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Frontiers in Microbiology 2022Bivalve shellfish consumption (ark shells, clams, cockles, and oysters) has increased over the last decades. Following this trend, infectious disease outbreaks... (Review)
Review
Bivalve shellfish consumption (ark shells, clams, cockles, and oysters) has increased over the last decades. Following this trend, infectious disease outbreaks associated with their consumption have been reported more frequently. Molluscs are a diverse group of organisms found wild and farmed. They are common on our tables, but unfortunately, despite their great taste, they can also pose a threat as a potential vector for numerous species of pathogenic microorganisms. Clams, in particular, might be filled with pathogens because of their filter-feeding diet. This specific way of feeding favors the accumulation of excessive amounts of pathogenic microorganisms like spp., including and , , spp., and fecal coliforms, and intestinal enterococci. The problems of pathogen dissemination and disease outbreaks caused by exogenous bacteria in many geographical regions quickly became an unwanted effect of globalized food supply chains, global climate change, and natural pathogen transmission dynamics. Moreover, some pathogens like spp., with high zoonotic potential, are spreading worldwide along with food transport. These bacteria, contained in food, are also responsible for the potential transmission of antibiotic-resistance genes to species belonging to the human microbiota. Finally, they end up in wastewater, thus colonizing new areas, which enables them to introduce new antibiotic-resistance genes (ARG) into the environment and extend the existing spectrum of ARGs already present in local biomes. Foodborne pathogens require modern methods of detection. Similarly, detecting ARGs is necessary to prevent resistance dissemination in new environments, thus preventing future outbreaks, which could threaten associated consumers and workers in the food processing industry.
PubMed: 36699600
DOI: 10.3389/fmicb.2022.1061223 -
Frontiers in Microbiology 2022The is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other...
The is a globally emerging foodborne and zoonotic pathogen that can cause diarrhea in humans. It is relatively homogenous and clearly distinguishes the group from other . () is a heterogeneous species and little is known about its genomic characterization in China. This study aims to determine the genetic and plasmid features of based on whole-genome sequence (WGS). Average Nucleotide Identity (ANI) and DNA-DNA hybridization (DDH) were used for the species classification for 90 initially identified strains. One complete genome and 42 draft genomes were obtained by whole genome sequencing. The genomic characteristics were determined using various bioinformatics software. The genomes of the strains examined were estimated to vary from 1.81 to 2.28 Mb in length, with a G + C content of around 27%. ANI and DDH results indicated that 90 initially identified strains should be reclassified into four new species (ANI > 96% or DDH > 70%). Two clades (four subclades) were identified among 90 genomes with the phylogenetic analysis. The phylogenetic tree indicated these 90 genomes exhibited a high intra-species genomic diversity. No clustering was assorted with the host or geographic location among these genomes. Aminoglycoside resistance genes, such as , , , , and streptothricin resistance gene were detected in the chromosomes from a third of the Chinese strains. Virulence-related genes were identified in all the sequenced strains. A novel large multiple drug-resistant plasmid (named pCNAC48 with 161,992 bp in length) was identified in strain ICDCAC48. Two antibiotic-resistance islands were found in the plasmid with lengths of 7,950 and 25,137 bp and G + C content of 38.23 and 32.39%, respectively. The drug resistance genes and some transposable elements were cross-distributed among the islands in the plasmid. Antimicrobial susceptibility tests indicated these resistance genes in the plasmid were functional. Plasmid conjugation and curing experiments proved pCNAC48 was stable in strain ICDCAC48. It was the first identified multiple drug resistance plasmid in .
PubMed: 36212879
DOI: 10.3389/fmicb.2022.984450 -
Veterinary Medicine and Science Jul 2022Arcobacter spp. has been considered an emerging foodborne pathogen and a hazard to human health. The dairy chain has been isolated from different sources; nevertheless,...
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 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.
Topics: Animals; Anti-Bacterial Agents; Arcobacter; Drug Resistance, Microbial; Genotype; Humans; Milk; Multiplex Polymerase Chain Reaction; Prevalence; RNA, Ribosomal, 16S; Virulence Factors
PubMed: 35426255
DOI: 10.1002/vms3.800 -
Antibiotics (Basel, Switzerland) Mar 2021spp. are emerging waterborne and foodborne zoonotic pathogens responsible for gastroenteritis in humans. In this work, we evaluated the occurrence and the antimicrobial...
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 isolates recovered from different aquatic sources. Besides, we searched for spp. in seaweeds and the corresponding seawater samples. Bacteriological and molecular methods applied to 100 samples led to the isolation of 28 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 than the corresponding seawater samples. The isolates were identified as (96.4%) and (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 and/or This work confirms the occurrence and the continuous emergence of antibiotic-resistant strains in environmental samples; also, the presence of quinolone-resistant spp. in aquatic sources used for water supply and irrigation represents a potential risk for human health.
PubMed: 33802125
DOI: 10.3390/antibiotics10030288 -
Foods (Basel, Switzerland) Jul 2021This review maps the global research landscape of the public health implications of from the food-environment interphase using content analytics and integrated science... (Review)
Review
This review maps the global research landscape of the public health implications of from the food-environment interphase using content analytics and integrated science mapping. The search term "Arcobacter" was used to retrieve relevant articles published in Web of Science and Scopus between 1991 to 2019. The number of articles included in the review was 524, with 1304 authors, 172 journal sources, and a collaborative index of 2.55. The annual growth rate of the publications was 9.74%. The most contributing author in the field was Houf K., with 40 publications, 26 h-index, and 2020 total citations. The most productive country was the USA (13.33%). The majority of the articles were published in English (96%) and in the Journal of Food Protection (8.02%). The highest research outputs were in the field of Microbiology (264). The frequently occurred keywords were , poultry, shellfish, cattle, and chicken. This study revealed a fair increase in the growth rate of -related research-especially in the area of isolation and detection of the pathogen in foods and food environments, as well as the pathogenesis and genetic diversity of the pathogen. Research themes in the area of prevalence and epidemiology seem to be underexplored.
PubMed: 34359542
DOI: 10.3390/foods10071673 -
Frontiers in Microbiology 2023was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of utilizing the 16S...
was recognized as an emerging enteropathogen and controversies regarding its classification persisted. This study aimed to reevaluate the taxonomy of utilizing the 16S rRNA gene, 23S rRNA gene, single-copy orthologous genes, as well as genomic indices such as Average Nucleotide Identity (ANI) and DNA-DNA hybridization (). The taxonomy of this genus was reevaluated in this study using multiple indices with a dataset of 371 genomes comprising 34 known species and 14 potentially new species. Good discrimination could be achieved only in some species but not for the species with higher sequence similarity using the comparisons of the 16S rRNA gene and 23S rRNA gene sequences. A high-accuracy phylogenomic approach for was established using 84 single-copy orthologous genes obtained through various bioinformatics methods. One marker gene (gene711), which was found to possess the same distinguishing ability as ANI, and single-copy orthologous methods, was identified as a reliable locus for inferring the phylogeny of the genus. The effective species classification was achieved by employing gene711 with a sequence similarity exceeding 96%, even for species like , , and , which exhibited ambiguous classification using ANI and . Additionally, excellent subspecies categorizing among could be distinguished using gene711. In conclusion, this framework strategy had the potential advantage of developing rapid species identification, particularly for highly variable species, providing a novel insight into the behavior and characteristics of .
PubMed: 37881248
DOI: 10.3389/fmicb.2023.1278268 -
Journal of Environmental Management Jan 2022Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand...
Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; HS) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential HS producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The HS producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of HS consuming sulfate oxidizing bacteria (SOB) was 5-10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced HS and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.
Topics: Aquaculture; Bioreactors; Denitrification; Microbiota; Nitrates; RNA, Ribosomal, 16S
PubMed: 34592671
DOI: 10.1016/j.jenvman.2021.113852 -
Applied and Environmental Microbiology Oct 2020Rapid and accurate identification of is of great importance because it is considered an emerging food- and waterborne pathogen and potential zoonotic agent. Raman...
Rapid and accurate identification of is of great importance because it is considered an emerging food- and waterborne pathogen and potential zoonotic agent. Raman spectroscopy can differentiate bacteria based on Raman scattering spectral patterns of whole cells in a fast, reagentless, and easy-to-use manner. We aimed to detect and discriminate bacteria at the species level using confocal micro-Raman spectroscopy (785 nm) coupled with neural networks. A total of 82 reference and field isolates of 18 species from clinical, environmental, and agri-food sources were included. We determined that the bacterial cultivation time and growth temperature did not significantly influence the Raman spectral reproducibility and discrimination capability. The genus could be successfully differentiated from the closely related genera and using principal-component analysis. For the identification of to the species level, an accuracy of 97.2% was achieved for all 18 species using Raman spectroscopy combined with a convolutional neural network (CNN). The predictive capability of Raman-CNN was further validated using an independent data set of 12 strains. Furthermore, a Raman spectroscopy-based fully connected artificial neural network (ANN) was constructed to determine the actual ratio of a specific species in a bacterial mixture ranging from 5% to 100% by biomass (regression coefficient >0.99). The application of both CNN and fully connected ANN improved the accuracy of Raman spectroscopy for bacterial species determination compared to the conventional chemometrics. This newly developed approach enables rapid identification and species determination of within an hour following cultivation. Rapid identification of bacterial pathogens is critical for developing an early warning system and performing epidemiological investigation. is an emerging foodborne pathogen and has become more important in recent decades. The incidence of species in the agro-ecosystem is probably underestimated mainly due to the limitation in the available detection and characterization techniques. Raman spectroscopy combined with machine learning can accurately identify at the species level in a rapid and reliable manner, providing a promising tool for epidemiological surveillance of this microbe in the agri-food chain. The knowledge elicited from this study has the potential to be used for routine bacterial screening and diagnostics by the government, food industry, and clinics.
Topics: Arcobacter; Bacteriological Techniques; Neural Networks, Computer; Spectrum Analysis, Raman
PubMed: 32801186
DOI: 10.1128/AEM.00924-20 -
Iranian Journal of Microbiology Dec 2020species are food-borne and zoonotic enteropathogens. Defined breakpoints for the investigation of antimicrobial resistance of are missing.
BACKGROUND AND OBJECTIVES
species are food-borne and zoonotic enteropathogens. Defined breakpoints for the investigation of antimicrobial resistance of are missing.
MATERIALS AND METHODS
The study was performed to investigate the incidence and antimicrobial resistance of species in animals and poultry meat samples procured from slaughterhouses in Iran. To investigate the prevalence of antimicrobial resistance, samples were collected from cattle (n=100), sheep (n=100), goat (n=100), broiler chicken (n=100), turkey (n=100) and quail (n=100). isolates of meat samples were isolated, investigated by PCR method and antibiotic resistance was also investigated. The susceptibility was assessed by Kirby-Bauer disc diffusion.
RESULTS
The results showed that 52 samples (8.66%) were positive for spp. The most prevalence were observed in broiler chickens (26%, n=26 samples), quail (13%, n=13 samples), turkey (8%, n=8), cattle (3%, n=3), sheep (1%, n=1) and goat (1%, n=1). had highest prevalence among species. All the isolates showed sensitivity to gentamicin, streptomycin and tetracycline.
CONCLUSION
Poultry meat is a potential source of infection with that must be considered in slaughterhouses in Iran. species showed sensitivity for a broad spectrum of antibiotics that can be used during infection with species.
PubMed: 33613907
DOI: 10.18502/ijm.v12i6.5027 -
Journal of Food Protection Jan 2021Arcobacter species are gram-negative rods that have been implicated in food- and waterborne illness. Although various cultural isolation methods have been proposed, the...
ABSTRACT
Arcobacter species are gram-negative rods that have been implicated in food- and waterborne illness. Although various cultural isolation methods have been proposed, the current procedures are unable to fully suppress the growth of background microbiota present in food samples, which inhibits Arcobacter isolation. The purpose of this study was to develop a selective enrichment broth and chromogenic plating medium to detect three Arcobacter species that have been recognized as emerging foodborne pathogens: Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The developed Nguyen-Restaino-Juárez (NRJ) Arcobacter detection system consists of a selective enrichment broth (NRJ-B) and a selective-differential plating medium (NRJ-M). The protocol of the detection method was determined by evaluating the growth of A. butzleri, A. cryaerophilus, and A. skirrowii under various temperatures (30, 35, and 42°C) and incubation (aerobic, microaerophilic, and anaerobic) conditions. Additionally, 47 Arcobacter strains and 39 non-Arcobacter strains were tested in inclusivity and exclusivity evaluations of NRJ-B and NRJ-M. Overall, the study determined that the optimal growth conditions of Arcobacter species using the NRJ Arcobacter detection system were aerobic incubation at 30°C. NRJ-B supported good growth of A. butzleri, A. cryaerophilus, and A. skirrowii while effectively suppressing the growth of non-Arcobacter strains after 48 h. Furthermore, NRJ-M yielded 97.8% inclusivity and 100.0% exclusivity using the tested strains and resulted in salmon-pigmented Arcobacter colonies (1.0 to 1.5 mm in diameter) after 72 h. The novel protocol is the first to develop a chromogenic plating medium for the isolation of Arcobacter species. This simple and accurate test method would greatly contribute to understanding the distribution of pathogenic Arcobacter species in food samples.
Topics: Agar; Arcobacter; Culture Media
PubMed: 33411930
DOI: 10.4315/JFP-20-245