Phylogenomics of Enterococcus faecalis from wild birds: new insights into host‐associated differences in core and accessory genomes of the species

2019

Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone‐responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the sp…

Identification of multiplicatively acting modulatory mutational signatures in cancer

2022

Abstract Background A deep understanding of carcinogenesis at the DNA level underpins many advances in cancer prevention and treatment. Mutational signatures provide a breakthrough conceptualisation, as well as an analysis framework, that can be used to build such understanding. They capture somatic mutation patterns and at best identify their causes. Most studies in this context have focused on an inherently additive analysis, e.g. by non-negative matrix factorization, where the mutations within a cancer sample are explained by a linear combination of independent mutational signatures. However, other recent studies show that the mutational signatures exhibit non-additive interactions. Resu…

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov

2019

AbstractKlebsiella oxytocacauses opportunistic human infections and post-antibiotic haemorrhagic diarrhoea. ThisEnterobacteriaceaespecies is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4, Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from,Klebsiella michiganensis(Ko1),Klebsiella oxytoca(Ko2),K. huaxiensis(Ko8) andK. grimontii(Ko6). The average nucleotide identity of Ko3 and Ko4 were 90.7% withK. huaxiensisand 95.5% withK. grimontii, respectively. In addition, three strains ofK.…

Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex

2019

14 páginas, 6 figuras

Bayesian parameter inference for cognitive simulators

2022

Additional file 1 of Identification of multiplicatively acting modulatory mutational signatures in cancer

2023

Additional file 1. Supplementary Figures.