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to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy.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.

Keywords: Genomics; Identification; Phytobacter diazotrophicus; Phytobacter palmae; Phytobacter ursingii; Taxonomy.

Fig. 1

Core-genome tree, generated using EDGAR 3.0, with all available genomes of Phytobacter spp. (December 2021). Original descriptions as currently present in GenBank are indicated. Approximately maximum-likelihood phylogenetic trees were generated by aligning all core genes with MUSCLE, concatenation and tree generation with FastTree. The most optimal tree, based on 1424 genes per genome (476,326 amino acids per genome), is shown. Values at the branches are local support values computed by FastTree, using the Shimodaira–Hasegawa test. Line colours represent the different species: green: P. diazotrophicus, red: P. ursingii, blue: P. palmae, yellow: new Phytobacter sp.; purple: P. massiliensis. Type strains are indicated in bold. The origin of each strain is indicated as a dot: red, clinical; green, environmental; yellow, MAG sequence

Fig. 2

Phylogenetic tree showing the evolutionary relationship among Phytobacter species and other type species of the family Enterobacteriaceae based on 16S rRNA gene sequences (1457 bp). The tree was constructed by using the maximum likelihood method and the most optimal tree is shown. Line colours represent the different species: green: P. diazotrophicus, red: P. ursingii, blue: P. palmae, purple: P. massiliensis. Numbers at branching points are bootstrap percentage values (> 50%) based on 1000 replications. GenBank accession numbers are shown before the strain name. Bar, 0.005% nucleotide sequence difference

Fig. 3

Geographic overview of Phytobacter spp. distribution. Coloured squares and circles represent the different species for which genomes are available (Table 1): green: P. diazotrophicus, red: P. ursingii, blue: P. palmae, violet: P. massiliensis. A white “T” in the symbol represents the location of the type strain. Diamonds and triangles (orange) indicate the origins of potential findings as reported in Table 2. E: environmental isolate; H: hospital-associated isolate