Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Jean-Philippe Rasigade (1, 2, 3) , Maxime Barbier (2) , Oana Dumitrescu (1, 3) , Catherine Pichat (3) , Gérard Carret (3) , Anne-Sophie Ronnaux-Baron (4) , Ghislaine Blasquez (4) , Christine Godin-Benhaim (5) , Sandrine Boisset (6, 7) , Anne Carricajo (8) , Véronique Jacomo (9) , Isabelle Fredenucci (3) , Michèle Pérouse De Montclos (3) , Jean-Pierre Flandrois (3) , Florence Ader (10) , Philip Supply (11) , Gérard Lina (1, 3) , Thierry Wirth (2, 12)

1 StaPath - Pathogénie des Staphylocoques – Staphylococcal Pathogenesis
2 ISYEB - Institut de Systématique, Evolution, Biodiversité
3 IAI - Institut des Agents Infectieux [Lyon]
4 Comité Départemental d’Hygiène Sociale - CLAT69 [Lyon)
5 ARS - Agence régionale de santé Auvergne Rhône Alpes
6 Laboratoire de Bactériologie
7 TIMC-IMAG-TheREx - Thérapeutique Recombinante Expérimentale
8 CHU ST-E - Centre Hospitalier Universitaire de Saint-Etienne [CHU Saint-Etienne]
9 Eurofins Biomnis
10 LegioPath - Pathogenèse des légionelles- Legionella pathogenesis
11 CIIL - Centre d’Infection et d’Immunité de Lille - INSERM U 1019 - UMR 9017 - UMR 8204
12 ISYEB - Institut de Systématique, Evolution, Biodiversité

The transmission dynamics of tuberculosis involves complex interactions of socio-economic and, possibly, microbiological factors. We describe an analytical framework to infer factors of epidemic success based on the joint analysis of epidemiological, clinical and pathogen genetic data. We derive isolate-specific, genetic distance-based estimates of epidemic success, and we represent success-related time-dependent concepts, namely epidemicity and endemicity, by restricting analysis to specific time scales. The method is applied to analyze a surveillance-based cohort of 1,641 tuberculosis patients with minisatellite-based isolate genotypes. Known predictors of isolate endemicity (older age, native status) and epidemicity (younger age, sputum smear positivity) were identified with high confidence (P \textless 0.001). Long-term epidemic success also correlated with the ability of Euro-American and Beijing MTBC lineages to cause active pulmonary infection, independent of patient age and country of origin. Our results demonstrate how important insights into the transmission dynamics of tuberculosis can be gained from active surveillance data.

Domaines: Immunologie; Bactériologie; Virologie

Jean-Philippe Rasigade, Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, et al.. Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis. Scientific Reports, 2017, 7, pp.45326. ⟨10.1038/srep45326⟩. ⟨hal-01911199⟩