Vol.:(0123456789) 1 3 https://doi.org/10.1007/s10096-022-04413-8 REVIEW Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae Theo H. M. Smits 1  · Lavinia N. V. S. Arend 2  · Sofa Cardew 3  · Erika Tång‑Hallbäck 4  · Marcelo T. Mira 5  · Edward R. B. Moore 6,3  · Jorge L. M. Sampaio 7  · Fabio Rezzonico 1  · Marcelo Pillonetto 2,5 Received: 2 November 2021 / Accepted: 25 January 2022 © The Author(s) 2022 Abstract Although many clinically signifcant 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 classifcation and for which proper identifcation remains challenging. With the current improvements in the feld 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to identify past recurrences of a specifc organism, particularly those originally published under an incorrect or outdated taxonomy.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 identifcation 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 Phytobacter diazotrophicus · Phytobacter ursingii · Phytobacter palmae · Genomics · Identifcation · Taxonomy Introduction The taxonomy of Enterobacteriaceae, since its establish- ment and valid publication in the Approved Lists of Bacte- rial Names in 1980 [1], has been prone to constant updates, revisions and corrections [2, 3]. Over the years, many novel genus and species names have been validly published. Since about 1985, the use of improved molecular tools such as PCR, 16S rRNA gene and multi-locus sequence analysis (MLSA) has led to a more stable taxonomy [4]. It has been only in the last 10 years that genome-based taxonomic studies and the use of average nucleotide identities (ANI) [5] and digital DNA-DNA hybridization (dDDH) [6] have enabled reliable delineation and detailed analysis of the diferent taxa, at the species-level, and giving rise in 2016 to the revision of the Enterobacteriaceae, with the creation of several sister fami- lies, like the Erwiniaceae or Pectobacteriaceae [2]. A more detailed analysis has shown six distinct phylogenomic-based * Theo H. M. Smits theo.smits@zhaw.ch * Marcelo Pillonetto m.pilonetto@pucpr.br 1 Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland 2 Central Public Health Laboratory – State of Paraná – LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil 3 Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden 4 Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden 5 Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil 6 Department of Infectious Disease, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden 7 Faculdade de Ciências Farmacêuticas - University of São Paulo and Fleury Medicina Diagnóstica, São Paulo, SP, Brazil / Published online: 15 February 2022 European Journal of Clinical Microbiology & Infectious Diseases (2022) 41:547–558