Journal Article

Adaptation of host transmission cycle during Clostridium difficile speciation

Harcourt, Katherine, Kumar, Nitin, Lawley, Trevor D., Browne, Hilary P., Kuijper, Ed J., Wieler, Lothar H., Forster, Samuel C., Pirmohamed, Munir, Dougan, Gordon, Norén, Torbjörn, Stares, Mark D., Riley, Thomas V., Hargreaves, Katherine R., Seyboldt, Christian, Clokie, Martha R. J., Fairley, Derek J., Ip, Margaret, Wren, Brendan W., Clare, Simon, Viciani, Elisa, Roberts, Paul, Jensen, Mie Birgitte Frid

2019

Overview

Bacterial speciation is a fundamental evolutionary process characterized by diverging genotypic and phenotypic properties. However, the selective forces that affect genetic adaptations and how they relate to the biological changes that underpin the formation of a new bacterial species remain poorly understood. Here, we show that the spore-forming, healthcare-associated enteropathogen Clostridium difficile is actively undergoing speciation. Through large-scale genomic analysis of 906 strains, we demonstrate that the ongoing speciation process is linked to positive selection on core genes in the newly forming species that are involved in sporulation and the metabolism of simple dietary sugars. Functional validation shows that the new C. difficile produces spores that are more resistant and have increased sporulation and host colonization capacity when glucose or fructose is available for metabolism. Thus, we report the formation of an emerging C. difficil e species, selected for metabolizing simple dietary sugars and producing high levels of resistant spores, that is adapted for healthcare-mediated transmission. Genomic analysis of 906 Clostridium difficile strains shows that this enteropathogen is undergoing speciation, which is linked to the selection of genes involved in sporulation and in the metabolism of simple dietary sugars.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 45 / 45/23 / 631/326 / 631/326/1320 / 631/326/325 / 64 / 64/60 / Acclimatization - genetics / Acids / Adaptation / Agriculture / Animal Genetics and Genomics / Anti-Bacterial Agents - pharmacology / Bacteria / Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Carbohydrate metabolism / Clostridioides difficile - genetics / Clostridioides difficile - isolation & purification / Clostridium difficile / Clostridium Infections - metabolism / Clostridium Infections - microbiology / Clostridium Infections - transmission / Colonization / Diet therapy / Discriminant analysis / Disease transmission / Fructose / Gene Function / Genes / Genetic aspects / Genetic Speciation / Genome, Bacterial / Genomes / Genomic analysis / Genomics / Harbors / Health aspects / Health care / Human Genetics / Humans / Letter / Metabolism / Phylogenetics / Positive selection / Software / Speciation / Species / Spores / Spores, Bacterial - drug effects / Spores, Bacterial - genetics / Spores, Bacterial - growth & development / Spores, Bacterial - metabolism / Sporulation / Sugar / Sugar-free diet / Sugars - metabolism / Virulence - genetics