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Background   Aeromonas hydrophila  is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. Moreover, the potential pathogenic factors among the publicly available genomes in  A. hydrophila  strains of different origins have not yet been investigated.    Results  To identify the valid strains of  A. hydrophila  and their pathogenic factors, we performed a pan-genomic study. It revealed that there were 13 mislabelled strains and 49 valid strains that were further verified by Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and in silico multiple locus strain typing (MLST). Multiple numbers of phages were detected among the strains and among them Aeromonas phi 018 was frequently present. The diversity in type III secretion system (T3SS) and conservation of type II and type VI secretion systems (T2SS and T6SS, respectively) among all the strains are important to study for designing future strategies. The most prevalent antibiotic resistances were found to be beta-lactamase, polymyxin and colistin resistances. The comparative analyses of sequence type (ST) 251 and other ST groups revealed that there were higher numbers of virulence factors in ST-251 than in other STs group.    Conclusion  Publicly available genomes have 13 mislabelled organisms, and there are only 49 valid  A. hydrophila  strains. This valid pan-genome identifies multiple prophages that can be further utilized. Different  A. hydrophila  strains harbour multiple virulence factors and antibiotic resistance genes. Identification of such factors is important for designing future treatment regimes.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5100-4) contains supplementary material, which is available to authorized users.

Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors