Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea

Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater

A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2^T, was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2^T was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2^T was closely related to Arcobacter lekithochrous LFT 1.7^T and Arcobacter caeni RW17-10^T(95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2^T was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2^T represents a new Arcobacter species. The predominant fatty acids were C_16 : 1 ω7c/C_16 : 1 ω6c and C_18 : 1 ω7c/C_18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2^T as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2^T (DSM 29169^T=KCTC 52423^T).

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Prevalence, resistance to antimicrobials, and antibiotypes of Arcobacter species recovered from retail meat in Wasit marketplaces in Iraq

Background and Aim: Arcobacter is a food-borne pathogen associated with human and animal infections. In Iraq, these infections and their adverse effects on public health have not been well investigated. For this reason, as well as to submit data on the resistance to antimicrobials and antibiotypes of the Arcobacter spp. and their occurrence in retail meat in the Wasit marketplaces, this study was undertaken. Materials and Methods: A total of 83 samples of fresh raw (n=35) and chilled meat (n=48) were purchased randomly from marketplaces in various regions of the Wasit Governorate. Bacterial detection was conducted using cultural methods, biochemical analysis, and the Oxoid Biomedical Identification System Campy. Confirmation of these bacteria at the species level was performed using the multiplex polymerase chain reaction method. Susceptibility of the Arcobacter spp. to antimicrobials was investigated in 11 isolates comprising Arcobacter butzleri (n=9) and Arcobacter cryaerophilus (n=2) using the Kirby–Bauer disk diffusion method. Results: A total of 32 (38.6%) of the 83 fresh raw and chilled meat samples tested positive for Arcobacter spp.; of those, 27 (84.4%) and 5 (15.6%) were recognized as A. butzleri and A. cryaerophilus, respectively. Maximum resistance was perceived, respectively, to tetracycline, erythromycin, and ampicillin (90.9%, 81.8%, and 81.8%, respectively). In contrast, a low resistance rate against fluoroquinolones up to 9.09% was found. Antibiograms of the A. butzleri and A. cryaerophilus isolates yielded ten antibiotypes. The vast majority of the isolates (90.91%) were resistant to no fewer than three classes of antimicrobials, and 27.3% of these showed resistance to six antibiotics. A total of 91% of the analyzed isolates had a multiple antibiotic resistance index score between 0.27 and 0.73. Conclusion: Our outcomes demonstrated that retail meat can be a prospective vehicle for pathogenic Arcobacter, making these products a possible risk to human health. Our outcomes postulate that the contamination of retail meats by pathogenic Arcobacter is a global public health concern, particularly with the growing resistance to life-saving drugs, and emphasizes consumer understanding about the quality and safety of these products. To achieve healthy food products, good management practices, and successful control approaches must be implemented across the entire food chain, not only to protect consumers from these contaminants but also to minimize the risk of drug resistance.

Aliarcobacter vitoriensis sp. nov., isolated from carrot and urban wastewater

Two isolates, one recovered from a carrot and another one from urban wastewater, were characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates clustered together, and were most closely related to Aliarcobacter lanthieri. Multilocus phylogenetic analysis (MLPA) using the concatenated sequences of five housekeeping genes (atpA, gyrA, gyrB, hsp60 and rpoB) suggested that these isolates formed a distinct phylogenetic lineage among the genera derived from the former genus Arcobacter. Whole-genome sequence, in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) value between the genome of strain F199^T and those of related species confirmed that these isolates represent a novel species. These strains can be differentiated from its phylogenetically closest species A. lanthieri by its inability to growth on 1% glycine and by their enzyme activity of esterase lipase (C8) and acid phosphatase. Our results, by the application of a polyphasic analysis, confirmed that these two isolates represent a novel species of the genus Aliarcobacter, for which the name Aliarcobacter vitoriensis sp. nov. is proposed. The type strain is F199^T (=CECT 9230^T=LMG 30050^T).

Dynamics of the Pacific oyster pathobiota during mortality episodes in Europe assessed by 16S rRNA gene profiling and a new target enrichment next-generation sequencing strategy

Infectious agents such as the bacteria Vibrio aestuarianus or Ostreid herpesvirus 1 have been repeatedly associated with dramatic disease outbreaks of Crassostrea gigas beds in Europe. Beside roles played by these pathogens, microbial infections in C. gigas may derive from the contribution of a larger number of microorganisms than previously thought, according to an emerging view supporting the polymicrobial nature of bivalve diseases. In this study, the microbial communities associated with a large number of C. gigas samples collected during recurrent mortality episodes at different European sites were investigated by real-time PCR and 16SrRNA gene-based microbial profiling. A new target enrichment next-generation sequencing protocol for selective capturing of 884 phylogenetic and virulence markers of the potential microbial pathogenic community in oyster tissue was developed allowing high taxonomic resolution analysis of the bivalve pathobiota. Comparative analysis of contrasting C. gigas samples conducted using these methods revealed that oyster experiencing mortality outbreaks displayed signs of microbiota disruption associated with the presence of previously undetected potential pathogenic microbial species mostly belonging to genus Vibrio and Arcobacter. The role of these species and their consortia should be targeted by future studies aiming to shed light on mechanisms underlying polymicrobial infections in C. gigas.

High-throughput sequencing and analysis of microbial communities in the mangrove swamps along the coast of Beibu Gulf in Guangxi, China

Mangrove swamp is one of the world's richest and most productive marine ecosystems. This ecosystem also has a great ecological importance, but is highly susceptible to anthropogenic disturbances. The balance of mangrove ecosystem depends largely on the microbial communities in mangrove sediments. Thus, understanding how the mangrove microbial communities respond to spatial differences is essential for more accurate assessment of mangrove ecosystem health. To this end, we performed the first medium-distance (150 km) research on the biogeographic distribution of mangrove microbial communities. The hypervariable regions of 16S rRNA gene was sequenced by Illumina to compare the microbial communities in mangrove sediments collected from six locations (i.e. Zhenzhu harbor, Yuzhouping, Maowei Sea, Qinzhou harbor, Beihai city and Shankou) along the coastline of Beibu Gulf in Guangxi province, China. Collectively, Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Parvarchaeota, Acidobacteria and Cyanobacteria were the predominant phyla in the mangrove sediments of this area. At genus level, the heat map of microbial communities reflected similarities between study sites and was in agreement with their biogeographic characteristics. Interestingly, the genera Desulfococcus, Arcobacter, Nitrosopumilus and Sulfurimonas showed differences in abundance between study sites. Furthermore, the principal component analysis (PCA) and unweighted UniFrac cluster tree of beta diversity were used to study the biogeographic diversity of the microbial communities. Relatively broader variation of microbial communities was found in Beihai city and Qinzhou harbour, suggesting that environmental condition and historical events may play an important role in shaping the bacterial communities as well. This is the first report on medium-distance range distribution of bacteria in the mangrove swamp ecosystem. Our data is valuable for monitoring and evaluation of the impact of human activity on mangrove habitats from the perspective of microbiome.

Diversity, enumeration, and isolation of Arcobacter spp. in the giant abalone, Haliotis gigantea

Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter‐specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter‐specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F‐positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338‐positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%–100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%–94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.

A meta-analytic perspective on Arcobacter spp. antibiotic resistance

OBJECTIVES

Over the years, an increased prevalence of resistant strains of Arcobacter has been observed, which may be due to Arcobacter exposure to antibiotics used both in animal production and human medicine. A systematic review was performed with the objective of summarising the results of the rates of antimicrobial resistance of Arcobacter isolates.

METHODS

The systematic review was performed according to PRISMA (Preferred Reported Items for Systematic Reviews and Meta-Analysis) recommendations, followed by meta-analysis.

RESULTS

It was observed that the resistance rate ranged between 69.3-99.2% for penicillins and 30.5-97.4% for cephalosporins. The overall percentage of resistance to fluoroquinolones ranged from 4.3% to 14.0%, with the highest resistance percentage observed for levofloxacin. Resistance rates ranged between 10.7-39.8% for macrolides, 1.8-12.9% for aminoglycosides and 0.8-7.1% for tetracyclines.

CONCLUSIONS

These results show that Arcobacter spp. present resistance to various antibiotics commonly used and advocate further studies of the associated resistance mechanisms.

Complete Genome Sequence of the Arcobacter bivalviorum Type Strain LMG 26154

Arcobacters are routinely recovered from marine environments, and multiple Arcobacter species have been isolated from shellfish. Arcobacter bivalviorum was recovered from mussels collected in the Ebro Delta in northeastern Spain. This report describes the complete whole-genome sequence of the A. bivalviorum type strain LMG 26154 (= F4^T = CECT 7835^T).

Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan

Nitrous oxide (N₂O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N₂O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N₂O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N₂O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N₂O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N₂O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N₂O only. Collectively, these results suggest that the N₂O-reducing microbiome in eelgrass meadows is largely responsible for coastal N₂O mitigation.

Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.

Detection of Arcobacter spp. in food products collected from Sicilia region: A preliminary study

The aim of the study was to evaluate the occurrence of Arcobacter spp. in food samples collected from Sicilia region. A total of 91 food products of animal origin (41 meat, 17 fresh milk, 18 shellfish) and 15 samples of fresh vegetables, were examined by cultural method and confirmed by biochemical analysis and PCR methods. The detection of Arcobacter spp. was performed, after selective enrichment, on two selective agar plates: Arcobacter agar and mCCD (modified charcoal cefoperazone deoxycholate) agar supplemented with CAT (Cefoperazone, Amphotericin B and Teicoplanin). Arcobacter species were isolated using the membrane filtration technique. In 13 (14.3%) out of the 91 tested samples, the presence of Arcobacter spp. was found: the isolates were confirmed by multiplex PCR and identified as belonging to the species A. butzleri and A. cryaerophilus. The highest prevalence rate was observed in chicken meat (8.8%) followed by shellfish (3.3%). Negative results have been obtained for raw milks and vegetables samples. The preliminary study highlights the importance of this emerging pathogen and the need for further studies on its prevalence and distribution in different types of food for human consumption.

Do the Escherichia coli European Union shellfish safety standards predict the presence of Arcobacter spp., a potential zoonotic pathogen?

The genus Arcobacter comprises Campylobacter-related species, considered zoonotic emergent pathogens, the presence of which in water has been associated with fecal pollution. Discharges of fecal polluted water into the sea have been considered as one of the main reasons for the presence of Arcobacter in shellfish, and this may represent a risk for public health. In this study, the European Union shellfish food safety criteria based on levels of Escherichia coli were studied in relation to their capacity to predict the presence of Arcobacter species. In addition, the accumulation factor (AF) that measures the concentration ratio between the microbes present in the shellfish and in the water, was also studied for both bacteria. The results show that the presence of E. coli correlated with the presence of the potentially pathogenic species A. butzleri and A. cryaerophilus. However, in 26.1% of the shellfish samples (corresponding to those taken during summer months) E. coli failed to predict the presence of, for instance A. butzleri and A. skirrowii, among other species. In the rest of the samples a significant correlation between the concentration of E. coli and Arcobacter spp. (mussels and oyster; R²=0.744) was found. This study indicates that the presence of E. coli can predict the presence of pathogenic Arcobacter species in shellfish samples harvested from water with temperatures lower than 26.2°C. Consumption of shellfish collected at higher temperatures which may not be permissive to the growth of E. coli but does allow growth of Arcobacter spp., may represent a risk for consumers.

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291^T = LMG 9904^T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229^T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065^T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291^T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976^T).

Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage

Four bacterial strains recovered from shellfish (n=3) and from the water (n=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus Arcobacter (represented by strain F138-33^T) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being Arcobacter marinus and Arcobactermolluscorum. However, phylogenetic analyses using the concatenated sequences of housekeeping genes (atpA, gyrB, hsp60, gyrA and rpoB) showed that all the novel strains formed a distinct lineage within the genus Arcobacter. Results of in silico DNA-DNA hybridization and the average nucleotide identity between the genome of strain F138-33^T and those of the closely related species A. marinus and other relatively closely related species such as A. molluscorum and Arcobacterhalophilus were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name Arcobacter canalis sp. nov. is proposed, with the type strain F138-33^T (=CECT 8984^T=LMG 29148^T).