Aeromonas rivipollensis sp. nov., a novel species isolated from aquatic samples

Occurrence of Aeromonas Species in the Cutaneous Mucus of Barbour’s Seahorses (Hippocampus barbouri) as Revealed by High-Throughput Sequencing

Although several studies have described the bacterial community composition associated with marine fish, there is limited information related to seahorses. Moreover, previous studies have demonstrated that the skin microbiota is useful for determining health status and common disorders in the host. This study, therefore, aimed to explore the skin bacterial community composition in Barbour’s seahorse (Hippocampus barbouri) using high-throughput sequencing of 16S ribosomal RNA genes. Water and sediment samples from the surrounding environment were also analyzed for comparative purposes. The results revealed that sequences affiliated with the Shewanellaceae family were dominant in the skin of female Barbour’s seahorses and sediment samples, whereas sequences affiliated with the Bacillaceae family were dominant in the skin of male Barbour’s seahorses. Interestingly, sequences affiliated with the Aeromonas genus were found in the skin of Barbour’s seahorses, whose abundance was slightly similar between the female and male specimens. Further comparative analysis showed that the presence of Aeromonas species in the skin of Barbour’s seahorses was strongly influenced by the surrounding sediment. Given that some Aeromonas species are known to be important pathogens in humans and fish, these results may be used for further research on the dependency of the skin microbial composition on the environment as well as determine whether the presence of Aeromonas and other detected species has implications on seahorse health.

Comparative Genomics Revealed a Potential Threat of Aeromonas rivipollensis G87 Strain and Its Antibiotic Resistance

Aeromonas rivipollensis is an emerging pathogen linked to a broad range of infections in humans. Due to the inability to accurately differentiate Aeromonas species using conventional techniques, in-depth comparative genomics analysis is imperative to identify them. This study characterized 4 A. rivipollensis strains that were isolated from river water in Johannesburg, South Africa, by whole-genome sequencing (WGS). WGS was carried out, and taxonomic classification was employed to profile virulence and antibiotic resistance (AR). The AR profiles of the A. rivipollensis genomes consisted of betalactams and cephalosporin-resistance genes, while the tetracycline-resistance gene (tetE) was only determined to be in the G87 strain. A mobile genetic element (MGE), transposons TnC, was determined to be in this strain that mediates tetracycline resistance MFS efflux tetE. A pangenomic investigation revealed the G87 strain's unique characteristic, which included immunoglobulin A-binding proteins, extracellular polysialic acid, and exogenous sialic acid as virulence factors. The identified polysialic acid and sialic acid genes can be associated with antiphagocytic and antibactericidal properties, respectively. MGEs such as transposases introduce virulence and AR genes in the A. rivipollensis G87 genome. This study showed that A. rivipollensis is generally resistant to a class of beta-lactams and cephalosporins. MGEs pose a challenge in some of the Aeromonas species strains and are subjected to antibiotics resistance and the acquisition of virulence genes in the ecosystem.

The Isolation of Aeromonas Species and Other Common Enteric Bacterial Pathogens from Patients with Gastroenteritis in an Australian Population

Aeromonas species are emerging human enteric pathogens. However, systematic analysis of Aeromonas species infection in human gastroenteritis in comparison with other enteric bacterial pathogens in the Australian population is lacking. Here we analysed the isolation of Aeromonas species and other bacterial pathogens in five consecutive years (2015–2019) from 375,842 stool samples of patients with gastroenteritis in a large Australian diagnostic laboratory and identified a subset (48 isolates) of Aeromonas isolates to species level, using multilocus phylogenetic analysis. Aeromonas species were the third most common bacterial pathogens, following Campylobacter and Salmonella species. Aeromonas infection rate was significantly correlated with increasing age (p < 0.001). Aeromonas species were more often isolated in warm seasons and in males than females (p < 0.001). Five Aeromonas species were identified. Most of the infections were from three species, namely Aeromonas veronii (52%), Aeromonas caviae (27%) and Aeromonas hydrophila (12.5%). The majority of patients with Aeromonas species infection did not have a documented overseas travel history. The findings from this study support the importance of Aeromonas species in human gastroenteritis and suggest that the sources of Aeromonas infection in Australian patients should be further investigated.

Taxonomic Identification of Different Species of the Genus Aeromonas by Whole-Genome Sequencing and Use of Their Species-Specific β-Lactamases as Phylogenetic Markers

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 (bla_CphA, bla_AmpC and bla_OXA). A. veronii only showed class-B- and class-D-like matches (bla_CphA and bla_OXA), whereas those for A. media, A. rivipollensis and A. caviae were class C and D (bla_CMY, bla_MOX and bla_OXA427). 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.

Identification of Emerging Hazards in Mussels by the Galician Emerging Food Safety Risks Network (RISEGAL). A First Approach

Emerging risk identification is a priority for the European Food Safety Authority (EFSA). The goal of the Galician Emerging Food Safety Risks Network (RISEGAL) is the identification of emerging risks in foods produced and commercialized in Galicia (northwest Spain) in order to propose prevention plans and mitigation strategies. In this work, RISEGAL applied a systematic approach for the identification of emerging food safety risks potentially affecting bivalve shellfish. First, a comprehensive review of scientific databases was carried out to identify hazards most quoted as emerging in bivalves in the period 2016-2018. Then, identified hazards were semiquantitatively assessed by a panel of food safety experts, who scored them accordingly with the five evaluation criteria proposed by EFSA: novelty, soundness, imminence, scale, and severity. Scores determined that perfluorinated compounds, antimicrobial resistance, Vibrio parahaemolyticus, hepatitis E virus (HEV), and antimicrobial residues are the emerging hazards that are considered most imminent and severe and that could cause safety problems of the highest scale in the bivalve value chain by the majority of the experts consulted (75%). Finally, in a preliminary way, an exploratory study carried out in the Galician Rías highlighted the presence of HEV in mussels cultivated in class B production areas.

Eobania vermiculata as a potential indicator of nitrate contamination in soil

The effects of nitrates were analysed on the land snail Eobania vermiculata, a good bioindicator to assess the effects of certain pollutants in soil. It is known that the molluscs are very sensitive to contamination substances and can be used as sentinel organism for environmental pollution assessment. The nitrates are present in fertilizers and in food additives and their excess can not only be harmful to the environment but also dangerous for the humans. Indeed, in the mammals the nitrates are converted into nitrites and can cause a series of complications as the formation of methaemoglobin and cancers. In this study, adult organisms of E. vermiculata were exposed to soil containing 2000 mg/L of nitrates for 30 days to evaluate the stool microbiome and the histological changes at the level of the foot. Eggs of these snails were similarly treated to observe their hatching, survival and development. Histological changes were observed at level of the foot of adult snails exposed to nitrate and in their stools was evident an increase of bacteria, especially those that have a high ability to exploit nitrates and nitrogen as nutrients. Instead, the treated eggs showed changes in hatching, hypopigmentation of newborn snails and a decrease of their survival in time. The overall information obtained from these endpoints can provide important information regarding the quality of the environment. In addition, they also showed that the invertebrate organism E. vermiculata despite being a simple organism is very useful and efficient for ecotoxicological studies.

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

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.

Molecular Identification and Virulence Potential of the Genus Aeromonas Isolated from Wild Rainbow Trout (Oncorhynchus mykiss) in Mexico

The members of the Aeromonas genus are important foodborne pathogens, with a worldwide distribution. Wild rainbow trout, from the national protected area Santuario del Agua State Park, Corral de Piedra, were analyzed. Species of Aeromonas were isolated from the trout, and their pathogenic potential was analyzed based on different pathogenicity and virulence factors. The isolates were identified as A. allosaccharophila (n = 15), A. sobria (n = 8), A. veronii (n = 3), A. rivipollensis (n = 2), A. piscicola (n = 2), and A. popoffii (n = 1), by RNA polymerase sigma factor (rpoD) gene sequencing. Sequence similarity with the type strain was 92.2 to 99.6% for A. sobria isolates, 97.8 to 98.0% for A. allosaccharophila isolates, 99.2% for the A. popoffii isolate, 99.2 to 100% for A. piscicola isolates, and 98.2 to 99.2% for A. veronii isolates. Notably, isolates A30T2-gills and A30T2-spleen showed sequence similarity of 98.0% with strain A. media CECT 4232T and 99.0% with strain A. rivipollensis P2G1T. Virulence genes were detected by PCR at the following frequencies: fla and serine protease, 96.77%; aerA, 93.54%; aexT, 87.09%; lipases, 74.19%; ascV and ahyB, 67.74%; exu, 61.29%; act, 41.93%; ascF-G, 38.70%; lafA, 32.26%; alt, 6.46%; aopP, 9.67%; and ast, 3.23%. These results indicate that several Aeromonas species had the potential pathogenicity to infect wild rainbow trout in the waterway created by the Corral de Piedra dam, suggesting they could be an emerging zoonotic pathogen.

The Significance of Mesophilic Aeromonas spp. in Minimally Processed Ready-to-Eat Seafood

Minimally processed and ready-to-eat (RTE) seafood products are gaining popularity because of their availability in retail stores and the consumers' perception of convenience. Products that are subjected to mild processing and products that do not require additional heating prior to consumption are eaten by an increasing proportion of the population, including people that are more susceptible to foodborne disease. Worldwide, seafood is an important source of foodborne outbreaks, but the exact burden is not known. The increased interest in seafood products for raw consumption introduces new food safety issues that must be addressed by all actors in the food chain. Bacteria belonging to genus Aeromonas are ubiquitous in marine environments, and Aeromonas spp. has held the title "emerging foodborne pathogen" for more than a decade. Given its high prevalence in seafood and in vegetables included in many RTE seafood meals, the significance of Aeromonas as a potential foodborne pathogen and a food spoilage organism increases. Some Aeromonas spp. can grow relatively uninhibited in food during refrigeration under a broad range of pH and NaCl concentrations, and in various packaging atmospheres. Strains of several Aeromonas species have shown spoilage potential by the production of spoilage associated metabolites in various seafood products, but the knowledge on spoilage in cold water fish species is scarce. The question about the significance of Aeromonas spp. in RTE seafood products is challenged by the limited knowledge on how to identify the truly virulent strains. The limited information on clinically relevant strains is partly due to few registered outbreaks, and to the disputed role as a true foodborne pathogen. However, it is likely that illness caused by Aeromonas might go on undetected due to unreported cases and a lack of adequate identification schemes. A rather confusing taxonomy and inadequate biochemical tests for species identification has led to a biased focus towards some Aeromonas species. Over the last ten years, several housekeeping genes has replaced the 16S rRNA gene as suitable genetic markers for phylogenetic analysis. The result is a more clear and robust taxonomy and updated knowledge on the currently circulating environmental strains. Nevertheless, more knowledge on which factors that contribute to virulence and how to control the potential pathogenic strains of Aeromonas in perishable RTE seafood products are needed.

Complete Genome Sequence of Aeromonas rivipollensis KN-Mc-11N1, Isolated from a Wild Nutria (Myocastor coypus) in South Korea

We report here the complete genome sequence of Aeromonas rivipollensis KN-Mc-11N1, which was isolated from a wild nutria (Myocastor coypus) in South Korea. Genomic analysis indicated that A. rivipollensis may have zoonotic potential similar to that of other aeromonads, and nutria could be one of the sources of transmission of zoonotic pathogens to humans.

Simultaneous nitrogen and organics removal using membrane aeration and effluent ultrafiltration in an anaerobic fluidized membrane bioreactor

Dissolved methane and a lack of nutrient removal are two concerns for treatment of wastewater using anaerobic fluidized bed membrane bioreactors (AFMBRs). Membrane aerators were integrated into an AFMBR to form an aeration membrane fluidized bed membrane bioreactor (AeMFMBR) capable of simultaneous removal of organic matter and ammonia without production of dissolved methane. Good effluent quality was obtained with no detectable suspended solids, 93±5% of chemical oxygen demand (COD) removal to 14±11mg/L, and 74±8% of total ammonia (TA) removal to 12±3mg-N/L for domestic wastewater (COD of 193±23mg/L and TA of 49±5mg-N/L) treatment. Nitrate and nitrite concentrations were always low (<1mg-N/L) during continuous flow treatment. Membrane fouling was well controlled by fluidization of the granular activated carbon (GAC) particles (transmembrane pressures maintained <3kPa). Analysis of the microbial communities suggested that nitrogen removal was due to nitrification and denitrification based on the presence of microorganisms associated with these processes.

Distinct Aeromonas Populations in Water Column and Associated with Copepods from Estuarine Environment (Seine, France)

Aeromonas spp. are ubiquitous bacteria primarily recovered from aquatic ecosystems. They are found in fresh water as well as estuarine and marine waters, and in association with numerous autochthonous aquatic organisms in these environments. However, aeromonads are also etiologic agents of fish diseases and are now recognized as emerging pathogens in humans. The estuary is therefore a key environment, harboring autochthonous aeromonads, and aeromonads originating from humans and animals, mainly released by treated WWTP effluent or watershed run-off via tributaries. The present study compares the abundance and the diversity of Aeromonas populations. Over 2 years of monitoring (eight campaigns from February 2013 to November 2015), the occurrence of Aeromonas was investigated within the water column (water and fluid mud) and in association with copepods. Moreover, the diversity of Aeromonas populations was ascertained by analyzing gyrB and radA sequences, and the antibiotic-resistance phenotypes were determined using the disk diffusion method. This study shows, for the first time, the presence of Aeromonas spp. in water (1.1 × 10² to 1.2 ± 0.3 × 10³ CFU.100 mL^-1), fluid mud (2.6 ± 2.6 × 10² to 9.8 ± 0.9 × 10³ CFU.g^-1) and in association with living copepods (1.9 ± 0.7 × 10² to >1.1 × 10⁴ CFU.g^-1) in the Seine estuary. Moreover, the diversity study, conducted on 36 strains isolated from the water column and 47 strains isolated from copepods, indicates distinct populations within these two compartments. Strains distributed in five clusters corresponding to A. bestiarum (n = 6; 5.45%), A. encheleia (n = 1; 0.91%), A. media (n = 22; 20.0%), A. rivipollensis (n = 34; 30.91%) and A. salmonicida (n = 47; 42.73%). A. salmonicida is the most abundant species associated with Eurytemora affinis (n = 35; 74.47%). In contrast, A. salmonicida accounts for only 30.56% (n = 11) of isolates in the water column. This study shows the coexistence of distinct populations of Aeromonas in the oligohaline area of an anthropized estuary. Moreover, A. media, a putative human pathogen, present in the water column and abundant in the WWTP samples, was not detected in association with living copepods.

Assessment of MultiLocus Sequence Analysis As a Valuable Tool for the Classification of the Genus Salinivibrio

The genus Salinivibrio includes obligatory halophilic bacteria and is commonly isolated from hypersaline habitats and salted food products. They grow optimally between 7.5 and 10% salts and are facultative anaerobes. Currently, this genus comprises four species, one of them, S. costicola, with three subspecies. In this study we isolated and characterized an additional 70 strains from solar salterns located in different locations. Comparative 16S rRNA gene sequence analysis identified these strains as belonging to the genus Salinivibrio but could not differentiate strains into species-like groups. To achieve finer phylogenetic resolution, we carried out a MultiLocus Sequence Analysis (MLSA) of the new isolates and the type strains of the species of Salinivibrio based on the individual as well as concatenated sequences of four housekeeping genes: gyrB, recA, rpoA, and rpoD. The strains formed four clearly differentiated species-like clusters called phylogroups. All of the known type and subspecies strains were associated with one of these clusters except S. sharmensis. One phylogroup had no previously described species coupled to it. Further DNA–DNA hybridization (DDH) experiments with selected representative strains from these phylogroups permitted us to validate the MLSA study, correlating the species level defined by the DDH (70%) with a 97% cut-off for the concatenated MLSA gene sequences. Based on these criteria, the novel strains forming phylogroup 1 could constitute a new species while strains constructing the other three phylogroups are members of previously recognized Salinivibrio species. S. costicola subsp. vallismortis co-occurs with S. proteolyticus in phylogroup 4, and separately from other S. costicola strains, indicating its need for reclassification. On the other hand, genome fingerprinting analysis showed that the environmental strains do not form clonal populations and did not cluster according to their site of cultivation. In future studies regarding the classification and identification of new Salinivibrio strains we recommend the following strategy: (i) initial partial sequencing of the 16S rRNA gene for genus-level identification; (ii) sequencing and concatenation of the four before mentioned housekeeping genes for species-level discrimination; (iii) DDH experiments, only required when the concatenated MLSA similarity values among a new isolate and other Salinivibrio strains are above the 97% cut-off.

Delineation of Taxonomic Species within Complex of Species: Aeromonas media and Related Species as a Test Case

Aeromonas media is an opportunistic pathogen for human and animals mainly found in aquatic habitats and which has been noted for significant genomic and phenotypic heterogeneities. We aimed to better understand the population structure and diversity of strains currently affiliated to A. media and the related species A. rivipollensis. Forty-one strains were included in a population study integrating, multilocus genetics, phylogenetics, comparative genomics, as well as phenotypics, lifestyle, and evolutionary features. Sixteen gene-based multilocus phylogeny delineated three clades. Clades corresponded to different genomic groups or genomospecies defined by phylogenomic metrics ANI (average nucleotide identity) and isDDH (in silico DNA-DNA hybridization) on 14 whole genome sequences. DL-lactate utilization, cefoxitin susceptibility, nucleotide signatures, ribosomal multi-operon diversity, and differences in relative effect of recombination and mutation (i.e., in evolution mode) distinguished the two species Aeromonas media and Aeromonas rivipollensis. The description of these two species was emended accordingly. The genome metrics and comparative genomics suggested that a third clade is a distinct genomospecies. Beside the species delineation, genetic and genomic data analysis provided a more comprehensive knowledge of the cladogenesis determinants at the root and inside A. media species complex among aeromonads. Particular lifestyles and phenotypes as well as major differences in evolution modes may represent putative factors associated with lineage emergence and speciation within the A. media complex. Finally, the integrative and populational approach presented in this study is considered broadly in order to conciliate the delineation of taxonomic species and the population structure in bacterial genera organized in species complexes.

'Aeromonas intestinalis' and 'Aeromonas enterica' isolated from human faeces, 'Aeromonas crassostreae' from oyster and 'Aeromonas aquatilis' isolated from lake water represent novel species

Four Aeromonas strains from clinical and environmental samples differed from known species on the basis of rpoD gene sequence. Multilocus phylogenetic analysis and in silico DNA-DNA hybridization confirmed them as four new species even though their 16S rRNA gene sequence similarity with their closest relatives was >98.7%, as occurred for other Aeromonas spp.