Taxonomy, epidemiology, and clinical relevance of the genus Arcobacter

Human health implications of clinically relevant bacteria in wastewater habitats

The objective of this review is to reflect on the multiple roles of bacteria in wastewater habitats with particular emphasis on their harmful potential for human health. Indigenous bacteria promote a series of biochemical and metabolic transformations indispensable to achieve wastewater treatment. Some of these bacteria may be pathogenic or harbour antibiotic resistance or virulence genes harmful for human health. Several chemical contaminants (heavy metals, disinfectants and antibiotics) may select these bacteria or their genes. Worldwide studies show that treated wastewater contain antibiotic resistant bacteria or genes encoding virulence or antimicrobial resistance, evidencing that treatment processes may fail to remove efficiently these bio-pollutants. The contamination of the surrounding environment, such as rivers or lakes receiving such effluents, is also documented in several studies. The current state of the art suggests that only some of antibiotic resistance and virulence potential in wastewater is known. Moreover, wastewater habitats may favour the evolution and dissemination of new resistance and virulence genes and the emergence of new pathogens. For these reasons, additional research is needed in order to obtain a more detailed assessment of the long-term effects of wastewater discharges. In particular, it is important to measure the human and environmental health risks associated with wastewater reuse.

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.

Isolation and identification of zoonotic species of genus arcobacter from chicken viscera obtained from retail distributors of the metropolitan area of San José, Costa Rica

Arcobacter is a genus of growing importance worldwide; some of its species are considered emerging enteropathogens and potential zoonotic agents. In Costa Rica, as well as in other countries, its isolation has been reported, so the objective of this project was to evaluate and identify the presence of Arcobacter in chicken viscera sold in the metropolitan area of San José, Costa Rica, as well as to determine the antimicrobial resistance patterns associated with it. One hundred fifty samples of chicken viscera including heart, liver, and other gastrointestinal organs were purchased from 15 supermarkets and 15 local retailers. De Boer and Houf broths were used as enrichment media; isolation was done with Arcobacter-selective medium and with membrane filtration with blood agar. Typical colonies were identified with genus-specific PCR, and species identification was made with multiplex PCR. Susceptibility to ampicillin, ciprofloxacin, chloramphenicol, erythromycin, gentamicin, and tetracycline was done with the Epsilometer test. The isolation frequency of Arcobacter genus obtained in this study was of 17.3%. A total of 33 isolates were obtained from the poultry samples, and according to the multiplex PCR methodology, 22 (66.7%) isolates were identified as Arcobacter butzleri, 8 (24.2%) as Arcobacter cryaerophilus, and 1 (3.1%) as Arcobacter skirrowii. Two strains were not identified. No statistical significant difference was found when the source of samples was compared. Resistance toward chloramphenicol was 68.75%, followed by ampicillin (43.75%) and ciprofloxacin (18.75%); all strains were susceptible to tetracycline.

Occurrence and genetic diversity of Arcobacter spp. in a spinach-processing plant and evaluation of two Arcobacter-specific quantitative PCR assays

Some species of the genus Arcobacter are considered to be emerging food pathogens. With respect to recent vegetable-borne outbreaks, the aim of this work was to investigate the occurrence and diversity of Arcobacter within the production chain of a spinach-processing plant by a combination of cultivation and molecular methods. Samples including spinach, water, and surface biofilm were taken over a period of three years from the entire processing line. Ten 16S rRNA (rrs) gene clone libraries were constructed and analysed using amplified rRNA gene restriction analysis (ARDRA). Approximately 1200 clones were studied that resulted in 44 operational taxonomic units (OTUs). Sequences with high similarities to Arcobacter cryaerophilus (13% of clones, 3 OTUs), A. ellisii (4%, 6 OTUs), A. suis (15%, 3 OTUs), and the type strain of A. nitrofigilis (1%, 7 OTUs) were identified. This represents the first report of the detection of the recently described species A. ellisii, A. suis and, in addition, A. venerupis from alternative habitats. A total of 67% of the clones (22 OTUs) could not be assigned to a genus, which indicated the presence of uncharacterised Arcobacter species. For the cultivation-independent detection of Arcobacter, two genus-specific quantitative PCR (qPCR) assays were developed and tested on 15 Arcobacter species. When these assays were applied to samples from the spinach-processing plant, they showed positive results for up to 35% of the samples and supported the conclusion that there is a considerable risk for the transfer of pathogenic Arcobacter species on vegetables, which was also verified by a cultivation approach.

Antibiotic resistance, antimicrobial residues and bacterial community composition in urban wastewater

This study was based on the hypothesis that the occurrence of antimicrobial residues and antibiotic resistant bacteria in the sewage could be correlated with the structure and composition of the bacterial community and the antibiotic resistance loads of the final effluent. Raw and treated wastewater composite samples were collected from an urban treatment plant over 14 sampling dates. Samples were characterized for the i) occurrence of tetracyclines, penicillins, sulfonamides, quinolones, triclosan, arsenic, cadmium, lead, chromium and mercury; ii) antibiotic resistance percentages for tetracycline, sulfamethoxazole, ciprofloxacin and amoxicillin and iii) 16S rRNA gene-DGGE patterns. The data of corresponding samples, taking into account the hydraulic residence time, was analyzed using multivariate analysis. Variations on the bacterial community structure of the final effluent were significantly correlated with the occurrence of tetracyclines, penicillins, sulfonamides, quinolones and triclosan in the raw inflow. Members of the class Epsilonproteobacteria presented positive correlations with those antimicrobials, whereas negative correlations were observed with Beta and Gammaproteobacteria and Firmicutes. Antibiotic resistance percentages presented different trends of variation in heterotrophs/enterobacteria and in enterococci, varied over time and after wastewater treatment. Antibiotic resistance was positively correlated with the occurrence of tetracyclines residues and high temperature. A relationship between antibiotic residues, bacterial community structure and composition and antibiotic resistance is demonstrated. Further studies, involving more wastewater treatment plants may help to elucidate this complex relationship.

Presence of Campylobacter and Arcobacter species in in-line milk filters of farms authorized to produce and sell raw milk and of a water buffalo dairy farm in Italy

The objectives of this study were to investigate the presence of Campylobacter spp. and Arcobacter spp. in dairy herds authorized for the production and sale of raw milk and in a water buffalo dairy farm, and to test the antimicrobial susceptibility of the isolates. A total of 196 in-line milk filters were collected from 14 dairy farms (13 bovine and 1 water buffalo) for detection of Campylobacter spp. and Arcobacter spp. by microbiological culture. For each farm investigated, 1 isolate for each Campylobacter and Arcobacter species isolated was tested using the Etest method (AB Biodisk, Solna, Sweden) to evaluate the susceptibility to ciprofloxacin, tetracycline, chloramphenicol, ampicillin, erythromycin, and gentamicin. A total of 52 isolates were detected in 49 milk filters in 12 farms (85.7%) out of 14 and the isolates were identified as Campylobacter jejuni (6), Campylobacter hyointestinalis ssp. hyointestinalis (8), Campylobacter concisus (1), Campylobacter fetus ssp. fetus (1), Arcobacter butzleri (22), and Arcobacter cryaerophilus (14). The small number of isolates tested for antimicrobial susceptibility precludes any epidemiological consideration but highlights that all Campylobacter isolates were susceptible to macrolides, which are the first-choice drugs for the treatment of campylobacteriosis, and that resistance to fluoroquinolones and tetracycline was detected; for Arcobacter isolates, resistance to ampicillin and chloramphenicol was detected. The sale of raw milk for human consumption by self-service automatic vending machines has been allowed in Italy since 2004 and the presence of C. jejuni in in-line milk filters confirms that raw milk consumption is a significant risk factor for human infection. The high occurrence of emerging Campylobacter spp. and Arcobacter spp. discovered in dairy farms authorized for production and sale of raw milk represents an emerging hazard for human health.

Assessment of the prevalence and diversity of emergent campylobacteria in human stool samples using a combination of traditional and molecular methods

This study aims to assess the diversity of campylobacteria (Campylobacter and Arcobacter) in human fecal samples from patients with diarrhea (n = 140) and asymptomatic controls (n = 116) in Chile, using a combination of traditional culture and molecular methods. The culture methods detected campylobacteria in 10.7% of the patients with diarrhea and in 1.7% of the controls. In contrast, the molecular methods detected campylobacteria more often than the traditional culture, with a prevalence of 25.7% and 5.2%, respectively. The traditional methods only recovered the species Campylobacter jejuni, Campylobacter coli, and Arcobacter butzleri, whereas the molecular methods additionally detected the emergent species Campylobacter concisus and Campylobacter ureolyticus.

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.

Small changes in pH have direct effects on marine bacterial community composition: a microcosm approach

As the atmospheric CO(2) concentration rises, more CO(2) will dissolve in the oceans, leading to a reduction in pH. Effects of ocean acidification on bacterial communities have mainly been studied in biologically complex systems, in which indirect effects, mediated through food web interactions, come into play. These approaches come close to nature but suffer from low replication and neglect seasonality. To comprehensively investigate direct pH effects, we conducted highly-replicated laboratory acidification experiments with the natural bacterial community from Helgoland Roads (North Sea). Seasonal variability was accounted for by repeating the experiment four times (spring, summer, autumn, winter). Three dilution approaches were used to select for different ecological strategies, i.e. fast-growing or low-nutrient adapted bacteria. The pH levels investigated were in situ seawater pH (8.15-8.22), pH 7.82 and pH 7.67, representing the present-day situation and two acidification scenarios projected for the North Sea for the year 2100. In all seasons, both automated ribosomal intergenic spacer analysis and 16S ribosomal amplicon pyrosequencing revealed pH-dependent community shifts for two of the dilution approaches. Bacteria susceptible to changes in pH were different members of Gammaproteobacteria, Flavobacteriaceae, Rhodobacteraceae, Campylobacteraceae and further less abundant groups. Their specific response to reduced pH was often context-dependent. Bacterial abundance was not influenced by pH. Our findings suggest that already moderate changes in pH have the potential to cause compositional shifts, depending on the community assembly and environmental factors. By identifying pH-susceptible groups, this study provides insights for more directed, in-depth community analyses in large-scale and long-term experiments.

Regulation of energy metabolism by the extracytoplasmic function (ECF) σ factors of Arcobacter butzleri

The extracytoplasmic function (ECF) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. The emerging pathogen Arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ECF family. Here, we report the identification of the genes regulated by five out of the seven A. butzleri ECF σ factors. Three of the ECF σ factors play an apparent role in transport, energy generation and the maintenance of redox balance. Several genes like the nap, sox and tct genes are regulated by more than one ECF σ factor, indicating that the A. butzleri ECF σ factors form a network of overlapping regulons. In contrast to other eubacteria, these A. butzleri ECF regulons appear to primarily regulate responses to changing environments in order to meet metabolic needs instead of an obvious role in stress adaptation.

Emerging pathogen Arcobacter spp. in acute gastroenteritis: molecular identification, antibiotic susceptibilities and genotyping of the isolated arcobacters

The aims of this study were as follows: (i) to isolate Arcobacter spp. from the stool samples of patients with gastroenteritis; (ii) to identify them with molecular methods; (iii) to genotype them using enterobacterial repetitive intergenic consensus (ERIC)-PCR; and (iv) to determine their antibiotic susceptibilities. For the study, a total of 3287 diarrhoeal stool samples submitted to the Microbiology Laboratory of the Kayseri Training and Research Hospital, Kayseri, Turkey, between 2010 and 2011 were analysed. Campylobacter blood-free selective medium supplemented with cefoperazone, amphotericin B and teicoplanin was used for isolation. Medium inoculated with stool samples was incubated microaerobically at 37 °C for 72-96 h. Phenotypic tests, a genus-specific PCR and a multiplex PCR were used to identify the arcobacters, whilst ERIC-PCR was used for genotyping and the antibiotic susceptibilities of the isolates were detected by E-test. Arcobacter spp. were isolated from nine of the 3287 samples. These nine isolates were identified as Arcobacter butzleri and all showed different ERIC-PCR profiles. All nine isolates were resistant to ampicillin and susceptible to gentamicin, tetracycline, erythromycin and ciprofloxacin. As far as is known, this is the first study in which A. butzleri has been isolated from human acute gastrointestinal infections in Turkey. According to these results, it is recommended that, when investigating the aetiology of infections of the digestive system in humans, Arcobacter spp. be considered for inclusion. The results of this study should contribute to our knowledge related to A. butzleri infections in humans.

Genetic characterization of Arcobacter isolates from various sources

Arcobacter is getting more attention due to its detection from wide host-range and foods of animal origin. The objective of this study was to determine the prevalence of Arcobacter spp. in various sources at farm level and beef retailed in markets in Malaysia and to assess the genetic relatedness among them. A total of 273 samples from dairy cattle including cattle (n=120), floor (n=30), water (n=18) and milk (n=105) as well as 148 beef samples collected from retail markets were studied. The overall prevalence of Arcobacter in various sources was 15% (63/421). However, source-wise detection rate of Arcobacter spp. was recorded as 26.66% (8/30) in floor, 26.3% (39/148) in beef, 11.11% (2/18) in water, 7.6% (8/105) in milk and 6.66% (8/120) in cattle. Arcobacter butzleri was the frequently isolated species however, a total of 75%, 66.7%, 53.8%, 50% and 12.5%% samples from floor, milk, beef, water and cattle, respectively, were carrying more than one species simultaneously. One (12.5%) cattle and beef sample (2.5%) found to be carrying one Arcobacter spp., A. skirrowii, only. Typing of Arcobacter isolates was done though pulsed field gel electrophoresis (PFGE) after digested with Eag1 restriction endonuclease (RE). Digestion of genomic DNA of Arcobacter from various sources yielded 12 major clusters (≥ 50% similarity) which included 29 different band patterns. A number of closely related A. butzleri isolates were found from beef samples which indicate cross contamination of common type of Arcobacter. Fecal shedding of Arcobacter by healthy animals can contaminate water and milk which may act as source of infection in humans.

Arcobacter in Lake Erie beach waters: an emerging gastrointestinal pathogen linked with human-associated fecal contamination

The genus Arcobacter has been associated with human illness and fecal contamination by humans and animals. To better characterize the health risk posed by this emerging waterborne pathogen, we investigated the occurrence of Arcobacter spp. in Lake Erie beach waters. During the summer of 2010, water samples were collected 35 times from the Euclid, Villa Angela, and Headlands (East and West) beaches, located along Ohio's Lake Erie coast. After sample concentration, Arcobacter was quantified by real-time PCR targeting the Arcobacter 23S rRNA gene. Other fecal genetic markers (Bacteroides 16S rRNA gene [HuBac], Escherichia coli uidA gene, Enterococcus 23S rRNA gene, and tetracycline resistance genes) were also assessed. Arcobacter was detected frequently at all beaches, and both the occurrence and densities of Arcobacter spp. were higher at the Euclid and Villa Angela beaches (with higher levels of fecal contamination) than at the East and West Headlands beaches. The Arcobacter density in Lake Erie beach water was significantly correlated with the human-specific fecal marker HuBac according to Spearman's correlation analysis (r = 0.592; P < 0.001). Phylogenetic analysis demonstrated that most of the identified Arcobacter sequences were closely related to Arcobacter cryaerophilus, which is known to cause gastrointestinal diseases in humans. Since human-pathogenic Arcobacter spp. are linked to human-associated fecal sources, it is important to identify and manage the human-associated contamination sources for the prevention of Arcobacter-associated public health risks at Lake Erie beaches.

Arcobacter bivalviorum sp. nov. and Arcobacter venerupis sp. nov., new species isolated from shellfish

A group of ten Arcobacter isolates (Gram negative, slightly curved motile rods, oxidase positive) was recovered from mussels (nine) and from clams (one). These isolates could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR). The aim of this study is to establish the taxonomic position of these isolates. The 16S rRNA gene sequence similarity of mussel strain F4(T) to the type strains of all other Arcobacter species ranged from 91.1% to 94.8%. The species most similar to the clams' strain F67-11(T) were Arcobacter defluvii (CECT 7697(T), 97.1%) and Arcobacter ellisii (CECT 7837(T), 97.0%). On the basis of phylogenetic analyses with 16S rRNA, rpoB, gyrB and hsp60 genes, the mussel and clam strains formed two different, new lineages within the genus Arcobacter. These data, together with their different phenotypic characteristics and MALDI-TOF mass spectra, revealed that these strains represent two new species, for which the names Arcobacter bivalviorum (type strain F4(T)=CECT 7835(T)=LMG 26154(T)) and Arcobacter venerupis (type strain F67-11(T)=CECT 7836(T)=LMG 26156(T)) are proposed.

Prevalence, distribution and antibiotic resistance of emergent Arcobacter spp. from clinically healthy cattle and goats

Prevalence, distribution and antibiotic resistance of Arcobacter spp. were investigated in cattle, goats, floor and treated water samples in this study. The prevalence of Arcobacter in adult and young was recorded as 8/110 (7.27%) and 4/83 (4.81%), respectively, which showed insignificant difference (P = 0.3503) in detection rates between adult and young cattle. A total of 33.33% of the floor samples and 11.11% of the treated water samples analysed were determined as positive for Arcobacter. Among the species isolated, over all, A. butzleri (45%) was the most frequently detected species, followed by A. skirrowii (5%). A. butzleri was isolated from adult cattle, floor and water samples at the rates of 75.0%, 33.4% and 50%, respectively. Co-colonization of species was not uncommon, and 50% of the samples were carrying more than one Arcobacter species. Only 12.5% sample from cattle (adult) was detected positive for only A. skirrowii. All samples from young animals, floor and water contained mixed isolates. None of the samples from goat farm was found to be carrying Arcobacter species. On profiling of antimicrobial resistance patterns, it was found that only one A. butzleri isolate (3.7%) was sensitive to all nine antibiotics tested. A. butzleri was found highly resistant to ampicillin (55.6%), followed by cefotaxime (33.4%) and ciprofloxacin (33.4%). Overall, 20% of the isolates showed multidrug resistance (resistant ≥4 antibiotics). Gentamicin and enrofloxacin can be used as drugs of choice for the treatment for Arcobacter infections.

Microbial community composition and dynamics of moving bed biofilm reactor systems treating municipal sewage

Moving bed biofilm reactor (MBBR) systems are increasingly used for municipal and industrial wastewater treatment, yet in contrast to activated sludge (AS) systems, little is known about their constituent microbial communities. This study investigated the community composition of two municipal MBBR wastewater treatment plants (WWTPs) in Wellington, New Zealand. Monthly samples comprising biofilm and suspended biomass were collected over a 12-month period. Bacterial and archaeal community composition was determined using a full-cycle community approach, including analysis of 16S rRNA gene libraries, fluorescence in situ hybridization (FISH) and automated ribosomal intergenic spacer analysis (ARISA). Differences in microbial community structure and abundance were observed between the two WWTPs and between biofilm and suspended biomass. Biofilms from both plants were dominated by Clostridia and sulfate-reducing members of the Deltaproteobacteria (SRBs). FISH analyses indicated morphological differences in the Deltaproteobacteria detected at the two plants and also revealed distinctive clustering between SRBs and members of the Methanosarcinales, which were the only Archaea detected and were present in low abundance (<5%). Biovolume estimates of the SRBs were higher in biofilm samples from one of the WWTPs which receives both domestic and industrial waste and is influenced by seawater infiltration. The suspended communities from both plants were diverse and dominated by aerobic members of the Gammaproteobacteria and Betaproteobacteria. This study represents the first detailed analysis of microbial communities in full-scale MBBR systems and indicates that this process selects for distinctive biofilm and planktonic communities, both of which differ from those found in conventional AS systems.