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Saint-André-lez-Lille, France

Vadwai V.,Medical Research Center | Shetty A.,Medical Research Center | Supply P.,Center for Infection and Immunity of Lille | Supply P.,French Institute of Health and Medical Research | And 3 more authors.
Tuberculosis | Year: 2012

Genotyping of Mycobacterium tuberculosis isolates is a useful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. There is a lack of information on the discriminatory power of standard 24-locus mycobacterial interspersed repetitive unit (MIRU) - variable number tandem repeats (VNTR) in India, which has the highest tuberculosis (TB) burden worldwide. Therefore, we assessed its utility on 69 M. tuberculosis (MTB) isolates from patients with extrapulmonary tuberculosis, in comparison to standard insertion sequence (IS) 6110-Restriction fragment length polymorphism (RFLP) fingerprinting and spoligotyping. IS6110-RFLP (HGDI, 0.9987) identified a single cluster of 3 (4.3%) single-copy IS6110 isolates. Spoligotyping showed 69.5% clustering (HGDI, 0.8857). In contrast, MIRU-VNTR analysis identified 69 (100%) unique strains (HGDI, 1.0000). Within the study limits, this observed high discriminatory power suggests that 24-locus MIRU-VNTR genotyping could potentially be used to study long-term transmission of MTB infection in Mumbai. Moreover, high congruence between the MIRU-VNTR-based and spoligotyping-based strain groupings suggests that CAS, EAI and Beijing are the predominant strain lineages in the Mumbai TB patient population. The Beijing lineage isolates were found to be more significantly associated with multi-drug resistance (p < 0.01) than CAS and EAI lineages. © 2012 Elsevier Ltd. All rights reserved.

Pouseele H.,Applied Maths | Supply P.,Center for Infection and Immunity of Lille | Supply P.,French Institute of Health and Medical Research | Supply P.,French National Center for Scientific Research | And 2 more authors.
Methods in Microbiology | Year: 2015

Efficient molecular-guided epidemiological control of tuberculosis is especially important, because of the complex epidemiology, the insidious transmission and the specific biological features of its etiologic agent Mycobacterium tuberculosis. The most used typing system for epidemiological tracing of the pathogen is MIRU-VNTR typing, which has been internationally standardised under two formats (standard 24-locus based and 4 hypervariable locus based), optionally combined with spoligotyping. This generalised use has been facilitated by the portable numerical genotypes that are generated, the precisely calibrated molecular cluster definition and the option to use published protocols or ready-to-go kits directly compatible with multifunctional web-based databases. However, such classical typing systems can inherently not capture all possible micro-variation that can occur in the genome. Near complete capture of the available genetic information is increasingly performed by whole-genome sequencing (WGS). Such approaches take advantage of the rapid advances and increasing affordability of next-generation sequencing technologies, including benchtop platforms meeting the needs of routine clinical microbiology. However, such technologies rely on a number of key technical steps that are important, including in particular the critical bioinformatics analysis step. This chapter will therefore provide an overview of analysis parameters that are determinant for accurate WGS-based epidemiological surveillance of M. tuberculosis, linked to its restricted genetic diversity and the particular richness of its genome in repetitive regions. © 2015 Elsevier Ltd.

Yanokura E.,Yakult Central Institute | Oki K.,Yakult Honsha European Research Center for Microbiology | Makino H.,Yakult Central Institute | Modesto M.,University of Bologna | And 7 more authors.
Systematic and Applied Microbiology | Year: 2015

The species Bifidobacterium longum is currently divided into three subspecies, B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis. This classification was based on an assessment of accumulated information on the species' phenotypic and genotypic features. The three subspecies of B. longum were investigated using genotypic identification [amplified-fragment length polymorphism (AFLP), multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST)]. By using the AFLP and the MLSA methods, we allocated 25 strains of B. longum into three major clusters corresponding to the three subspecies; the cluster comprising the strains of B. longum subsp. suis was further divided into two subclusters differentiable by the ability to produce urease. By using the MLST method, the 25 strains of B. longum were divided into eight groups: four major groups corresponding to the results obtained by AFLP and MLSA, plus four minor disparate groups. The results of AFLP, MLSA and MLST analyses were consistent and revealed a novel subspeciation of B. longum, which comprised three known subspecies and a novel subspecies of urease-negative B. longum, for which the name B. longum subsp. suillum subsp. nov. is proposed, with type strain Su 851T=DSM 28597T=JCM 19995T. © 2015 Elsevier GmbH.

Villemagne B.,University of Lille Nord de France | Villemagne B.,French Institute of Health and Medical Research | Crauste C.,University of Lille Nord de France | Crauste C.,French Institute of Health and Medical Research | And 10 more authors.
European Journal of Medicinal Chemistry | Year: 2012

Tuberculosis is a major disease causing every year 1.8 million deaths worldwide and represents the leading cause of mortality resulting from a bacterial infection. Introduction in the 60's of first-line drug regimen resulted in the control of the disease and TB was perceived as defeating. However, since the progression of HIV leading to co-infection with AIDS and the emergence of drug resistant strains, the need of new anti-tuberculosis drugs was not overstated. However in the past 40 years any new molecule did succeed in reaching the market. Today, the pipeline of potential new treatments has been fulfilled with several compounds in clinical trials or preclinical development with promising activities against sensitive and resistant Mycobacterium tuberculosis strains. Compounds as gatifloxacin, moxifloxacin, metronidazole or linezolid already used against other bacterial infections are currently evaluated in clinical phases 2 or 3 for treating tuberculosis. In addition, analogues of known TB drugs (PA-824, OPC-67683, PNU-100480, AZD5847, SQ609, SQ109, DC-159a) and new chemical entities (TMC207, BTZ043, DNB1, BDM31343) are under development. In this review, we report the chemical synthesis, mode of action when known, in vitro and in vivo activities and clinical data of all current small molecules targeting tuberculosis. © 2012 Elsevier Masson SAS. All rights reserved.

Corbiere V.,Free University of Colombia | Pottier G.,Free University of Colombia | Bonkain F.,Free University of Colombia | Schepers K.,Free University of Colombia | And 12 more authors.
PLoS ONE | Year: 2012

Background: Most individuals infected with Mycobacterium tuberculosis develop latent tuberculosis infection (LTBI). Some may progress to active disease and would benefit from preventive treatment yet no means currently exists to predict who will reactivate. Here, we provide an approach to stratify LTBI based on IFN-γ responses to two antigens, the recombinant Early-Secreted Antigen Target-6 (rESAT-6) and the latency antigen Heparin-Binding Haemagglutinin (HBHA). Methods: We retrospectively analyzed results from in-house IFN-γ-release assays with HBHA (HBHA-IGRA) and rESAT-6 (rESAT-6-IGRA) performed during a 12-year period on serial blood samples (3 to 9) collected from 23 LTBI subjects in a low-TB incidence country. Both the kinetics of the absolute IFN-γ concentrations secreted in response to each antigen and the dynamics of HBHA/rESAT-6-induced IFN-γ concentrations ratios were examined. Results: This analysis allowed the identification among the LTBI subjects of three major groups. Group A featured stable HBHA and rESAT-6-IGRA profiles with an HBHA/rESAT-6 ratio persistently higher than 1, and with high HBHA- and usually negative rESAT-6-IGRA responses throughout the study. Group B had changing HBHA/rESAT-6 ratios fluctuating from 0.0001 to 10,000, with both HBHA and rESAT-6 responses varying over time at least once during the follow-up. Group C was characterized by a progressive disappearance of all responses. Conclusions: By combining the measures of IFN-γ concentrations secreted in response to an early and a latency antigens, LTBI subjects can be stratified into different risk groups. We propose that disappearing responses indicate cure, that persistent responses to HBHA with HBHA/rESAT-6 ratios ≥1 represent stable LTBI subjects, whereas subjects with ratios varying from ≥1 to <1 should be closely monitored as they may represent the highest-risk group, as illustrated by a case report, and should therefore be prioritized for preventive treatment. © 2012 Corbière et al.

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