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Akkemik Y, Güner A. Determination of the presence and antimicrobial resistance of Arcobacter species in broiler carcasses at different stages of slaughter line. Food Sci Nutr 2024; 12:3461-3468. [PMID: 38726459 PMCID: PMC11077200 DOI: 10.1002/fsn3.4013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 05/12/2024] Open
Abstract
In this study, to investigate Arcobacter spp. contamination post-scalding and de-feathering, post-evisceration, post-chilling, and packaged products, which are the most essential contamination stages of broiler slaughter, a total of 108 samples were taken from three different broiler slaughterhouses at different times. Isolates obtained by cultural methods in 104 of 108 samples were analyzed by mPCR method to identify pathogen Arcobacter spp. Arcobacter butzleri, Arcobacter cryaerophilus, and mixed contamination of both Arcobacter species were detected in 51 samples. Of the 51 isolates, 27 (52.9%) were A. butzleri, 16 (31.4%) were A. cryaerophilus, and 8 (15.7%) were mixed contamination of A. butzleri and A. cryaerophilus, while Arcobacter skirrowii was not detected. A. butzleri and A. cryaerophilus contamination was 59.2% post-scalding and de-feathering, 43.4% post-evisceration, 44.4% and 48.1% post-chilling and in packaged products, respectively. All A. butzleri strains were found to be 100% resistant to cefoperazone and penicillin and sensitive to tetracycline. A. cryaerophilus strains were 100% resistant to cefoperazone, penicillin, and cloxacillin and susceptible to tetracycline and erythromycin. In the study, it was determined that Arcobacter spp. caused a very intense contamination (85.18%-100%) and also contamination rates of identified pathogen strains (A. butzleri and A. cryaerophilus) were very high (59.2% and 43.4%) in broiler slaughtering stages. Considering that each step in broiler slaughter could contaminate the next stage, developing a safe slaughter and minimizing the risk toward the final product, it was concluded that critical control points could not be well managed in broiler slaughterhouses, and broiler meat may pose a significant risk to public health.
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Affiliation(s)
- Yasin Akkemik
- Department of Food Hygiene and TechnologyKastamonu University Faculty of Veterinary MedicineKastamonuTurkey
| | - Ahmet Güner
- Department of Food Hygiene and TechnologySelcuk University Faculty of Veterinary MedicineKonyaTurkey
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2
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Pascual J, Lepleux C, Methner A, Spröer C, Bunk B, Overmann J. Arcobacter roscoffensis sp. nov., a marine bacterium isolated from coastal seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37200211 DOI: 10.1099/ijsem.0.005895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Abstract
A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2T, was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2T was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2T was closely related to Arcobacter lekithochrous LFT 1.7T and Arcobacter caeni RW17-10T(95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2T was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2T represents a new Arcobacter species. The predominant fatty acids were C16 : 1 ω7c/C16 : 1 ω6c and C18 : 1 ω7c/C18 : 1 ω6c. The results of a polyphasic analysis supported the description of strain ARW1-2F2T as representing a novel species of the genus Arcobacter, for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2T (DSM 29169T=KCTC 52423T).
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Affiliation(s)
- Javier Pascual
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
- Present address: Darwin Bioprospecting Excellence S.L., Paterna, Spain
| | - Cendrella Lepleux
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Anika Methner
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
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3
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A Review on the Prevalence of Arcobacter in Aquatic Environments. WATER 2022. [DOI: 10.3390/w14081266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Arcobacter is an emerging pathogen that is associated with human and animal diseases. Since its first introduction in 1991, 33 Arcobacter species have been identified. Studies have reported that with the presence of Arcobacter in environmental water bodies, animals, and humans, a possibility of its transmission via water and food makes it a potential waterborne and foodborne pathogen. Therefore, this review article focuses on the general characteristics of Arcobacter, including its pathogenicity, antimicrobial resistance, methods of detection by cultivation and molecular techniques, and its presence in water, fecal samples, and animal products worldwide. These detection methods include conventional culture methods, and rapid and accurate Arcobacter identification at the species level, using quantitative polymerase chain reaction (qPCR) and multiplex PCR. Arcobacter has been identified worldwide from feces of various hosts, such as humans, cattle, pigs, sheep, horses, dogs, poultry, and swine, and also from meat, dairy products, carcasses, buccal cavity, and cloacal swabs. Furthermore, Arcobacter has been detected in groundwater, river water, wastewater (influent and effluent), canals, treated drinking water, spring water, and seawater. Hence, we propose that understanding the prevalence of Arcobacter in environmental water and fecal-source samples and its infection of humans and animals will contribute to a better strategy to control and prevent the survival and growth of the bacteria.
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Heins A, Amann RI, Harder J. Cultivation of particle-associated heterotrophic bacteria during a spring phytoplankton bloom in the North Sea. Syst Appl Microbiol 2021; 44:126232. [PMID: 34399113 DOI: 10.1016/j.syapm.2021.126232] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/21/2021] [Accepted: 07/05/2021] [Indexed: 11/29/2022]
Abstract
Seawater contains free-living and particle-attached bacteria. Only a small fraction is cultivable on plates. As free-living and particle-associated bacteria differ in their physiological traits, their cultivability on plates may coincide with particle association. Using filtration and Imhoff sedimentation cones, particles were collected during a spring phytoplankton bloom off Helgoland (North Sea) in order to obtain particle-associated bacteria as inocula. Direct dilution plating resulted in 526 strains from 3 µm filtration retentates and 597 strains from settled particles. Motile Gammaproteobacteria from the genera Pseudoalteromonas, Shewanella, Psychrobacter, Vibrio and Colwellia, as well as particle-attached Flavobacteriia affiliating with the genera Tenacibaculum and Gramella, were frequently isolated. As a result, a diverse collection comprised of 266 strains was deposited. Two strains were most likely to represent novel genera and 78 strains were probably novel species. Recently, a high-throughput cultivation study from the same site using seawater as an inoculum had retrieved 271 operational phylogenetic units (OPUs) that represented 88% of the 4136 characterized strains at the species level. A comparison of 16S rRNA gene sequences revealed that the collection obtained matched 104 of the 271 seawater OPUs at the species level and an additional 113 at the genus level. This large overlap indicated a significant contribution of particle-associated bacteria to the cultivable microbiome from seawater. The presence of 49 genera not identified in the larger seawater study suggested that sample fractionation was an efficient strategy to cultivate rare members of the planktonic microbiome. The diverse collection of heterotrophic bacteria retrieved in this study will be a rich source for future studies on the biology of particle-associated bacteria.
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Affiliation(s)
- Anneke Heins
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Characterization of Arcobacter spp. Isolated from human diarrheal, non-diarrheal and food samples in Thailand. PLoS One 2021; 16:e0246598. [PMID: 33544770 PMCID: PMC7864401 DOI: 10.1371/journal.pone.0246598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/21/2021] [Indexed: 11/19/2022] Open
Abstract
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.
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Turgay E, Steinum TM, Eryalçın KM, Yardımcı RE, Karataş S. The influence of diet on the microbiota of live-feed rotifers (Brachionus plicatilis) used in commercial fish larviculture. FEMS Microbiol Lett 2021; 367:5719568. [PMID: 32005987 DOI: 10.1093/femsle/fnaa020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
Live-feed is indispensable to commercial fish larviculture. However, high bacterial loads in rotifers could pose a biosecurity risk. While this may be true, live-feed associated bacteria could also be beneficial to fish larvae through improved feed utilization or pathogen inhibition following host microbiota modification. The study objective was to elucidate the largely unexplored microbiota of rotifers propagated on five different diets through bacterial community profiling by 16S rRNA gene amplicon sequencing. Investigated rotifer samples had a median observed alpha-diversity of 338 ± 87 bacterial species. Alpha- and Gamma-Proteobacteria dominated the rotifer microbiota followed by members of classes Flavobacteriia, Cytophagia, Mollicutes, Phycisphaerae and Bacteroidia. Different diets significantly altered the bacterial communities associated with rotifers according to PERMANOVA test results and beta dispersion calculations. A common core rotifer microbiome included 31 bacterial species present in relative abundances over 0.01%. We discuss the functional role of some microbiome members. Our data suggested the presence of several known fish pathogens in stock rotifers. However, we found no evidence for increased loads of these presumptive taxa in propagated live-feed rotifers during this field trial.
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Affiliation(s)
- Emre Turgay
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Terje Marken Steinum
- Department of Molecular Biology and Genetics, Faculty of Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Kamil Mert Eryalçın
- Fish Nutrition & Phytoplankton-Zooplankton Culture Laboratory, Aquaculture Department, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Remziye Eda Yardımcı
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
| | - Süheyla Karataş
- Department of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Ordu Cad. No:8, 34134 Istanbul, Turkey
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Kim MJ, Baek MG, Shin SK, Yi H. Poseidonibacter parvus sp. nov., isolated from a squid. Int J Syst Evol Microbiol 2020; 71. [PMID: 33269998 DOI: 10.1099/ijsem.0.004590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, short rod-shaped, motile, brownish-coloured bacterium, termed strain LPB0137T, was isolated from a squid. Its cells could grow weakly on marine agar 2216 with 0.04 % 2,3,5-triphenyl tetrazolium chloride (TTC). Each cell of strain LPB0137T has a circular chromosome with a length of 2.87 Mb and 27.7 mol% DNA G+C content. The genome includes 2698 protein-coding genes and six rRNA operons. In 16S rRNA gene sequence trees, strain LPB0137T formed a robust monophyletic clade with Poseidonibacter antarcticus SM1702T with a sequence similarity of 98.3 %. However, the average nucleotide identity and in silico DNA-DNA hybridization values between the two type strains were low (83.9 and 28.1 %, respectively). The overall phenotypic and genomic features of strain LPB0137T supported its assignment to the genus Poseidonibacter. However, the relatively low gene and genome sequence similarity between this strain and other type strains of the genus Poseidonibacter and several enzymatic characteristics indicated the taxonomic novelty of the isolated strain as a new member of the genus Poseidonibacter. Therefore, based on the phylogenetic and phenotypic characteristics of LPB0137T, we proposed a novel species of the genus Poseidonibacter for it, with the name Poseidonibacter parvus sp. nov. The type strain of this new species is thus LPB0137T (=KACC 18888T=JCM 31548T).
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Affiliation(s)
- Min Ji Kim
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Min-Gyung Baek
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
| | - Su-Kyoung Shin
- Institute for Biomaterials, Korea University, Seoul, Republic of Korea
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, Republic of Korea.,Department of Public Health Sciences, Graduate School, Korea University, Seoul, Republic of Korea
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8
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On SLW, Miller WG, Biggs PJ, Cornelius AJ, Vandamme P. A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Syst Appl Microbiol 2020; 43:126108. [PMID: 32847783 DOI: 10.1016/j.syapm.2020.126108] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA-DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G+C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of "aerotolerant campylobacters" as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].
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Affiliation(s)
- Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Springs Road, Lincoln 7467, New Zealand.
| | - William G Miller
- US Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Patrick J Biggs
- Bioinformatics and Statistics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Angela J Cornelius
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Miltenburg MG, Cloutier M, Craiovan E, Lapen DR, Wilkes G, Topp E, Khan IUH. Real-time quantitative PCR assay development and application for assessment of agricultural surface water and various fecal matter for prevalence of Aliarcobacter faecis and Aliarcobacter lanthieri. BMC Microbiol 2020; 20:164. [PMID: 32546238 PMCID: PMC7298852 DOI: 10.1186/s12866-020-01826-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/18/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Aliarcobacter faecis and Aliarcobacter lanthieri are recently identified as emerging human and animal pathogens. In this paper, we demonstrate the development and optimization of two direct DNA-based quantitative real-time PCR assays using species-specific oligonucleotide primer pairs derived from rpoB and gyrA genes for A. faecis and A. lanthieri, respectively. Initially, the specificity of primers and amplicon size of each target reference strain was verified and confirmed by melt curve analysis. Standard curves were developed with a minimum quantification limit of 100 cells mL- 1 or g- 1 obtained using known quantities of spiked A. faecis and A. lanthieri reference strains in autoclaved agricultural surface water and dairy cow manure samples. RESULTS Each species-specific qPCR assay was validated and applied to determine the rate of prevalence and quantify the total number of cells of each target species in natural surface waters of an agriculturally-dominant and non-agricultural reference watershed. In addition, the prevalence and densities were determined for human and various animal (e.g., dogs, cats, dairy cow, and poultry) fecal samples. Overall, the prevalence of A. faecis for surface water and feces was 21 and 28%, respectively. The maximum A. faecis concentration for water and feces was 2.3 × 107 cells 100 mL- 1 and 1.2 × 107 cells g- 1, respectively. A. lanthieri was detected at a lower frequency (2%) with a maximum concentration in surface water of 4.2 × 105 cells 100 mL- 1; fecal samples had a prevalence and maximum density of 10% and 2.0 × 106 cells g- 1, respectively. CONCLUSIONS The results indicate that the occurrence of these species in agricultural surface water is potentially due to fecal contamination of water from livestock, human, or wildlife as both species were detected in fecal samples. The new real-time qPCR assays can facilitate rapid and accurate detection in < 3 h to quantify total numbers of A. faecis and A. lanthieri cells present in various complex environmental samples.
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Affiliation(s)
- Mary G Miltenburg
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.,Canadian Food Inspection Agency (CFIA), Ottawa, ON, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.,Natural Resources Canada, Ottawa, ON, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario, K1A 0C6, Canada.
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10
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Chieffi D, Fanelli F, Fusco V. Arcobacter butzleri: Up-to-date taxonomy, ecology, and pathogenicity of an emerging pathogen. Compr Rev Food Sci Food Saf 2020; 19:2071-2109. [PMID: 33337088 DOI: 10.1111/1541-4337.12577] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/19/2022]
Abstract
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.
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Affiliation(s)
- Daniele Chieffi
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), Bari, Italy
| | - Francesca Fanelli
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), Bari, Italy
| | - Vincenzina Fusco
- Institute of Sciences of Food Production, National Research Council of Italy (CNR-ISPA), Bari, Italy
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11
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Alonso R, Girbau C, Martinez-Malaxetxebarria I, Pérez-Cataluña A, Salas-Massó N, Romalde JL, Figueras MJ, Fernandez-Astorga A. Aliarcobacter vitoriensis sp. nov., isolated from carrot and urban wastewater. Syst Appl Microbiol 2020; 43:126091. [PMID: 32690190 DOI: 10.1016/j.syapm.2020.126091] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/27/2020] [Accepted: 04/30/2020] [Indexed: 10/24/2022]
Abstract
Two isolates, one recovered from a carrot and another one from urban wastewater, were characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both isolates clustered together, and were most closely related to Aliarcobacter lanthieri. Multilocus phylogenetic analysis (MLPA) using the concatenated sequences of five housekeeping genes (atpA, gyrA, gyrB, hsp60 and rpoB) suggested that these isolates formed a distinct phylogenetic lineage among the genera derived from the former genus Arcobacter. Whole-genome sequence, in silico DNA-DNA hybridization (isDDH) and the average nucleotide identity (ANI) value between the genome of strain F199T and those of related species confirmed that these isolates represent a novel species. These strains can be differentiated from its phylogenetically closest species A. lanthieri by its inability to growth on 1% glycine and by their enzyme activity of esterase lipase (C8) and acid phosphatase. Our results, by the application of a polyphasic analysis, confirmed that these two isolates represent a novel species of the genus Aliarcobacter, for which the name Aliarcobacter vitoriensis sp. nov. is proposed. The type strain is F199T (=CECT 9230T=LMG 30050T).
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Affiliation(s)
- Rodrigo Alonso
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Cecilia Girbau
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Irati Martinez-Malaxetxebarria
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
| | - Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología & Instituto CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782 Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Aurora Fernandez-Astorga
- Department of Immunology, Microbiology and Parasitology, Faculty of Pharmacy. University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
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12
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Pérez-Cataluña A, Salas-Massó N, Figueras MJ. Arcobacter lacus sp. nov. and Arcobacter caeni sp. nov., two novel species isolated from reclaimed water. Int J Syst Evol Microbiol 2019; 69:3326-3331. [DOI: 10.1099/ijsem.0.003101] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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13
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Guo XH, Wang N, Yuan XX, Zhang XY, Chen XL, Zhang YZ, Song XY. Poseidonibacter antarcticus sp. nov., isolated from Antarctic intertidal sediment. Int J Syst Evol Microbiol 2019; 69:2717-2722. [DOI: 10.1099/ijsem.0.003539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Xiao-Han Guo
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Ning Wang
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiao-Xue Yuan
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Yu-Zhong Zhang
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, PR China
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Xiao-Yan Song
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
- Marine Biotechnology Research Center, Shandong University, Qingdao 266237, PR China
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Mizutani Y, Iehata S, Mori T, Oh R, Fukuzaki S, Tanaka R. Diversity, enumeration, and isolation of Arcobacter spp. in the giant abalone, Haliotis gigantea. Microbiologyopen 2019; 8:e890. [PMID: 31168933 PMCID: PMC6813453 DOI: 10.1002/mbo3.890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/16/2019] [Accepted: 05/20/2019] [Indexed: 01/04/2023] Open
Abstract
Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter‐specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter‐specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F‐positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338‐positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%–100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%–94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.
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Affiliation(s)
- Yukino Mizutani
- Graduate School of Bioresources, Laboratory of Marine Microbiology, Mie University, Tsu, Japan
| | - Shunpei Iehata
- School of Fisheries and Aquaculture Science, Universiti Malaysia Terengganu, Kuala Terengganu, Terengganu, Malaysia
| | - Tetsushi Mori
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Japan
| | - Ryota Oh
- Graduate School of Bioresources, Laboratory of Marine Microbiology, Mie University, Tsu, Japan
| | - Satoshi Fukuzaki
- Graduate School of Bioresources, Laboratory of Marine Microbiology, Mie University, Tsu, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Laboratory of Marine Microbiology, Mie University, Tsu, Japan
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15
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Zambri M, Cloutier M, Adam Z, Lapen DR, Wilkes G, Sunohara M, Topp E, Talbot G, Khan IUH. Novel virulence, antibiotic resistance and toxin gene-specific PCR-based assays for rapid pathogenicity assessment of Arcobacter faecis and Arcobacter lanthieri. BMC Microbiol 2019; 19:11. [PMID: 30634926 PMCID: PMC6330389 DOI: 10.1186/s12866-018-1357-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/28/2018] [Indexed: 11/30/2022] Open
Abstract
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.
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Affiliation(s)
- Matthew Zambri
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.,Department of Biology, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Zaky Adam
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.,School of Information Technology and Engineering, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Mark Sunohara
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Edward Topp
- London Research and Development Centre (LRDC), Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Guylaine Talbot
- Sherbrooke Research and Development Centre (SRDC), Agriculture and Agri-Food Canada, Sherbrooke, Quebec, J1M 0C8, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada.
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16
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A meta-analytic perspective on Arcobacter spp. antibiotic resistance. J Glob Antimicrob Resist 2019; 16:130-139. [PMID: 30611931 DOI: 10.1016/j.jgar.2018.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 12/22/2018] [Accepted: 12/27/2018] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Over the years, an increased prevalence of resistant strains of Arcobacter has been observed, which may be due to Arcobacter exposure to antibiotics used both in animal production and human medicine. A systematic review was performed with the objective of summarising the results of the rates of antimicrobial resistance of Arcobacter isolates. METHODS The systematic review was performed according to PRISMA (Preferred Reported Items for Systematic Reviews and Meta-Analysis) recommendations, followed by meta-analysis. RESULTS It was observed that the resistance rate ranged between 69.3-99.2% for penicillins and 30.5-97.4% for cephalosporins. The overall percentage of resistance to fluoroquinolones ranged from 4.3% to 14.0%, with the highest resistance percentage observed for levofloxacin. Resistance rates ranged between 10.7-39.8% for macrolides, 1.8-12.9% for aminoglycosides and 0.8-7.1% for tetracyclines. CONCLUSIONS These results show that Arcobacter spp. present resistance to various antibiotics commonly used and advocate further studies of the associated resistance mechanisms.
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Complete Genome Sequence of the Arcobacter bivalviorum Type Strain LMG 26154. Microbiol Resour Announc 2018; 7:MRA01076-18. [PMID: 30533664 PMCID: PMC6256687 DOI: 10.1128/mra.01076-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Arcobacters are routinely recovered from marine environments, and multiple Arcobacter species have been isolated from shellfish. Arcobacter bivalviorum was recovered from mussels collected in the Ebro Delta in northeastern Spain. This report describes the complete whole-genome sequence of the A. bivalviorum type strain LMG 26154 (= F4T = CECT 7835T).
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18
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Complete Genome Sequence of the Arcobacter halophilus Type Strain CCUG 53805. Microbiol Resour Announc 2018; 7:MRA01077-18. [PMID: 30533711 PMCID: PMC6256642 DOI: 10.1128/mra.01077-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Many Arcobacter spp. are free living and are routinely recovered from marine environments. Many Arcobacter spp. are free living and are routinely recovered from marine environments. Arcobacter halophilus was isolated from hypersaline lagoon water in the Hawaiian islands, and it was demonstrated to be an obligate halophile. This study describes the complete whole-genome sequence of the A. halophilus type strain, CCUG 53805 (= LA31BT = ATCC BAA-1022T).
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19
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Nakagawa T, Tsuchiya Y, Ueda S, Fukui M, Takahashi R. Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan. Microbes Environ 2018; 34:13-22. [PMID: 30504642 PMCID: PMC6440730 DOI: 10.1264/jsme2.me18103] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. Sulfur-oxidizing Gammaproteobacteria within nosZ gene clade II dominated in the lineage Dechloromonas-Magnetospirillum-Thiocapsa. Alphaproteobacteria within nosZ gene clade I were predominant in both zones. The proportions of Epsilonproteobacteria within nosZ gene clade II increased after incubations in the eelgrass zone microcosm supplemented with N2O only. Collectively, these results suggest that the N2O-reducing microbiome in eelgrass meadows is largely responsible for coastal N2O mitigation.
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Affiliation(s)
| | | | - Shingo Ueda
- College of Bioresource Sciences, Nihon University
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University
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20
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter molluscorum Type Strain LMG 25693. Microbiol Resour Announc 2018; 7:e01293-18. [PMID: 30533749 PMCID: PMC6256585 DOI: 10.1128/mra.01293-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 09/26/2018] [Indexed: 12/22/2022] Open
Abstract
As components of freshwater and marine microflora, Arcobacter spp. are often recovered from shellfish, such as mussels, clams, and oysters. Arcobacter molluscorum was isolated from mussels from the Ebro Delta in Catalonia, Spain. This article describes the whole-genome sequence of the A. molluscorum strain LMG 25693T (= F98-3T = CECT 7696T).
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Affiliation(s)
- William G. Miller
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, California, USA
| | - Emma Yee
- U.S. Department of Agriculture, Produce Safety and Microbiology Research Unit, Agricultural Research Service, Albany, California, USA
| | - James L. Bono
- U.S. Department of Agriculture, Meat Safety and Quality Research Unit, Agricultural Research Service, Clay Center, Nebraska, USA
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21
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter ellisii Type Strain LMG 26155. Microbiol Resour Announc 2018; 7:e01268-18. [PMID: 30533751 PMCID: PMC6256587 DOI: 10.1128/mra.01268-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/30/2018] [Indexed: 01/05/2023] Open
Abstract
Arcobacter spp. are highly prevalent in contaminated environmental waters and have been recovered from both freshwater and seawater, with several species isolated from shellfish. Arcobacter ellisii was recovered from mussels collected in Catalonia, Spain. This study describes the whole-genome sequence of the A. ellisii type strain LMG 26155 (=F79-6T =CECT 7837T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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22
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos. Front Microbiol 2018; 9:2077. [PMID: 30233547 PMCID: PMC6131481 DOI: 10.3389/fmicb.2018.02077] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 08/14/2018] [Indexed: 11/16/2022] Open
Abstract
Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.
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Affiliation(s)
- Alba Pérez-Cataluña
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
| | - Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Maria J Figueras
- Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Reus, Spain
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23
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Diéguez AL, Pérez-Cataluña A, Figueras MJ, Romalde JL. Arcobacter haliotis Tanaka et al. 2017 is a later heterotypic synonym of Arcobacter lekithochrous Diéguez et al. 2017. Int J Syst Evol Microbiol 2018; 68:2851-2854. [DOI: 10.1099/ijsem.0.002909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ana L. Diéguez
- 1Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Alba Pérez-Cataluña
- 2Departament de Ciéncies Médiques Bàsiques, Facultat de Medicina, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Maria José Figueras
- 2Departament de Ciéncies Médiques Bàsiques, Facultat de Medicina, IISPV, Universitat Rovira i Virgili, Sant Llorenç 21, 43201 Reus, Spain
| | - Jesús L. Romalde
- 1Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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Salas-Massó N, Figueras MJ, Andree KB, Furones MD. Do the Escherichia coli European Union shellfish safety standards predict the presence of Arcobacter spp., a potential zoonotic pathogen? THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 624:1171-1179. [PMID: 29929229 DOI: 10.1016/j.scitotenv.2017.12.178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/07/2017] [Accepted: 12/16/2017] [Indexed: 06/08/2023]
Abstract
The genus Arcobacter comprises Campylobacter-related species, considered zoonotic emergent pathogens, the presence of which in water has been associated with fecal pollution. Discharges of fecal polluted water into the sea have been considered as one of the main reasons for the presence of Arcobacter in shellfish, and this may represent a risk for public health. In this study, the European Union shellfish food safety criteria based on levels of Escherichia coli were studied in relation to their capacity to predict the presence of Arcobacter species. In addition, the accumulation factor (AF) that measures the concentration ratio between the microbes present in the shellfish and in the water, was also studied for both bacteria. The results show that the presence of E. coli correlated with the presence of the potentially pathogenic species A. butzleri and A. cryaerophilus. However, in 26.1% of the shellfish samples (corresponding to those taken during summer months) E. coli failed to predict the presence of, for instance A. butzleri and A. skirrowii, among other species. In the rest of the samples a significant correlation between the concentration of E. coli and Arcobacter spp. (mussels and oyster; R2=0.744) was found. This study indicates that the presence of E. coli can predict the presence of pathogenic Arcobacter species in shellfish samples harvested from water with temperatures lower than 26.2°C. Consumption of shellfish collected at higher temperatures which may not be permissive to the growth of E. coli but does allow growth of Arcobacter spp., may represent a risk for consumers.
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Affiliation(s)
- Nuria Salas-Massó
- IRTA Sant Carles de la Ràpita, Carretera Poble Nou, Km 5.5, 43540 Sant Carles de la Ràpita, Spain; Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - M José Figueras
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain.
| | - Karl B Andree
- IRTA Sant Carles de la Ràpita, Carretera Poble Nou, Km 5.5, 43540 Sant Carles de la Ràpita, Spain
| | - M Dolors Furones
- IRTA Sant Carles de la Ràpita, Carretera Poble Nou, Km 5.5, 43540 Sant Carles de la Ràpita, Spain
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25
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Pérez-Cataluña A, Collado L, Salgado O, Lefiñanco V, Figueras MJ. A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars. Front Microbiol 2018; 9:805. [PMID: 29755434 PMCID: PMC5934430 DOI: 10.3389/fmicb.2018.00805] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/10/2018] [Indexed: 12/01/2022] Open
Abstract
The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291T = LMG 9904T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976T).
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Affiliation(s)
- Alba Pérez-Cataluña
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
| | - Luis Collado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - Oscar Salgado
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile.,Laboratory of Microbial Ecology of Extreme Systems, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Violeta Lefiñanco
- Faculty of Sciences, Institute of Biochemistry and Microbiology, Universidad Austral de Chile, Valdivia, Chile
| | - María J Figueras
- Unit of Microbiology, Department of Basic Health Sciences, Faculty of Medicine and Health Sciences, IISPV, University Rovira i Virgili, Reus, Spain
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Vicente-Martins S, Oleastro M, Domingues FC, Ferreira S. Arcobacter spp. at retail food from Portugal: Prevalence, genotyping and antibiotics resistance. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pérez-Cataluña A, Salas-Massó N, Figueras MJ. Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage. Int J Syst Evol Microbiol 2018; 68:1258-1264. [PMID: 29488868 DOI: 10.1099/ijsem.0.002662] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Four bacterial strains recovered from shellfish (n=3) and from the water (n=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus Arcobacter (represented by strain F138-33T) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being Arcobacter marinus and Arcobactermolluscorum. However, phylogenetic analyses using the concatenated sequences of housekeeping genes (atpA, gyrB, hsp60, gyrA and rpoB) showed that all the novel strains formed a distinct lineage within the genus Arcobacter. Results of in silico DNA-DNA hybridization and the average nucleotide identity between the genome of strain F138-33T and those of the closely related species A. marinus and other relatively closely related species such as A. molluscorum and Arcobacterhalophilus were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name Arcobacter canalis sp. nov. is proposed, with the type strain F138-33T (=CECT 8984T=LMG 29148T).
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Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - Nuria Salas-Massó
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
| | - María José Figueras
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, IISPV, Universitat Rovira i Virgili, Reus, Spain
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Ramees TP, Dhama K, Karthik K, Rathore RS, Kumar A, Saminathan M, Tiwari R, Malik YS, Singh RK. Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review. Vet Q 2017; 37:136-161. [PMID: 28438095 DOI: 10.1080/01652176.2017.1323355] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Thadiyam Puram Ramees
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Kuldeep Dhama
- b Division of Pathology , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Kumaragurubaran Karthik
- c Central University Laboratory , Tamil Nadu Veterinary and Animal Sciences University , Chennai , India
| | - Ramswaroop Singh Rathore
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Ashok Kumar
- a Division of Veterinary Public Health , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Mani Saminathan
- b Division of Pathology , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Ruchi Tiwari
- d Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences , UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan (DUVASU) , Mathura , India
| | - Yashpal Singh Malik
- e Division of Biological Standardization , ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
| | - Raj Kumar Singh
- f ICAR-Indian Veterinary Research Institute (IVRI) , Bareilly , India
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Rathlavath S, Kohli V, Singh AS, Lekshmi M, Tripathi G, Kumar S, Nayak BB. Virulence genotypes and antimicrobial susceptibility patterns of Arcobacter butzleri isolated from seafood and its environment. Int J Food Microbiol 2017; 263:32-37. [DOI: 10.1016/j.ijfoodmicro.2017.10.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/05/2017] [Accepted: 10/03/2017] [Indexed: 11/28/2022]
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Pérez-Cataluña A, Tapiol J, Benavent C, Sarvisé C, Gómez F, Martínez B, Terron-Puig M, Recio G, Vilanova A, Pujol I, Ballester F, Rezusta A, Figueras MJ. Antimicrobial susceptibility, virulence potential and sequence types associated with Arcobacter strains recovered from human faeces. J Med Microbiol 2017; 66:1736-1743. [PMID: 29120301 DOI: 10.1099/jmm.0.000638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Alba Pérez-Cataluña
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
| | | | | | | | | | | | | | - Gemma Recio
- Hospital Universitari Joan XXIII, Tarragona, Spain
| | | | | | | | | | - María Jose Figueras
- Unitat de Microbiología, Departament de Ciències Mèdiques Bàsiques, Facultat de Medicina i Ciències de la Salut, Universitat Rovira i Virgili, Reus, Spain
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Rathlavath S, Kumar S, Nayak BB. Comparative isolation and genetic diversity of Arcobacter sp. from fish and the coastal environment. Lett Appl Microbiol 2017; 65:42-49. [PMID: 28394467 DOI: 10.1111/lam.12743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/05/2017] [Accepted: 03/22/2017] [Indexed: 12/13/2022]
Abstract
Arcobacter species are emerging food-borne and water-borne human pathogens associated mostly with food animals and their environment. The present study was aimed to isolate Arcobacter species from fish, shellfish and coastal water samples using two methods and to determine their genetic diversity. Of 201 samples of fish, shellfish and water samples analysed, 66 (32·8%) samples showed the presence of Arcobacter DNA from both Arcobacter enrichment broth and Bolton broth. Arcobacters were isolated from 58 (87·8%) and 38 (57·5%) of Arcobacter DNA-positive samples using Arcobacter blood agar and Preston blood agar, respectively. Arcobacter sp. identified by biochemical tests were further analysed by a genus-specific PCR, followed by a multiplex-PCR and 16S rRNA-RFLP. From both the methods, four different Arcobacter species namely Arcobacter butzleri, Arcobacter skirrowii, Arcobacter mytili and Arcobacter defluvii were isolated, of which A. butzleri was the predominant species. Enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprint analysis revealed that the arcobacters isolated in this study were genetically very diverse and no specific genotype was found associated with a specific source (seafood or water). Since pathogenic arcobacters are not known to be natural inhabitants of coastal marine environment, identifying the sources of contamination will be crucial for effective management of this problem. SIGNIFICANCE AND IMPACT OF THE STUDY Arcobacter sp. are emerging food- and water-borne human pathogens. In this study, comparison of two selective media suggested Arcobacter blood agar to be more efficient in yielding Arcobacter sp. from seafood. Furthermore, the isolation of Arcobacter sp. such as Arcobacter butzleri, A. skirrowii, A. mytili and A. defluvii from seafood suggests diverse sources of contamination of seafood by Arcobacter sp. Analysis of enterobacterial repetitive intergenic consensus sequence-PCR patterns of A. butzleri showed high genetic diversity and lack of clonality among the isolates. Arcobacter contamination of seafood is an emerging issue both from seafood safety and seafood trade point of view.
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Affiliation(s)
- S Rathlavath
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, India
| | - S Kumar
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, India
| | - B B Nayak
- Quality Control Laboratory, Post-Harvest Technology Department, ICAR-Central Institute of Fisheries Education (CIFE), Mumbai, India
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