Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp

Abstract

Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla _MOX-9 and bla _OXA-427 β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes.

Keywords: Aeromonas media; antimicrobial resistance; intrinsic–extrinsic; plasmid; virulence; whole genome sequencing.

Figure 1

Circular map showing a comparison of the genome of Aeromonas media strain SD/21–15 together with genomes retrieved from the National Center for Biotechnology Information (NCBI) public databank obtained from different host species and environmental samples from different geographical areas in the world (See Table 1). Note strain SD/21–15 (JAJVCY000000000; outermost) shows a complete circular map similar with other 25 A. media strains. Figure 1 was created in Proksee (https://proksee.ca/).

Figure 2

Heatmap/cladogram combined with phylogenetic comparison of Aeromonas media strain SD/21–15 isolated from an aquatic environment in Denmark with other strains retrieved from the National Center for Biotechnology Information (NCBI) public databank isolated from different host species and environments in the world. Note the high similarity among all 25 A. media strains with homology varying between 93 and 100%.

Figure 3

Schematic diagram of virulence genes on Aeromonas media included investigated showing (i) adherence proteins consisting of the Msh and type tap IV pili as well as the polar and lateral flagella, (ii) iron acquisition components comprising of the ferric uptake regulator (Fur), heme, and siderophore proteins, (iii) secretion system consisting of T2SS and T6SS, (iv) hemolysins consisting of hemolysin A (hylA), hemolysin III (hylIII), and thermostable heat (TH) protein, (v) biofilm and quorum sensing components consisting of S-ribosylhomocysteinase (LuxS) and MQS, (iv) Immune proteins consisting of capsule, lipopolysaccharide (LPS), and somatic O-antigen. In addition, schematic diagram shows A. media components associated with antimicrobial resistance (AMR) components consisting of (vii) efflux pumps and (viii) plasmid. Figure 3 was created in BioRender.com (https://biorender.com/).

Figure 4

Circular maps of plasmids (i) pSD/21–15 isolated from Denmark (A), (ii) pTR3_1 waste water treatment from United States (B), (iii) pR50_22 from a sludge in China (C), (iv) pMC64 from a hospital in China (D), (v) pE31 from water in China (E), and (vi) pT5-1 from a sludge in China (F). Note that the location of virulence factors, antimicrobial resistance (AMR) genes, transposases, efflux pumps, secretion system, and other genes are shown in the circular map for each the plasmid.