Un nouveau scénario pour les premières étapes de l'évolution de Mycobacterium tuberculosis.

Mycobacterium tuberculosis, the causative agent of tuberculosis, is a pathogen of world-wide impact. Since its discovery in 1882 by Robert Koch many studies have been focusing on the characteristics of this bacterium and of the most closely related strains known as the Mycobacterium tuberculosis complex (MTBC). In this work we started by studying the closest neighbor to the MTBC, the "Mycobacterium canettii" taxon, which is only found in one particular region of the world, the Horn of Africa. It t has been first identified in the middle of the XXth century as being able to cause tuberculosis in humans, but having at the same time peculiar phenotypic characteristics. Through the study of some phylogenetic markers we have been able to establish that this bacterium does not belong to the MTBC sensu stricto and can therefore be used as an outgroup in order to root the phylogeny to study the emergence of the MTBC.The next step was to study the genetic diversity of a collection of strains of "M. canettii",using the “next generation sequencing” (NGS) approach.. The analysis of this collection, built along the years by the French Army Health Service (SSA), has permitted to show the rapid emergence of a particular clone, as well as to get information enabling to precise the position of the most recent common ancestor (MRCA) of the MTBC. Because of the restricted geographic location of this species, it was also decided to assess the genetic diversity of strains of M. tuberculosis coming from the same part of the globe.This second part of the study, performed on a collection of strains also gathered by the SSA, has lead to the identification of a new, previously unknown, lineage of the MTBC. This discovery has a profound impact on the comprehension of the emergence of M. tuberculosis, as it permits to develop a new model of appearance by interpreting this lineage as the founder ecotype of the MTBC. The evolution of M. tuberculosis can therefore by understood along a path linking "M. canettii", opportunistic pathogen supposedly environmental, and this new lineage. After this proposal of a new model, we tried to date it by extrapolatingMycobacterium tuberculosis, la bactérie causant la tuberculose, est un pathogène d'importance majeure à l'échelle mondiale. Depuis sa découverte en 1882 par Robert Koch, de nombreuses études se sont penchées sur les caractéristiques de cette bactérie et des souches proches, connues sous le nom de complexe Mycobacterium tuberculosis (MTBC). Dans le cadre de ce travail nous avons commencé par nous intéresser à l'espèce proche "Mycobacterium canettii", qui avait été identifiée au milieu du XXème siècle comme étant également capable de causer des cas de tuberculose chez l'Homme, tout en possédant des caractéristiques phénotypiques propres. Par le biais de l'étude de certains marqueurs phylogénétiques, nous avons pu établir que cette bactérie n'appartenait pas au MTBC au sens strict et pouvait donc être utilisée comme point d'ancrage dans le cadre de l'étude de la phylogénie et de l'émergence de ce dernier.C'est pourquoi nous avons choisi d'étudier la diversité de la collection de souches de "Mycobacterium canettii", qui proviennent toutes d'une même région du globe, la Corne de l'Afrique. L'étude de cette collection, construite au fil des ans par le Service de Santé des Armées (SSA), a permis de mettre en évidence l'émergence d'un groupe particulier de souches au sein de cette espèce, ainsi que d'obtenir des éléments permettant de préciser le positionnement du dernier ancêtre commun (MRCA) du MTBC. Du fait de l'origine géographique exclusive de ce taxon, nous avons ensuite décidé d'évaluer la diversité génétique des souches de Mycobacterium tuberculosis provenant de cette même région du globe.Cette seconde partie de l'étude, menée sur une collection à nouveau constituée par le SSA, a conduit à l'identification d'une nouvelle lignée au sein du MTBC, jusqu'alors inconnue. Cette découverte a un impact important sur la compréhension de l'émergence de Mycobacterium tuberculosis, car elle permet d'envisager un nouveau modèle d'apparition en interprétant cette lignée comme le descendant contemporain de l'écotype fondateur du MTBC. L'évolution de Mycobacterium tuberculosis peut ainsi être comprise suivant une progression liant "Mycobacterium canettii", pathogène occasionnel supposé environnemental, et cette nouvelle lignée. Une fois ce nouveau modèle proposé, nous avons tenté de le dater en extrapolant le taux de mutations observé lors d'évènements épidémiques contemporains, ce qui nous a permis de dater le MRCA du MTBC à environ 10 000 ans. Enfin nous avons mis en parallèle ces éléments concrets avec les connaissances paléo-ethnographiques actuelles concernant la Corne de l'Afrique pour proposer un modèle historiquement argumenté permettant d'expliquer la structuration phylogénétique actuelle du MTBC

Mineral content and biomechanical properties of fibrolamellar bone

editorial reviewe

Breast Cancer Risk Estimation and Personal Insurance: A Qualitative Study Presenting Perspectives from Canadian Patients and Decision Makers

Genetic stratification approaches in personalized medicine may considerably improve our ability to predict breast cancer risk for women at higher risk of developing breast cancer. Notwithstanding these advantages, concerns have been raised about the use of the genetic information derived in these processes, outside of the research and medical health care settings, by third parties such as insurers. Indeed, insurance applicants are asked to consent to insurers accessing their medical information (implicitly including genetic) to verify or determine their insurability level, or eligibility to certain insurance products. This use of genetic information may result in the differential treatment of individuals based on their genetic information, which could lead to higher premium, exclusionary clauses or even the denial of coverage. This phenomenon has been commonly referred to as “Genetic Discrimination” (GD). In the Canadian context, where federal Bill S-201, An Act to prohibit and prevent genetic discrimination, has recently been enacted but may be subject to constitutional challenges, information about potential risks to insurability may raise issues in the clinical context. We conducted a survey with women in Quebec who have never been diagnosed with breast cancer to document their perspectives. We complemented the research with data from 14 semi-structured interviews with decision-makers in Quebec to discuss institutional issues raised by the use of genetic information by insurers. Our results provide findings on five main issues: (1) the reluctance to undergo genetic screening test due to insurability concerns, (2) insurers' interest in genetic information, (3) the duty to disclose genetic information to insurers, (4) the disclosure of potential impacts on insurability before genetic testing, and (5) the status of genetic information compared to other health data. Overall, both groups of participants (the women surveyed and the decision-makers interviewed) acknowledged having concerns about GD and reported a need for better communication tools discussing insurability risk. Our conclusions regarding concerns about GD and the need for better communication tools in the clinical setting may be transferable to the broader Canadian context

Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Background: Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 50-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains.Results: A total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays. Conclusions: This work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France

Figure 1: Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis

Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis. A. Minimum spanning tree based on 3987 chromosomal SNPs (obtained with BioNumerics 6.6 from Applied Maths). The 3 canSNP groups present in France are color-coded: B.Br CNEVA in light blue, A.Br 011/009 in purple and A.Br 001/002 in green. The African lineage A.Br 005/006 is indicated in red. Positions of the B. anthracis Sterne (in green), Ames ancestor (in yellow) and A1055 (in black) strains are also marked. Each circle represents a unique SNP genotype. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of the new identified French canSNPs. The star marks the approximate branching point of the B. anthracis lineage within the B. cereus group. Based on a parsimony approach, the tree size is 4018, i.e. it contains approximately 0.77% of homoplasia. B. Linear phylogenetic tree rooted with the B. cereus AH820 strain as outgroup. This figure illustrates the relationship between French and globally diverse B. anthracis strains

Data from: High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery

Background: Single nucleotide polymorphisms (SNPs) are ideal signatures for subtyping monomorphic pathogens such as Bacillus anthracis. Here we report the use of next-generation sequencing technology to investigate the historical, geographic and genetic diversity of Bacillus anthracis in France. 122 strains isolated over a 50-years period throughout the country were whole-genome sequenced and comparative analyses were carried out with a focus on SNPs discovery to discriminate regional sub-groups of strains.Results: A total of 1581 chromosomal SNPs precisely establish the phylogenetic relationships existing between the French strains. Phylogeography patterns within the three canSNP sub-lineages present in France (i.e. B.Br.CNEVA, A.Br.011/009 and A.Br.001/002) were observed. One of the more remarkable findings was the identification of a variety of genotypes within the A.Br.011/009 sub-group that are persisting in the different regions of France. The 560 SNPs defining the A.Br.011/009- affiliated French strains split the Trans-Eurasian sub-group into six distinct branches without any intermediate nodes. Distinct sub-branches, with some geographic clustering, were resolved. The 345 SNPs defining the major B.Br CNEVA sub-lineage clustered three main phylogeographic clades, the Alps, the Pyrenees, and the Massif Central, with a small Saône-et-Loire sub-cluster nested within the latter group. The French strains affiliated to the minor A.Br.001/002 group were characterized by 226 SNPs. All recent isolates collected from the Doubs department were closely related. Identification of SNPs from whole-genome sequences facilitates high-resolution strain tracking and provides the level of discrimination required for outbreak investigations. Eight diagnostic SNPs, representative of the main French-specific phylogeographic clusters, were therefore selected and developed into high-resolution melting SNP discriminative assays. Conclusions: This work has established one of the most accurate phylogenetic reconstruction of B. anthracis population structure in a country. An extensive next-generation sequencing (NGS) dataset of 122 French strains have been created that allowed the identification of novel diagnostic SNPs useful to rapidly determine the geographic origin of any strain found in France

A novel Pseudomonas aeruginosa bacteriophage, Ab31, a chimera formed from temperate phage PAJU2 and P. putida lytic phage AF: characteristics and mechanism of bacterial resistance.

A novel temperate bacteriophage of Pseudomonas aeruginosa, phage vB_PaeP_Tr60_Ab31 (alias Ab31) is described. Its genome is composed of structural genes related to those of lytic P. putida phage AF, and regulatory genes similar to those of temperate phage PAJU2. The virion structure resembles that of phage AF and other lytic Podoviridae (S. enterica Epsilon 15 and E. coli phiv10) with similar tail spikes. Ab31 was able to infect P. aeruginosa strain PA14 and two genetically related strains called Tr60 and Tr162, out of 35 diverse strains from cystic fibrosis patients. Analysis of resistant host variants revealed different phenotypes, including induction of pigment and alginate overproduction. Whole genome sequencing of resistant variants highlighted the existence of a large deletion of 234 kbp in two strains, encompassing a cluster of genes required for the production of CupA fimbriae. Stable lysogens formed by Ab31 in strain Tr60, permitted the identification of the insertion site. During colonization of the lung in cystic fibrosis patients, P. aeruginosa adapts by modifying its genome. We suggest that bacteriophages such as Ab31 may play an important role in this adaptation by selecting for bacterial characteristics that favor persistence of bacteria in the lung

Figure 2: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage

Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 345 chromosomal SNPs (A), 14 pXO1 SNPs (B) and 15 pXO2 SNPs (C). The geographic clustering of the French strains is color-coded: Alps in green (34 strains), Pyrenees in purple (9 strains), Massif Central in red (18 strains) and Saône et Loire department in yellow (6 strains). The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of four French canSNPs described in this study. Based on a parsimony approach, the tree size is 352, i.e. it contains approximately 1.98% of homoplasia. Concerning the plasmids, the tree sizes are 14 and 15 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia

Figure 3: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup

Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup (obtained with BioNumerics 6.6 from Applied Maths). Data are based on 560 chromosomal SNPs (A), 20 pXO1 SNPs (B) and 18 pXO2 SNPs (C). The six resolved branches are color-coded. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the positions and names for two canSNPs described in this study. NE: North-East, SW: South-West, SE: South-East. Based on a parsimony approach, the tree size is 561, i.e. it contains approximately 0.18% of homoplasia. Concerning the plasmids, the tree sizes are 20 and 18 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia