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

Furqan Awan,Yongjie Liu,Yuhao Dong,Muhammad Hassan Mushtaq,Chengping Lu,Jin Liu,Nannan Wang

doi:10.1186/s12864-018-5100-4

Furqan Awan, Yongjie Liu + Show 5 more

Open Access

https://doi.org/10.1186/s12864-018-5100-4

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Abstract

BackgroundAeromonas 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.ResultsTo 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.ConclusionPublicly 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.

Highlights

Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen
Core and pangenome analysis of 62 strains It was revealed that there were 13 mislabelled strains included in the pan-genome of A. hydrophila (Fig. 1a)
As similar bacterial species have conserved virulence factors [3], this study showed that T2SS and Type VI secretion systems (T6SS) were conserved among the A. hydrophila strains, whereas the occurrence of Type III secretion system (T3SS) was variable among the strains

Summary

Introduction

Aeromonas hydrophila is a potential zoonotic pathogen and primary fish pathogen. With overlapping characteristics, multiple isolates are often mislabelled and misclassified. The potential pathogenic factors among the publicly available genomes in A. hydrophila strains of different origins have not yet been investigated. A. hydrophila can cause gastroenteritis, necrotizing fasciitis, septicaemia and meningitis [2]. It has multifactorial virulence factors, such as type III, type IV and type VI secretion systems (T3SS, T4SS and T6SS, respectively), exotoxins and endotoxins [3]. Aeromonas species have dynamic characteristics and are hard to classify into defined taxonomic groups [1]. This overlapping classification has caused a great deal of ambiguity among A. hydrophila strains [3]. Traditional classification of A. hydrophila is based on multiple hybridization groups (HGs), 16S

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