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 (blaCphA, blaAmpC and blaOXA). A. veronii only showed class-B- and class-D-like matches (blaCphA and blaOXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (blaCMY, blaMOX and blaOXA427). 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.

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

“…examined in this study could be that they intrinsically are encoded in the genomes. Despite so, suffice to point out that the MBL genes detected in this study have been reported from different bacteria species isolated from humans, animals, fish, chickens, mussel and the environments in different countries ( Maravić et al, 2013 ; Bottoni et al, 2015 ; Hilt et al, 2020 ; Ramsamy et al, 2020 ; Bertran et al, 2021 ; Wang Y. et al, 2021 ). Thus, it is likely that these AMR genes exist in other bacteria species in different aquatic environments and a wide range of host species in India.…”

“…from reservoir water in Singapore (Zhong et al, 2021), A. media in Nebraska watershed (Donner et al, 2022), A. salmonicida from Atlantic salmon (Salmo salar L) in Chile (Vásquez-Ponce et al, 2022), and pork processing plant in Spain (Cobo-Díaz et al, 2021). Similarly, bla OXA-724 has been detected from A. dhakensis isolated from humans in Spain (Bertran et al, 2021), A. hydrophila from pigs in South Africa (Ramsamy et al, 2021) as well as A. jandaei and A. hydrophila from chicken and , while in the present study it was found in A. hydrophila from carp and A. veronii from sardine from India. bla OXA-72 has been detected from Acinetobacter baumannii in humans where it has been associated with pneumonia, septic shock, and respiratory failure (Jia et al, 2019).…”

“…isolated from humans, pigs, catfish, chicken, frogs, mullet and the environment while bla AQU-2 has been reported from Aeromonas spp. isolated from humans and chicken in different countries ( Walsh et al, 1997 ; Ramadan et al, 2018 ; Seo and Lee, 2018 ; Wang et al, 2019 ; Bertran et al, 2021 ; Kimera et al, 2021 ; Wang Y. et al, 2021 ). Similarly, bla FOX-2 , bla FOX- 4 , bla FOX- 5 and bla MOX-7 , have been detected from different bacteria species including Aeromonas spp.…”

Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary

“…Nonetheless, in certain cases such associations may be established with sufficient confidence, such as for linking the cphA4 carbapenemase and the ampS β-lactamase genes detected in the carp intestinal microbiome with Aeromonas spp. [ 51 , 52 ], or the association of the bla ACI-1 β-lactamase gene (at 100% coverage and 100% identity) with the anaerobic coccus Acidaminococcus intestinii ( Acidaminococcaceae ) in the pig fecal microbiome [ 53 , 54 ] ( Supplementary Table S3 ). Moreover, BLASTN searches of metagenomic contigs in some further cases also yielded database hits with both the coverage and identity at >99% and coupled with a specific bacterial genus for the highest alignment scores.…”

“…strains highlighted the role of water as a vehicle for the dissemination of the qnrS -resistance determinants [ 74 ], similar to the environment of fish production in aquaculture. Indeed, two of the ARGs that were detected only in the carp intestine in the current study, cphA4 and ampS , are characteristic ARGs of Aeromonas spp., an important genus for fish-pathogenic bacteria [ 52 ].…”