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Sheikh AA, Schneiderman D, Sykes EME, Kumar A, Chen W, Lapen DR, Khan IUH. Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species. Lett Appl Microbiol 2024; 77:ovae027. [PMID: 38460955 DOI: 10.1093/lambio/ovae027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 03/11/2024]
Abstract
The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.
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Affiliation(s)
- Alexander A Sheikh
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Danielle Schneiderman
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Ellen M E Sykes
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, R3T 2N2, MB, Canada
| | - Wen Chen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - David R Lapen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
| | - Izhar U H Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, K1A 0C6, ON, Canada
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2
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Khan IUH, Chen W, Cloutier M, Lapen DR, Craiovan E, Wilkes G. Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water. BMC Microbiol 2024; 24:17. [PMID: 38191309 PMCID: PMC10773081 DOI: 10.1186/s12866-023-03119-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites. RESULTS All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic. CONCLUSIONS The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.
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Affiliation(s)
- Izhar U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada.
| | - Wen Chen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - David R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Emilia Craiovan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Graham Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
- Natural Resources Canada, Ottawa, ON, Canada
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3
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Gabucci C, Baldelli G, Amagliani G, Schiavano GF, Savelli D, Russo I, Di Lullo S, Blasi G, Napoleoni M, Leoni F, Primavilla S, Massacci FR, Garofolo G, Petruzzelli A. Widespread Multidrug Resistance of Arcobacter butzleri Isolated from Clinical and Food Sources in Central Italy. Antibiotics (Basel) 2023; 12:1292. [PMID: 37627712 PMCID: PMC10451661 DOI: 10.3390/antibiotics12081292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
The Arcobacter genus comprises a group of bacteria widely distributed in different habitats that can be spread throughout the food chain. Fluoroquinolones and aminoglycosides represent the most common antimicrobial agents used for the treatment of Arcobacter infections. However, the increasing trend of the antimicrobial resistance of this pathogen leads to treatment failures. Moreover, the test implementation and interpretation are hindered by the lack of reference protocols and standard interpretive criteria. The purpose of our study was to assess the antibiotic resistance pattern of 17 A. butzleri strains isolated in Central Italy from fresh vegetables, sushi, chicken breast, and clinical human samples to provide new and updated information about the antimicrobial resistance epidemiology of this species. Antimicrobial susceptibility testing was carried out by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)'s disc diffusion method. All the strains were multidrug resistant, with 100% resistance to tetracyclines and cefotaxime (third generation cephalosporins). Some differences were noticed among the strains, according to the isolation source (clinical isolates, food of animal origin, or fresh vegetables), with a higher sensitivity to streptomycin detected only in the strains isolated from fresh vegetables. Our data, together with other epidemiological information at the national or European Union (EU) level, may contribute to developing homogeneous breakpoints. However, the high prevalence of resistance to a wide range of antimicrobial classes makes this microorganism a threat to human health and suggests that its monitoring should be considered by authorities designated for food safety.
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Affiliation(s)
- Claudia Gabucci
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Giulia Baldelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (G.B.); (I.R.)
| | - Giulia Amagliani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (G.B.); (I.R.)
| | | | - David Savelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Ilaria Russo
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, Italy; (G.B.); (I.R.)
| | - Stefania Di Lullo
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Giuliana Blasi
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Maira Napoleoni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Francesca Leoni
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Sara Primavilla
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Francesca Romana Massacci
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
| | - Giuliano Garofolo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, 64100 Teramo, Italy;
| | - Annalisa Petruzzelli
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati”, 06126 Perugia, Italy; (C.G.); (D.S.); (S.D.L.); (G.B.); (M.N.); (F.L.); (S.P.); (F.R.M.); (A.P.)
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Khan IUH, Becker A, Cloutier M, Plötz M, Lapen DR, Wilkes G, Topp E, Abdulmawjood A. Loop-mediated isothermal amplification: Development, validation and application of simple and rapid assays for quantitative detection of species of Arcobacteraceae family- and species-specific Aliarcobacter faecis and Aliarcobacter lanthieri. J Appl Microbiol 2020; 131:288-299. [PMID: 33174331 PMCID: PMC8359143 DOI: 10.1111/jam.14926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 11/29/2022]
Abstract
Aim The family Arcobacteraceae formerly genus Arcobacter has recently been reclassified into six genera. Among nine species of the genus Aliarcobacter, Aliarcobacter faecis and Aliarcobacter lanthieri have been identified as emerging pathogens potentially cause health risks to humans and animals. This study was designed to develop/optimize, validate and apply Arcobacteraceae family‐ and two species‐specific (A. faecis and A. lanthieri) loop‐mediated isothermal amplification (LAMP) assays to rapidly detect and quantify total number of cells in various environmental niches. Methods and Results Three sets of LAMP primers were designed from conserved and variable regions of 16S rRNA (family‐specific) and gyrB (species‐specific) genes. Optimized Arcobacteraceae family‐specific LAMP assay correctly amplified and detected 24 species, whereas species‐specific LAMP assays detected A. faecis and A. lanthieri reference strains as well as 91 pure and mixed culture isolates recovered from aquatic and faecal sources. The specificity of LAMP amplification of A. faecis and A. lanthieri was further confirmed by restriction fragment length polymorphism analysis. Assay sensitivities were tested using variable DNA concentrations extracted from simulated target species cells in an autoclaved agricultural water sample by achieving a minimum detection limit of 10 cells mL−1 (10 fg). Direct DNA‐based quantitative detection, from agricultural surface water, identified A. faecis (17%) and A. lanthieri (1%) at a low frequency compared to family‐level (93%) with the concentration ranging from 2·1 × 101 to 2·2 × 105 cells 100 mL−1. Conclusions Overall, these three DNA‐based rapid and cost‐effective novel LAMP assays are sensitive and can be completed in less than 40 min. They have potential for on‐site quantitative detection of species of family Arcobacteraceae, A. faecis and A. lanthieri in food, environmental and clinical matrices. Significance and Impact of the Study The newly developed LAMP assays are specific, sensitive, accurate with higher reproducibility that have potential to facilitate in a less equipped lab setting and can help in early quantitative detection and rate of prevalence in environmental niches. The assays can be adopted in the diagnostic labs and epidemiological studies.
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Affiliation(s)
- I U H Khan
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - A Becker
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - M Cloutier
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - M Plötz
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
| | - D R Lapen
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - G Wilkes
- Ottawa Research and Development Centre (ORDC), Agriculture and Agri-Food Canada, Ottawa, ON, Canada.,Natural Resources Canada, Ottawa, ON, Canada
| | - E Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - A Abdulmawjood
- Institute of Food Quality and Food Safety, Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Foundation, Hannover, Germany
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5
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Arcobacter Identification and Species Determination Using Raman Spectroscopy Combined with Neural Networks. Appl Environ Microbiol 2020; 86:AEM.00924-20. [PMID: 32801186 DOI: 10.1128/aem.00924-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
Rapid and accurate identification of Arcobacter 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 Arcobacter 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 Arcobacter 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 Arcobacter could be successfully differentiated from the closely related genera Campylobacter and Helicobacter using principal-component analysis. For the identification of Arcobacter to the species level, an accuracy of 97.2% was achieved for all 18 Arcobacter 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 Arcobacter strains. Furthermore, a Raman spectroscopy-based fully connected artificial neural network (ANN) was constructed to determine the actual ratio of a specific Arcobacter 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 Arcobacter within an hour following cultivation.IMPORTANCE Rapid identification of bacterial pathogens is critical for developing an early warning system and performing epidemiological investigation. Arcobacter is an emerging foodborne pathogen and has become more important in recent decades. The incidence of Arcobacter 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 Arcobacter 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.
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6
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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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7
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Kopprio GA, Neogi SB, Rashid H, Alonso C, Yamasaki S, Koch BP, Gärdes A, Lara RJ. Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers. Front Microbiol 2020; 11:594. [PMID: 32351470 PMCID: PMC7174592 DOI: 10.3389/fmicb.2020.00594] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/18/2020] [Indexed: 01/23/2023] Open
Abstract
The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.
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Affiliation(s)
- Germán A Kopprio
- Department of Chemical Analytics and Biogeochemistry, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.,Tropical Marine Microbiology, Leibniz Centre for Tropical Marine Research, Bremen, Germany.,Marine Biogeochemistry, Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Sur, Bahía Blanca, Argentina
| | - Sucharit B Neogi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Harunur Rashid
- Department of Fisheries Management, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Cecilia Alonso
- Microbial Ecology of Aquatic Systems, Centro Universitario Región Este, Universidad de la República, Rocha, Uruguay
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Boris P Koch
- Ecological Chemistry, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Astrid Gärdes
- Tropical Marine Microbiology, Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | - Rubén J Lara
- Marine Biogeochemistry, Instituto Argentino de Oceanografía, Consejo Nacional de Investigaciones Científicas y Técnicas - Universidad Nacional del Sur, Bahía Blanca, Argentina
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8
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Xiong J, Huang B, Guo SL, Xu JS, Huang W. A novel multiplex PCR assay for rapid detection of virulent Aeromonas in cultured eels. J Appl Microbiol 2019; 127:418-428. [PMID: 31136041 DOI: 10.1111/jam.14311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/30/2019] [Accepted: 05/08/2019] [Indexed: 01/01/2023]
Abstract
AIMS Under intensive and stressful aquaculture conditions, cultured eels are highly susceptible to virulent Aeromonas sp. infections. To rapidly and simultaneously confirm Aeromonas isolate and its virulence, a two-tube multiplex PCR (mPCR) assay incorporating gyrB gene for genus-specific recognition and seven major virulence genes for virulence assessment was developed. METHODS AND RESULTS Eight pairs of primers were designed and divided into two groups-gyrB, ahpA, epr and aerA in tube 1 and alt, act, ast and hlyA in tube 2. The optimized mPCR conditions were the same except for their final concentrations. The specificity of the mPCR was validated by the extracted DNA of 10 Aeromonas and 8 non-Aeromonas species, or mixed DNA templates. Detection limits were determined to be 200 copies per μl in tube 1 and 20 copies per μl in tube 2. The mPCR reproducibility was tested by both artificial challenge and clinical samples. CONCLUSIONS The results showed this two-tube mPCR assay was rapid, specific, sensitive and reliable. SIGNIFICANCE AND IMPACT OF THE STUDY To our knowledge, this is the first report to distinguish virulent Aeromonas isolates from nonvirulent ones by seven popular and major virulence genes at the genus-specific level. And it will be useful for large-scale screening of virulent Aeromonas sp. in cultured eels.
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Affiliation(s)
- J Xiong
- Fisheries College, Jimei University, Xiamen, China.,Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Xiamen, China
| | - B Huang
- Fisheries College, Jimei University, Xiamen, China.,Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Xiamen, China
| | - S-L Guo
- Fisheries College, Jimei University, Xiamen, China.,Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Xiamen, China
| | - J-S Xu
- Fisheries College, Jimei University, Xiamen, China.,Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Xiamen, China
| | - W Huang
- Fisheries College, Jimei University, Xiamen, China.,Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education of the People's Republic of China, Xiamen, 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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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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11
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Occurrence of virulence-associated genes in Arcobacter butzleri and Arcobacter cryaerophilus isolates from foodstuff, water, and clinical samples within the Czech Republic. Folia Microbiol (Praha) 2018; 64:25-31. [PMID: 29936647 DOI: 10.1007/s12223-018-0628-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 06/19/2018] [Indexed: 01/22/2023]
Abstract
Bacteria of the Arcobacter (A.) genus, originating mainly from food and water, are dreaded germs for humans as well as animals. However, the virulence of these bacteria has not been fully elucidated yet. This study looked at the occurrence of eight virulence-associated factors (ciaB, cj1349, pldA, irgA, hecA, tlyA, mviN, hecB) in a total of 80 isolates of Arcobacter butzleri and 22 isolates of A. cryaerophilus. The isolates were derived from food, water, and clinical samples. A polymerase chain reaction using specific primers was used to detect these virulence-associated genes. The presence of all genes in the isolates of A. butzleri (98.8% ciaB, 95.0% cj1349, 98.8% pldA, 22.5% irgA, 31.3% hecA, 95.0% tlyA, 97.5% mviN, 38.8% hecB) and A. cryaerophilus (95.5% ciaB, 0.0% cj1349, 9.1% pldA, 0.0% irgA, 0.0% hecA, 31.8% tlyA, 90.9% mviN, 0.0% hecB) was monitored. Among the tested isolates, there were 13 isolates (12.7%) of A. butzleri, in which the presence of all eight virulence-associated genes was recorded in the genome. In contrast, in one A. cryaerophilus strain, none of the observed genes were detected. The presence of ciaB and mviN genes was significantly more frequent in A. cryaerophilus isolates than other genes (P < 0.05). In general, more virulence-associated genes have been detected in A. butzleri isolates compared to A. cryaerophilus. The most common gene combination (ciaB, cj1349, pldA, tlyA, mviN) was detected in case of 39 isolates. In 50.0% of A. butzleri isolates derived from clinical samples, all eight virulence-associated genes were significantly more frequently detected (P < 0.05). The tlyA gene occurred significantly more frequent in A. butzleri isolates from meat and water samples and irgA and hecB genes in clinical samples. Therefore, our study provides information about occurrence of virulence-associated genes in genome of Arcobacter isolates. These findings could be hazardous to human health, because the presence of virulence-associated genes is the assumption for potential dangerousness of these bacteria. Our results indicate high incidence of virulence-associated genes in Arcobacter genomes and hence potentially pathogenic properties of the studied strains.
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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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