AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland

Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangement

Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins

Aeromonas salmonicida subsp. salmonicida is a fish pathogen. Analysis of its genomic characteristics is required to determine the worldwide distribution of the various populations of this bacterium. Genomic alignments between the 01-B526 pathogenic strain and the A449 reference strain have revealed a 51-kb chromosomal insertion in 01-B526. This insertion (AsaGEI1a) has been identified as a new genomic island (GEI) bearing prophage genes. PCR assays were used to detect this GEI in a collection of 139 A. salmonicida subsp. salmonicida isolates. Three forms of this GEI (AsaGEI1a, AsaGEI1b, AsaGEI2a) are now known based on this analysis and the sequencing of the genomes of seven additional isolates. A new prophage (prophage 3) associated with AsaGEI2a was also discovered. Each GEI appeared to be strongly associated with a specific geographic region. AsaGEI1a and AsaGEI2a were exclusively found in North American isolates, except for one European isolate bearing AsaGEI2a. The majority of the isolates bearing AsaGEI1b or no GEI were from Europe. Prophage 3 has also a particular geographic distribution and was found only in North American isolates. We demonstrated that A. salmonicida subsp. salmonicida possesses unsuspected elements of genomic heterogeneity that could be used as indicators to determine the geographic origins of isolates of this bacterium.Keywords : Bacteria, Genomics-functional genomics-comparative genomics; Furunculosis; Aeromonas salmonicida; Fish pathogen; Genomic island; Geographical distributio

Une approche de support aux décisions non structurées

Supposons un moment que vous dirigez ABC Inc., moyenne entreprise en croissance. Ingénieur et MBA, vous avez mis en marché un produit révolutionnaire qui, encore aujourd'hui, se vend comme des petits pains chauds. De plus en plus vous êtes assailli par la publicité et les représentants des différents constructeurs informatiques. Néophyte en la matière, vous embauchez un consultant pour voir à la définition et - au respect de vos besoins. Il est probable que votre comptabilité, votre gestion des stocks et une portion de votre production soient informatisables. Pour un investissement de 10 000 ou 100 000 dollars vos employés augmenterons leur efficacité (et vos profits sous-entend le représentant). Mais vous? Vous qui êtes chargé ce trouver de nouveaux débouchés, de planifier ou de trouver des stratégies de développement, mis à part les rapports historiques consolidés et à jour, que vous apporte ce système d'information? Les concepts de système d'aide à la décision, et, plus récemment, de centre d'information sont sensés offrir ces réponses sur mesure pour vos besoins

Network-level prediction of set-shifting deterioration after lower-grade glioma resection

International audienceOBJECTIVE The aim of this study was to predict set-shifting deterioration after resection of low-grade glioma. METHODS The authors retrospectively analyzed a bicentric series of 102 patients who underwent surgery for low-grade glioma. The difference between the completion times of the Trail Making Test parts B and A (TMT B-A) was evaluated preoperatively and 3–4 months after surgery. High dimensionality of the information related to the surgical cavity topography was reduced to a small set of predictors in four different ways: 1) overlap between surgical cavity and each of the 122 cortical parcels composing Yeo’s 17-network parcellation of the brain; 2) Tractotron: disconnection by the cavity of the major white matter bundles; 3) overlap between the surgical cavity and each of Yeo’s networks; and 4) disconets: signature of structural disconnection by the cavity of each of Yeo’s networks. A random forest algorithm was implemented to predict the postoperative change in the TMT B-A z-score. RESULTS The last two network-based approaches yielded significant accuracies in left-out subjects (area under the receiver operating characteristic curve [AUC] approximately equal to 0.8, p approximately equal to 0.001) and outperformed the two alternatives. In single tree hierarchical models, the degree of damage to Yeo corticocortical network 12 (CC 12) was a critical node: patients with damage to CC 12 higher than 7.5% (cortical overlap) or 7.2% (disconets) had much higher risk to deteriorate, establishing for the first time a causal link between damage to this network and impaired set-shifting. CONCLUSIONS The authors’ results give strong support to the idea that network-level approaches are a powerful way to address the lesion-symptom mapping problem, enabling machine learning–powered individual outcome predictions

Dissociating motor–speech from lexico-semantic systems in the left frontal lobe: insight from a series of 17 awake intraoperative mappings in glioma patients

International audienc

AsaGEI2b: a new variant of a genomic island identified in the Aeromonas salmonicida subsp. salmonicida JF3224 strain isolated from a wild fish in Switzerland.

Aeromonas salmonicida subsp. salmonicida is the causal agent of furunculosis in salmonids. We recently identified a group of genomic islands (AsaGEI) in this bacterium. AsaGEI2a, one of these genomic islands, has almost exclusively been identified in isolates from North America. To date, Aeromonas salmonicida subsp. salmonicida JF3224, a strain isolated from a wild brown trout (Salmo trutta) caught in Switzerland, was the only European isolate that appeared to bear AsaGEI2a. We analyzed the genome of JF3224 and showed that the genomic island in JF3224 is a new variant of AsaGEI, which we have called AsaGEI2b. While AsaGEI2b shares the same integrase gene and insertion site as AsaGEI2a, it is very different in terms of many other features. Additional genomic investigations combined with PCR genotyping revealed that JF3224 is sensitive to growth at 25°C, leading to insertion sequence-dependent rearrangement of the locus on the pAsa5 plasmid that encodes a type three secretion system, which is essential for the virulence of the bacterium. The analysis of the JF3224 genome confirmed that AsaGEIs are accurate indicators of the geographic origins of A. salmonicida subsp. salmonicida isolates and is another example of the susceptibility of the pAsa5 plasmid to DNA rearrangements