Open AccessGlobal population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex
Author(s) -
Tomoyuki Ono,
Itsuki Taniguchi,
Keiji Nakamura,
Débora Satie Nagano,
Ruriko Nishida,
Yasuhiro Gotoh,
Yoshitoshi Ogura,
Mitsuhiko Sato,
Atsushi Iguchi,
Kazunori Murase,
Dai Yoshimura,
Takehiko Itoh,
Ayaka Shima,
Damien Dubois,
Éric Oswald,
Akira Shiose,
Naomasa Gotoh,
Tetsuya Hayashi
Publication year - 2022
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.476
H-Index - 28
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000793
Subject(s) - serratia marcescens , biology , clade , mobile genetic elements , prophage , genome , population , phylogenetic tree , genetics , horizontal gene transfer , microbiology and biotechnology , gene , bacteriophage , escherichia coli , medicine , environmental health
Serratia marcescens is an important nosocomial pathogen causing various opportunistic infections, such as urinary tract infections, bacteremia and sometimes even hospital outbreaks. The recent emergence and spread of multidrug-resistant (MDR) strains further pose serious threats to global public health. This bacterium is also ubiquitously found in natural environments, but the genomic differences between clinical and environmental isolates are not clear, including those between S. marcescens and its close relatives. In this study, we performed a large-scale genome analysis of S. marcescens and closely related species (referred to as the ‘ S. marcescens complex’), including more than 200 clinical and environmental strains newly sequenced here. Our analysis revealed their phylogenetic relationships and complex global population structure, comprising 14 clades, which were defined based on whole-genome average nucleotide identity. Clades 10, 11, 12 and 13 corresponded to S. nematodiphila , S. marcescens sensu stricto , S. ureilytica and S. surfactantfaciens , respectively. Several clades exhibited distinct genome sizes and GC contents and a negative correlation of these genomic parameters was observed in each clade, which was associated with the acquisition of mobile genetic elements (MGEs), but different types of MGEs, plasmids or prophages (and other integrative elements), were found to contribute to the generation of these genomic variations. Importantly, clades 1 and 2 mostly comprised clinical or hospital environment isolates and accumulated a wide range of antimicrobial resistance genes, including various extended-spectrum β-lactamase and carbapenemase genes, and fluoroquinolone target site mutations, leading to a high proportion of MDR strains. This finding suggests that clades 1 and 2 represent hospital-adapted lineages in the S. marcescens complex although their potential virulence is currently unknown. These data provide an important genomic basis for reconsidering the classification of this group of bacteria and reveal novel insights into their evolution, biology and differential importance in clinical settings.