Draft genome sequences of three arcobacter strains of pig and dairy cattle manure origin

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

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

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.

Novel virulence, antibiotic resistance and toxin gene-specific PCR-based assays for rapid pathogenicity assessment of Arcobacter faecis and Arcobacter lanthieri

Background

Arcobacter faecis and A. lanthieri are two newly classified species of genus Arcobacter. The prevalence and distribution of virulence, antibiotic resistance and toxin (VAT) genes in these species are required to assess their potential pathogenic health impacts to humans and animals. This study (i) developed species- and gene-specific primer pairs for the detection of six virulence, two antibiotic resistance, and three toxin genes in two target species; (ii) optimized eight single-tube multiplex and three monoplex PCR protocols using the newly developed species- and gene-specific primers; and (iii) conducted specificity and sensitivity evaluations as well as validation of eleven mono- and multiplex PCR assays by testing A. faecis (n= 29) and A. lanthieri (n= 10) strains isolated from various fecal and agricultural water sources to determine the prevalence and distribution of VAT genes and assess the degree of pathogenicity within the two species.

Results

Detection of all ten and eleven target VAT genes, and expression of cytolethal distending toxin (cdtA, cdtB and cdtC) genes in A. faecis and A. lanthieri reference strains with high frequency in field isolates suggest that they are potentially pathogenic strains. These findings indicate that these two species can pose a health risk to humans and animals.

Conclusions

The study results show that the developed mono- and multiplex PCR (mPCR) assays are simple, rapid, reliable and sensitive for the simultaneous assessment of the potential pathogenicity and antibiotic resistance profiling of tet(O) and tet(W) genes in these two newly discovered species. Also, these assays can be useful in diagnostic and analytical laboratories to determine the pathotypes and assessment of the virulence and toxin factors associated to human and animal infections.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1357-7) contains supplementary material, which is available to authorized users.

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.

Genome Sequence of Arcobacter sp. Strain LA11, Isolated from the Abalone Haliotis discus

Arcobacter sp. strain LA11 was isolated from the gut of the abalone Haliotis discus Here, we present the annotation and analysis of the draft genome of this strain, which is involved in nitrogen metabolism.

Global Distribution and Prevalence of Arcobacter in Food and Water

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

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

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