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 < 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.

In a 5-year retrospective study, we used spoligotyping and mycobacterial interspersed repetitive units to type 13 strains of Mycobacterium bovis isolated from human sources. Despite the relatively high incidence of human tuberculosis caused by M. bovis (2%), these tools showed no clonal evolution and no relationships between the isolates.

BackgroundThe present work relates to identification and a deep molecular characterization of circulating Mycobacterium tuberculosis complex (MTBC) strains in the Rhône-Alpes region, France from 2000 to 2010. It aimed to provide with a first snapshot of MTBC genetic diversity in conjunction with bacterial drug resistance, type of disease and available demographic and epidemiologic characteristics over an eleven-year period, in the south-east of France.MethodsMycobacterium tuberculosis complex (MTBC) strains isolated in the Rhône-Alpes region, France (n = 2257, 1 isolate per patient) between 2000 and 2010 were analyzed by spoligotyping. MIRU-VNTR typing was applied on n = 1698 strains (with full results available for 974 strains). The data obtained were compared with the SITVIT2 database, followed by detailed genotyping, phylogenetic, and epidemiologic analyses in correlation with anonymized data on available demographic, and epidemiologic characteristics, and location of disease (pulmonary or extrapulmonary TB).ResultsThe most predominant spoligotyping clusters were SIT53/T1 (n = 346, 15.3%) > SIT50/H3 (n = 166, 7.35%) > SIT42/LAM9 (n = 125, 5.5%) > SIT1/Beijing (n = 72, 3.2%) > SIT47/H1 (n = 71, 3.1%). Evolutionary-recent strains belonging to the Principal Genetic Group (PGG) 2/3, or Euro-American lineages (T, LAM, Haarlem, X, S) were predominant and represented 1768 or 78.33% of all isolates. For strains having drug resistance information (n = 1119), any drug resistance accounted for 14.83% cases vs. 1.52% for multidrug resistance (MDR); and was significantly more associated with age group 21–40 years (p-value<0.001). Extra-pulmonary TB was more common among female patients while pulmonary TB predominated among men (p-value<0.001; OR = 2.16 95%CI [1.69; 2.77]). Also, BOV and CAS lineages were significantly well represented in patients affected by extra-pulmonary TB (p-value<0.001). The origin was known for 927/2257 patients: 376 (40.6%) being French-born vs. 551 (59.4%) Foreign-born. French patients were significantly older (mean age: 58.42 yrs 95%CI [56.04; 60.80]) than Foreign-born patients (mean age: 42.38 yrs. 95%CI [40.75; 44.0]).ConclusionThe study underlined the importance of imported TB cases on the genetic diversity and epidemiologic characteristics of circulating MTBC strains in Rhône-Alpes region, France over a large time-period. It helps better understand intricate relationships between certain lineages and geographic origin of the patients, and pinpoints genotypic and phylogenetic specificities of prevailing MTBC strains. Lastly, it also demonstrated a slow decline in isolation of M. africanum lineage in this region between 2000 and 2010.

While isoniazid and rifampin have been the cornerstone of tuberculosis therapy caused by drug-susceptible for more than 40 years, their combined action has never been thoroughly assessed by modern quantitative pharmacology approaches. The aims of this work were to perform experiments and mathematical modeling of the antibacterial effect of isoniazid and rifampin alone and in combination against various strains of After MIC determination of H37Rv and three strains belonging to the Beijing, Euro-American, and Indo-Oceanic lineages, the antibacterial effects of isoniazid and rifampin alone and in combination were studied in static time-kill experiments. A sigmoidal maximum effect model (Hill equation) and a response-surface model were used to describe the effect of the drugs alone and in combination, respectively. The killing effect of isoniazid and rifampin alone were well described by the Hill equation. Rifampin displayed a more concentration-dependent effect than isoniazid around the MIC. The pharmacodynamics parameters of each drug (maximal effect, median effect concentration, and coefficient of sigmoidicity) were quite similar between the four strains. The response-surface model from Minto et al. fit data of combined effect very well with low bias and imprecision (C. F. Minto, T. W. Schnider, T. G. Short, K. M. Gregg, A. Gentilini, Anesthesiology1603-1616, 2000, https://doi.org/10.1097/00000542-200006000-00017). Response-surface modeling showed that the combined action of isoniazid and rifampin was synergistic for the H37Rv, Beijing, and Euro-American strains but only additive for the Indo-Oceanic strain. This study can serve as a motivating example for preclinical evaluation of combined action of antituberculous drugs.

Control of Mycobacterium tuberculosis transmission in high-income healthcare settings and in low tuberculosis (TB) prevalence countries remains a public health priority given the constant changes in M. tuberculosis epidemiology worldwide. Though Europe is a low prevalence area [1], TB burden among precarious and migrant populations contributes to this evolving landscape, as addressed by the action framework towards TB elimination [2]. At the core of the national healthcare system, tertiary care hospitals manage both patients with greater susceptibility to TB, and patients with complex and/or advanced TB disease. Key measures for TB control rely on enabling linkage of cases and identification of transmission chains, often supported by molecular survey tools [3,4]. This is achieved by highlighting matched genotypes through a population-based systematic molecular TB survey in order to uncover outbreaks, even between apparently unrelated cases [5]. On that basis, further investigations can be triggered to understand the circumstances of transmission. In case of healthcare-related transmission, the origin of TB exposure is difficult to track as clinical disease develops months or years after patient discharge [6]. Therefore, understanding nosocomial TB transmission is essential for implementing control measures preventing such events. Herein, we bring evidence of the usefulness of molecular survey programmes to detect unsuspected TB transmission events among highly susceptible populations, and from a multidrug-resistant (MDR)-TB patient to a community-based individual. Subsequent corrective interventions implemented to prevent further nosocomial TB transmission are also described.Since 2008, the laboratory of the Lyon University Hospital has implemented a prospective population-based survey by systematic genotyping of M. tuberculosis isolates from the surrounding geographic districts (ORAM: Observatoire Rhône-Alpes des Mycobactéries), to facilitate the reporting of clinical microbiology results from TB laboratories to an operational network including TB management and control centres, and a centralised regional health agency [7]. In addition to spoligo-and MIRU-VNTR15-typing performed as described [7], from 2016 onwards, whole genome sequencing (WGS) was implemented as previously reported [5]. Sampling and testing were performed upon diagnosis and in accordance with the French bioethics laws. Contact-tracing was conducted as recommended by the French guidelines [8].From 2008 to 2018, 3230 cases of microbiologically proven TB were recorded; 20.5% of these cases were clustered, representing 662 patients distributed in 217 clusters. Among 96 clusters (341 cases) with confirmed transmission ( patients knew each other), four were healthcare-related (transmission occurring in hospital area), representing eight patients, including a single MDR-TB transmission event (figure 1a). Among them, three cases in lung transplant recipients resulted from nosocomial transmission of drug-susceptible TB. All index cases were men aged fro...