Christophe Sola holds since September 2007 a Full Professorship position in Microbiology at University of Paris-Saclay (UPSay) where he was the Principal Investigator of his research team IGEPE between 2007 and 2019. He is now a senior scientist in an INSERM-University-Paris -Cité Joint Research Unit, named IAME, that stands for “Infection, Antimicrobials, Modeling and Evolution”, working in a lab associated to the French National Research Center Laboratory for Mycobacetriology. His research work focus on Mycobacterium tuberculosis genetic diversity and especially on CRISPR polymorphisms. He was at the origin of the International Spoligotyping Databases created and maintained at the Institut Pasteur, databases that were instrumental in helping to decipher the population structure of the Mycobacterium tuberculosis complex before the Whole-Genome-Sequence era. He is now working in Big Dataset management systems, by developing and analyzing data for public health and academic research
EDUCATION
PharmD PhD
RESEARCH, TEACHING, or OTHER INTERESTS
Microbiology, Applied Microbiology and Biotechnology, Infectious Diseases, Ecology, Evolution, Behavior and Systematics
Developing a Tuberculosis Q&A Database Using Q&A-ET: Question and Answer Evaluator Toolkit Jihad Al Akl, Chady Abou Jaoude, Zahi Chami, Christophe Guyeux, David Laiymani, et al. 5th IEEE Middle East and North Africa Communications Conference Breaking Boundaries Pioneering the Next Era of Communication Menacomm 2025, 2025 Large language models (LLMs) have shown remarkable potential in various natural language processing tasks, including text generation, question-answering, etc. However, their application in specialized domains like medical research remains limited due to their tendency to produce harmful or inaccurate responses. This is especially true in the field of microbiology, here on Mycobacterium tuberculosis (MTB), where generating reliable and safe medical advice is critical. Creating domain-specific question-answer datasets essential for fine-tuning LLMs is labor-intensive and time-consuming. In this study, we present Q&A-ET (Question and Answer Evaluator Toolkit), a framework designed to streamline the generation of high-quality question-answer datasets by leveraging both human feedback and the capabilities of LLMs. Our approach not only reduces the time and effort required to build datasets but also enhances the accuracy and reliability of LLMs in the medical domain. We will open-source both the toolkit and the MTB question-answer dataset, which consist of two articles with 55 unique questions and 124 expert-evaluated question-answer pairs reviewed by a medical expert, offering valuable resources for future research in this critical area.
Newly Identified Mycobacterium africanum Lineage 10, Central Africa Christophe Guyeux, Gaetan Senelle, Adrien Le Meur, Philip Supply, Cyril Gaudin, et al. Emerging Infectious Diseases, 2024 Analysis of genome sequencing data from >100,000 genomes of Mycobacterium tuberculosis complex using TB-Annotator software revealed a previously unknown lineage, proposed name L10, in central Africa. Phylogenetic reconstruction suggests L10 could represent a missing link in the evolutionary and geographic migration histories of M. africanum.
Advanced Machine Learning for Predicting Drug Resistance in Clinical Isolates of Mycobacterium Tuberculosis Complex Naoufal Sirri, Christophe Guyeux, Christophe Sola Proceedings 2024 World Conference on Complex Systems Wccs 2024, 2024 Tuberculosis remains a significant public health issue, and addressing multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains is a critical global health priority. Resistance primarily results from mutations in genes related to drug targets or enzyme conversions, though our understanding of these mutations is still incomplete. Whole-genome sequencing (WGS) has become a prevalent method for rapidly characterizing bacterial isolates and detecting mutations associated with drug resistance. Despite its widespread use, WGS has limitations, particularly in accounting for the evolutionary aspects of resistance. Conversely, machine learning techniques have shown great promise in predicting Mycobacterium tuberculosis (MTB) resistance to specific drugs and in identifying resistance markers efficiently. In this study, machine learning models were applied to a dataset of 28,073 MTB isolates, which had undergone both WGS analysis and laboratory-based drug susceptibility testing (DST) for ten antituberculosis drugs. Advanced boosting algorithms, including extreme gradient boosting (XGBoost), light gradient boosting machine (LightGBM), and a novel deep neural network model, were employed to forecast drug resistance. Separate models were constructed for each drug, using the 10 most impactful feature classes as input variables during the training phase to optimize performance. The effectiveness of the models was evaluated using various metrics, such as sensitivity, specificity, F1 score, receiver operating characteristic (ROC) curve, and the area under the curve (AUC). All three models accurately predicted drug resistance, with the deep learning model outperforming existing methods. AU C values for nine drugs ranged from 0.97 to 0.99, demonstrating model robustness. This study underscores the utility of machine learning for drug resistance prediction, effectively integrating multiple predictors and aiding clinical decision-making while improving SNP detection as WGS data increases.
Spolmap: An Enriched Visualization of CRISPR Diversity Christophe Guyeux, Guislaine Refrégier, Christophe Sola Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, 2022
Direct genomic and viral DNA electrochemical sensing at the sub-femtomolar level: Importance of the carbon-based transducer 20th International Conference on Miniaturized Systems for Chemistry and Life Sciences Microtas 2016, 2016
Evaluation of a new molecular test for the identification of drug resistance in mycobacterium tuberculosis clinical isolates Problems of Infectious and Parasitic Diseases, 2012
Evaluation of a new molecular test for the identification of drug resistance in mycobacterium tuberculosis clinical isolates Problems of Infectious and Parasitic Diseases, 2010
Beijing/w and major spoligotype families of Mycobacterium tuberculosis strains isolated from tuberculosis patients in Eastern Turkey New Microbiologica, 2009
Markov Models to classify M. tuberculosis spoligotypes Georges Valetudie, Jacky Desachy, Christophe Sola Proceedings 21st International Conference on Advanced Information Networking and Applications Workshops Symposia Ainaw 07, 2007
Molecular epidemiology of drug-resistant Mycobacterium tuberculosis strains isolated from patients with pulmonary tuberculosis in Poland: A 1-year study International Journal of Tuberculosis and Lung Disease, 2004
Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: Recommendations for standardised nomenclature International Journal of Tuberculosis and Lung Disease, 2001
Mycobaterium avium intracellulare complex: Phenotypic and genotypic markers and molecular basis of inter-species transmission Bulletin De La Societe De Pathologie Exotique, 2000
Recent developments of spoligotyping as applied to the study of epidemiology, biodiversity and molecular phylogeny of the Mycobacterium tuberculosis complex Pathologie Biologie, 2000
Migrations and Tuberculosis: A comparative study of Mycobacterium tuberculosis genomic population structure in Brazil and Mozambique to historical triangular slave trade … T Morel-Journel, C Guyeux, C Sola Tuberculosis, 102734 , 2026 2026
Genomic characterization and epidemiology of Mycobacterium tuberculosis lineage 2 isolates from Kazakhstan D Auganova, S Atavliyeva, N Gharbi, E Zholdybayeva, Y Skiba, ... Scientific Reports 15 (1), 37715 , 2025 2025 Citations: 2
Building a Large Dataset of Genome Mutations Associated with Antibiotic Resistance in Mycobacterium tuberculosis J Al Akl, C Abou Jaoude, Z Al Chami, C Guyeux, D Laiymani, C Sola 2025 IEEE/ACS 22nd International Conference on Computer Systems and … , 2025 2025
An insight into the characterization of L2 Beijing multi-drug resistant tuberculosis: Description of resistance-associated-variants and discovery of Modern 7 L2 sublineage MA Soutou, C Allam, M Abifadel, J Najjar, C Guyeux, E Cambau, C Sola Infection, Genetics and Evolution, 105797 , 2025 2025 Citations: 1
In-depth analysis of predominant Mycobacterium tuberculosis L. 2.2. M3 strain from Panama, using TB-Annotator JE Ku, F Acosta, E Shitikov, P Patel, D Sambrano, C Guyeux, I Mokrousov, ... 45th Annual Congress of the European Society for Mycobacteriology , 2025 2025
Developing a tuberculosis q&a database using q&a-et: Question and answer evaluator toolkit J Al Akl, C Abou Jaoude, Z Chami, C Guyeux, D Laiymani, C Sola 2025 5th IEEE Middle East and North Africa Communications Conference … , 2025 2025
Advanced Machine Learning for Predicting Drug Resistance in Clinical Isolates of Mycobacterium Tuberculosis Complex N Sirri, C Guyeux, C Sola 2024 World Conference on Complex Systems (WCCS), 1-8 , 2024 2024
Leveraging LLM-Powered Systems to Accelerate Mycobacterium Tuberculosis Research Step One: From Documents to the Vectorstore C Guyeux, D Laiymani, C Sola International Conference on Machine Learning, Optimization, and Data Science … , 2024 2024 Citations: 1
The hidden diversity of mycobacterium tuberculosis complex in africa: the new l10 and the possible diversification histories of the complex C Guyeux, G Senelle, A Le Meur, C Sola, G Refrégier Annual Congress of the European Society of Mycobacteriology , 2024 2024 Citations: 1
Study and implementation of a new machine learning algorithm to predict drug resistance in Mycobacterium tuberculosis complex clinical isolates N SIRRI, C Guyeux, C Sola 2024 Citations: 1
Newly identified Mycobacterium africanum lineage 10, central Africa C Guyeux, G Senelle, A Le Meur, P Supply, C Gaudin, JE Phelan, ... Emerging infectious diseases 30 (3), 560 , 2024 2024 Citations: 49
Evolution, Phylogenetics, and Phylogeography of Mycobacterium tuberculosis complex C Sola, I Mokrousov, MR Sahal, K La, G Senelle, C Guyeux, G Refrégier, ... Genetics and Evolution of Infectious Diseases, 683-772 , 2024 2024 Citations: 8
The paradoxes of Mycobacterium tuberculosis molecular evolution and consequences for the inference of tuberculosis emergence date R Zein-Eddine, F Hak, A Le Meur, C Genestet, O Dumitrescu, C Guyeux, ... Tuberculosis 143, 102378 , 2023 2023 Citations: 2
Towards a better understanding of the long-lasting evolutionary history of Mycobacterium tuberculosis G Senelle, C Guyeux, G Refrégier, C Sola Tuberculosis 143, 102374 , 2023 2023 Citations: 3
Towards the reconstruction of a global TB history using a new pipeline “TB-Annotator G Senelle, MR Sahal, K La, T Billard-Pomares, J Marin, F Mougari, ... Tuberculosis 143, 102376 , 2023 2023 Citations: 6
A de novo diploid genome assembly allows dissecting the transcriptomic differences underlying the clonal phenotypic diversity in cultivar'Malbec' L Calderón, P Carbonell-Bejerano, C Muñoz, L Bree, C Sola, D Bergamin, ... LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular … , 2023 2023
Mycobacterium tuberculosis complex drug-resistance, phylogenetics, and evolution in Nigeria: Comparison with Ghana and Cameroon MR Sahal, G Senelle, K La, TW Panda, DW Taura, C Guyeux, E Cambau, ... PLOS Neglected Tropical Diseases 17 (10), e0011619 , 2023 2023 Citations: 6
Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data G Napier, D Couvin, G Refrégier, C Guyeux, CJ Meehan, C Sola, ... Scientific reports 13 (1), 11368 , 2023 2023 Citations: 14
TB-annotator: a scalable web application that allows in-depth analysis of very large sets of publicly available Mycobacterium tuberculosis complex genomes G Senelle, C Guyeux, G Refrégier, C Sola bioRxiv, 2023.06. 12.526393 , 2023 2023 Citations: 4
Paleopathology and evolution of tuberculosis editorial MA Coqueugniot Tuberculosis 143, 102428 , 2023 2023
MOST CITED SCHOLAR PUBLICATIONS
Proposal for Standardization of Optimized Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing of Mycobacterium tuberculosis P Supply, C Allix, S Lesjean, M Cardoso-Oelemann, S Rüsch-Gerdes, ... Journal of clinical microbiology 44 (12), 4498-4510 , 2006 2006 Citations: 1850
Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and … K Brudey, JR Driscoll, L Rigouts, WM Prodinger, A Gori, SA Al-Hajoj, ... BMC microbiology 6 (1), 23 , 2006 2006 Citations: 1422
SITVITWEB–a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology C Demay, B Liens, T Burguière, V Hill, D Couvin, J Millet, I Mokrousov, ... Infection, genetics and evolution 12 (4), 755-766 , 2012 2012 Citations: 618
Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic … I Filliol, AS Motiwala, M Cavatore, W Qi, MH Hazbón, ... Journal of bacteriology 188 (2), 759-772 , 2006 2006 Citations: 583
Characterization of Mycobacterium tuberculosis Complex DNAs from Egyptian Mummies by Spoligotyping AR Zink, C Sola, U Reischl, W Grabner, N Rastogi, H Wolf, AG Nerlich Journal of clinical microbiology 41 (1), 359-367 , 2003 2003 Citations: 516
Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis F Coll, J Phelan, GA Hill-Cawthorne, MB Nair, K Mallard, S Ali, ... Nature genetics 50 (2), 307-316 , 2018 2018 Citations: 423
The mycobacteria: an introduction to nomenclature and pathogenesis N Rastogi, E Legrand, C Sola Revue Scientifique Et Technique-Office International Des Epizooties 20 (1 … , 2001 2001 Citations: 422
Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics C Sola, I Filliol, E Legrand, S Lesjean, C Locht, P Supply, N Rastogi Infection, genetics and evolution 3 (2), 125-133 , 2003 2003 Citations: 380
CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections L Fabre, J Zhang, G Guigon, S Le Hello, V Guibert, M Accou-Demartin, ... PloS one 7 (5), e36995 , 2012 2012 Citations: 310
Global distribution of Mycobacterium tuberculosis spoligotypes I Filliol, JR Driscoll, D Van Soolingen, BN Kreiswirth, K Kremer, ... Emerging infectious diseases 8 (11), 1347 , 2002 2002 Citations: 309
Spacer oligonucleotide typing of bacteria of the Mycobacterium tuberculosis complex: recommendations for standardised nomenclature JW Dale, D Brittain, AA Cataldi, D Cousins, JT Crawford, J Driscoll, ... International Journal of Tuberculosis and Lung Disease 5 (3), 216-219 , 2001 2001 Citations: 271
Genetic Biodiversity of Mycobacterium tuberculosis Complex Strains from Patients with Pulmonary Tuberculosis in Cameroon SN Niobe-Eyangoh, C Kuaban, P Sorlin, P Cunin, J Thonnon, C Sola, ... Journal of clinical microbiology 41 (6), 2547-2553 , 2003 2003 Citations: 236
Spoligotype database of Mycobacterium tuberculosis: biogeographic distribution of shared types and epidemiologic and phylogenetic perspectives C Sola, I Filliol, MC Gutierrez, I Mokrousov, V Vincent, N Rastogi Emerging infectious diseases 7 (3), 390 , 2001 2001 Citations: 235
Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis T Dos Vultos, O Mestre, J Rauzier, M Golec, N Rastogi, V Rasolofo, ... PloS one 3 (2), e1538 , 2008 2008 Citations: 191
Mycobacterium tuberculosis Phylogeny Reconstruction Based on Combined Numerical Analysis with IS 1081, IS 6110, VNTR, and DR-Based Spoligotyping … C Sola, I Filliol, E Legrand, I Mokrousov, N Rastogi Journal of molecular evolution 53 (6), 680-689 , 2001 2001 Citations: 179
Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of ‘spoligotyping’ with new spacers and a … J Zhang, E Abadia, G Refregier, S Tafaj, ML Boschiroli, B Guillard, ... Journal of medical microbiology 59 (3), 285-294 , 2010 2010 Citations: 162
Spoligotype Signatures in the Mycobacterium tuberculosis Complex EM Streicher, TC Victor, G Van Der Spuy, C Sola, N Rastogi, ... Journal of clinical microbiology 45 (1), 237-240 , 2007 2007 Citations: 159
E-DNA Sensor of Mycobacterium tuberculosis Based on Electrochemical Assembly of Nanomaterials (MWCNTs/PPy/PAMAM) A Miodek, N Mejri, M Gomgnimbou, C Sola, H Korri-Youssoufi Analytical chemistry 87 (18), 9257-9264 , 2015 2015 Citations: 142
A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis M Sebban, I Mokrousov, N Rastogi, C Sola Bioinformatics 18 (2), 235-243 , 2002 2002 Citations: 134
Methods used in the molecular epidemiology of tuberculosis P Moström, M Gordon, C Sola, M Ridell, N Rastogi Clinical microbiology and infection 8 (11), 694-704 , 2002 2002 Citations: 128