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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the

Tomoyuki Ono1,2, Itsuki Taniguchi1, Keiji Nakamura1

  • 1Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, 812-8582, Japan.

Microbial Genomics
|March 22, 2022
PubMed

Insights

Multidrug-resistant Serratia marcescens strains are a global threat. Genomic analysis reveals hospital-adapted lineages (clades 1 and 2) with numerous antimicrobial resistance genes, distinct from environmental strains.

Area of Science:

  • Microbiology
  • Genomics
  • Evolutionary Biology

Background:

  • Serratia marcescens is a significant nosocomial pathogen responsible for opportunistic infections and hospital outbreaks.
  • The emergence of multidrug-resistant (MDR) strains presents a growing public health concern.
  • Genomic distinctions between clinical and environmental S. marcescens isolates and related species remain unclear.

Purpose of the Study:

  • To conduct a large-scale genome analysis of the S. marcescens complex, including clinical and environmental strains.
  • To elucidate phylogenetic relationships, population structure, and genomic variations within the S. marcescens complex.
  • To identify potential hospital-adapted lineages and understand the genetic basis of antimicrobial resistance.

Main Methods:

  • Whole-genome sequencing of over 200 clinical and environmental S. marcescens complex strains.
  • Phylogenetic analysis based on whole-genome average nucleotide identity to define clades.
  • Comparative genomic analysis to assess genome size, GC content, and mobile genetic element acquisition.

Main Results:

  • The S. marcescens complex comprises 14 distinct clades, with specific clades identified as S. nematodiphila, S. marcescens sensu stricto, S. ureilytica, and S. surfactantfaciens.
  • Genome size and GC content varied across clades, negatively correlated and influenced by mobile genetic elements like plasmids and prophages.
  • Clades 1 and 2, predominantly clinical/hospital isolates, possess extensive antimicrobial resistance genes and fluoroquinolone resistance mutations, indicating MDR potential and hospital adaptation.

Conclusions:

  • Genomic analysis provides a framework for reclassifying the S. marcescens complex.
  • Hospital-adapted lineages (clades 1 and 2) have accumulated significant antimicrobial resistance genes.
  • These findings offer insights into the evolution, biology, and clinical relevance of S. marcescens complex bacteria.
Keywords:
Serratia marcescens complexantimicrobial resistancegenomicshospital-adapted lineagepopulation structure

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