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

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.

Investigation and characterization of Aliarcobacter spp. isolated from cattle slaughterhouse in Türkiye

Aliarcobacter spp. have been isolated from numerous food products at retail and from animal carcasses and feces at slaughter. The objectives of this study were as follows: (i) to isolate Aliarcobacter species from different slaughterhouses' samples and (ii) to detect genetic diversity, antibiotic resistance, biofilm ability, and putative virulence gene profiles of the isolates. A molecular investigation of antibiotic resistance and virulence factors was also conducted using polymerase chain reaction (PCR). Among 150 samples, a total of 22 (14.6%) Aliarcobacter spp. isolates were obtained, with varying levels of antibiotic resistance observed. The genes tetO, tetW, and gyrA were detected in 0%, 31.8%, and 27.2% of the isolates, respectively. All isolates were resistant to ampicillin, rifampin, and erythromycin, while tetracycline was found to be the most effective antibiotic, with 81.8% of the isolates showing susceptibility to it. All isolates (100%) harbored more than one of the nine putative virulence genes tested, with 18.1% of isolates carrying more than three. Regarding biofilm formation, 7 (31.8%) and 4 (18.1%) isolates were found to form strong and moderate biofilms, respectively, while one (4.5%) isolate was classified as a weak biofilm producer. ERIC-PCR band patterns suggested that the isolated Aliarcobacter spp. from slaughterhouses had different sources of contamination. These findings highlight the potential risk posed by pathogenic and multidrug-resistant Aliarcobacter spp. in food and the need for control measures throughout the food chain to prevent the spread of these strains. The results indicate that foods of animal origin and cattle slaughterhouses are significant sources of antimicrobial resistant Aliarcobacter.

Genetic characteristics, antimicrobial resistance, and prevalence of Arcobacter spp. isolated from various sources in Shenzhen, China

Arcobacter spp. is a globally emerging zoonotic and foodborne pathogen. However, little is known about its prevalence and antimicrobial resistance in China. To investigate the prevalence of Arcobacter spp. isolated from various sources, 396 samples were collected from human feces, chicken cecum, and food specimens including chicken meat, beef, pork, lettuce, and seafood. Arcobacter spp. was isolated by the membrane filtration method. For 92 strains, the agar dilution method and next-generation sequencing were used to investigate their antimicrobial resistance and to obtain whole genome data, respectively. The virulence factor database (VFDB) was queried to identify virulence genes. ResFinder and the Comprehensive Antibiotic Resistance Database (CARD) were used to predict resistance genes. A phylogenetic tree was constructed using the maximum likelihood (ML) method with core single-nucleotide polymorphisms (SNPs). We found that 27.5% of the samples (n = 109) were positive for Arcobacter spp., comprising Arcobacter butzleri (53.0%), Arcobacter cryaerophilus (39.6%), and Arcobacter skirrowii (7.4%). Chicken meat had the highest prevalence (81.2%), followed by seafood (51.9%), pork (43.3%), beef (36.7%), lettuce (35.5%), chicken cecum (8%), and human fecal samples (0%, 0/159). Antimicrobial susceptibility tests revealed that 51 A. butzleri and 40 A. cryaerophilus strains were resistant to streptomycin (98.1, 70%), clindamycin (94.1, 90%), tetracycline (64.7, 52.5%), azithromycin (43.1%, 15%), nalidixic acid (33.4, 35%), and ciprofloxacin (31.3, 35%) but were susceptible to erythromycin, gentamicin, chloramphenicol, telithromycin, and clindamycin (≤10%). A. skirrowii was sensitive to all experimental antibiotics. The virulence factors tlyA, mviN, cj1349, ciaB, and pldA were carried by all Arcobacter spp. strains at 100%, and the following percentages were cadF (95.7%), iroE (23.9%), hecB (2.2%), hecA, and irgA (1.1%). Only one A. butzleri strain (F061-2G) carried a macrolide resistance gene (ereA). One A. butzleri and one A. cryaerophilus harbored resistance island gene clusters, which were isolated from pork and chicken. Phylogenetic tree analysis revealed that A. butzleri, A. cryaerophilus, and A. skirrowii were separated from each other. To our knowledge, this is the first report of the isolation of Arcobacter spp. from vegetables and seafood in China. The resistance island gene cluster found in pork and chicken meat and the presence of virulence factors could be a potential risk to human health.

Genotyping, antibiotic resistance and prevalence of Arcobacter species in milk and dairy products

BACKGROUND

Arcobacter spp. has been considered an emerging foodborne pathogen and a hazard to human health. The dairy chain has been isolated from different sources; nevertheless, data on Arcobacter occurrence in raw milk and dairy products in Iran are still scant.

OBJECTIVE

The present study investigates the prevalence, antimicrobial susceptibility and the presence of virulence genes of Arcobacters species isolated from milk and dairy products.

METHODS

Then, a total of 350 raw milk samples and 400 dairy product samples were collected from dairy supply centers in Isfahan, Iran. Presumptive Arcobacter strains were obtained by enriching samples in Oxoid Arcobacter enrichment broth (AEB) followed by the filtration of enrichment product through 0.45-μm pore size membrane filters laid onto non-selective blood at 30°C under microaerophilic conditions. Molecular identification of Arcobacter cryaerophilus and A. butzleri was performed by Polymerase chain reaction (PCR) amplification of the 16S rRNA gene, followed by sequencing. The disc diffusion method was used to determine the antimicrobial susceptibility of isolates. Targeted resistance and virulence genes were detected using multiplex PCR.

RESULTS

The results show a low recovery rate of Arcobacter spp. in milk. Arcobacters were found in all types of milk, except raw camel milk, but were absent from all dairy products. Arcobacter butzleri was the predominant species in raw milk. Detection of virulence genes shows that all virulence genes targeted were found among A. butzleri, and six (cadF, cj1349, irgA, mviN, pldA, tlyA) were found among A. cryaerophilus. All A. butzleri strains and some A. cryaerophilus strains isolated from milk were resistant to amoxicillin-clavulanic acid and tetracycline. All A. cryaerophilus isolates from milk were susceptible to gentamycin, streptomycin, erythromycin and ciprofloxacin. The distribution of resistance genes in Arcobacter strains in milk shows that all isolates carried tet(O) and bla_OXA-61 genes.

CONCLUSIONS

In conclusion, the results indicate a low recovery rate of Arcobacter spp. in milk and milk products. However, a significant number of Arcobacter strains with putative virulence genes may be potential pathogens for humans and an overall increase in Arcobacter resistance to first-line antibiotics. These results highlight the need for regular surveillance of Arcobacter strains in milk and milk products in Iran.

Metagenomic profiling of antibiotic resistance and virulence removal: Activated sludge vs. algal wastewater treatment system

Conventional activated sludge-based (CAS) wastewater treatment plants are known to be a source of antibiotic resistance genes (ARGs) and virulence genes (VGs). As an alternative, a single-step mixotrophic algal wastewater treatment (A-WWT) system is proposed here to effectively reduce ARGs and VGs in the final effluent while meeting all the discharge standards. In this study, we applied the metagenomic profiling approach to compare the A-WWT system against the CAS system in terms of removal efficacy of ARG and VGs. A total of 111 ARG and 93 VG subtypes belonging to 10 antibiotic resistant classes and 19 virulence classes were detected in this study. Although the CAS system reduced the relative abundance of most classes of ARGs (7 of 10) and VGs (11 of 19), 3 ARG classes and 7 VG classes had increased abundances. On the other hand, the A-WWT system reduced the relative abundance of all classes of ARGs and VGs, and effectively eliminated most subtypes of ARGs and VGs. In the CAS system, the bacterial genera carrying ARGs and VGs was expanded, and the diversity index was increased greatly, suggesting the occurrence of horizontal gene transfer (HGT). In contrast, the A-WWT system narrowed down the potential host range and decreased their diversity substantially. Results of this study highlight the potential risk of ARGs and VGs in CAS system and demonstrate the feasibility of the algal-based system in removing ARGs and VGs.

Occurrence and Antimicrobial Resistance of Arcobacter spp. Recovered from Aquatic Environments

Arcobacter spp. are emerging waterborne and foodborne zoonotic pathogens responsible for gastroenteritis in humans. In this work, we evaluated the occurrence and the antimicrobial resistance profile of Arcobacter isolates recovered from different aquatic sources. Besides, we searched for Arcobacter spp. in seaweeds and the corresponding seawater samples. Bacteriological and molecular methods applied to 100 samples led to the isolation of 28 Arcobacter isolates from 27 samples. The highest prevalence was detected in rivers followed by artificial ponds, streams, well waters, and spring waters. Seaweeds contained a higher percentage of Arcobacter than the corresponding seawater samples. The isolates were identified as Arcobacter butzleri (96.4%) and Arcobacter cryaerophilus (3.6%). All the isolates showed a multi-drug resistance profile, being resistant to at least three different classes of antibiotics. Molecular analysis of genetic determinants responsible for tetracycline resistance in nine randomly chosen isolates revealed the presence of tetO and/or tetW. This work confirms the occurrence and the continuous emergence of antibiotic-resistant Arcobacter strains in environmental samples; also, the presence of quinolone-resistant Arcobacter spp. in aquatic sources used for water supply and irrigation represents a potential risk for human health.

Antimicrobial Resistance and in silico Virulence Profiling of Aliarcobacter butzleri Strains From German Water Poultry

Aliarcobacter butzleri is an emerging foodborne and zoonotic pathogen that is usually transmitted via contaminated food or water. A. butzleri is not only the most prevalent Aliarcobacter species, it is also closely related to thermophilic Campylobacter, which have shown increasing resistance in recent years. Therefore, it is important to assess its resistance and virulence profiles. In this study, 45 Aliarcobacter butzleri strains from water poultry farms in Thuringia, Germany, were subjected to an antimicrobial susceptibility test using the gradient strip diffusion method and whole-genome sequencing. In the phylogenetic analysis, the genomes of the German strains showed high genetic diversity. Thirty-three isolates formed 11 subgroups containing two to six strains. The antimicrobial susceptibility testing showed that 32 strains were resistant to erythromycin, 26 to doxycycline, and 20 to tetracycline, respectively. Only two strains were resistant to ciprofloxacin, while 39 strains were resistant to streptomycin. The in silico prediction of the antimicrobial resistance profiles identified a large repertoire of potential resistance mechanisms. A strong correlation between a gyrA point mutation (Thr-85-Ile) and ciprofloxacin resistance was found in 11 strains. A partial correlation was observed between the presence of the bla3 gene and ampicillin resistance. In silico virulence profiling revealed a broad spectrum of putative virulence factors, including a complete lipid A cluster in all studied genomes.

Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance

Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases. The custom-made databases identified a large repertoire of potential resistance and virulence-associated genes. This study provides the first resistance and virulence determinants database for A. butzleri.

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.

Antimicrobial Resistance in Veterinary Medicine: An Overview

Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.