Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific β-Lactamases as Phylogenetic Markers

Abstract

Some Aeromonas species, potentially pathogenic for humans, are known to express up to three different classes of chromosomal β-lactamases, which may become hyperproduced and cause treatment failure. The aim of this study was to assess the utility of these species-specific β-lactamase genes as phylogenetic markers using whole-genome sequencing data. Core-genome alignments were generated for 36 Aeromonas genomes from seven different species and scanned for antimicrobial resistance genes. Core-genome alignment confirmed the MALDI-TOF identification of most of the isolates and re-identified an A. hydrophila isolate as A. dhakensis. Three (B, C and D) of the four Ambler classes of β-lactamase genes were found in A. sobria, A. allosacharophila, A. hydrophila and A. dhakensis (bla_CphA, bla_AmpC and bla_OXA). A. veronii only showed class-B- and class-D-like matches (bla_CphA and bla_OXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (bla_CMY, bla_MOX and bla_OXA427). The phylogenetic tree derived from concatenated sequences of β-lactamase genes successfully clustered each species. Some isolates also had resistance to sulfonamides, quinolones and aminoglycosides. Whole-genome sequencing proved to be a useful method to identify Aeromonas at the species level, which led to the unexpected identification of A. dhakensis and A.rivipollensis and revealed the resistome of each isolate.

Keywords: Aeromonas dhakensis; Aeromonas rivipollensis; FOX; MOX; beta-lactamases; cephamicinases; core-genome.

Figure 1

Maximum likelihood phylogenetic tree derived from the core-genome alignment of the Aeromonas spp. isolates and type strain genomes. All strains with names beginning with D are isolates from the laboratory. Bootstrap values above 80% are shown in branch nodes (premutation = 100). The different clusters within the phylogenetic tree contain previously identified sequences posted on GenBank. Type strain information and accession numbers are presented in Table S1.

Figure 2

UPGMA tree containing all β-lactamase resistance genes found in Aeromonas isolates. Class B β-lactamase branch is coloured in blue, Class C β-lactamase branch is coloured in green, and Class D β-lactamase branch is coloured in red. Analyses of the 65 nucleotide sequences were performed using MEGA X.