Escherichia marmotae - a human pathogen easily misidentified as Escherichia coli

Abstract

AbstractWe hereby present the first descriptions of human invasive infections caused by Escherchia marmotae, a recently described species that encompasses the former “Escherichia cryptic clade V”. We report four cases, one acute sepsis of unknown origin, one post-operative sepsis after cholecystectomy, one spondylodiscitis and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab during six months. Through genome sequencing of the causative strains combined with available genomes from elsewhere we demonstrate E. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of non-human sources, thus indicating inherent virulence in multiple phylogenetic lineages. Pan genome analyses indicate that E. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits like genes encoding antimicrobial resistance. Reliable identification might be possible by MALDI-ToF MS, but relevant spectra are missing in commercial databases. E. marmotae can be identified through 16S rRNA sequencing. Escherichia marmotae could represent a relatively common human pathogen and improved diagnostics will provide a better understanding of its clinical importance.