Reexamining the Association of AmpC Variants with Enterobacter Species in the Context of Updated Taxonomy

Abstract

We performed whole-genome sequencing for 17 Enterobacter clinical strains and analyzed all available Enterobacter genomes and those of its closely related genera (n = 3,389) from NCBI. The exact origins of plasmid-borne bla_CMH and bla_MIR genes are Enterobacter cloacae and Enterobacter roggenkampii, respectively, while plasmid-borne bla_ACT genes originated from multiple other Enterobacter species, including Enterobacter xiangfangensis, Enterobacter hoffmannii, Enterobacter asburiae, Enterobacter ludwigii, and Enterobacter kobei. The genus Enterobacter represents a large reservoir of plasmid-borne AmpC β-lactamase.

Keywords: AmpC; Enterobacter; taxonomy; β-lactamase.

FIG 1

A phylogenetic tree of all ACT, CMH, and MIR variants and AmpC variants of the type or reference strain of each Enterobacter species. This tree was inferred from the multialignment of amino acid sequences using IQ-TREE v2.1.2 (14) and was visualized and annotated using iTOL v6.1.2 (15). A phylogenetic tree of all Enterobacter AmpC variants and all ACT, CMH, and MIR variants is shown in Fig. S2. Amino acid sequence accession numbers of AmpC variants are indicated, and those seen in Enterobacter are also shown with the species names. Taxon refers to tentative unnamed species based on genome analysis, as the proposal of appropriate species names also needs phenotypic characterizations under current International Code of Nomenclature of Prokaryotes (17). AmpC variants from the type strain of named Enterobacter species or the reference strain from unnamed taxa are shown in red, while those that have not been identified in Enterobacter genomes are depicted in blue.