Abstract
Aeromonas are Gram-negative rods widely distributed in the environment. They can cause severe infections in fish related to financial losses in the fish industry, and are considered opportunistic pathogens of humans causing infections ranging from diarrhea to septicemia. The objective of this study was to determine in silico the contribution of genomic islands to A. hydrophila. The complete genomes of 17 A. hydrophila isolates, which were separated into two phylogenetic groups, were analyzed using a genomic island (GI) predictor. The number of predicted GIs and their characteristics varied among strains. Strains from group 1, which contains mainly fish pathogens, generally have a higher number of predicted GIs, and with larger size, than strains from group 2 constituted by strains recovered from distinct sources. Only a few predicted GIs were shared among them and contained mostly genes from the core genome. Features related to virulence, metabolism, and resistance were found in the predicted GIs, but strains varied in relation to their gene content. In strains from group 1, O Ag biosynthesis clusters OX1 and OX6 were identified, while strains from group 2 each had unique clusters. Metabolic pathways for myo-inositol, L-fucose, sialic acid, and a cluster encoding QueDEC, tgtA5, and proteins related to DNA metabolism were identified in strains of group 1, which share a high number of predicted GIs. No distinctive features of group 2 strains were identified in their predicted GIs, which are more diverse and possibly better represent GIs in this species. However, some strains have several resistance attributes encoded by their predicted GIs. Several predicted GIs encode hypothetical proteins and phage proteins whose functions have not been identified but may contribute to Aeromonas fitness. In summary, features with functions identified on predicted GIs may confer advantages to host colonization and competitiveness in the environment.
Highlights
The bacterial genome is composed of a core genome containing the genetic information required for essential functions, and a flexible gene pool, which encodes additional traits that can be beneficial under certain circumstances
Strains of A. schubertii, A. veronii, A. salmonicida, A. dhakensis, A. hydrophila, A. encheleia, A. media, A. rivipollensis, A. jandaei, and A. caviae were separated into distinct branches of the phylogenetic tree according to their species
There were some exceptions, with A. veronii WP2_S18_CRE03 grouped with A. jandaei strains 3299 and 3348; A. hydrophila YL17 grouped together A. dhakensis KN_Mc_6U21, and A. hydrophila 4AK4 with A. media T0-1-19 and A. rivipollensis KN_Mc_11N1, suggesting that these strains were misidentified at the species level
Summary
The bacterial genome is composed of a core genome containing the genetic information required for essential functions, and a flexible gene pool, which encodes additional traits that can be beneficial under certain circumstances. Genomic islands are syntenic blocks of accessory genes acquired by horizontal gene transfer (HGT) which contribute to the diversification and adaptation of microorganisms and offer a selective advantage for host bacteria According to their gene content, GIs are described as pathogenicity, resistance, symbiosis, metabolic or fitness islands (Weinstock et al, 2000; Juhas et al, 2009; Rao et al, 2020). GIs usually differ from chromosomes in terms of GC content, tetranucleotide frequency, and codon usage They are often flanked by small directly repeated (DR) sequences and are often inserted into tRNA genes. Bioinformatics tools developed for GI prediction (Vernikos and Parkhill, 2006; Pundhir et al, 2008; Che et al, 2014; Soares et al, 2016; Wei et al, 2016; Bertelli et al, 2017) are available for the study of these mobile elements
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