Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae

Abstract

Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.

Genomic Identification of Two Phytobacter diazotrophicus Isolates from a Neonatal Intensive Care Unit in Singapore

“…Members of the genus Phytobacter (order Enterobacterales ) are isolated from the natural environment and clinical settings ( 1 , 2 ). They are known as saprobes but increasingly reported in clinical infections ( 1 , 2 ).…”

“…Members of the genus Phytobacter (order Enterobacterales ) are isolated from the natural environment and clinical settings ( 1 , 2 ). They are known as saprobes but increasingly reported in clinical infections ( 1 , 2 ). Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories ( 1 ).…”

“…They are known as saprobes but increasingly reported in clinical infections ( 1 , 2 ). Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories ( 1 ). Here, we report the identification of two Phytobacter diazotrophicus isolates using whole-genome sequencing (WGS) data.…”

Gram-negative sepsis caused by a rare pathogenPhytobacter ursingii

“…Phytobacter ursingii is a rarely encountered bacterium first categorised within the Enterobacteriaceae family in 2018 1. Since the discovery of the Phytobacter genus in 2008, there has been a growing body of evidence that species within this genus, mainly P. diazothrophicus , play a role in opportunistic nosocomial infections 2–4. Currently, there are no published case reports describing P .…”

“…ursingii infection. However, retrospective genomic analysis has confirmed P. ursingii’ s presence in a prior sepsis outbreak of contaminated intravenous fluids in 1972 and showed its potential misidentification as Pantoea agglomerans in prior outbreaks 4. This report serves to describe the first case of P. ursingii sepsis that was identified at the time of illness and may serve as a basis for the literature on clinical features, antibiotic susceptibility, prognosis for sepsis and microbiological identification pitfalls with this bacterium in the adult age group.…”