Arcobacter butzleri: underestimated enteropathogen

Occurrence, Sources and Virulence Potential of Arcobacter butzleri in Urban Municipal Stormwater Systems

A. butzleri is an underappreciated emerging global pathogen, despite growing evidence that it is a major contributor of diarrheal illness. Few studies have investigated the occurrence and public health risks that this organism possesses from waterborne exposure routes including through stormwater use. In this study, we assessed the prevalence, virulence potential, and primary sources of stormwater-isolated A. butzleri in fecally contaminated urban stormwater systems. Based on qPCR, A. butzleri was the most common enteric bacterial pathogen [25%] found in stormwater among a panel of pathogens surveyed, including Shiga-toxin producing Escherichia coli (STEC) [6%], Campylobacter spp. [4%], and Salmonella spp. [<1%]. Concentrations of the bacteria, based on qPCR amplification of the single copy gene hsp60, were as high as 6.2 log10 copies/100 mL, suggesting significant loading of this pathogen in some stormwater systems. Importantly, out of 73 unique stormwater culture isolates, 90% were positive for the putative virulence genes cadF, ciaB, tlyA, cjl349, pldA, and mviN, while 50-75% of isolates also possessed the virulence genes irgA, hecA, and hecB. Occurrence of A. butzleri was most often associated with the human fecal pollution marker HF183 in stormwater samples. These results suggest that A. butzleri may be an important bacterial pathogen in stormwater, warranting further study on the risks it represents to public health during stormwater use.

Opportunistic Pathogens in Drinking Water Distribution Systems-A Review

In contrast to "frank" pathogens, like Salmonella entrocolitica, Shigella dysenteriae, and Vibrio cholerae, that always have a probability of disease, "opportunistic" pathogens are organisms that cause an infectious disease in a host with a weakened immune system and rarely in a healthy host. Historically, drinking water treatment has focused on control of frank pathogens, particularly those from human or animal sources (like Giardia lamblia, Cryptosporidium parvum, or Hepatitis A virus), but in recent years outbreaks from drinking water have increasingly been due to opportunistic pathogens. Characteristics of opportunistic pathogens that make them problematic for water treatment include: (1) they are normally present in aquatic environments, (2) they grow in biofilms that protect the bacteria from disinfectants, and (3) under appropriate conditions in drinking water systems (e.g., warm water, stagnation, low disinfectant levels, etc.), these bacteria can amplify to levels that can pose a public health risk. The three most common opportunistic pathogens in drinking water systems are Legionella pneumophila, Mycobacterium avium, and Pseudomonas aeruginosa. This report focuses on these organisms to provide information on their public health risk, occurrence in drinking water systems, susceptibility to various disinfectants, and other operational practices (like flushing and cleaning of pipes and storage tanks). In addition, information is provided on a group of nine other opportunistic pathogens that are less commonly found in drinking water systems, including Aeromonas hydrophila, Klebsiella pneumoniae, Serratia marcescens, Burkholderia pseudomallei, Acinetobacter baumannii, Stenotrophomonas maltophilia, Arcobacter butzleri, and several free-living amoebae including Naegleria fowleri and species of Acanthamoeba. The public health risk for these microbes in drinking water is still unclear, but in most cases, efforts to manage Legionella, mycobacteria, and Pseudomonas risks will also be effective for these other opportunistic pathogens. The approach to managing opportunistic pathogens in drinking water supplies focuses on controlling the growth of these organisms. Many of these microbes are normal inhabitants in biofilms in water, so the attention is less on eliminating these organisms from entering the system and more on managing their occurrence and concentrations in the pipe network. With anticipated warming trends associated with climate change, the factors that drive the growth of opportunistic pathogens in drinking water systems will likely increase. It is important, therefore, to evaluate treatment barriers and management activities for control of opportunistic pathogen risks. Controls for primary treatment, particularly for turbidity management and disinfection, should be reviewed to ensure adequacy for opportunistic pathogen control. However, the major focus for the utility's opportunistic pathogen risk reduction plan is the management of biological activity and biofilms in the distribution system. Factors that influence the growth of microbes (primarily in biofilms) in the distribution system include, temperature, disinfectant type and concentration, nutrient levels (measured as AOC or BDOC), stagnation, flushing of pipes and cleaning of storage tank sediments, and corrosion control. Pressure management and distribution system integrity are also important to the microbial quality of water but are related more to the intrusion of contaminants into the distribution system rather than directly related to microbial growth. Summarizing the identified risk from drinking water, the availability and quality of disinfection data for treatment, and guidelines or standards for control showed that adequate information is best available for management of L. pneumophila. For L. pneumophila, the risk for this organism has been clearly established from drinking water, cases have increased worldwide, and it is one of the most identified causes of drinking water outbreaks. Water management best practices (e.g., maintenance of a disinfectant residual throughout the distribution system, flushing and cleaning of sediments in pipelines and storage tanks, among others) have been shown to be effective for control of L. pneumophila in water supplies. In addition, there are well documented management guidelines available for the control of the organism in drinking water distribution systems. By comparison, management of risks for Mycobacteria from water are less clear than for L. pneumophila. Treatment of M. avium is difficult due to its resistance to disinfection, the tendency to form clumps, and attachment to surfaces in biofilms. Additionally, there are no guidelines for management of M. avium in drinking water, and one risk assessment study suggested a low risk of infection. The role of tap water in the transmission of the other opportunistic pathogens is less clear and, in many cases, actions to manage L. pneumophila (e.g., maintenance of a disinfectant residual, flushing, cleaning of storage tanks, etc.) will also be beneficial in helping to manage these organisms as well.

Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water

BACKGROUND

Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites.

RESULTS

All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic.

CONCLUSIONS

The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.

Widespread Multidrug Resistance of Arcobacter butzleri Isolated from Clinical and Food Sources in Central Italy

The Arcobacter genus comprises a group of bacteria widely distributed in different habitats that can be spread throughout the food chain. Fluoroquinolones and aminoglycosides represent the most common antimicrobial agents used for the treatment of Arcobacter infections. However, the increasing trend of the antimicrobial resistance of this pathogen leads to treatment failures. Moreover, the test implementation and interpretation are hindered by the lack of reference protocols and standard interpretive criteria. The purpose of our study was to assess the antibiotic resistance pattern of 17 A. butzleri strains isolated in Central Italy from fresh vegetables, sushi, chicken breast, and clinical human samples to provide new and updated information about the antimicrobial resistance epidemiology of this species. Antimicrobial susceptibility testing was carried out by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)'s disc diffusion method. All the strains were multidrug resistant, with 100% resistance to tetracyclines and cefotaxime (third generation cephalosporins). Some differences were noticed among the strains, according to the isolation source (clinical isolates, food of animal origin, or fresh vegetables), with a higher sensitivity to streptomycin detected only in the strains isolated from fresh vegetables. Our data, together with other epidemiological information at the national or European Union (EU) level, may contribute to developing homogeneous breakpoints. However, the high prevalence of resistance to a wide range of antimicrobial classes makes this microorganism a threat to human health and suggests that its monitoring should be considered by authorities designated for food safety.

Comparison of Two Culture-Based Detection Systems for the Isolation of Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii in Raw Ground Poultry

Arcobacters are emerging pathogens that have been underestimated due to a lack of a standardized isolation method. The aim of this research was to evaluate the ability to isolate Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii using two Arcobacter-specific culture detection systems: (i) the Houf broth and modified charcoal cefoperazone deoxycholate agar supplemented with cefoperazone, amphotericin B, and teicoplanin (HB/mCCDA+CAT), and (ii) the Nguyen-Restaino-Juárez Arcobacter enrichment broth and chromogenic agar (NRJ-B/M). Both detection systems were evaluated for productivity ratio, sensitivity, and specificity. As a result, the productivity ratio for both plating agars were >90%, which indicates that the selective agents used in the two plating agars did not inhibit Arcobacter growth. Moreover, sensitivity evaluations using artificially inoculated retail ground poultry (n = 780) determined that both detection systems were able to isolate A. butlzeri with >95% sensitivity at the 0.1 and 1.0-2.0 CFU/g detection level. The sensitivity in A. cryaerophilus isolation was higher for NRJ-B/M (78.0% at 0.1 CFU/g; 95.1% at 1.0-2.0 CFU/g) when compared with HB/mCCDA+CAT (34.1% at 0.1 CFU/g; 51.2% at 1.0-2.0 CFU/g). Both detection systems resulted in <50% sensitivity when isolating A. skirrowii at 0.1 and 1.0-2.0 CFU/g; however, the sensitivity for NRJ-B/M was significantly higher than HB/mCCDA+CAT. At the detection level of 5.0 CFU/g, both detection systems were able to isolate A. skirrowii with 100% sensitivity. Specificity comparisons using uninoculated ground poultry samples (n = 40) indicated the growth of background microbiota were significantly inhibited or could be easily differentiated on NRJ-B/M (90.0%, specificity) when compared with HB/mCCDA+CAT (30.0%, specificity). Overall, these results show that the NRJ-B/M detection system is a more sensitive and specific detection system when isolating Arcobacter spp. from ground chicken.

Antimicrobial Resistance and Pathogenicity of Aliarcobacter butzleri Isolated from Poultry Meat

Aliarcobacter butzleri (A. butzleri) is an emergent zoonotic food-related pathogen that can be transmitted through the consumption of poultry meat. Data regarding the pathogenicity and resistance of A. butzleri are still scarce, and the presence of virulent MDR strains of this zoonotic pathogen in poultry meat is an issue of particular concern to public health. This study aimed to characterize the pathogenicity and antimicrobial resistance profiles of A. butzleri strains isolated from poultry meat sold at retail markets in São Paulo, Brazil. The minimum inhibitory concentrations of 27 strains were determined using the broth microdilution method. The results showed that 77.7% of the isolates were resistant to clindamycin, 62.9% to florfenicol, 59.2% to nalidixic acid, 11.1% to azithromycin, 7.4% to ciprofloxacin and telithromycin, and 3.7% to erythromycin and tetracycline, although all were susceptible to gentamicin. Moreover, 55.5% of the virulent isolates were also multidrug-resistant (MDR). Three strains were selected for pathogenicity tests in vitro and in vivo. The tested strains expressed weak/moderate biofilm production and showed a diffuse adhesion pattern (3 h) in HeLa cells and toxicity in Vero cells (24 h). Experimental inoculation in 11-week-old chicks induced a transitory inflammatory enteritis. Intestinal hemorrhage and destruction of the intestinal crypts were observed in the rabbit ileal loop test. Considering the fact that Brazil is a major exporter of poultry meat, the data from this study point to the need of improvement of the diagnostic tools, as well as of the adoption of surveillance guidelines and more specific control strategies to ensure food safety, reducing the presence of pathogenic MDR strains in broilers.

Arcobacter species in milk contamination: a prevalence-based systematic review and meta-analysis

AIMS

Milk is consumed raw or minimally processed and plays a role in the dissemination of pathogens of public health concerns. The present investigation is aimed at assessing the occurrence of pathogenic Arcobacter species in 2945 milk samples.

METHODS AND RESULTS

Arcobacter data systematically retrieved from five repositories until 20 February 2022 according to PRISMA principles were logit transformed and fitted using a generalized linear mixed-effects model. The between-study heterogeneity was estimated as I2-value. Leave-one-out cross-validation and funnel plot with Egger's tests were used to assess the hardiness and bias in the model. The global prevalence of Arcobacter genus in the milk was 12% [95% confidence interval (CI): 7-19%; I2 = 87.3%, 95% CI: 83.0-90.6%] and no publication bias observed (Egger's test: P = 0.112). Arcobacter genus prevalence in milk was 13% (95% CI: 5-30%), 10% (95% CI: 1-46%), and 9% (95% CI: 4-19%) in Europe, South America, and Asia, respectively. Arcobacter butzleri was the most prevalent [8% (95% CI: 4-13%)], followed by A. cryaerophilus [0.6% (95% CI: 0.2-33.2%)] and A. skirrowii [0.19% (95% CI: 0.03-1.2%)]. Also, species-specific prevalence of A. butzleri, A. cryaerophilus, and A. skirrowii varied continentally, but the test for species-specific/continental differences was not significantly different (P > 0.5).

Investigation of Antibiotic Resistome in Hospital Wastewater during the COVID-19 Pandemic: Is the Initial Phase of the Pandemic Contributing to Antimicrobial Resistance?

Since the COVID-19 pandemic started, there has been much speculation about how COVID-19 and antimicrobial resistance may be interconnected. In this study, untreated wastewater was sampled from Hospital A designated to treat COVID-19 patients during the first wave of the COVID-19 pandemic alongside Hospital B that did not receive any COVID-19 patients. Metagenomics was used to determine the relative abundance and mobile potential of antibiotic resistant genes (ARGs), prior to determining the correlation of ARGs with time/incidence of COVID-19. Our findings showed that ARGs resistant to macrolides, sulfonamides, and tetracyclines were positively correlated with time in Hospital A but not in Hospital B. Likewise, minor extended spectrum beta-lactamases (ESBLs) and carbapenemases of classes B and D were positively correlated with time, suggesting the selection of rare and/or carbapenem-resistant genes in Hospital A. Non-carbapenemase bla_VEB also positively correlated with both time and intI1 and was copresent with other ARGs including carbapenem-resistant genes in 6 metagenome-assembled genomes (MAGs). This study highlighted concerns related to the dissemination of antimicrobial resistance (AMR) during the COVID-19 pandemic that may arise from antibiotic use and untreated hospital wastewater.

Molecular Cut-off Values for Aliarcobacter butzleri Susceptibility Testing

Aliarcobacter butzleri is an emerging gastrointestinal pathogen found in many countries worldwide. In France, it has become the third most commonly isolated bacterial species from the stools of patients with intestinal infections. No interpretative criteria for antimicrobial susceptibility testing have been proposed for A. butzleri, and most strains are categorized using the recommendations of the Clinical and Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing for Campylobacter or Enterobacterales. In the present study, the genomes of 30 resistant A. butzleri isolates were analyzed to propose specific epidemiological cut-off values for ampicillin, ciprofloxacin, erythromycin, and tetracycline. The identification of a β-lactamase and the T85I GyrA mutation associated with ampicillin and ciprofloxacin resistance, respectively, allowed us to adjust the disk diffusion (DD) and MIC cut-off values for these molecules. However, epidemiological cut-off values for erythromycin and tetracycline could not be estimated due to the absence of known resistance mechanisms. The present study paves the way for building a consensus for antimicrobial susceptibility testing for this concerning pathogen.

IMPORTANCEAliarcobacter butzleri is an emerging and concerning intestinal pathogen. Very few studies have focused on this particular species, and antimicrobial susceptibility testing (AST) is based on methods that have been mostly developed for Campylobacter spp. In fact, no disk diffusion and E-tests adapted cut-offs for A. butzleri are available which leads to misinterpretations. We have shown here that NGS approach to identify genes and mutations in close relation to phenotypic resistance levels is a robust way to solve that issue and precisely differentiate WT and NWT A. butzleri isolates for frequently used antimicrobials. MIC and DD cut-off values have been significantly adjusted and answer the need for a global consensus regarding AST for A. butzleri.

Arcobacter Butzleri in an AIDS Patient

Background

Arcobacter butzleri (A. butzleri) is an emerging enteric pathogen increasingly identified in Europe and is likely under-reported in other global regions. We describe to our knowledge the first case report of A. butzleri in an AIDS patient, along with the first documented local (Singapore) case of A. butzleri infection. Case Presentation. A 38-year-old AIDS patient presented with diarrhoea of 2 weeks' duration. Stool cultures yielded A. butzleri. The patient was treated with 3 days of ciprofloxacin with clinical resolution of diarrhoea.

Conclusion

A. butzleri is likely to be present, although under-reported in AIDS patients, and it should be noted as a pathogen of increasing significance.

NRJ Media as the Gold-Standard Arcobacter-Specific Detection System: Applications in Poultry Testing

Arcobacter species are ubiquitous emerging pathogens with an impact that has been underestimated due to limitations in isolation and detection methods. Our group recently developed the novel NRJ Arcobacter-detection system, with major improvements in specificity and selectivity compared to other culture-based methods. In this work, the NRJ detection system was evaluated using retail whole broiler chicken carcass. Nanopore 16S rRNA gene amplicon sequencing demonstrated that Arcobacter species are found in very low abundance in retail chicken and that indigenous microbiota could be a major factor interfering with detection. Comparison of the microbiome obtained from modified Houf broth (HB) method, as the standard detection system, and the novel NRJ method, showed Arcobacter abundances of <15% and >97%, respectively. The NRJ system significantly inhibits the growth of non-target microbiota, and specifically allows the multiplication of Arcobacter species. In this report, we describe the gold-standard of Arcobacter-specific culture-based method to test food matrices, which can be used for other applications, such as clinical and environmental sampling.

Microbial community origin and fate through a rural wastewater treatment plant

Conventional wastewater treatment relies on a complex microbiota; however, much of this community is still to be characterised. To better understand the origin, dynamics and fate of bacteria within a wastewater treatment plant: untreated primary wastewater, activated sludge, and post-treatment effluent were characterised. From 3,163 Exact Sequence Variants (ESVs), 860 were annotated to species-level. In primary wastewater, 28% of ESVs were putative bacterial species previously associated with humans, 14% with animals and 5% as common to the environment. Differential abundance analysis revealed significant relative reductions in ESVs from potentially humans-associated species from primary wastewater to activated sludge, and significant increases in ESVs from species associated with nutrient cycling. Between primary wastewater and effluent, 51% of ESVs from human-associated species did not significantly differ, and species such as Bacteroides massiliensis and Bacteroides dorei increased. These findings illustrate that activated sludge increased extracellular protease and urease-producing species, ammonia and nitrite oxidizers, denitrifiers and specific phosphorus accumulators. Although many human-associated species declined, some persisted in effluent, including strains of potential health or environmental concern. Species-level microbial assessment may be useful for understanding variation in wastewater treatment efficiency as well as for monitoring the release of microbes into surface water and the wider ecosystem. This article is protected by copyright. All rights reserved.

First case of diarrhea due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador

The first case of acute watery diarrhea disease due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador is reported. An infant presented with moderate protein-calorie malnutrition, dehydration and anemia. A curved Gram-negative organism was isolated from stools, having been preliminarily identified by phenotypic characteristics. Definitive identification was achieved by multiplex PCR. Aliarcobacter butzleri was the only pathogenic microorganism isolated. No other entero-pathogens, enterovirus or parasites were found. Our findings strongly suggest that in this specific case, A. butzleri was the etiological agent. Further investigations are needed to develop standardized diagnostic protocols and to establish the prevalence and significance of Aliarcobacter infections in humans.

Bacterial diversity assessment of world's largest sewage-fed fish farms with special reference to water quality: a Ramsar site

Bacterial community structure is one of the essential components of aquaculture dynamics and plays an important role in maintaining wetland health. The present work is an effort to study the structure of bacterial communities in the world's largest sewage-fed fish farms, the East Kolkata Wetlands (EKWs), along with their predicted functional metabolic pathways and correlation with environmental variables. Sequencing data analysis revealed the abundance of genera such as Arcobacter (0-50%), Pseudomonas (0-15%), Sulfurospirillum (0-9%), Cloacibacterium (0-6%), hgcI clade (7-29%), C39 (0-9%), V6 (3-36%), Fluiivicola (1-6%) and Cyanobium (3-8%) in the EKWs. Further, water quality analysis of three treatment groups, i.e. Sewage, Sewage F-1 and Sewage F-2, revealed that dissolved oxygen (DO), biochemical oxygen demand (BOD) and chemical oxygen demand (COD) differed significantly and violated the standard prescribed norms (Central Pollution Control Board, CPCB, New Delhi) for fishery propagation and irrigation in India. Further, the correlation matrix analysis between the abundance of bacterial genera and environmental variables indicated that DO, BOD and COD were mainly responsible for bacterial community structure and their proliferation in the EKWs. Our results indicated that the abundance of genera such as Arcobacter, Pseudomonas, Sulfurospirillum and Cloacibacterium has an inverse relationship with BOD and COD. Our observations based on the bacterial community structure and deteriorated water quality indicate the ineffective functioning and poor management of this man-made constructed wetland.

Presence and quantification of pathogenic Arcobacter and Campylobacter species in retail meats available in Japan

We present estimations for the amounts of Arcobacter (A. butzleri, A. cryaerophilus and A. skirrowii) and Campylobacter (C. jejuni, C. coli and C. fetus) species in retail chicken, pork and beef meat using PCR-MPN. Arcobacter butzleri, A. cryaerophilus and C. jejuni were found in 100, 60 and 55% of chicken samples, respectively. No other Arcobacter or Campylobacter species were found in chicken. The MPNs of A. butzleri, A. cryaerophilus and C. jejuni were greater than 10³ per 100 g in 50, 0 and 5% of samples, respectively. The MPN of A. butzleri was higher than that of C. jejuni in 95% of samples. In pork, A. butzleri and A. cryaerophilus were detected in 10 and 11 (50 and 55%) of 20 samples, respectively. No other Arcobacter or Campylobacter species were found in pork. Only one pork sample had more than 10³ MPN per 100 g of A. cryaerophilus. For beef, only two samples tested positive for A. cryaerophilus, at 4600 and 92 MPN per 100 g. Overall, we found that the presence and MPNs of Arcobacter species are very high in chicken. In contrast, the positive ratios of Arcobacter in pork were high as chicken samples, but MPNs were lower than in chicken.

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

Converting conventional farms to organic systems to improve ecosystem health is an emerging trend in recent decades, yet little is explored to what extent and how this process drives the taxonomic diversity and functional capacity of above-ground microbes. This study was, therefore, conducted to investigate the effects of agricultural management, i.e., organic, transition, and conventional, on the structure and function of sugarcane phyllosphere microbial community using the shotgun metagenomics approach. Comparative metagenome analysis exhibited that farming practices strongly influenced taxonomic and functional diversities, as well as co-occurrence interactions of phyllosphere microbes. A complex microbial network with the highest connectivity was observed in organic farming, indicating strong resilient capabilities of its microbial community to cope with the dynamic environmental stressors. Organic farming also harbored genus Streptomyces as the potential keystone species and plant growth-promoting bacteria as microbial signatures, including Mesorhizobium loti, Bradyrhizobium sp. SG09, Lactobacillus plantarum, and Bacillus cellulosilyticus. Interestingly, numerous toxic compound-degrading species were specifically enriched in transition farming, which might suggest their essential roles in the transformation of conventional to organic farming. Moreover, conventional practice diminished the abundance of genes related to cell motility and energy metabolism of phyllosphere microbes, which could negatively contribute to lower microbial diversity in this habitat. Altogether, our results demonstrated the response of sugarcane-associated phyllosphere microbiota to specific agricultural managements that played vital roles in sustainable sugarcane production.

Antimicrobial Susceptibility and Genomic Analysis of Aliarcobacter cibarius and Aliarcobacter thereius, Two Rarely Detected Aliarcobacter Species

Aliarcobacter cibarius and Aliarcobacter thereius are two rarely detected Aliarcobacter species. In the study, we analyzed the antimicrobial susceptibility and provide detailed insights into the genotype and phylogeny of both species using whole-genome sequencing. Thermophilic Campylobacter species are the most common bacterial foodborne pathogens causing gastroenteritis in humans worldwide. The genus Aliarcobacter is part of the Campylobacteraceae family and includes the species Aliarcobacter butzleri, Aliarcobacter cryaerophilus, Aliarcobacter skirrowii, and the rarely described Aliarcobacter cibarius, Aliarcobacter faecis, Aliarcobacter lanthieri, Aliarcobacter thereius, and Acrobarter trophiarum. Aliarcobacter are emergent enteropathogens and potential zoonotic agents. Here, we generated, analyzed, and characterized whole-genome sequences of Aliarcobacter cibarius and Aliarcobacter thereius. They were isolated from water poultry farms in Germany, cultured and identified by MALDI-TOF MS. With PCR the identity was verified. Antibiotic susceptibility testing was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, streptomycin, ampicillin, and cefotaxime using the gradient strip method (E-test). Whole-genome sequences were generated including those of reference strains. Complete genomes for six selected strains are reported. These provide detailed insights into the genotype. With these, we predicted in silico known AMR genes, virulence-associated genes, and plasmid replicons. Phenotypic analysis of resistance showed differences between the presence of resistance genes and the prediction of phenotypic resistance profiles. In Aliarcobacter butzleri, the nucleotide sequence of the gyrA gene (DQ464331) can show a signature mutation resulting in an amino acid change T85>I. Acrobarter cibarius and Acrobarter thereius showed the same gene as assessed by similarity annotation of the mutations 254C>G. Most of the isolates were found to be sensitive to ciprofloxacin. The ciprofloxacin-resistant Aliarcobacter thereius isolate was associated with the amino acid change T85>I. But this was not predicted with antibiotic resistance databases, before. Ultimately, a phylogenetic analysis was done to facilitate in future outbreak analysis.

Characterization of Arcobacter spp. Isolated from human diarrheal, non-diarrheal and food samples in Thailand

Arcobacter butzleri is an emerging zoonotic food-borne and water-borne pathogen that can cause diarrhea in humans. The global prevalence of A. butzleri infection is underestimated, and little is known about their phenotypic and genotypic characterization. The aim of this study was to determine antimicrobial susceptibility (AST) profiles, detect related virulence genes, and classify sequence type (ST) of A. butzleri isolates obtained from human stool and food samples. A total of 84 A. butzleri isolates were obtained from human diarrheal (n = 25), non-diarrheal (n = 24) stool, and food (n = 35) samples in Thailand. They were evaluated for phenotypic identification by conventional microbiological procedures and AST by Kirby-Bauer disc diffusion method as well as virulence genes detection. Representative isolates from each origin were selected based on the presence of virulence genes and AST profiles to analyze genetic diversity by multilocus sequence typing (MLST). All isolates showed resistance to nalidixic acid 40.5% (34/84), ciprofloxacin 11.9% (10/84), azithromycin 8.3% (7/84), and erythromycin 3.6% (3/84). Regarding the ten virulence genes detected, cj1349, mviN and pldA had the highest prevalence 100% (84/84), followed by tlyA 98.8% (83/84), cadF 97.6% (82/84), ciaB 71.4% (60/84), hecA and hecB 22.6% (19/84), iroE 15.5% (13/84) and irgA 10.7% (9/84), respectively. Three virulence genes were present among A. butzleri isolates of human diarrheal stool and food samples, with a significant difference observed among isolates; hecB [36% (9/25) and 8.6% (3/35)], hecA [36% (9/25) and 5.7% (2/35)], and irgA [24% (6/25) and 2.9% (1/35)] (p < 0.05), respectively. The hecA and hecB virulence genes functions are related to the mechanism of hemolysis, while irgA supports a bacterial nutritional requirement. MLST analysis of 26 A. butzleri isolates revealed that 16 novel STs exhibited high genetic diversity. The results of this study is useful for understanding potentially pathogenic and antimicrobial-resistant A. butzleri in Thailand. The pathogenic virulence markers hecB, hecA, and irgA have the potential to be developed for rapid diagnostic detection in human diarrheal stool. No significant relationships among STs and sources of origin were observed. Little is known about A. butzleri, the mechanism of action of these virulence genes, is a topic that needs further investigation.

Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream

Water quality monitoring is essential to safeguard human and environmental health. The advent of next-generation sequencing techniques in recent years, which allow a more in-depth study of environmental microbial communities in the environment, could broaden the perspective of water quality monitoring to include impact of faecal pollution bacteria on ecosystem. In this study, 16 S rRNA amplicon sequencing was used to evaluate the impact of wastewater treatment plant (WWTP) effluent on autochthonous microbial communities of a temporary Mediterranean stream characterized by high flow seasonality (from 0.02 m³/s in winter to 0.006 m³/s in summer). Seven sampling campaigns were performed under different temperatures and streamflow conditions (winter and summer). Water samples were collected upstream (Upper) of the WWTP, the secondary effluent (EF) discharge and 75 m (P75) and 1000 m (P1000) downstream of the WWTP. A total of 5,593,724 sequences were obtained, giving rise to 20,650 amplicon sequence variants (ASV), which were further analysed and classified into phylum, class, family and genus. Each sample presented different distribution and abundance of taxa. Although taxon distribution and abundance differed in each sample, the microbial community structure of P75 resembled that of EF samples, and Upper and P1000 samples mostly clustered together. Alpha diversity showed the highest values for Upper and P1000 samples and presented seasonal differences, being higher in winter conditions of high streamflow and low temperature. Our results suggest the microbial ecology re-establishment, since autochthonous bacterial communities were able to recover from the impact of the WWTP effluent in 1 km. Alpha diversity results indicates a possible influence of environmental factors on the bacterial community structure. This study shows the potential of next-generation sequencing techniques as useful tools in water quality monitoring and management within the climate change scenario.

Arcobacter butzleri: Up-to-date taxonomy, ecology, and pathogenicity of an emerging pathogen

Arcobacter butzleri, recently emended to the Aliarcobacter butzleri comb. nov., is an emerging pathogen causing enteritis, severe diarrhea, septicaemia, and bacteraemia in humans and enteritis, stillbirth, and abortion in animals. Since its recognition as emerging pathogen on 2002, advancements have been made in elucidating its pathogenicity and epidemiology, also thanks to advent of genomics, which, moreover, contributed in emending its taxonomy. In this review, we provide an overview of the up-to-date taxonomy, ecology, and pathogenicity of this emerging pathogen. Moreover, the implication of A. butzleri in the safety of foods is pinpointed, and culture-dependent and independent detection, identification, and typing methods as well as strategies to control and prevent the survival and growth of this pathogen are provided.

Prevalence and antimicrobial susceptibility of Arcobacter species in human stool samples derived from out- and inpatients: the prospective German Arcobacter prevalence study Arcopath

Background

Arcobacter species, particularly A. butzleri, but also A. cryaerophilus constitute emerging pathogens causing gastroenteritis in humans. However, isolation of Arcobacter may often fail during routine diagnostic procedures due to the lack of standard protocols. Furthermore, defined breakpoints for the interpretation of antimicrobial susceptibilities of Arcobacter are missing. Hence, reliable epidemiological data of human Arcobacter infections are scarce and lacking for Germany. We therefore performed a 13-month prospective Arcobacter prevalence study in German patients.

Results

A total of 4636 human stool samples was included and Arcobacter spp. were identified from 0.85% of specimens in 3884 outpatients and from 0.40% of specimens in 752 hospitalized patients. Overall, A. butzleri was the most prevalent species (n = 24; 67%), followed by A. cryaerophilus (n = 10; 28%) and A. lanthieri (n = 2; 6%). Whereas A. butzleri, A. cryaerophilus and A. lanthieri were identified in outpatients, only A. butzleri could be isolated from samples of hospitalized patients. Antimicrobial susceptibility testing of Arcobacter isolates revealed high susceptibilities to ciprofloxacin, whereas bimodal distributions of MICs were observed for azithromycin and ampicillin.

Conclusions

In summary, Arcobacter including A. butzleri, A. cryaerophilus and A. lanthieri could be isolated in 0.85% of German outpatients and ciprofloxacin rather than other antibiotics might be appropriate for antibiotic treatment of infections. Further epidemiological studies are needed, however, to provide a sufficient risk assessment of Arcobacter infections in humans.

Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen

Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.

Human campylobacteriosis: A public health concern of global importance

Campylobacter species are among the leading cause of bacterial foodborne and waterborne infections. In addition, Campylobacter is one of the major causative agent of bacterial gastrointestinal infections and the rise in the incidence of Campylobacter infections have been reported worldwide. Also, the emergence of some Campylobacter species as one of the main causative agent of diarrhea and the propensity of these bacteria species to resist the actions of antimicrobial agents; position them as a serious threat to the public health. This paper reviews Campylobacter pathogenicity, infections, isolation and diagnosis, their reservoirs, transmission pathways, epidemiology of Campylobacter outbreaks, prevention and treatment option, antibiotics resistance and control of antibiotics use.

Identification of virulence and antibiotic resistance factors in Arcobacter butzleri isolated from bovine milk by Whole Genome Sequencing

Arcobacter butzleri is a pathogenic aerobic bacterium responsible for diarrhea and septicemia in humans. It is frequently isolated from food products of animal origin, including milk and dairy products. To data, few reports are currently available on the genetic characteristics and virulence profiles of A. butzleri. The aim of this study was to investigate the genetic diversity and to characterize the virulence and antibiotic resistance profiles of 10 A. butzleri strains isolated from bovine milk samples by Whole Genome Sequence (WGS). Multi-Locus Sequence Typing (MLST) revealed that three isolates belonged to the ST66, two to the ST420 and the remaining five strains to the ST627, ST629, ST630, ST633 and ST637, respectively. The 100% of the strains carried cadF, pldA, ciaB, cj1349, mviN and tlyA virulence factors genes; 60% iroE; 50% irgA; 10% hecB. Resistome prediction showed a multidrug resistance: 100% of isolates resulted resistant to fluoroquinolones and tetracycline; 90% of strains to rifampicin and cephalosporins and a minor percentage to other antibiotics. Furthermore, the 50% of strains harbored four mutations in Mycobacterium tuberculosis katG gene conferring resistance to isoniazid. The study provided interesting data on the virulence characteristics and on the genetic endowment related to the antimicrobial resistance of A. butzleri isolates from milk. The determination of the STs also added information concerning the genetic variability of this microorganism. To date, a very limited number of studies have been published on the typing of A. butzleri using WGS, so this paper proposes an innovative methodological approach that allows a rapid and complete characterization of pathogenic microorganisms.

Urbanization Impacts the Physicochemical Characteristics and Abundance of Fecal Markers and Bacterial Pathogens in Surface Water

Urbanization is increasing worldwide and is happening at a rapid rate in China in line with economic development. Urbanization can lead to major changes in freshwater environments through multiple chemical and microbial contaminants. We assessed the impact of urbanization on physicochemical characteristics and microbial loading in canals in Suzhou, a city that has experienced rapid urbanization in recent decades. Nine sampling locations covering three urban intensity classes (high, medium and low) in Suzhou were selected for field studies and three locations in Huangshan (natural reserve) were included as pristine control locations. Water samples were collected for physicochemical, microbiological and molecular analyses. Compared to medium and low urbanization sites, there were statistically significant higher levels of nutrients and total and thermotolerant coliforms (or fecal coliforms) in highly urbanized locations. The effect of urbanization was also apparent in the abundances of human-associated fecal markers and bacterial pathogens in water samples from highly urbanized locations. These results correlated well with land use types and anthropogenic activities at the sampling sites. The overall results indicate that urbanization negatively impacts water quality, providing high levels of nutrients and a microbial load that includes fecal markers and pathogens.

Antimicrobial Susceptibility and Genomic Structure of Arcobacter skirrowii Isolates

Campylobacter spp. are considered the most common bacterial cause of foodborne gastroenteritis in the world. The family Campylobacteraceae includes the genus Arcobacter with the three species Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii as emergent enteropathogens and potential zoonotic agents. Here, we characterized genome sequences of Arcobacter that were isolated from water poultry on farms in Germany. Isolates were cultured, identified by MALDI-TOF MS and identification was verified with PCR assays. Antibiotic susceptibility testing of isolates was carried out with erythromycin, ciprofloxacin, doxycycline, tetracycline, gentamicin, and streptomycin using the gradient strip method (E-test). We also sequenced whole genomes and predicted antibiotic resistance determinants, virulence factors, performed a phylogenetic analysis to determine the genetic relatedness of these isolates and searched for plasmids.

Filling the gaps in clinical proteomics: a do-it-yourself guide for the identification of the emerging pathogen Arcobacter by matrix-assisted laser desorption ionization-time of flight mass spectrometry

Arcobacters are considered emerging gastrointestinal pathogens. Rapid, reliable and species-specific identification of these bacteria is important. Biochemical tests commonly yield negative or variable results. Molecular methods prove more reliable but are time consuming and lack specificity. Matrix assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a fast, cheap and robust technique that has revolutionized genus and species identification in clinical microbiology. The performance of an in vitro diagnostic (RUO) spectral database of MALDI-TOF MS for the identification of human clinically relevant Arcobacter isolates was validated and compared to an in house created Reference Spectral database (RS) containing a representative set of deposited Arcobacter strains of zoonotic interest. A challenge panel of clinical, human and veterinary, unique Campylobacteraceae strains was used to test accuracy. Using direct colony transfer, sensitivity with RS was significantly better than with RUO for A. butzleri and A. cryaerophilus identification (100% and 92% versus 74% and 16%). For A. skirrowii, sensitivity remained low (21% versus 0%). Reanalysis using formic acid overlay (on-target extraction) augmented sensitivity for the latter species to 64%. Specificity of RS database remained excellent without any misidentifications of human clinical strains including Campylobacter fetus and C. jejuni/coli. The use of an enriched database for MALDI-TOF MS identification of Arcobacter spp. of human interest produced high-confidence identifications to species level resulting in a significantly improved sensitivity with conservation of excellent specificity. Misidentifications, which can have therapeutic and public health consequences, were not encountered.

Antimicrobial susceptibility testing of Arcobacter butzleri: development and application of a new protocol for broth microdilution

Objectives

To develop a standard reference broth microdilution method for antimicrobial susceptibility testing (AST) of Arcobacter butzleri. The protocol was subsequently applied to a collection of A. butzleri isolates from different sources.

Methods

Broth microdilution susceptibility testing was performed on eight A. butzleri isolates in three media: non-supplemented CAMHB, CAMHB + 2% FBS and CAMHB + 5% FBS. The MIC values were read after 24 and 48 h of incubation at 35 ± 2 °C in ambient air. A logistic regression model was used to determine the combination of medium and incubation time yielding the most homogeneous results. Subsequently, the protocol was applied to 65 A. butzleri isolates to determine their MICs of 31 antimicrobial agents.

Results

The statistical analysis revealed that the most homogeneous MIC values were obtained with CAMHB + 5% FBS and reading of MIC values after 24 h of incubation. The standardized method was successful for AST of all 65 A. butzleri isolates. MIC values were distributed unimodally for most antimicrobial agents. However, one field isolate showed elevated MIC values of gentamicin, streptomycin, tetracycline and trimethoprim/sulfamethoxazole.

Conclusions

This study presents a new protocol for AST of A. butzleri by broth microdilution and shows the distribution of MIC values of 31 antimicrobial agents for a collection of A. butzleri isolates from different origins.

Quantitative real-time PCR-based assessment of tile drainage management influences on bacterial pathogens in tile drainage and groundwater

This study compared the impact of controlled tile drainage (CD) and freely draining (FD) systems on the prevalence and quantitative real-time PCR-based enumeration of four major pathogens including Arcobacter butzleri, Campylobacter jejuni, Campylobacter coli, and Helicobacter pylori in tile- and groundwater following a fall liquid swine manure (LSM) application on clay loam field plots. Although the prevalence of all target pathogens were detected in CD and FD systems, the loads of A. butzleri, C. jejuni, and C. coli were significantly lower in CD tile-water (p<0.05), in relation to FD tile-water. However, concentrations of A. butzleri were significantly greater in CD than FD tile-water (p<0.05). In shallow groundwater (1.2m depth), concentrations of A. butzleri, C. coli, and H. pylori showed no significant difference between CD and FD plots, while C. jejuni concentrations were significantly higher in FD plots (p<0.05). No impact of CD on the H. pylori was observed since quantitative detection in tile- and groundwater was scarce. Although speculative, H. pylori occurrence may have been related to the application of municipal biosolids four years prior to the LSM experiment. Overall, CD can be used to help minimize off-field export of pathogens into surface waters following manure applications to land, thereby reducing waterborne pathogen exposure risks to humans.

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.

Antimicrobial susceptibility, virulence potential and sequence types associated with Arcobacter strains recovered from human faeces

PURPOSE

The genus Arcobacter includes bacteria that are considered emergent pathogens because they can produce infections in humans and animals. The most common symptoms are bloody and non-bloody persistent diarrhea but cases with abdominal cramps without diarrhea or asymptomatic cases have also been described as well as cases with bacteremia. The objective was to characterize Arcobacter clinical strains isolated from the faeces of patients from three Spanish hospitals.

METHODOLOGY

We have characterized 28 clinical strains (27 of A. butzleri and one of A. cryaerophilus) isolated from faeces, analysing their epidemiological relationship using the multilocus sequence typing (MLST) approach and screening them for their antibiotic susceptibility and for the presence of virulence genes.Results/Key findings. Typing results showed that only one of the 28 identified sequence types (i.e. ST 2) was already present in the MLST database. The other 27 STs constituted new records because they included new alleles for five of the seven genes or new combinations of known alleles of the seven genes. All strains were positive for the ciaB virulence gene and sensitive to tetracycline. However, 7.4 % of the A. butzleri and A. cryaerophilus strains showed resistance to ciprofloxacin.

CONCLUSION

The fact that epidemiological unrelated strains show the same ST indicates that other techniques with higher resolution should be developed to effectively recognize the infection source. Resistance to ciprofloxacin, one of the antibiotics recommended for the treatment of Arcobacter intestinal infections, demonstrated in 10.7 % of the strains, indicates the importance of selecting the most appropriate effective treatment.

[Arcobacter - an underestimated zoonotic pathogen?]

The relevance for public health of the agent Arcobacter is mostly unclear despite of an increasing number of studies. Recent evidence shows that especially Arcobacter (A.) butzleri but also A. cryaerophilus and A. skirrowii may be involved in human enteric diseases. However, little is currently known about pathogenicity or potential virulence factors. Livestock animals, particularly poultry and pigs, might be a significant reservoir of Arcobacter spp. Furthermore, Arcobacter spp. could be isolated from retail raw meat products of these animals as well as from drinking water. There are currently no standardized isolation and detection methods to collect comparable data. Further studies and efforts of both human and veterinary medicine are needed to elucidate prevalence, epidemiology, the pathogenic role and potential virulence factors of Arcobacter spp. These data are the necessary basis for further risk assessment.

Pathogens of Food Animals: Sources, Characteristics, Human Risk, and Methods of Detection

Pathogens associated with food production (livestock) animals come in many forms causing a multitude of disease for humans. For the purpose of this review, these infectious agents can be divided into three broad categories: those that are associated with bacterial disease, those that are associated with viruses, and those that are parasitic in nature. The goal of this chapter is to provide the reader with an overview of the most common pathogens that cause disease in humans through exposure via the food chain and the consequence of this exposure as well as risk and detection methods. We have also included a collection of unusual pathogens that although rare have still caused disease, and their recognition is warranted in light of emerging and reemerging diseases. These provide the reader an understanding of where the next big outbreak could occur. The influence of the global economy, the movement of people, and food makes understanding production animal-associated disease paramount to being able to address new diseases as they arise.

Genetic diversity of Arcobacter isolated from bivalves of Adriatic and their interactions with Mytilus galloprovincialis hemocytes

The human food-borne pathogens Arcobacter butzleri and A. cryaerophilus have been frequently isolated from the intestinal tracts and fecal samples of different farm animals and, after excretion, these microorganisms can contaminate the environment, including the aquatic one. In this regard, A. butzleri and A. cryaerophilus have been detected in seawater and bivalves of coastal areas which are affected by fecal contamination. The capability of bivalve hemocytes to interact with bacteria has been proposed as the main factor inversely conditioning their persistence in the bivalve. In this study, 12 strains of Arcobacter spp. were isolated between January and May 2013 from bivalves of Central Adriatic Sea of Italy in order to examine their genetic diversity as well as in vitro interactions with bivalve components of the immune response, such as hemocytes. Of these, seven isolates were A. butzleri and five A. cryaerophilus, and were genetically different. All strains showed ability to induce spreading and respiratory burst of Mytilus galloprovincialis hemocytes. Overall, our data demonstrate the high genetic diversity of these microorganisms circulating in the marine study area. Moreover, the Arcobacter-bivalve interaction suggests that they do not have a potential to persist in the tissues of M. galloprovincialis.

Occurrence of Arcobacter spp. and correlation with the bacterial indicator of faecal contamination Escherichia coli in bivalve molluscs from the Central Adriatic, Italy

A total of 162 samples of bivalve molluscs (45 mussels and 117 clams) collected between December 2012 and 2014 from harvesting areas of the Central Adriatic were analysed by a culturing method for the presence of Arcobacter spp. Species identification was performed by PCR and sequencing analysis of a fragment of the rpoB gene. Overall, Arcobacter species were detected in 30% of samples, specifically 33% clams and 22% mussels. A. butzleri was the most common species (20% of the samples), followed by A. cryaerophilus (9%) and A. skirrowii (1%). A seasonal association of A. butzleri contamination was detected. A. butzleri was significantly more commonly recovered from samples collected during the winter-spring period (29%) than from those of the summer-autumn (8%). A. cryaerophilus was cultured from 6% to 11% of the samples collected in summer-autumn and winter-spring, respectively, but these differences were not statistically significant. A. skirrowii was recovered from a sample of mussels harvested in May 2014. To identify associations between the occurrence of Arcobacter spp. and E. coli levels, samples were divided into groups generating results with E. coli at >230MPN/100g and E. coli at ≤230MPN/100g, the latter corresponding to EU microbiological criteria allowed for live bivalve molluscs at retail level. A. butzleri was significantly more commonly detected in samples with higher E. coli levels (48%) than in those with lower levels of E. coli (10%), providing evidence for considering E. coli as an index organism for A. butzleri contamination in bivalve molluscs.

Microbial community structure in a full-scale anaerobic treatment plant during start-up and first year of operation revealed by high-throughput 16S rRNA gene amplicon sequencing

High-throughput amplicon sequencing of six biomass samples from a full-scale anaerobic reactor at a Norwegian wood and pulp factory using Biothane Biobed Expanded Granular Sludge Bed (EGSB) technology during start-up and first year of operation was performed. A total of 106,166 16S rRNA gene sequences (V3-V5 region) were obtained. The number of operational taxonomic units (OTUs) ranged from 595 to 2472, and a total of 38 different phyla and 143 families were observed. The predominant phyla were Bacteroidetes, Chloroflexi, Firmicutes, Proteobacteria, and Spirochaetes. A more diverse microbial community was observed in the inoculum biomass coming from an Upflow Anaerobic Sludge Blanket (USAB) reactor, reflecting an adaptation of the inoculum diversity to the specific conditions of the new reactor. In addition, no taxa classified as obligate pathogens were identified and potentially opportunistic pathogens were absent or observed in low abundances. No Legionella bacteria were identified by traditional culture-based and molecular methods.

The Use of Two Culturing Methods in Parallel Reveals a High Prevalence and Diversity of Arcobacter spp. in a Wastewater Treatment Plant

The genus Arcobacter includes species considered emerging food and waterborne pathogens. Despite Arcobacter has been linked to the presence of faecal pollution, few studies have investigated its prevalence in wastewater, and the only isolated species were Arcobacter butzleri and Arcobacter cryaerophilus. This study aimed to establish the prevalence of Arcobacter spp. at a WWTP using in parallel two culturing methods (direct plating and culturing after enrichment) and a direct detection by m-PCR. In addition, the genetic diversity of the isolates was established using the ERIC-PCR genotyping method. Most of the wastewater samples (96.7%) were positive for Arcobacter and a high genetic diversity was observed among the 651 investigated isolates that belonged to 424 different ERIC genotypes. However, only few strains persisted at different dates or sampling points. The use of direct plating in parallel with culturing after enrichment allowed recovering the species A. butzleri, A. cryaerophilus, Arcobacter thereius, Arcobacter defluvii, Arcobacter skirrowii, Arcobacter ellisii, Arcobacter cloacae, and Arcobacter nitrofigilis, most of them isolated for the first time from wastewater. The predominant species was A. butzleri, however, by direct plating predominated A. cryaerophilus. Therefore, the overall predominance of A. butzleri was a bias associated with the use of enrichment.

The Immunopathogenic Potential of Arcobacter butzleri - Lessons from a Meta-Analysis of Murine Infection Studies

Background

Only limited information is available about the immunopathogenic properties of Arcobacter infection in vivo. Therefore, we performed a meta-analysis of published data in murine infection models to compare the pathogenic potential of Arcobacter butzleri with Campylobacter jejuni and commensal Escherichia coli as pathogenic and harmless reference bacteria, respectively.

Methodology / Principal Findings

Gnotobiotic IL-10^-/- mice generated by broad-spectrum antibiotic compounds were perorally infected with A. butzleri (strains CCUG 30485 or C1), C. jejuni (strain 81-176) or a commensal intestinal E. coli strain. Either strain stably colonized the murine intestines upon infection. At day 6 postinfection (p.i.), C. jejuni infected mice only displayed severe clinical sequelae such as wasting bloody diarrhea. Gross disease was accompanied by increased numbers of colonic apoptotic cells and distinct immune cell populations including macrophages and monocytes, T and B cells as well as regulatory T cells upon pathogenic infection. Whereas A. butzleri and E. coli infected mice were clinically unaffected, respective colonic immune cell numbers increased in the former, but not in the latter, and more distinctly upon A. butzleri strain CCUG 30485 as compared to C1 strain infection. Both, A. butzleri and C. jejuni induced increased secretion of pro-inflammatory cytokines such as IFN-γ, TNF, IL-6 and MCP-1 in large, but also small intestines. Remarkably, even though viable bacteria did not translocate from the intestines to extra-intestinal compartments, systemic immune responses were induced in C. jejuni, but also A. butzleri infected mice as indicated by increased respective pro-inflammatory cytokine concentrations in serum samples at day 6 p.i.

Conclusion / Significance

A. butzleri induce less distinct pro-inflammatory sequelae as compared to C. jejuni, but more pronounced local and systemic immune responses than commensal E. coli in a strain-dependent manner. Hence, data point towards that A. butzleri is more than a commensal in vertebrate hosts.

Evaluation of Various Campylobacter-Specific Quantitative PCR (qPCR) Assays for Detection and Enumeration of Campylobacteraceae in Irrigation Water and Wastewater via a Miniaturized Most-Probable-Number-qPCR Assay

Campylobacter spp. are the leading cause of bacterial gastroenteritis worldwide, and water is increasingly seen as a risk factor in transmission. Here we describe a most-probable-number (MPN)-quantitative PCR (qPCR) assay in which water samples are centrifuged and aliquoted into microtiter plates and the bacteria are enumerated by qPCR. We observed that commonly used Campylobacter molecular assays produced vastly different detection rates. In irrigation water samples, detection rates varied depending upon the PCR assay and culture method used, as follows: 0% by the de Boer Lv1-16S qPCR assay, 2.5% by the Van Dyke 16S and Jensen glyA qPCR assays, and 75% by the Linton 16S endpoint PCR when cultured at 37°C. Primer/probe specificity was the major confounder, with Arcobacter spp. routinely yielding false-positive results. The primers and PCR conditions described by Van Dyke et al. (M. I. Van Dyke, V. K. Morton, N. L. McLellan, and P. M. Huck, J Appl Microbiol 109:1053-1066, 2010, http://dx.doi.org/10.1111/j.1365-2672.2010.04730.x) proved to be the most sensitive and specific for Campylobacter detection in water. Campylobacter occurrence in irrigation water was found to be very low (<2 MPN/300 ml) when this Campylobacter-specific qPCR was used, with the most commonly detected species being C. jejuni, C. coli, and C. lari Campylobacters in raw sewage were present at ∼10(2)/100 ml, with incubation at 42°C required for reducing microbial growth competition from arcobacters. Overall, when Campylobacter prevalence and/or concentration in water is reported using molecular methods, considerable validation is recommended when adapting methods largely developed for clinical applications. Furthermore, combining MPN methods with molecular biology-based detection algorithms allows for the detection and quantification of Campylobacter spp. in environmental samples and is potentially suited to quantitative microbial risk assessment for improved public health disease prevention related to food and water exposures.

IMPORTANCE

The results of this study demonstrate the importance of assay validation upon data interpretation of environmental monitoring for Campylobacter when using molecular biology-based assays. Previous studies describing Campylobacter prevalence in Canada utilized primers that we have determined to be nonspecific due to their cross-amplification of Arcobacter spp. As such, Campylobacter prevalence may have been vastly overestimated in other studies. Additionally, the development of a quantitative assay described in this study will allow accurate determination of Campylobacter concentrations in environmental water samples, allowing more informed decisions to be made about water usage based on quantitative microbial risk assessment.

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.

MicroRNA Response of Primary Human Macrophages to Arcobacter Butzleri Infection

The role of microRNAs (miRNAs) in infectious diseases is becoming more and more apparent, and the use of miRNAs as a diagnostic tool and their therapeutic application has become the major focus of investigation. The aim of this study was to identify miRNAs involved in the immune signaling of macrophages in response to Arcobacter (A.) butzleri infection, an emerging foodborne pathogen causing gastroenteritis. Therefore, primary human macrophages were isolated and infected, and miRNA expression was studied by means of RNAseq. Analysis of the data revealed the expression of several miRNAs, which were previously associated with bacterial infections such as miR-155, miR-125, and miR-212. They were shown to play a key role in Toll-like receptor signaling where they act as fine-tuners to establish a balanced immune response. In addition, miRNAs which have yet not been identified during bacterial infections such as miR-3613, miR-2116, miR-671, miR-30d, and miR-629 were differentially regulated in A. butzleri-infected cells. Targets of these miRNAs accumulated in pathways such as apoptosis and endocytosis – processes that might be involved in A. butzleri pathogenesis. Our study contributes new findings about the interaction of A. butzleri with human innate immune cells helping to understand underlying regulatory mechanisms in macrophages during infection.

Toll-Like Receptor-4 Dependent Intestinal Gene Expression During Arcobacter Butzleri Infection of Gnotobiotic Il-10 Deficient Mice

We have previously shown that Arcobacter butzleri infection induces Toll-like receptor (TLR) -4 dependent immune responses in perorally infected gnotobiotic IL-10^–/– mice. Here, we analyzed TLR-4-dependent expression of genes encoding inflammatory mediators and matrix-degrading gelatinases MMP-2 and -9 in the small and large intestines of gnotobiotic TLR-4-deficient IL-10^–/– mice that were perorally infected with A. butzleri strains CCUG 30485 or C1, of human and chicken origin, respectively. At day 6 following A. butzleri infection, colonic mucin-2 mRNA, as integral part of the intestinal mucus layer, was downregulated in the colon, but not ileum, of IL-10^–/– but not TLR-4^–/– IL-10^–/– mice. CCUG 30485 strain-infected TLR-4-deficient IL-10^–/– mice displayed less distinctly upregulated IFN-γ, IL-17A, and IL-1β mRNA levels in ileum and colon, which was also true for colonic IL-22. These changes were accompanied by upregulated colonic MMP-2 and ileal MMP-9 mRNA exclusively in IL-10^–/– mice. In conclusion, TLR-4 is essentially involved in A. butzleri mediated modulation of gene expression in the intestines of gnotobiotic IL-10^–/– mice.

Tracing enteric pathogen contamination in sub-Saharan African groundwater

Quantitative PCR (qPCR) can rapidly screen for an array of faecally-derived bacteria, which can be employed as tracers to understand groundwater vulnerability to faecal contamination. A microbial DNA qPCR array was used to examine 45 bacterial targets, potentially relating to enteric pathogens, in 22 groundwater supplies beneath the city of Kabwe, Zambia in both the dry and subsequent wet season. Thermotolerant (faecal) coliforms, sanitary risks, and tryptophan-like fluorescence, an emerging real-time reagentless faecal indicator, were also concurrently investigated. There was evidence for the presence of enteric bacterial contamination, through the detection of species and group specific 16S rRNA gene fragments, in 72% of supplies where sufficient DNA was available for qPCR analysis. DNA from the opportunistic pathogen Citrobacter freundii was most prevalent (69% analysed samples), with Vibrio cholerae also perennially persistent in groundwater (41% analysed samples). DNA from other species such as Bifidobacterium longum and Arcobacter butzleri was more seasonally transient. Bacterial DNA markers were most common in shallow hand-dug wells in laterite/saprolite implicating rapid subsurface pathways and vulnerability to pollution at the surface. Boreholes into the underlying dolomites were also contaminated beneath the city highlighting that a laterite/saprolite overburden, as occurs across much of sub-Saharan aquifer, does not adequately protect underlying bedrock groundwater resources. Nevertheless, peri-urban boreholes all tested negative establishing there is limited subsurface lateral transport of enteric bacteria outside the city limits. Thermotolerant coliforms were present in 97% of sites contaminated with enteric bacterial DNA markers. Furthermore, tryptophan-like fluorescence was also demonstrated as an effective indicator and was in excess of 1.4μg/L in all contaminated sites.

Toll-Like Receptor-4 is Essential for Arcobacter Butzleri-Induced Colonic and Systemic Immune Responses in Gnotobiotic IL-10(-/-) Mice

Arcobacter butzleri causes sporadic cases of gastroenteritis, but the underlying immunopathological mechanisms of infection are unknown. We have recently demonstrated that A. butzleri-infected gnotobiotic IL-10^–/– mice were clinically unaffected but exhibited intestinal and systemic inflammatory immune responses. For the first time, we here investigated the role of Toll-like receptor (TLR)-4, the main receptor for lipopolysaccharide and lipooligosaccharide of Gram-negative bacteria, in murine arcobacteriosis. Gnotobiotic TLR-4/IL-10-double deficient (TLR-4^–/– IL-10^–/–) and IL-10^–/– control mice generated by broad-spectrum antibiotics were perorally infected with A. butzleri. Until day 16 postinfection, mice of either genotype were stably colonized with the pathogen, but fecal bacterial loads were approximately 0.5–2.0 log lower in TLR-4^–/– IL-10^–/– as compared to IL-10^–/– mice. A. butzleri-infected TLR-4^–/– IL-10^–/– mice displayed less pronounced colonic apoptosis accompanied by lower numbers of macrophages and monocytes, T lymphocytes, regulatory T-cells, and B lymphocytes within the colonic mucosa and lamina propria as compared to IL-10^–/– mice. Furthermore, colonic concentrations of nitric oxide, TNF, IL-6, MCP-1, and, remarkably, IFN-γ and IL-12p70 serum levels were lower in A. butzleri-infected TLR-4^–/– IL-10^–/– versus IL-10^–/– mice. In conclusion, TLR-4 is involved in mediating murine A. butzleri infection. Further studies are needed to investigate the molecular mechanisms underlying Arcobacter–host interactions in more detail.