Arcobacter defluvii sp. nov., isolated from sewage samples

Microbial diversity characterizations, associated pathogenesis and antimicrobial resistance profiling of Najafgarh drain

The Najafgarh drain plays a significant role in the pollution of the Yamuna River, accounting for 40% of the total pollution. Therefore, it is crucial to investigate and analyze the microbial diversity, metabolic functional capacity, and antibiotic resistance genes (ARGs) present in the Najafgarh drain. Additionally, studying the water quality and its relationship with the proliferation of microorganisms in the drain is of utmost importance. Results obtained confirmed the deteriorated water quality as physico-chemical parameters such as biochemical oxygen demand (BOD), chemical oxygen demand (COD), dissolved oxygen (DO), and total suspended solids (TSS) in the range of 125-140, 400-460, 0-0.2, 25-140.4 mg/l respectively violated the standard permissible national and global standards. In addition, the next generation sequencing (NGS) analysis confirm the presence of genus such as Thauera, Arcobacter, Pseudomonas, Geobacter, Dechloromonas, Tolumonas, Sulfurospirullum, Desulfovibrio, Aeromonas, Bacteroides, Prevotella, Cloacibacterium, Bifidobacterium, Clostridium etc. along with 864 ARGs in the wastewater obtained from the Najafgarh drain. Findings confirm that the pathogenic species reported from this dataset possess severe detrimental impact on faunal and human health. Further, Pearson's r correlation analysis indicated that environmental variables, mainly total dissolved solids (TDS) and chemical oxygen demand (COD), play a pivotal role in driving microbial community structure of this heavily polluted drain. Thus, the poor water quality, presence of a microbial nexus, pathogenic markers, and ARGs throughout this drain confirmed that it would be one potential contributor to the dissemination of disease-causing agents (pathogens) to the household and drinking water supplies in the near future.

Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary

Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10 µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain community dissimilarities between locations were TDP, PN, modelled temperature and salinity (r = 0.73) for the free living bacteria, TP for the associated bacteria (r = 0.43), and modelled temperature (r = 0.28) for the microbial eukaryotic communities. Overall, these results show that a minor disturbance such as a brief rainfall event can significantly shift the microbial assemblage of an anthropogenically impacted area within an urban estuary to a greater degree than a seasonal change, but may result in a lesser response to the same disturbance at a buffered, more oceanic influenced location. Fine scale research into the factors driving the response of microbial communities in urban estuaries to climate related disturbances will be necessary to understand and implement changes to maintain future estuarine ecosystem services.

Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

Dinitrogen (N₂) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N₂ fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N₂ fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.

Rainfall leads to elevated levels of antibiotic resistance genes within seawater at an Australian beach

Anthropogenic waste streams can be major sources of antibiotic resistant microbes within the environment, creating a potential risk to public health. We examined patterns in the occurrence of a suite of antibiotic resistance genes (ARGs) and their links to enteric bacteria at a popular swimming beach in Australia that experiences intermittent contamination by sewage, with potential points of input including stormwater drains and a coastal lagoon. Samples were collected throughout a significant rainfall event (40.8 mm over 3 days) and analysed using both qPCR and 16S rRNA amplicon sequencing. Before the rainfall event, low levels of faecal indicator bacteria and a microbial source tracking human faeces (sewage) marker (Lachno3) were observed. These levels increased over 10x following rainfall. Within lagoon, drain and seawater samples, levels of the ARGs sulI, dfrA1 and qnrS increased by between 1 and 2 orders of magnitude after 20.4 mm of rain, while levels of tetA increased by an order of magnitude after a total of 40.8 mm. After 40.8 mm of rain sulI, tetA and qnrS could be detected 300 m offshore with levels remaining high five days after the rain event. Highest levels of sewage markers and ARGs were observed adjacent to the lagoon (when opened) and in-front of the stormwater drains, pinpointing these as the points of ARG input. Significant positive correlations were observed between all ARGs, and a suite of Amplicon Sequence Variants that were identified as stormwater drain indicator taxa using 16S rRNA amplicon sequencing data. Of note, some stormwater drain indicator taxa, which exhibited correlations to ARG abundance, included the human pathogens Arcobacter butzleri and Bacteroides fragilis. Given that previous research has linked high levels of ARGs in recreationally used environments to antimicrobial resistant pathogen infections, the observed patterns indicate a potentially elevated human health risk at a popular swimming beach following significant rainfall events.

Molecular microbiological approaches reduce ambiguity about the sources of faecal pollution and identify microbial hazards within an urbanised coastal environment

Urbanised beaches are regularly impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard Faecal Indicator Bacteria (FIB) analyses to discriminate sources of faecal material or detect other microbial hazards, including antibiotic resistance genes (ARGs). We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating at 9 stormwater drains located on Rose Bay beach over the course of a significant (67.5 mm) rainfall event, whereby samples were taken 6 days prior to any rain, on the day of initial rainfall (3.8 mm), three days later after 43 mm of rain and then four days after any rain. Quantitative PCR (qPCR) was used to target marker genes from bacteria (i.e., Lachnospiraceae and Bacteroides) that have been demonstrated to be specific to human faeces (sewage), along with gene sequences from Heliobacter and Bacteriodes that are specific to bird and dog faeces respectively, and ARGs (sulI, tetA, qnrS, dfrA1 and vanB). 16S rRNA gene amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Prior to the rain event, low FIB levels (mean: 2.4 CFU/100 ml) were accompanied by generally low levels of the human and animal faecal markers, with the exception of one transect, potentially indicative of a dry weather sewage leak. Following 43 mm of rain, levels of both human faecal markers increased significantly in stormwater drain and seawater samples, with highest levels of these markers pinpointing several stormwater drains as sources of sewage contamination. During this time, sewage contamination was observed up to 1000 m from shore and was significantly and positively correlated with often highly elevated levels of the ARGs dfrA1, qnrS, sulI and vanB. Significantly elevated levels of the dog faecal marker in stormwater drains at this time also indicated that rainfall led to increased input of dog faecal material from the surrounding catchment. Using 16S rRNA gene amplicon sequencing, several indicator taxa for stormwater contamination such as Arcobacter spp. and Comamonadaceae spp. were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event, with the microbial signature of one particular drain contributing up to 50% of bacterial community in the seawater directly adjacent. By applying a suite of molecular microbiological approaches, we have precisely pinpointed the causes and point-sources of faecal contamination and other associated microbiological hazards (e.g., ARGs) at an urbanised beach, which has helped to identify the most suitable locations for targeted management of water quality at the beach.

A Review on the Prevalence of Arcobacter in Aquatic Environments

Arcobacter is an emerging pathogen that is associated with human and animal diseases. Since its first introduction in 1991, 33 Arcobacter species have been identified. Studies have reported that with the presence of Arcobacter in environmental water bodies, animals, and humans, a possibility of its transmission via water and food makes it a potential waterborne and foodborne pathogen. Therefore, this review article focuses on the general characteristics of Arcobacter, including its pathogenicity, antimicrobial resistance, methods of detection by cultivation and molecular techniques, and its presence in water, fecal samples, and animal products worldwide. These detection methods include conventional culture methods, and rapid and accurate Arcobacter identification at the species level, using quantitative polymerase chain reaction (qPCR) and multiplex PCR. Arcobacter has been identified worldwide from feces of various hosts, such as humans, cattle, pigs, sheep, horses, dogs, poultry, and swine, and also from meat, dairy products, carcasses, buccal cavity, and cloacal swabs. Furthermore, Arcobacter has been detected in groundwater, river water, wastewater (influent and effluent), canals, treated drinking water, spring water, and seawater. Hence, we propose that understanding the prevalence of Arcobacter in environmental water and fecal-source samples and its infection of humans and animals will contribute to a better strategy to control and prevent the survival and growth of the bacteria.

Prevalence, virulence genes and anti­microbial resistance of Arcobacter isolates from animal meat in Iran

Arcobacter spp. are food-borne and zoonotic entero-pathogens. Obtaining information in relation to antimicrobial resistance helps us for utilisation of an appropriate agent for the treatment of Arcobacter infections. This study aimed to investigate the prevalence, antimicrobial resistance and virulence factors in animal raw meat in Iran. The samples were collected from cattle (n=80), sheep (n=80), goats (n=80), camels (n=80), and buffaloes (n=60) from Khuzestan (n=110), Isfahan (n=80), Gilan (n=110) and Chaharmahal and Bakhtiari (n=80) provinces. Arcobacter isolates of meat samples were isolated, investigated by PCR method. The antibiotic resistance was also investigated. All isolates were screened for 6 virulence genes: cadF, ciaB, cj1349, Mvin, pldA and tlyA by PCR assays. The results showed that the prevalence of Arcobacter species had no significant difference among provinces and animals (P>0.05), so that positive samples were 1.25%, 1.25%, and 0.9% in Isfafhan, Chaharmahal and Bakhtiari, and Gilan, respectively. Virulence genes were observed for A. butzleri species (n=3, 100%). The results showed that Arcobacter spp. were resistant to streptomycin (100%), tetracycline (100%) and vancomycin (100%), but were susceptible to azithromycin (33.33%). In sum, the different regions of the Iran had a relative incidence of 1% for Arcobacter spp. The species showed a resistance of 100% for streptomycin, tetracycline and vancomycin. These findings could help to identify Arcobacter spp. and select the best agent against infection in case of Arcobacter infection in animals.

Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig

A study on the polyphasic taxonomic classification of an Arcobacter strain, R-73987^T, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus Arcobacter and suggested that strain R-73987^T belongs to a novel undescribed species. Comparative analysis of the rpoB gene sequence confirmed the findings. Arcobacter faecis LMG 28519^T was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and in silico DNA-DNA hybridization between the genome of strain R-73987^T and the genomes of validly named Arcobacter species resulted in values below 95-96 and 70  %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987^T represents a novel Arcobacter species, for which the name Arcobacter vandammei sp. nov. is proposed. The type strain is R-73987^T (=LMG 31429^T=CCUG 75005^T). This appears to be the first Arcobacter species recovered from porcine intestinal mucus.

Changes in bacterial diversity of activated sludge exposed to titanium dioxide nanoparticles

The rapid growth of the use of nanomaterials in different modern industrial branches makes the study of the impact of nanoparticles on the human health and environment an urgent matter. For instance, it has been reported that titanium dioxide nanoparticles (TiO₂ NPs) can be found in wastewater treatment plants. Previous studies have found contrasting effects of these nanoparticles over the activated sludge process, including negative effects on the oxygen uptake. The non-utilization of oxygen reflects that aerobic bacteria were inhibited or decayed. The aim of this work was to study how TiO₂ NPs affect the bacterial diversity and metabolic processes on an activated sludge. First, respirometry assays of 8 h were carried out at different concentrations of TiO₂ NPs (0.5-2.0 mg/mL) to measure the oxygen uptake by the activated sludge. The bacterial diversity of these assays was determined by sequencing the amplified V3-V4 region of the 16S rRNA gene using Illumina MiSeq. According to the respirometry assays, the aerobic processes were inhibited in a range from 18.5 ± 4.8% to 37.5 ± 2.0% for concentrations of 0.5-2.0 mg/mL TiO₂ NPs. The oxygen uptake rate was affected mainly after 4.5 h for concentrations higher than 1.0 mg/mL of these nanoparticles. Results indicated that, in the presence of TiO₂ NPs, the bacterial community of activated sludge was altered mainly in the genera related to nitrogen removal (nitrogen assimilation, nitrification and denitrification). The metabolic pathways prediction suggested that genes related to biofilm formation were more sensitive than genes directly related to nitrification-denitrification and N-assimilation processes. These results indicated that TiO₂ NPs might modify the bacteria diversity in the activated sludge according to their concentration and time of exposition, which in turn impact in the performance of the wastewater treatment processes.

Nitrogen transformation processes and mass balance in deep constructed wetlands treating sewage, exploring the anammox contribution

This work was aimed to assess the contribution of classical nitrogen removal pathways in two deep constructed wetlands CW1 and CW2 located at Jaipur, India. Nitrogen mass balance revealed that 44.87% and 43.77% losses of T-N in CW1 and CW2 were unaccounted for. To elucidate these significant losses, the study was extended to assess the occurrence and contribution of a novel pathway (ANAMMOX) in overall nitrogen removal. The ratio of NH⁴⁺-N (removed) & NO₃^--N (produced) in CW1 & CW2 indicated that ANAMMOX could be one of the key pathways for nitrogen removal in the CWs besides nitrification-denitrification in microbial films. The molecular analysis confirmed bands of ANAMMOX bacteria developed intrinsically. The study revealed that deep wetlands can offer a feasible option for the sustenance of ANAMMOX bacteria and may help develop design parameters for CWs for achieving higherT-N removal withsimilarsurface area as that of conventional wetlands.

Real-time quantitative PCR assay development and application for assessment of agricultural surface water and various fecal matter for prevalence of Aliarcobacter faecis and Aliarcobacter lanthieri

BACKGROUND

Aliarcobacter faecis and Aliarcobacter lanthieri are recently identified as emerging human and animal pathogens. In this paper, we demonstrate the development and optimization of two direct DNA-based quantitative real-time PCR assays using species-specific oligonucleotide primer pairs derived from rpoB and gyrA genes for A. faecis and A. lanthieri, respectively. Initially, the specificity of primers and amplicon size of each target reference strain was verified and confirmed by melt curve analysis. Standard curves were developed with a minimum quantification limit of 100 cells mL^- 1 or g^- 1 obtained using known quantities of spiked A. faecis and A. lanthieri reference strains in autoclaved agricultural surface water and dairy cow manure samples.

RESULTS

Each species-specific qPCR assay was validated and applied to determine the rate of prevalence and quantify the total number of cells of each target species in natural surface waters of an agriculturally-dominant and non-agricultural reference watershed. In addition, the prevalence and densities were determined for human and various animal (e.g., dogs, cats, dairy cow, and poultry) fecal samples. Overall, the prevalence of A. faecis for surface water and feces was 21 and 28%, respectively. The maximum A. faecis concentration for water and feces was 2.3 × 10⁷ cells 100 mL^{- 1} and 1.2 × 10⁷ cells g^- 1, respectively. A. lanthieri was detected at a lower frequency (2%) with a maximum concentration in surface water of 4.2 × 10⁵ cells 100 mL^- 1; fecal samples had a prevalence and maximum density of 10% and 2.0 × 10⁶ cells g^- 1, respectively.

CONCLUSIONS

The results indicate that the occurrence of these species in agricultural surface water is potentially due to fecal contamination of water from livestock, human, or wildlife as both species were detected in fecal samples. The new real-time qPCR assays can facilitate rapid and accurate detection in < 3 h to quantify total numbers of A. faecis and A. lanthieri cells present in various complex environmental samples.

Large genetic diversity of Arcobacter butzleri isolated from raw milk in Southern Italy

Arcobacter butzleri is a zoonotic foodborne pathogen able to cause enteric and extraintestinal diseases. Its occurrence in foodstuff is well recognized worldwide but data on its presence in foods from Southern Italy are scarce. In this study the results on the occurrence and genotyping of Arcobacter spp. in bulk milk samples collected in Southern Italy are reported. Out of 484 samples, 64 (13.2%) resulted positive for the presence of Arcobacter spp. Using Real Time PCR but as few as 31.2% of these samples turned out as positive by using the cultural method, showing an overall prevalence of 4.1%. All isolates were identified as A. cryaerophilus using the biochemical identification whilst the sequencing of the atpA gene revealed that all the isolates were A. butzleri. Among the confirmed isolates, 16 different Sequence Types (ST) were identified using the Multi Locus Sequence Typing (MLST), 14 (87.5%) of which were previously unreported. Our survey reveals the presence of A. butzleri in bulk tank milk from Southern Italy and highlights the discrepancy between the two approaches used both for the detection (i.e., real time PCR vs cultural method) and the identification (i.e., biochemical test vs aptA sequencing) of Arcobacter spp In addition, a large genetic diversity among the isolates was detected and this makes the identification of source of the infections very challenging in outbreaks investigation.

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.

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.

Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation

We analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, organisms related to Azoarcus spp. were identified as key players in the degradation of toluene and ethylbenzene. An organism highly related to Georgfuchsia toluolica G5G6 was enriched with p-xylene, a particularly recalcitrant compound. The anaerobic degradation of p-xylene requires a metabolic trait that was not described for members of the genus Georgfuchsia before. In line with this, we were able to identify a putative 4-methylbenzoyl-CoA reductase gene cluster in the respective enrichment culture, which is possibly involved in the anaerobic degradation of p-xylene.

Isolation and molecular characterization of Arcobacter butzleri and Arcobacter cryaerophilus from the pork production chain in Brazil

ABSTRACT: Arcobacter is an emerging zoonotic pathogen, and the major transmission routes to humans are the handling or consumption of contaminated raw/undercooked food products of animal origin, water and seafood. The isolation and identification of Arcobacter species are not routine in clinical laboratories; therefore, its true incidence in human infections may be underestimated. The present study aimed to isolate and characterize Arcobacter from carcasses and fecal samples collected at swine slaughterhouses and from meat markets in São Paulo State, Brazil. The isolates were identified using multiplex-PCR to differentiate the species and analyzed by single-enzyme amplified fragment length polymorphism (SE-AFLP). Arcobacter spp. were isolated from 73.0% of swine carcasses, 4% of fecal samples and 10% of pork samples. A. butzleri was the most prevalent species identified, followed by A. cryaerophilus. Interestingly, the carcasses presented higher frequency of A. butzleri isolation, whereas only A. cryaerophilus was isolated from fecal samples. SE-AFLP enabled the characterization of A. butzleri and A. cryaerophilus into 51 and 63 profiles, respectively. The great genetic heterogeneity observed for both species corroborates previous reports. This study confirms the necessity for a standard isolation protocol and the improvement of molecular tools to further elucidate Arcobacter epidemiology.

Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review

Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries. Arcobacters are implicated as causative agents of diarrhea, mastitis and abortion in animals, while causing bacteremia, endocarditis, peritonitis, gastroenteritis and diarrhea in humans. Three species including A. butzleri, A. cryaerophilus and A. skirrowii are predominantly associated with clinical conditions. Arcobacters are primarily transmitted through contaminated food and water sources. Identification of Arcobacter by biochemical tests is difficult and isolation remains the gold standard method. Current diagnostic advances have provided various molecular methods for efficient detection and differentiation of the Arcobacters at genus and species level. To overcome the emerging antibiotic resistance problem there is an essential need to explore the potential of novel and alternative therapies. Strengthening of the diagnostic aspects is also suggested as in most cases Arcobacters goes unnoticed and hence the exact epidemiological status remains uncertain. This review updates the current knowledge and many aspects of this important food-borne pathogen, namely etiology, evolution and emergence, genetic diversity, epidemiology, the disease in animals and humans, public health concerns, and advances in its diagnosis, prevention and control.

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

A Gram-negative, aerobic, polar-flagellated and rod-shaped, sometimes slightly curved bacterium, designated MA5T, was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan. Phylogenetic analyses based on 16S rRNA, gyrB, hsp60 and rpoB gene sequences placed strain MA5T in the genus Arcobacter in an independent phylogenetic line. Comparison of the 16S rRNA gene sequence of this strain with those of the type strains of the established Arcobacter species revealed A. nitrofigilis (95.1 %) as nearest neighbour. Strain MA5T grew optimally at 25 °C, pH 6.0 to 9.0 and in the presence of 2 to 5 % (w/v) NaCl under both aerobic and microaerobic conditions. The predominant fatty acids found were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C12 : 0 3-OH and C18 : 1 ω7c. Menaquinone-6 (MK-6) and menaquinone-7 (MK-7) were found as the major respiratory quinones. The major polar lipids detected were phosphatidylethanolamine and phosphatidylglycerol. Strain MA5T could be differentiated phenotypically from the phylogenetic closest Arcobacter species by its ability to grow on 0.05 % safranin and 0.01 % 2,3,5-triphenyl tetrazolium chloride (TTC), but not on 0.5 % NaCl. The obtained DNA G+C content of strain MA5T was 27.9 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic distinctiveness of MA5T, this strain is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter haliotis sp. nov. is proposed. The type strain is MA5T (=LMG 28652T=JCM 31147T).

Comparative isolation and genetic diversity of Arcobacter sp. from fish and the coastal environment

Arcobacter species are emerging food-borne and water-borne human pathogens associated mostly with food animals and their environment. The present study was aimed to isolate Arcobacter species from fish, shellfish and coastal water samples using two methods and to determine their genetic diversity. Of 201 samples of fish, shellfish and water samples analysed, 66 (32·8%) samples showed the presence of Arcobacter DNA from both Arcobacter enrichment broth and Bolton broth. Arcobacters were isolated from 58 (87·8%) and 38 (57·5%) of Arcobacter DNA-positive samples using Arcobacter blood agar and Preston blood agar, respectively. Arcobacter sp. identified by biochemical tests were further analysed by a genus-specific PCR, followed by a multiplex-PCR and 16S rRNA-RFLP. From both the methods, four different Arcobacter species namely Arcobacter butzleri, Arcobacter skirrowii, Arcobacter mytili and Arcobacter defluvii were isolated, of which A. butzleri was the predominant species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprint analysis revealed that the arcobacters isolated in this study were genetically very diverse and no specific genotype was found associated with a specific source (seafood or water). Since pathogenic arcobacters are not known to be natural inhabitants of coastal marine environment, identifying the sources of contamination will be crucial for effective management of this problem.

SIGNIFICANCE AND IMPACT OF THE STUDY

Arcobacter sp. are emerging food- and water-borne human pathogens. In this study, comparison of two selective media suggested Arcobacter blood agar to be more efficient in yielding Arcobacter sp. from seafood. Furthermore, the isolation of Arcobacter sp. such as Arcobacter butzleri, A. skirrowii, A. mytili and A. defluvii from seafood suggests diverse sources of contamination of seafood by Arcobacter sp. Analysis of enterobacterial repetitive intergenic consensus sequence-PCR patterns of A. butzleri showed high genetic diversity and lack of clonality among the isolates. Arcobacter contamination of seafood is an emerging issue both from seafood safety and seafood trade point of view.

Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery

Four bacterial strains, LFT 1.7T, LT2C 2.5, LT4C 2.8 and TM 4.6, were isolated from great scallop (Pecten maximus) larvae and tank seawater in a Norwegian hatchery and characterized by a polyphasic approach including determination of phenotypic, chemotaxonomic and genomic traits. All were Gram-stain-negative, motile rods, oxidase- and catalase-positive and required sea salts for growth. Major fatty acids present were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0, C14 : 0, summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I), C12 : 0 3-OH and C12 : 0. Strain LFT 1.7T contained menaquinone MK-6 as the sole respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that all strains formed a distinct lineage within the genus Arcobacter with a low similarity to known species (94.77-95.32 %). The DNA G+C content was 28.7 mol%. Results of in silico DNA-DNA hybridization and average nucleotide identity confirmed that the isolates constitute a novel species of Arcobacter, for which the name Arcobacter lekithochrous sp. nov. is proposed. The type strain is LFT 1.7T (=CECT 8942T=DSM 100870T).

Detection, Identification, and Antimicrobial Susceptibility of Arcobacter spp. Isolated from Shellfish in Spain

This work aimed to determine the presence of Arcobacter spp. in shellfish and to determine its susceptibility to quinolones. One hundred samples (41 mussels, 37 clams, and 22 cockles) were purchased from different local retail shops in Valencia, Spain, from September 2013 to June 2015. All samples were analyzed simultaneously by culture, after an enrichment step, and by polymerase chain reaction (PCR), directly and after enrichment. The susceptibility to levofloxacin and ciprofloxacin of the isolates was tested using the disk-diffusion test and E-test strips method. To clarify the mechanism of quinolone resistance, a fragment of the quinolone resistance-determining region of the gyrA gene was sequenced. Thirty-seven samples were positive and 49 isolates were obtained by culture, and Arcobacter spp. DNA was detected in 32% of the samples by PCR. However, after 48-h enrichment, the number of positive samples increased, and 68 of the 100 samples yielded the specific Arcobacter spp. PCR product. In addition, 49 isolates were identified by PCR-restriction fragment length polymorphism. The most commonly found species was Arcobacter butzleri (25 isolates, 51.03%) followed by Arcobacter cryaerophilus (19 isolates, 38.77%) and Arcobacter defluvii (5 isolates, 10.20%). Only three isolates of A. butzleri were resistant to both antibiotics. A mutation C to T transition in the position 254 of the gyrA gene was present in the three resistant isolates. This study confirms that pathogenic arcobacters are frequently found in edible shellfish samples. Moreover, this is the first time that A. butzleri and A. cryaerophilus have been isolated from cockles.

Arcobacter acticola sp. nov., isolated from seawater on the East Sea in South Korea

A Gram-stain-negative, facultative aerobic, non-flagellated, and rod-shaped bacterium, designated AR-13(T), was isolated from a seawater on the East Sea in South Korea, and subjected to a polyphasic taxonomic study. Strain AR-13(T) grew optimally at 30°C, at pH 7.0-8.0 and in the presence of 0-0.5% (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain AR-13(T) fell within the clade comprising the type strains of Arcobacter species, clustering coherently with the type strain of Arcobacter venerupis. Strain AR-13(T) exhibited 16S rRNA gene sequence similarity values of 98.1% to the type strain of A. venerupis and of 93.2-96.9% to the type strains of the other Arcobacter species. Strain AR-13(T) contained MK-6 as the only menaquinone and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C16:0, C18:1 ω7c, and summed feature 2 (iso-C16:1 I and/or C14:0 3-OH) as the major fatty acids. The major polar lipids detected in strain AR-13(T) were phosphatidylethanolamine, phosphatidylglycerol, and one unidentified aminophospholipid. The DNA G+C content was 28.3 mol% and its mean DNA-DNA relatedness value with the type strain of A. venerupis was 21%. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain AR-13(T) is separated from recognized Arcobacter species. On the basis of the data presented, strain AR-13(T) is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter acticola sp. nov. is proposed. The type strain is AR-13(T) (=KCTC 52212(T) =NBRC 112272(T)).

Occurrence of emerging food-borne pathogenic Arcobacter spp. isolated from pre-cut (ready-to-eat) vegetables

Given that changes in consumer food behaviours have led to an increase in the demand for pre-cut ready-to-eat (RTE) vegetables, and that few data are currently available on the occurrence of Arcobacter spp. in such foods, the aim of the present study was to assess the occurrence of Arcobacter spp. that carry virulence-associated genes on pre-cut RTE vegetables, using cultural and molecular methods. Arcobacter was detected using biomolecular identification methods in 44/160 (27.5%) of the samples, of which 40/44 (90.9%) isolates corresponded to A. butzleri and 4/44 (9.1%) to A. cryaerophilus. Studying the incidence of 9 virulence-associated genes revealed the widespread distribution of these genes among the Arcobacter isolates tested. The results obtained in our research provided plenty of information on the health risks associated with the direct consumption of raw vegetables, and highlight the need to implement further studies at each level of the production chain, in order to obtain further information to help protect human health.

Development and evaluation of multiplex PCR assays for rapid detection of virulence-associated genes in Arcobacter species

As the pathogenicity of Arcobacter species might be associated with various virulence factors, this study was aimed to develop and optimize three single-tube multiplex PCR (mPCR) assays that can efficiently detect multiple virulence-associated genes (VAGs) in Arcobacter spp. including the Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii, respectively. The recognized target virulence factors used in the study were fibronectin binding protein (cj1349), filamentous hemagglutinin (hecA), hemolysin activation protein (hecB), hemolysin (tlyA), integral membrane protein virulence factor (mviN), invasin (ciaB), outer membrane protein (irgA) and phospholipase (pldA). Identical results were obtained between singleplex PCR and mPCR assays and no cross- and/or non-specific amplification products were obtained when tested against other closely related bacterial species. The sensitivities of these three mPCR assays were ranging from 1ngμL(-1) to 100ngμL(-1) DNA. The developed assays with combinations of duplex or triplex PCR primer pairs of VAGs were further evaluated and validated by applying them to isolates of the A. butzleri, A. cryaerophilus and A. skirrowii recovered from fecal samples of human and animal origins. The findings revealed that the distribution of the ciaB (90%), mviN (70%), tlyA (50%) and pldA (45%) genes among these target species was significantly higher than the hecA (16%), hecB (10%) and each of irgA and cj1349 (6%) genes, respectively. The newly developed mPCR assays can be used as rapid technique and useful markers for the detection, prevalence and profiling of VAGs in the Arcobacter spp. Moreover, these assays can easily be performed with a high throughput to give a presumptive identification of the causal pathogen in epidemiological investigation of human infections.

Comparison of bacterial communities of conventional and A-stage activated sludge systems

The bacterial community structure of 10 different wastewater treatment systems and their influents has been investigated through pyrosequencing, yielding a total of 283486 reads. These bioreactors had different technological configurations: conventional activated sludge (CAS) systems and very highly loaded A-stage systems. A-stage processes are proposed as the first step in an energy producing municipal wastewater treatment process. Pyrosequencing analysis indicated that bacterial community structure of all influents was similar. Also the bacterial community of all CAS bioreactors was similar. Bacterial community structure of A-stage bioreactors showed a more case-specific pattern. A core of genera was consistently found for all influents, all CAS bioreactors and all A-stage bioreactors, respectively, showing that different geographical locations in The Netherlands and Spain did not affect the functional bacterial communities in these technologies. The ecological roles of these bacteria were discussed. Influents and A-stage bioreactors shared several core genera, while none of these were shared with CAS bioreactors communities. This difference is thought to reside in the different operational conditions of the two technologies. This study shows that bacterial community structure of CAS and A-stage bioreactors are mostly driven by solids retention time (SRT) and hydraulic retention time (HRT), as suggested by multivariate redundancy analysis.

Identification, characterization and description of Arcobacter faecis sp. nov., isolated from a human waste septic tank

A study on the taxonomic classification of Arcobacter species was performed on the cultures isolated from various fecal sources where an Arcobacter strain AF1078(T) from human waste septic tank near Ottawa, Ontario, Canada was characterized using a polyphasic approach. Genetic investigations including 16S rRNA, atpA, cpn60, gyrA, gyrB and rpoB gene sequences of strain AF1078(T) are unique in comparison with other arcobacters. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is most closely related to Arcobacter lanthieri and Arcobacter cibarius. Analyses of atpA, cpn60, gyrA, gyrB and rpoB gene sequences suggested that strain AF1078(T) formed a phylogenetic lineage independent of other species in the genus. Whole-genome sequence, DNA-DNA hybridization, fatty acid profile and phenotypic analysis further supported the conclusion that strain AF1078(T) represents a novel Arcobacter species, for which the name Arcobacter faecis sp. nov. is proposed, with type strain AF1078(T) (=LMG 28519(T); CCUG 66484(T)).

Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria

In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

Characterization of Arcobacter suis isolated from water buffalo (Bubalus bubalis) milk

During a survey in a dairy plant in Italy, the second strain (strain FG 206) of Arcobacter suis described in the literature was isolated from raw water buffalo milk. The objective of this study was to confirm the species identification, better define the species by comparing its characteristics with those of the reference strain (F41(T) = CECT 7833(T) = LMG 26152(T)) and to investigate its potential clinical relevance by detecting the virulence gene pattern of the new strain. Phenotypical characterization and 16S rRNA-RFLP gave a complete overlap of results for the two strains. As expected, an RFLP pattern common to A. suis and Arcobacter defluvii was obtained by MseI endonuclease digestion, and a pattern specific for A. suis was obtained by BfaI endonuclease digestion. 16S rRNA sequencing and multilocus phylogenetic analysis (MLPA) showed a robust relatedness of strain FG 206 to the A. suis type strain F41(T). The recovery of strain FG 206 from a dairy plant shows that this species of Arcobacter is present in the food chain. Like the type strain recovered from pig meat, the species A. suis may not be confined to a single type of food.

Global Distribution and Prevalence of Arcobacter in Food and Water

The emerging foodborne and waterborne pathogen, Arcobacter, has been linked to various gastrointestinal diseases. Currently, 19 species are established or proposed; consequently, there has been an increase in the number of publications regarding Arcobacter since it was first introduced in 1991. To better understand the potential public health risks posed by Arcobacter, this review summarizes the current knowledge concerning the global distribution and the prevalence of Arcobacter in food and water. Arcobacter spp. were identified in food animals, food-processing environments and a variety of foods, including vegetables, poultry, beef, dairy products, seafood, pork, lamb and rabbit. A wide range of waterbodies has been reported to be contaminated with Arcobacter spp., such as wastewater, seawater, lake and river water, drinking water, groundwater and recreational water. In addition, Arcobacter has also been isolated from pets, domestic birds, wildlife, zoo and farm animals. It is expected that advancements in molecular techniques will facilitate better detection worldwide and aid in understanding the pathogenicity of Arcobacter. However, more extensive and rigorous surveillance systems are needed to better understand the occurrence of Arcobacter in food and water in various regions of the world, as well as uncover other potential public health risks, that is antibiotic resistance and disinfection efficiency, to reduce the possibility of foodborne and waterborne infections.

Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure

A study was undertaken to determine the prevalence and diversity of species of the genus Arcobacter in pig and dairy cattle manure, which led to the identification of strains AF1440T, AF1430 and AF1581. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains confirmed that they belonged to the genus Arcobacter and were different from all known species of the genus. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. Their unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of the strains from other species of the genus Arcobacter. The isolates were found to be oxidase, catalase and esterase positive and urease negative; they grew well at 30 °C under microaerophilic conditions and produced nitrite and acetoin. Based on their common origin and various physiological properties, it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov. The type strain is AF1440T ( = LMG 28516T = CCUG 66485T); strains AF1430 ( = LMG 28515 = CCUG 66486) and AF1581 ( = LMG 28517 = CCUG 66487) are reference strains.

Insights in the pathogenesis and resistance of Arcobacter: A review

Arcobacter genus currently comprises 18 recognized species, among which Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii have been associated with human and animal disease. Although these organisms, with special emphasis A. butzleri, are emerging as clinical pathogens, several aspects of their epidemiology and virulence are only starting to be clarified. In vitro human and animal cell culture assays have been used to show that several Arcobacter species can adhere to and invade eukaryotic cells, induce an immune response and produce toxins that damage host cells. In addition, data from genome sequencing highlighted several potential markers that may be helpful candidates for the study and understanding of these mechanisms; however, more work is necessary to clarify the molecular mechanisms involved in Arcobacter virulence. Arcobacter can be considered a relatively robust organism showing to be able to survive in adverse conditions, as the ones imposed by food processing and storage. Moreover, these bacteria have shown increased antibiotic resistance, along with high multidrug resistance. In this review, we seek to update the state-of-the-art concerning Arcobacter distribution, its interaction with the host, the trends of antibiotic resistance, its ability to survive, and finally the use of natural antimicrobials for control of Arcobacter.

Arcobacter ebronensis sp. nov. and Arcobacter aquimarinus sp. nov., two new species isolated from marine environment

Two strains recovered from mussels (F128-2(T)) and sea water (W63(T)) were characterized as Arcobacter sp., but they could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR) and rpoB gene analysis. The 16S rRNA gene sequence similarity to the type strains of all Arcobacter species ranged from 92.2% to 96.7% with strain F128-2(T), and from 94.1% to 99.4% with strain W63(T), the most similar being A. bivalviorum (CECT 7835(T)) and A. defluvii (CECT 7697(T)), respectively. The phylogenetic analyses of 16S rRNA, and the concatenated sequences of gyrB, gyrA, rpoB, atpA and hsp60 genes confirmed that strains F128-2(T) and W63(T) belonged to two new lineages within the genus Arcobacter. Moreover, both strains showed differential phenotypic characteristics and MALDI-TOF mass spectra from all other Arcobacter species. Therefore, it has been demonstrated the existence of two new Arcobacter species and the proposed names are Arcobacter ebronensis (type strain F128-2(T)=CECT 8441(T)=LMG 27922(T)), and Arcobacter aquimarinus (type strain W63(T)=CECT 8442(T)=LMG 27923(T)).

Population dynamics and ecology of Arcobacter in sewage

Arcobacter species are highly abundant in sewage where they often comprise approximately 5-11% of the bacterial community. Oligotyping of sequences amplified from the V4V5 region of the 16S rRNA gene revealed Arcobacter populations from different cities were similar and dominated by 1-3 members, with extremely high microdiversity in the minor members. Overall, nine subgroups within the Arcobacter genus accounted for >80% of the total Arcobacter sequences in all samples analyzed. The distribution of oligotypes varied by both sample site and temperature, with samples from the same site generally being more similar to each other than other sites. Seven oligotypes matched with 100% identity to characterized Arcobacter species, but the remaining 19 abundant oligotypes appear to be unknown species. Sequences representing the two most abundant oligotypes matched exactly to the reference strains for A. cryaerophilus group 1B (CCUG 17802) and group 1A (CCUG 17801(T)), respectively. Oligotype 1 showed generally lower relative abundance in colder samples and higher relative abundance in warmer samples; the converse was true for Oligotype 2. Ten other oligotypes had significant positive or negative correlations between temperature and proportion in samples as well. The oligotype that corresponded to A. butzleri, the Arcobacter species most commonly isolated by culturing in sewage studies, was only the eleventh most abundant oligotype. This work suggests that Arcobacter populations within sewer infrastructure are modulated by temperature. Furthermore, current culturing methods used for identification of Arcobacter fail to identify some abundant members of the community and may underestimate the presence of species with affinities for growth at lower temperatures. Understanding the ecological factors that affect the survival and growth of Arcobacter spp. in sewer infrastructure may better inform the risks associated with these emerging pathogens.

Arcobacter spp. isolated from untreated domestic effluent

Arcobacter butzleri and Arcobacter cryaerophilus were isolated from samples of raw untreated domestic sewage influent from nine separate wastewater treatment facilities in Cheshire, UK. This is the first report of Arcobacter spp. from sewage in the UK and suggests that Arcobacter spp. may be present in the human community.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies have shown Arcobacter spp. to be present in domestic sewage in several European countries. This study supports previous findings with the first report of Arcobacter spp. in domestic sewage in the UK. This study suggests that Arcobacter spp. is present amongst local human populations, implicating it as an underestimated gastrointestinal pathogen in the UK and contributing to our understanding of this emerging pathogen and its presence within the UK. Providing a confirmation of the presence of Arcobacter in sewage, which supports previous studies, this paper will appeal to fellow researchers of Arcobacter, as well as healthcare and water treatment professionals concerned with microbiology, water safety and gastroenterology, potentially having a wide impact.

Genus-specific PCR assay for screening Arcobacter spp. in chicken meat

BACKGROUND

The number of emerging pathogenic species described within the genus Arcobacter has increased rapidly during the last few years. In this work a genus-specific polymerase chain reaction (PCR) assay was developed for detection of the species of Arcobacter most commonly associated with foods. The assay uses primers designed to amplify an 85 bp DNA fragment on the 16S rRNA gene and was applied to the detection of Arcobacter spp. in retail chicken meat.

RESULTS

Primer specificity was tested against a panel of Arcobacter spp., related Campylobacter and Helicobacter spp. and other food bacteria. Arcobacter primers consistently and selectively amplified the expected DNA fragment in all tested Arcobacter spp. Bacterial control primers confirmed the presence of amplifiable DNA in the samples. The applicability of the PCR assay to food was validated through screening of fresh retail chicken samples for the presence of Arcobacter spp., with a result of 45% (23 out of 51) positive samples.

CONCLUSION

The genus-specific PCR assay developed has the potential to be used as a quick and sensitive alternative method for the survey of Arcobacter contamination in meats.

Comparison of conventional PCR, multiplex PCR, and loop-mediated isothermal amplification assays for rapid detection of Arcobacter species

This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species.

Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter

Two strains (JC83, JC84T) of obligately anaerobic, H2S-producing bacteria were isolated from estuarine sediment samples collected from Gangasagar, West Bengal, India. Cells were Gram-stain-negative, non-motile rods. Both strains were positive for oxidase, negative for catalase, hydrolysed casein, reduced nitrate and utilized citrate. Both strains grew chemoorganoheterotrophically with optimal pH of 7–8 (range 7–10) and at 30 °C (range 25–37 °C). C16 : 1ω7c, C18 : 1ω7c, C16 : 0 and C12 : 0 were the major fatty acids of both strains with minor amounts of C14 : 0, C12 : 0 3-OH and C18 : 0. Polar lipids of both strains included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, phosphatidylcholine, phosphatidylinositol, an unidentified aminolipid (AL2), an unidentified phospholipid (PL2) and an unidentified lipid (L3). MK-6 was the major respiratory quinone. The DNA G+C content of strains JC83 and JC84T was 25.0 and 24.6 mol%, respectively. The strains showed DNA reassociation >85 % (86.0±0.5 %) (based on DNA–DNA hybridization). Based on 16S rRNA gene sequence analysis, both strains were identified as belonging to the family Campylobacteraceae of the class Epsilonproteobacteria with Arcobacter marinus CL-S1T (95.4 % sequence similarity) as their closest phylogenetic neighbour. On the basis of morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strains JC83 and JC84T are considered to represent a novel species, for which the name Arcobacter anaerophilus sp. nov. is proposed. The type strain is JC84T ( = KCTC 15071T = MTCC 10956T = DSM 24636T). An emended description of the genus Arcobacter is provided.

Higher water temperature and incubation under aerobic and microaerobic conditions increase the recovery and diversity of Arcobacter spp. from shellfish

Some Arcobacter species are considered emerging food-borne and waterborne pathogens, and shellfish have been suggested as one of their reservoirs. However, only a few studies have investigated the presence of Arcobacter in this kind of food. This study assesses the prevalence and diversity of Arcobacter spp. in shellfish by multiplex PCR (m-PCR) and culturing methods (under different atmospheric conditions) and evaluates the possible influence of environmental parameters (temperature, salinity, and harvesting bay). Arcobacter was detected by m-PCR and/or culturing in 61 (29.9%) of 204 shellfish samples. Of the positive samples by culturing, 41.1% were obtained under only aerobic incubation conditions, while 23.2% were obtained under only microaerobic conditions. Of 476 investigated isolates, 118 belonged to different enterobacterial repetitive intergenic consensus (ERIC)-PCR genotypes (strains) and to 11 different species. This study shows the highest diversity of Arcobacter species ever observed in samples from any origin. The most prevalent species was Arcobacter butzleri (60.2%), followed by Arcobacter molluscorum (21.2%). The prevalence of Arcobacter was significantly higher during the summer than in other seasons, being associated with an increase in water temperature. Results confirm that shellfish are a reservoir for a remarkable diversity of Arcobacter spp.

Performance of five molecular methods for monitoring Arcobacter spp

Background

Bacteria belonging to the Arcobacter genus are emerging enteropathogens and potential zoonotic agents. Their taxonomy has evolved very rapidly, and there are presently 18 recorded species. The prevalence of species belonging to Arcobacter is underestimated because of the limitations of currently available methods for species identification.

The aim of this study was to compare the performance of five PCR based methods that target regions of 16S rRNA, 23S rRNA or gyrA genes to identify Arcobacter species, and to review previous results reported in the literature using these methods.

Results

The five tested methods were found not to be reliable. They misidentified between 16.8% and 67.4% of the studied strains; this was dependent upon the target regions of the tested genes. The worst results obtained were for the identification of Arcobacter cryaerophilus and Arcobacter butzleri when the 23S rRNA gene was used as the target. These species were confused with many non-targeted species.

Conclusion

Our results suggest that the known diversity of Arcobacter spp. in different environments could be expanded if reliable identification methods are applied in future studies.

Adherence to and invasion of human intestinal cells by Arcobacter species and their virulence genotypes

The genus Arcobacter is composed of 17 species which have been isolated from various sources. Of particular interest are A. butzleri, A. cryaerophilus, and A. skirrowii, as these have been associated with human cases of diarrhea, the probable transmission routes being through the ingestion of contaminated drinking water and food. To date, only limited studies of virulence traits in this genus have been undertaken. The present study used 60 Arcobacter strains isolated from different sources, representing 16 of the 17 species of the genus, to investigate their ability to adhere to and invade the human intestinal cell line Caco-2. In addition, the presence of five putative virulence genes (ciaB, cadF, cj1349, hecA, and irgA) was screened for in these strains by PCR. All Arcobacter species except A. bivalviorum and Arcobacter sp. strain W63 adhered to Caco-2 cells, and most species (10/16) were invasive. The most invasive species were A. skirrowii, A. cryaerophilus, A. butzleri, and A. defluvii. All invasive strains were positive for ciaB (encoding a putative invasion protein). Other putative virulence genes were present in other species, i.e., A. butzleri (cadF, cj1349, irgA, and hecA), A. trophiarum (cj1349), A. ellisii (cj1349), and A. defluvii (irgA). No virulence genes were detected in strains which showed little or no invasion of Caco-2 cells. These results indicate that many Arcobacter species are potential pathogens of humans and animals.

Physiological and genetic description of dissimilatory perchlorate reduction by the novel marine bacterium Arcobacter sp. strain CAB

A novel dissimilatory perchlorate-reducing bacterium (DPRB), Arcobacter sp. strain CAB, was isolated from a marina in Berkeley, CA. Phylogenetically, this halophile was most closely related to Arcobacter defluvii strain SW30-2 and Arcobacter ellisii. With acetate as the electron donor, strain CAB completely reduced perchlorate (ClO₄⁻) or chlorate (ClO₃⁻) [collectively designated (per)chlorate] to innocuous chloride (Cl⁻), likely using the perchlorate reductase (Pcr) and chlorite dismutase (Cld) enzymes. When grown with perchlorate, optimum growth was observed at 25 to 30°C, pH 7, and 3% NaCl. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations were dominated by free-swimming straight rods with 1 to 2 polar flagella per cell. Strain CAB utilized a variety of organic acids, fructose, and hydrogen as electron donors coupled to (per)chlorate reduction. Further, under anoxic growth conditions strain CAB utilized the biogenic oxygen produced as a result of chlorite dismutation to oxidize catechol via the meta-cleavage pathway of aerobic catechol degradation and the catechol 2,3-dioxygenase enzyme. In addition to (per)chlorate, oxygen and nitrate were alternatively used as electron acceptors. The 3.48-Mb draft genome encoded a distinct perchlorate reduction island (PRI) containing several transposases. The genome lacks the pcrC gene, which was previously thought to be essential for (per)chlorate reduction, and appears to use an unrelated Arcobacter c-type cytochrome to perform the same function.

The study of dissimilatory perchlorate-reducing bacteria (DPRB) has largely focused on freshwater, mesophilic, neutral-pH environments. This study identifies a novel marine DPRB in the genus Arcobacter that represents the first description of a DPRB associated with the Campylobacteraceae. Strain CAB is currently the only epsilonproteobacterial DPRB in pure culture. The genome of strain CAB lacks the pcrC gene found in all other DPRB tested, demonstrating a new variation on the (per)chlorate reduction pathway. The ability of strain CAB to oxidize catechol via the oxygenase-dependent meta-cleavage pathway in the absence of external oxygen by using the biogenic oxygen produced from the dismutation of chlorite provides a valuable model for understanding the anaerobic degradation of a broad diversity of xenobiotics which are recalcitrant to anaerobic metabolism but labile to oxygenase-dependent mechanisms.

Updated 16S rRNA-RFLP method for the identification of all currently characterised Arcobacter spp

BACKGROUND

Arcobacter spp. (family Campylobacteraceae) are ubiquitous zoonotic bacteria that are being increasingly recognised as a threat to human health. A previously published 16S rRNA-RFLP Arcobacter spp. identification method produced specific RFLP patterns for the six species described at that time, using a single endonuclease (MseI). The number of characterised Arcobacter species has since risen to 17. The aim of the present study was to update the 16S rRNA-RFLP identification method to include all currently characterised species of Arcobacter.

RESULTS

Digestion of the 16S rRNA gene with the endonuclease MseI produced clear, distinctive patterns for 10 of the 17 species, while the remaining species shared a common or very similar RFLP pattern. Subsequent digestion of the 16S rRNA gene from these species with the endonucleases MnlI and/or BfaI generated species-specific RFLP patterns.

CONCLUSIONS

16S rRNA-RFLP analysis identified 17 Arcobacter spp. using either polyacrylamide or agarose gel electrophoresis. Microheterogeneities within the 16S rRNA gene, which interfered with the RFLP identification, were also documented for the first time in this genus, particularly in strains of Arcobacter cryaerophilus isolated from animal faeces and aborted foetuses.