Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Barbier, Maxime; Dumitrescu, Oana; Pichat, Catherine; Carret, G.; Ronnaux-Baron, Anne-Sophie; Blasquez, Ghislaine; Godin-Benhaïm, Christine; Boisset, Sandrine; Carricajo, Anne; Jacomo, Véronique; Frédénucci, Isabelle; Montclos, Michèle Pérouse de; Genestet, Charlotte; Ader, Florence; Supply, Philip; Lina, Gérard; Wirth, Thierry; Rasigade, Jean-Philippe

doi:10.1038/s41598-018-24034-6

Cited by 12 publications

(10 citation statements)

References 26 publications

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“…The median [interquartile range (IQR)] age of the study population was 35 [25-58] years, and a majority were male (66.2%). Most of the patients originated from Europe or Africa, which is consistent with the local epidemiology 19,20 . No difference was found in terms of comorbidities according to severity group ( Table 1 ).…”

Section: Resultssupporting

confidence: 82%

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Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Genestet

Refrégier

Hodille

et al. 2022

Preprint

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Mycobacterium tuberculosis (Mtb) infections result in a wide spectrum of clinical presentations but without proven Mtb genetic determinants. Herein, 234 pulmonary tuberculosis (TB) patients were stratified according to TB disease severity and Mtb genetic features were explored using whole genome sequencing, including heterologous single nucleotide polymorphism (SNP) calling to explore micro-diversity. Clinical isolates from patients with mild TB carried mutations in genes associated with host-pathogen interaction, while those from patients with moderate/severe TB carried mutations associated with regulatory mechanisms. Genome-wide association study identified a SNP in the promoter of the gene coding for the virulence regulator EspR associated with moderate/severe disease. Structural equation modelling and model comparisons indicated that TB severity was associated with the detection of Mtb micro-diversity within clinical isolates and to the espR SNP. Taken together, these results provide a new insight to better understand TB pathophysiology and could provide new prognosis tool for pulmonary TB severity.

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Section: Resultssupporting

confidence: 82%

“…Most of the patients originated from Europe or Africa, which is consistent with the local epidemiology 19,20 . No difference was found in terms of comorbidities according to severity group (Table 1).…”

Section: Tb Cohort Characterisationsupporting

confidence: 80%

Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Genestet

Refrégier

Hodille

et al. 2022

Preprint

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“…The THD approach converts genetic distances to a density measure in the space of haplotypes, which captures the number of putative between-host transmission events in the isolate's ancestry during a user-specified time window or timescale. This approach was previously shown to accurately capture the influence of well-established drivers of epidemic transmission of Mycobacterium tuberculosis and to detect novel potential drivers 25,59 . User-defined parameters were a mutation rate of 1.51 × 10 −6 substitutions per position per year, as defined under the best-fitting evolutionary model (Fig.…”

Section: Nature Microbiologymentioning

confidence: 99%

Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Wirth¹,

Bergot²,

Rasigade³

et al. 2020

Nat Microbiol

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first aligned the genome sequences of the 250 isolates against the NRCS-A reference genome CR01, resulting in a total of 22,621 single nucleotide polymorphisms (SNPs). To quantify recombination, we used ClonalFrameML 12 , which is specifically aimed at analysing whole-genome sequence data (see Supplementary Information). The results indicated that the impact of recombination (r) on the genome-wide substitution rate in S. capitis overall is almost equal to the impact of mutation (m), with r/m = 0.85. ClonalFrameML identified 190 recombination events in the global genealogy (Extended Data Fig. 1). The largest detected events (up to 26 kb) are probably products of horizontal gene transfer, some of which correspond to the insertion of pathogenicity islands. Clonal specialization and geographical dispersion of NRCS-A.The reconstructed maximum-likelihood tree (Fig. 1a) enabled us to draw a clear distinction between NRCS-A isolates that harbour the previously described specific NRCS-A pulsed-field gel electrophoresis pattern 8 (n = 197) and all the other strains found in basal positions (n = 53; hereafter 'basal'). These reconstructions revealed that this NRCS-A population is composed of at least three sublineages, which we named in chronological order of divergence on the basis of the observed branching order in the tree: 'proto-outbreak 1' (n = 18), 'proto-outbreak 2' (n = 17) and 'outbreak' (n = 162) (Fig. 1a,b). These three clades are supported both by bootstrap values greater than 95% and by the trimodal distribution of the

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“…TB was declared a global emergency by the WHO in 1994 but incessantly exists as a public health threat by affecting a large portion of the world population in many low‐income countries (Barbier et al., 2018; WHO, 2019). The actively flourishing globalization, migration of people, and rapid urbanization have boosted this airborne disease spread (Medie et al., 2011; WHO, 2019).…”

Section: Introductionmentioning

confidence: 99%

Glycoconjugates, hypothetical proteins, and post‐translational modification: Importance in host–pathogen interaction and antitubercular intervention development

Arega

Mahapatra

2021

Chem Biol Drug Des

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With the emergence of multidrug‐resistant bacteria, insufficiency of the established chemotherapy, and the existing vaccine BCG, tuberculosis (TB) subsists as the chief cause of death in different parts of the world. Thus, identification of novel target proteins is urgently required to develop more effective TB interventions. However, the novel vaccine and drug target knowledge based on the essentiality of the pathogen cell envelope components such as glycoconjugates, glycans, and the peptidoglycan layer of the lipid‐rich capsule are limited. Furthermore, most of the genes encoding proteins are characterized as hypothetical and functionally unknown. Correspondingly, some researchers have shown that the lipid and sugar components of the envelope glycoconjugates are largely in charge of TB pathogenesis and encounter many drugs and vaccines. Therefore, in this review we provide an insight into a comprehensive study concerning the importance of cell envelope glycoconjugates and hypothetical proteins, the impact of post‐translational modification, and the bioinformatics‐based implications for better antitubercular intervention development.

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Cited by 12 publications

References 26 publications

Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Niche specialization and spread of Staphylococcus capitis involved in neonatal sepsis

Glycoconjugates, hypothetical proteins, and post‐translational modification: Importance in host–pathogen interaction and antitubercular intervention development

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