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

Awan, Furqan; Dong, Yuhao; Jin, Lan; Wang, Nannan; Mushtaq, Muhammad; Chen, Lu; Liu, Yongjie

doi:10.1186/s12864-018-5100-4

Cited by 33 publications

(27 citation statements)

References 65 publications

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“…Preliminary analysis detected virulence factors similar to the genes of the type III secretion system in the seabass’ GIs as described elsewhere [66]. In addition, the analogy of prophages per genome detected in the current study, although not intact, is mentioned before in another species of the genus, A hydrophila [54,67,68]. Prophage genes are widely distributed within the aeromonads [69,70], but in the course of evolution there is a constant process of losing and acquiring such genetic material.…”

Section: Discussionsupporting

confidence: 59%

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

Smyrli

Triga

Dourala³

et al. 2019

Microorganisms

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Aeromonas veronii is an emerging pathogen causing severe pathology and mortalities in European seabass aquaculture in the Aegean Sea, Mediterranean. More than 50 strains of the pathogen were characterized biochemically and genetically in order to study the epidemiology of the disease, as well as the phylogeny and virulence of the bacterium. Based on the phenotypic characteristics, the isolates form three groups consisting of: (a) the West Aegean Sea, non-motile, non-pigment-producing strains, (b) the West Aegean Sea, motile, and pigment-producing strains and (c) the East Aegean Sea motile strains that produce minute amounts of pigment. All strains were highly similar at the genomic level; however, the pattern of West/East geographic origin was reflected in biochemical properties, in general genomic level comparison and in the putative virulent factors studied. Type VI secretion system was not detected in the western strains. The outer membrane protein (OMP) profile which contains proteins that are putative antigenic factors, was very similar between strains from the different areas. Although most of the OMPs were detected in all strains with great sequence similarity, diversification according to geographic origin was evident in known antigenic factors such as the maltoporin LamB. A systematic comparative analysis of the strains is presented and discussed in view of the emergence of A. veronii as a significant pathogen for the Mediterranean aquaculture.

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Section: Discussionsupporting

confidence: 59%

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

Smyrli

Triga

Dourala³

et al. 2019

Microorganisms

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“…were incorrectly labeled. Recently, different studies used the genomic indices to increase the correct identification of ambiguous Aeromonas strains, supporting the notion that these methods are essential in taxonomy [94][95][96].…”

Section: Genomicsmentioning

confidence: 78%

An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity

2020

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The genus Aeromonas belongs to the Aeromonadaceae family and comprises a group of Gram-negative bacteria widely distributed in aquatic environments, with some species able to cause disease in humans, fish, and other aquatic animals. However, bacteria of this genus are isolated from many other habitats, environments, and food products. The taxonomy of this genus is complex when phenotypic identification methods are used because such methods might not correctly identify all the species. On the other hand, molecular methods have proven very reliable, such as using the sequences of concatenated housekeeping genes like gyrB and rpoD or comparing the genomes with the type strains using a genomic index, such as the average nucleotide identity (ANI) or in silico DNA–DNA hybridization (isDDH). So far, 36 species have been described in the genus Aeromonas of which at least 19 are considered emerging pathogens to humans, causing a broad spectrum of infections. Having said that, when classifying 1852 strains that have been reported in various recent clinical cases, 95.4% were identified as only four species: Aeromonas caviae (37.26%), Aeromonas dhakensis (23.49%), Aeromonas veronii (21.54%), and Aeromonas hydrophila (13.07%). Since aeromonads were first associated with human disease, gastroenteritis, bacteremia, and wound infections have dominated. The literature shows that the pathogenic potential of Aeromonas is considered multifactorial and the presence of several virulence factors allows these bacteria to adhere, invade, and destroy the host cells, overcoming the immune host response. Based on current information about the ecology, epidemiology, and pathogenicity of the genus Aeromonas, we should assume that the infections these bacteria produce will remain a great health problem in the future. The ubiquitous distribution of these bacteria and the increasing elderly population, to whom these bacteria are an opportunistic pathogen, will facilitate this problem. In addition, using data from outbreak studies, it has been recognized that in cases of diarrhea, the infective dose of Aeromonas is relatively low. These poorly known bacteria should therefore be considered similarly as enteropathogens like Salmonella and Campylobacter.

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“…Recently, it was estimated that ∼18% of the organisms are misclassified in microbial genome databases 2 . This high rate of error led to investigation of misclassification of specific organisms, including Aeromonas 6 Fusobacterium 7 , and ultimately entire reference databases 2 . These studies found misclassified type strains, which calls into question the foundation of the taxonomy and inferred relatedness when population genomes are being used for epidemiological purposes, especially with rare organisms that are not well represented in the reference database.…”

Section: Introductionmentioning

confidence: 99%

Misclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies

Bandoy

Huang²,

Weimer

2019

Preprint

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Taxonomic classification is an essential step in the analysis of microbiome data that depends on a reference database of whole genome sequences. Taxonomic classifiers are built on established reference species, such as the Human Microbiome Project database, that is growing rapidly. While constructing a population wide pangenome of the bacterium Hungatella, we discovered that the Human Microbiome Project reference species Hungatella hathewayi (WAL 18680) was significantly different to other members of this genus. Specifically, the reference lacked the core genome as compared to the other members. Further analysis, using average nucleotide identity (ANI) and 16s rRNA comparisons, indicated that WAL18680 was misclassified as Hungatella. The error in classification is being amplified in the taxonomic classifiers and will have a compounding effect as microbiome analyses are done, resulting in inaccurate assignment of community members and will lead to fallacious conclusions and possibly treatment. As automated genome homology assessment expands for microbiome analysis, outbreak detection, and public health reliance on whole genomes increases this issue will likely occur at an increasing rate. These observations highlight the need for developing reference free methods for epidemiological investigation using whole genome sequences and the criticality of accurate reference databases.

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

Cited by 33 publications

References 65 publications

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

Comparative Study on A Novel Pathogen of European Seabass. Diversity of Aeromonas veronii in the Aegean Sea

An Update on the Genus Aeromonas: Taxonomy, Epidemiology, and Pathogenicity

Misclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies

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