On the forces shaping diversity and adaptation in the opportunistic pathogen Serratia marcescens

Serratia marcescens is an opportunistic pathogen able to cause fatal outbreaks in intensive care units. The bacterium shows genomic flexibility and ability to colonise diverse ecological niches, with recent genomic studies proposing the existence of hospital-associated lineages. In this study, we investigated the genetic and ecological drivers underlying the species’ evolution. Comparative genomic analyses revealed a population composed of five deeply-demarcated genetic clusters, with independent adaptive trajectories emphasised by profound genetic differences and diverse isolation sources. The clusters also show limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. The clusters emergence dates back to thousands years ago, suggesting that major adaptation events long pre-dated the origin of modern hospitals. Furthermore, metagenomic investigation revealed that the hospital-associated cluster is not enriched in the human gut, possibly having a fresh/marine water reservoir. Overall, this study revisits the diversity of Serratia marcescens in light of ecological and genetic barriers. ### Competing Interest Statement The authors have declared no competing interest.