre de Lutte Anti Tuberculeuse , CLAT 01, Bourg-en-Bresse, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Sophie Barabotti 6 Centres de Santé et de Prévention du Comité Départemental d’Hygiène Sociale, Centre de Lutte Anti Tuberculeuse , CLAT 69, Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Florence Ader 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 4 Hospices Civils de Lyon, Service des Maladies Infectieuses et Tropicales , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Cédric Dananché 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 7 Service Hygiène, Épidémiologie, Infectiovigilance et Prévention, Hôpital de la Croix-Rousse , Hospices Civils de Lyon, Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Elisabeth Hodille 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 2 Laboratoire de bactériologie, Hospices Civils de Lyon, Institut des Agents Infectieux , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Oana Dumitrescu 1 CIRI - Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1 , Inserm U1111, CNRS UMR5308, Lyon, France 2 Laboratoire de bactériologie, Hospices Civils de Lyon, Institut des Agents Infectieux , Lyon, France Find this author on Google Scholar Find this author on PubMed Search for this author on this site Abstract Full Text Info/History Metrics Supplementary material Data/Code Preview PDF SUMMARY Background In low-burden countries such as France, whole-genome sequencing (WGS) is increasingly integrated into routine tuberculosis (TB) surveillance to improve case management and transmission monitoring. However, applying WGS to all TB cases generates large volumes of data, requiring automated tools for timely interpretation and outbreak response. Methods Since November 2016, all clinical M. tuberculosis isolates diagnosed in eight hospitals from three cities of Auvergne-Rhône-Alpes in France have undergone WGS. In July 2023, an automated pipeline for anti-TB drug resistance prediction and unbiased detection of transmission clusters based on SNP distances was implemented. Epidemiological, microbiological and clinical data were collected, with contact duration classified as household, frequent, or occasional. Index cases were stratified by their level of extra-household transmission (EHT), and statistical analyses were performed to identify associated factors. Findings Among 1,152 TB patients diagnosed between 2016 and 2025, 75 clusters involving 247 patients (21·4%) were identified. WGS reliably detected resistance to first-line anti-TB drugs, leveraging the WHO mutation catalogue. Routine WGS enabled real-time alerts for TB control centres, leading to expanded field investigations, including community spillover, nosocomial transmissions, and school outbreak. Classical indicators of contagiousness (smear results, cavitary disease) were not associated with EHT level. Instead, lower TB severity indices and longer duration of symptoms were linked to higher EHT level. Interpretation Systematic WGS supports timely identification of drug resistance and transmission events and provides new insights into contagiousness factors. The automated pipeline enables direct interpretation by clinical microbiologists, facilitating real-time public health action. In this study, we demonstrate how, with the appropriate pipeline, WGS offered a time- and cost-effective solution for routine TB management. Funding This work was supported by SHAPE-Med@Lyon, a French government grant managed by the French National Research Agency under the France 2030 program (reference ANR-22-EXES-0012). Evidence before this study A systematic literature search was conducted using PubMed up to October 2025, with the following keywords: “tuberculosis” AND “whole genome sequencing” AND “contact tracing” OR “population based” OR “genomic surveillance” OR “investigation”. The review encompassed studies addressing the use of whole-genome sequencing (WGS) for tuberculosis (TB) surveillance, transmission cluster detection, and integration into routine epidemiological practice. Most published studies have focused on using WGS to retrospectively confirm or refute transmission events or to distinguish relapse from reinfection and therefore have not used genomic data to trigger real-time alerts to TB control centres. Even in the rare studies adopting a more proactive approach, the operational integration of WGS into routine diagnostic workflows is not described. No prospective study has provided a clear framework for the real-time use of WGS by clinical microbiologists to enable routine implementation and direct public health action. Added value of this study To our knowledge, this is the first study presenting the implementation of an automated WGS pipeline that enables unbiased detection of TB transmission clusters, based on single nucleotide polymorphism (SNP) distance, in routine surveillance across multiple hospitals. It shows how WGS data can be directly interpreted by clinical microbiologists for anti-TB drugs susceptibility prediction as well as facilitating real-time notification of TB control centres and immediate field investigations. By integrating genomic, epidemiological and clinical data, this comprehensive approach provides new insights into the factors associated with extra-household transmission and moves beyond the retrospective use of WGS, establishing its role as a proactive tool in TB diagnosis and public health practice. Implications of all the available evidence These findings highlight the need for national and international guidelines to evolve and support the widespread integration of WGS into routine TB management. The adoption of automated pipelines, such as the one presented herein, would not only enhance epidemiological surveillance but also streamline resistance detection and species identification, providing a time- and cost-effective all-in-one tool. Broad implementation of WGS-based approaches could significantly improve public health responses and the overall management of TB. Competing Interest Statement The authors have declared no competing interest. Funding Statement This work was supported by SHAPE-Med@Lyon, a French government grant managed by the French National Research Agency under the France 2030 program (reference ANR-22-EXES-0012). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All data were collected in a database in accordance with the decision 20-216 of the ethics committee of the Lyon University Hospital and French legislation in place at the time of the study (reference methodology MR-004 that covers the processing of personal data for purposes of study, evaluation, or research that does not involve the individual). Relevant approval regarding access to patient-identifiable information are granted by the French data protection agency (Commission Nationale de l'Informatique et des Libertes, CNIL). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data sharing Raw sequencing data is publicly available on the European Nucleotide Archive ( https://www.ebi.ac.uk/ena/browser/home ) using the accession numbers: PRJEB106242. Copyright The copyright holder for this preprint is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Back to top Previous Next Posted March 19, 2026. Download PDF Supplementary Material Data/Code Email Thank you for your interest in spreading the word about medRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. 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Share Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights Charlotte Genestet , Quentin Testard , Genna Ben-Hassen , Claire Bardel , Maxime Vallée , Chloé Bourg , Olivier Bahuaud , Brune Joannard , Caroline Tatai , Sophie Barabotti , Florence Ader , Cédric Dananché , Elisabeth Hodille , Oana Dumitrescu medRxiv 2026.03.16.26348245; doi: https://doi.org/10.64898/2026.03.16.26348245 Share This Article: Copy Citation Tools Automated bioinformatic pipeline for unbiased detection of tuberculosis transmission clusters: Real-time impact and retrospective insights Charlotte Genestet , Quentin Testard , Genna Ben-Hassen , Claire Bardel , Maxime Vallée , Chloé Bourg , Olivier Bahuaud , Brune Joannard , Caroline Tatai , Sophie Barabotti , Florence Ader , Cédric Dananché , Elisabeth Hodille , Oana Dumitrescu medRxiv 2026.03.16.26348245; doi: https://doi.org/10.64898/2026.03.16.26348245 Citation Manager Formats BibTeX Bookends EasyBib EndNote (tagged) EndNote 8 (xml) Medlars Mendeley Papers RefWorks Tagged Ref Manager RIS Zotero Tweet Widget Facebook Like Google Plus One Subject Area Epidemiology Subject Areas All Articles Addiction Medicine (638) Allergy and Immunology (917) Anesthesia (350) Cardiovascular Medicine (4998) Dentistry and Oral Medicine (494) Dermatology (427) Emergency Medicine (676) Endocrinology (including Diabetes Mellitus and Metabolic Disease) (1690) Epidemiology (16252) Forensic Medicine (36) Gastroenterology (1241) Genetic and Genomic Medicine (7274) Geriatric Medicine (751) Health Economics (1093) Health Informatics (5283) Health Policy (1467) Health Systems and Quality Improvement (1832) Hematology (599) HIV/AIDS (1380) Infectious Diseases (except HIV/AIDS) (16483) Intensive Care and Critical Care Medicine (1203) Medical Education (699) Medical Ethics (156) Nephrology (751) Neurology (7585) Nursing (377) Nutrition (1127) Obstetrics and Gynecology (1295) Occupational and Environmental Health (1039) Oncology (3742) Ophthalmology (1092) Orthopedics (407) Otolaryngology (465) Pain Medicine (501) Palliative Medicine (143) Pathology (721) Pediatrics (1858) Pharmacology and Therapeutics (755) Primary Care Research (786) Psychiatry and Clinical Psychology (6122) Public and Global Health (9984) Radiology and Imaging (2528) Rehabilitation Medicine and Physical Therapy (1516) Respiratory Medicine (1268) Rheumatology (658) Sexual and Reproductive Health (804) Sports Medicine (595) Surgery (802) Toxicology (109) Transplantation (318) Urology (307)

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