1
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Rivadulla M, Lois M, Elena AX, Balboa S, Suarez S, Berendonk TU, Romalde JL, Garrido JM, Omil F. Occurrence and fate of CECs (OMPs, ARGs and pathogens) during decentralised treatment of black water and grey water. Sci Total Environ 2024; 915:169863. [PMID: 38190906 DOI: 10.1016/j.scitotenv.2023.169863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/13/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024]
Abstract
Decentralised wastewater treatment is becoming a suitable strategy to reduce cost and environmental impact. In this research, the performance of two technologies treating black water (BW) and grey water (GW) fractions of urban sewage is carried out in a decentralised treatment of the wastewater produced in three office buildings. An Anaerobic Membrane Bioreactor (AnMBR) treating BW and a Hybrid preanoxic Membrane Bioreactor (H-MBR) containing small plastic carrier elements, treating GW were operated at pilot scale. Their potential on reducing the release of contaminants of emerging concern (CECs) such as Organic Micropollutants (OMPs), Antibiotic Resistance Genes (ARGs) and pathogens was studied. After 226 d of operation, a stable operation was achieved in both systems: the AnMBR removed 92.4 ± 2.5 % of influent COD, and H-MBR removed 89.7 ± 3.5 %. Regarding OMPs, the profile of compounds differed between BW and GW, being BW the matrix with more compounds detected at higher concentrations (up to μg L-1). For example, in the case of ibuprofen the concentrations in BW were 23.63 ± 3.97 μg L-1, 3 orders of magnitude higher than those detected in GW. The most abundant ARGs were sulfonamide resistant genes (sul1) and integron class 1 (intl1) in both BW and GW. Pathogenic bacteria counts were reduced between 1 and 3 log units in the AnMBR. Bacterial loads in GW were much lower than in BW, being no bacterial re-growth observed for the GW effluents after treatment in the H-MBR. None of the selected enteric viruses was detected in GW treatment line.
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Affiliation(s)
- M Rivadulla
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain.
| | - M Lois
- CRETUS, Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - A X Elena
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - S Balboa
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - S Suarez
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - T U Berendonk
- Technische Universität Dresden, Institute of Hydrobiology, Dresden, Germany
| | - J L Romalde
- CRETUS, Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - J M Garrido
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
| | - F Omil
- CRETUS, Department of Chemical Engineering, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Galicia, Spain
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2
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Duarte J, Máximo C, Costa P, Oliveira V, Gomes NCM, Romalde JL, Pereira C, Almeida A. Potential of an Isolated Bacteriophage to Inactivate Klebsiella pneumoniae: Preliminary Studies to Control Urinary Tract Infections. Antibiotics (Basel) 2024; 13:195. [PMID: 38391581 PMCID: PMC10885952 DOI: 10.3390/antibiotics13020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/13/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
Urinary tract infections (UTIs) caused by resistant Klebsiella pneumoniae can lead to severe clinical complications and even death. An alternative treatment option for infected patients is using bacteriophages. In the present study, we isolated phage VB_KPM_KP1LMA (KP1LMA) from sewage water using a K. pneumoniae strain as a host. Whole-genome analysis indicated that the genome was a double-stranded linear 176,096-bp long DNA molecule with 41.8% GC content and did not contain virulence or antibiotic resistance genes. The inactivation potential of phage KP1LMA was assessed in broth at an MOI of 1 and 10, and a maximum inactivation of 4.9 and 5.4 log CFU/mL, respectively, was observed after 9 h. The efficacy at an MOI of 10 was also assessed in urine to evaluate the phage's performance in an acidic environment. A maximum inactivation of 3.8 log CFU/mL was observed after 9 h. The results suggest that phage KP1LMA could potentially control a UTI caused by this strain of K. pneumoniae, indicating that the same procedure can be used to control UTIs caused by other strains if new specific phages are isolated. Although phage KP1LMA has a narrow host range, in the future, efforts can be made to expand its spectrum of activity and also to combine this phage with others, potentially enabling its use against other K. pneumoniae strains involved in UTIs.
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Affiliation(s)
- João Duarte
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carolina Máximo
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Costa
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS, Faculty of Biology, University of Santiago de Compostela, CP 15782 Santiago de Compostela, Spain
| | - Carla Pereira
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- CESAM, Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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3
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Duman M, Altun S, Saticioglu IB, Romalde JL. A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022. J Fish Dis 2023. [PMID: 37965781 DOI: 10.1111/jfd.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Jesús L Romalde
- Cross-disciplinary Research Center in Environmental Technologies (CRETUS), Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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4
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Kudo R, Yamano R, Yu J, Koike S, Haditomo AHC, de Freitas MAM, Tsuchiya J, Mino S, Thompson F, Romalde JL, Kasai H, Sakai Y, Sawabe T. Genome taxonomy of the genus Neptuniibacter and proposal of Neptuniibacter victor sp. nov. isolated from sea cucumber larvae. PLoS One 2023; 18:e0290060. [PMID: 37582072 PMCID: PMC10426996 DOI: 10.1371/journal.pone.0290060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/26/2023] [Indexed: 08/17/2023] Open
Abstract
A Gram-staining-negative, oxidase-positive, strictly aerobic rod-shaped bacterium, designated strain PT1T, was isolated from the laboratory-reared larvae of the sea cucumber Apostichopus japonicus. A phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT1T was closely related to Neptuniibacter marinus ATR 1.1T (= CECT 8938T = DSM 100783T) and Neptuniibacter caesariensis MED92T (= CECT 7075T = CCUG 52065T) showing 98.2% and 98.1% sequence similarity, respectively. However, the average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) values among these three strains were 72.0%-74.8% and 18.3%-19.5% among related Neptuniibacter species, which were below 95% and 70%, respectively, confirming the novel status of PT1T. The average amino acid identity (AAI) values of PT1T showing 74-77% among those strains indicated PT1T is a new species in the genus Neptuniibacter. Based on the genome-based taxonomic approach, Neptuniibacter victor sp. nov. is proposed for PT1T. The type strain is PT1T (JCM 35563T = LMG 32868T).
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Affiliation(s)
- Rika Kudo
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Ryota Yamano
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Juanwen Yu
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Shotaro Koike
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Alfabetian Harjuno Condro Haditomo
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
- Aquaculture Department, Faculty of Fisheries and Marine Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Mayanne A. M. de Freitas
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Jiro Tsuchiya
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Fabiano Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago, Spain
| | - Hisae Kasai
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Yuichi Sakai
- Hakodate Fisheries Research, Hokkaido Research Organization, Local Independent Administrative Agency, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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5
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Yamano R, Yu J, Haditomo AHC, Jiang C, Mino S, Romalde JL, Kang K, Sakai Y, Sawabe T. Genome taxonomy of the genus Thalassotalea and proposal of Thalassotalea hakodatensis sp. nov. isolated from sea cucumber larvae. PLoS One 2023; 18:e0286693. [PMID: 37267301 DOI: 10.1371/journal.pone.0286693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
The genus Thalassotalea is ubiquitous in marine environments, and up to 20 species have been described so far. A Gram-staining-negative, aerobic bacterium, designated strain PTE2T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PTE2T was closely related to Thalassotalea sediminis N211T (= KCTC 42588T = MCCC 1H00116T) with 97.9% sequence similarity. ANI and in silico DDH values against Thalassotalea species were 68.5-77.0% and 19.7-24.6%, respectively, indicating the novelty of PTE2T. Based on genome-based taxonomic approaches, strain PTE2T (= JCM 34608T = KCTC 82592T) is proposed as a new species, Thalassotalea hakodatensis sp. nov.
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Affiliation(s)
- Ryota Yamano
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Juanwen Yu
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Alfabetian Harjuno Condro Haditomo
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
- Aquaculture Department, Faculty of Fisheries and Marine Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
- Atmosphere and Ocean Research Institute, University of Tokyo, Chiba, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago, Spain
| | - Kyuhee Kang
- Korean Collection for Type Cultures (KCTC), Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, South Korea
| | - Yuichi Sakai
- Hakodate Fisheries Research, Hokkaido Research Organization, Local Independent Administrative Agency, Hakodate, Japan
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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6
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Cahier K, Piel D, Barcia-Cruz R, Goudenège D, Wegner KM, Monot M, Romalde JL, Le Roux F. Environmental vibrio phage-bacteria interaction networks reflect the genetic structure of host populations. Environ Microbiol 2023. [PMID: 36876921 DOI: 10.1111/1462-2920.16366] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/04/2023] [Indexed: 03/07/2023]
Abstract
Phages depend on their bacterial hosts to replicate. The habitat, density and genetic diversity of host populations are therefore key factors in phage ecology, but our ability to explore their biology depends on the isolation of a diverse and representative collection of phages from different sources. Here, we compared two populations of marine bacterial hosts and their phages collected during a time series sampling program in an oyster farm. The population of Vibrio crassostreae, a species associated specifically to oysters, was genetically structured into clades of near clonal strains, leading to the isolation of closely related phages forming large modules in phage-bacterial infection networks. For Vibrio chagasii, which blooms in the water column, a lower number of closely related hosts and a higher diversity of isolated phages resulted in small modules in the phage-bacterial infection network. Over time, phage load was correlated with V. chagasii abundance, indicating a role of host blooms in driving phage abundance. Genetic experiments further demonstrated that these phage blooms can generate epigenetic and genetic variability that can counteract host defence systems. These results highlight the importance of considering both the environmental dynamics and the genetic structure of the host when interpreting phage-bacteria networks.
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Affiliation(s)
- Karine Cahier
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, Plouzané, France
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff cedex, France
| | - Damien Piel
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, Plouzané, France
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff cedex, France
| | - Rubén Barcia-Cruz
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff cedex, France
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David Goudenège
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, Plouzané, France
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff cedex, France
| | - K Mathias Wegner
- AWI - Alfred Wegener Institut - Helmholtz-Zentrum für Polar- und Meeresforschung, Coastal Ecology, Waddensea Station Sylt, List, Germany
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Cross-Disciplinary Research Center in Environmental Technologies (CRETUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Frédérique Le Roux
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, Plouzané, France
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff cedex, France
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7
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Fernandez-Espinel C, Medina-Morillo M, Irgang R, Sotil G, Araya-León H, Flores-Dominick V, Romalde JL, Avendaño-Herrera R, Yunis-Aguinaga J. Co-existence of two Yersinia ruckeri biotypes and serotype O1a retrieved from rainbow trout (Oncorhynchus mykiss) farmed in Puno, Peru. J Fish Dis 2023; 46:157-163. [PMID: 36404601 DOI: 10.1111/jfd.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Yersinia ruckeri causes important economic losses for rainbow trout (Oncorhynchus mykiss) farms worldwide. This bacterial disease is likely the most common among trout in Peru; however, no commercial vaccine is available nationally, which is, in part, due to a lack of information on the bacterium. The aim of the current study was to characterize 29 Y. ruckeri isolates sampled from seven cage-reared farms in the Puno Region, the focal point for aquaculture activities in Peru. For this, samples were taken from fish with clinical signs (i.e. haemorrhages, uni- or bilateral exophthalmia, hyphaemia and/or melanosis). Notable among our findings was the existence of both Y. ruckeri biotype 1 (9 isolates) and biotype 2 (20 isolates; negative for sorbitol and Tween 80). The isolates further differed in API profiles 5307100 (21 isolates), 1307100 (4 isolates), 1305100 (2 isolates), 1307120 (1 isolate) and 5305100 (1 isolate), with the main differences being in the tests for lysine decarboxylase, gelatine hydrolysis and D-saccharose fermentation. Despite these differences, all isolates shared identical ERIC-PCR and REP-PCR profiles and belonged to the O1a serotype. Fingerprints were identical to the reference strain CECT 955 (serotype O1a). The information obtained will be used for epidemiological purposes by health authorities and for the development of a vaccine against Y. ruckeri, a prominent request made by fish farmers in Peru.
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Affiliation(s)
| | | | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Giovanna Sotil
- Laboratorio de Genética Molecular, Instituto del Mar del Perú (IMARPE), Peru
- Universidad Nacional Mayor de San Marcos, Peru
| | - Henry Araya-León
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | | | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ruben Avendaño-Herrera
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Chile
| | - Jefferson Yunis-Aguinaga
- Laboratorio de Patobiología Acuática, Instituto del Mar del Perú (IMARPE), Peru
- Universidad Científica del Sur, Peru
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8
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Jiang C, Kasai H, Mino S, Romalde JL, Sawabe T. The pan‐genome of Splendidus clade species in the family
Vibrionaceae
: insights into evolution, adaptation, and pathogenicity. Environ Microbiol 2022; 24:4587-4606. [DOI: 10.1111/1462-2920.16209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Hisae Kasai
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
| | - Jesús L. Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS‐Facultad de Biología. Universidade de Santiago de Compostela Spain
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences Hokkaido University Hakodate Japan
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9
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Nielsen SS, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Gortazar Schmidt C, Herskin M, Michel V, Miranda Chueca MA, Padalino B, Pasquali P, Roberts HC, Spoolder H, Stahl K, Velarde A, Viltrop A, Winckler C, Dewulf J, Guardabassi L, Hilbert F, Mader R, Romalde JL, Smith P, Baldinelli F, Kohnle L, Alvarez J. Assessment of animal diseases caused by bacteria resistant to antimicrobials: kept fish species. EFSA J 2022; 20:e07076. [PMID: 35136422 PMCID: PMC8808658 DOI: 10.2903/j.efsa.2022.7076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In this Opinion, the antimicrobial-resistant bacteria responsible for transmissible diseases that constitute a threat to the health of certain kept fish species have been assessed. Atlantic salmon (Salmo salar), carp (Cyprinus spp.), rainbow trout (Oncorhynchus mykiss), sea bream (Sparus aurata) and tilapia (Oreochromis spp.), selected as representative of the most important fish species and production systems that are commercially reared in fresh and saltwater farms, were the focus of this assessment. The assessment was performed following a methodology based on information collected by an extensive literature review and expert judgement. Details of the methodology used for this assessment are explained in a separate Opinion. The global state of play of antimicrobial resistance in Aeromonas hydrophila, Aeromonas salmonicida, Flavobacterium psychrophilum and Flavobacterium columnare is provided. Among these bacteria, none was identified as being among the most relevant antimicrobial-resistant bacteria in the assessed kept fish species in the EU due to the very limited scientific evidence available.
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10
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Söderlund-Venermo M, Varma A, Guo D, Gladue DP, Poole E, Pujol FH, Pappu H, Romalde JL, Kramer L, Baz M, Venter M, Moore MD, Nevels MM, Ezzikouri S, Vakharia VN, Wilson WC, Malik YS, Shi Z, Abdel-Moneim AS. World Society for Virology first international conference: Tackling global virus epidemics. Virology 2022; 566:114-121. [PMID: 34902730 PMCID: PMC8646940 DOI: 10.1016/j.virol.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 11/26/2021] [Indexed: 01/04/2023]
Abstract
This communication summarizes the presentations given at the 1st international conference of the World Society for Virology (WSV) held virtually during 16-18 June 2021, under the theme of tackling global viral epidemics. The purpose of this biennial meeting is to foster international collaborations and address important viral epidemics in different hosts. The first day included two sessions exclusively on SARS-CoV-2 and COVID-19. The other two days included one plenary and three parallel sessions each. Last not least, 16 sessions covered 140 on-demand submitted talks. In total, 270 scientists from 49 countries attended the meeting, including 40 invited keynote speakers.
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Affiliation(s)
| | - Anupam Varma
- Advanced Centre for Plant Virology Indian Agricultural Research Institute, New Delhi, India
| | - Deyin Guo
- Center for Infection and Immunity Study, School of Medicine, Sun Yat-sen University, Guangzhou, China
| | | | - Emma Poole
- Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Flor H. Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Hanu Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Jesús L. Romalde
- Department of Microbiology and Parasitology, CRETUS & CIBUS-Faculty of Biology, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Laura Kramer
- Arbovirus Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Mariana Baz
- WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute, Australia and Research Center in Infectious Diseases of the CHU of Québec and Université Laval, Melbourne, Victoria, Québec City, Quebec, Canada
| | - Marietjie Venter
- Zoonotic Arbo- and Respiratory Virus Research Program, Centre for Viral Zoonosis, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Matthew D. Moore
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Michael M. Nevels
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, UK
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Vikram N. Vakharia
- Institute of Marine & Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - William C. Wilson
- Foreign Arthropod Borne Animal Diseases Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS, USA
| | - Yashpal S. Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Zhengli Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Al-Taif, Saudi Arabia, Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt,Corresponding author
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11
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Jiang C, Tanaka M, Nishikawa S, Mino S, Romalde JL, Thompson FL, Gomez-Gil B, Sawabe T. Vibrio Clade 3.0: New Vibrionaceae Evolutionary Units Using Genome-Based Approach. Curr Microbiol 2021; 79:10. [PMID: 34905112 DOI: 10.1007/s00284-021-02725-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.
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Affiliation(s)
- Chunqi Jiang
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Mami Tanaka
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayo Nishikawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, España
| | - Fabiano L Thompson
- Institute of Biology and SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno Gomez-Gil
- CIAD, AC, Mazatlan Unit for Aquaculture and Environmental Management, Mazatlán, México
| | - Tomoo Sawabe
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan.
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12
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Hassoun-Kheir N, Stabholz Y, Kreft JU, de la Cruz R, Dechesne A, Smets BF, Romalde JL, Lema A, Balboa S, García-Riestra C, Torres-Sangiao E, Neuberger A, Graham D, Quintela-Baluja M, Stekel DJ, Graham J, Pruden A, Nesme J, Sørensen SJ, Hough R, Paul M. EMBRACE-WATERS statement: Recommendations for reporting of studies on antimicrobial resistance in wastewater and related aquatic environments. One Health 2021; 13:100339. [PMID: 34746357 PMCID: PMC8554267 DOI: 10.1016/j.onehlt.2021.100339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 10/17/2021] [Accepted: 10/17/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND A One Health approach requires integrative research to elucidate antimicrobial resistance (AMR) in the environment and the risks it poses to human health. Research on this topic involves experts from diverse backgrounds and professions. Shortcomings exist in terms of consistent, complete, and transparent reporting in many environmental studies. Standardized reporting will improve the quality of scientific papers, enable meta-analyses and enhance the communication among different experts. In this study, we aimed to generate a consensus of reporting standards for AMR research in wastewater and related aquatic environments. METHODS Based on a risk of bias assessment of the literature in a systematic review, we proposed a set of study quality indicators. We then used a multistep modified Delphi consensus to develop the EMBRACE-WATERS statement (rEporting antiMicroBial ResistAnCE in WATERS), a checklist of recommendations for reporting in studies of AMR in wastewater and related aquatic environments. FINDINGS Consensus was achieved among a multidisciplinary panel of twenty-one experts in three steps. The developed EMBRACE-WATERS statement incorporates 21 items. Each item contains essential elements of high-quality reporting and is followed by an explanation of their rationale and a reporting-example. The EMBRACE-WATERS statement is primarily intended to be used by investigators to ensure transparent and comprehensive reporting of their studies. It can also guide peer-reviewers and editors in evaluation of manuscripts on AMR in the aquatic environment. This statement is not intended to be used to guide investigators on the methodology of their research. INTERPRETATION We are hopeful that this statement will improve the reporting quality of future studies of AMR in wastewater and related aquatic environments. Its uptake would generate a common language to be used among researchers from different disciplines, thus advancing the One Health approach towards understanding AMR spread across aquatic environments. Similar initiatives are needed in other areas of One Health research.
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Affiliation(s)
- Nasreen Hassoun-Kheir
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - Yoav Stabholz
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
| | - Jan-Ulrich Kreft
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Roberto de la Cruz
- School of Biosciences, Institute of Microbiology and Infection (IMI), Centre for Computational Biology (CCB), University of Birmingham, Birmingham, UK
| | - Arnaud Dechesne
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Barth F. Smets
- Technical University of Denmark, Department of Environmental Engineering, bygning 115, Bygningstorvet, 2800 Kongens Lyngby, Denmark
| | - Jesús L. Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Alberto Lema
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Sabela Balboa
- CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos García-Riestra
- Department of Microbiology and Parasitology, University Hospital Complex of Santiago (CHUS), Spain
| | - Eva Torres-Sangiao
- Escherichia coli Group, Research Foundation Institute (FIDIS), University Hospital Complex (CHUS), Santiago de Compostela, ES, Spain
| | - Ami Neuberger
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, UK
| | | | - Dov J. Stekel
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, College Road, Loughborough LE12 5RD, UK
| | - Jay Graham
- University of California, Berkeley School of Public Health, Berkeley, CA, USA
| | - Amy Pruden
- The Charles Edward Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Joseph Nesme
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rupert Hough
- Information and Computational Sciences, The James Hutton Institute, Aberdeen AB15 8QH, Scotland, UK
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, HaAliya HaShniya St 8, Haifa 3109601, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
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13
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Quintela-Baluja M, Frigon D, Abouelnaga M, Jobling K, Romalde JL, Gomez Lopez M, Graham DW. Dynamics of integron structures across a wastewater network - Implications to resistance gene transfer. Water Res 2021; 206:117720. [PMID: 34673462 PMCID: PMC8626773 DOI: 10.1016/j.watres.2021.117720] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/14/2021] [Accepted: 09/24/2021] [Indexed: 05/19/2023]
Abstract
Class 1 and other integrons are common in wastewater networks, often being associated with antibiotic resistance genes (ARGs). However, the importance of different integron structures in ARG transfer within wastewater systems has only been implied, especially between community and hospital sources, among wastewater treatment plant compartments, and in receiving waters. This uncertainty is partly because current clinical class 1 integron qPCR assays (i.e., that target human-impacted structures, i.e., clintI1) poorly delineate clintI1 from non-impacted class 1 integron structures. They also say nothing about their ARG content. To fill these technical gaps, new real-time qPCR assays were developed for "impacted" class 1 structures (called aint1; i.e., anthropogenic class 1 integrons) and empty aint1 structures (i.e., carry no ARGs; called eaint1). The new assays and other integron assays then were used to examine integron dynamics across a wastewater network. 16S metagenomic sequencing also was performed to characterise associated microbiomes. aint1 abundances per bacterial cell were about 10 times greater in hospital wastewaters compared with other compartments, suggesting aint1 enrichment with ARGs in hospital sources. Conversely, the relative abundance of eaint1 structures were over double in recycled activated sludge compared with other compartments, except receiving waters (RAS; ∼30% of RAS class 1 structures did not carry ARGs). Microbiome analysis showed that human-associated bacterial taxa with mobile integrons also differed in RAS and river sediments. Further, class 1 integrons in RAS bacteria appear to have released ARGs, whereas hospital bacteria have accumulated ARGs. Results show that quantifying integron dynamics can help explain where ARG transfer occurs in wastewater networks, and should be considered in future studies on antibiotic resistance in the environment.
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Affiliation(s)
- Marcos Quintela-Baluja
- School of Engineering, Cassie Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK; Department of Analytical Chemistry, Nutrition and Bromatology, University of Santiago de Compostela, Spain.
| | - Dominic Frigon
- Department of Civil Engineering and Applied Mechanics, McGill University, Montréal (QC), Canada
| | - M Abouelnaga
- Department of Analytical Chemistry, School of Veterinary Sciences, Suez Canel University, Ismailia, Egypt
| | - Kelly Jobling
- School of Engineering, Cassie Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - David W Graham
- School of Engineering, Cassie Building, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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14
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Gerpe D, Lasa A, Lema A, Romalde JL. Metataxonomic analysis of tissue-associated microbiota in grooved carpet-shell (Ruditapes decussatus) and Manila (Ruditapes philippinarum) clams. Int Microbiol 2021; 24:607-618. [PMID: 34606012 PMCID: PMC8616884 DOI: 10.1007/s10123-021-00214-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/17/2021] [Accepted: 09/21/2021] [Indexed: 01/05/2023]
Abstract
Culture-dependent techniques only permit the study of a low percentage of the microbiota diversity in the environment. The introduction of next generation sequencing (NGS) technologies shed light into this hidden microbial world, providing a better knowledge on the general microbiota and, specifically, on the microbial populations of clams. Tissue-associated microbiota of Ruditapes decussatus and Ruditapes philippinarum (mantle, gills, gonad and hepatopancreas) was analysed in two different locations of Galicia (northwest of Spain) during Spring (April) and Autumn (October), employing a metataxonomic approach. High bacterial diversity and richness were found in all samples where a total of 22,044 OTUs were obtained. In most samples, phylum Proteobacteria was most frequently retrieved, although other phyla as Actinobacteria, Bacteroidetes, Tenericutes, Firmicutes or Chlamydiae also appeared at high relative abundances in the samples. At genus level, great variation was found across tissues and sampling periods. A Nonmetric Multidimensional Scaling (NMDS) and a hierarchical clustering analysis allowed to further analyse the factors responsible for the differences among groups of samples in the different sites. Results showed sample ordination based on tissue origin and sampling periods, pointing out that the microbiota was influenced by these factors. Indeed, predominance of certain genera was observed, such as Endozoicomonas or Methylobacterium in gills and gonads, respectively, suggesting that selection of specific bacterial taxa is likely to occur. So far, this study provided a general picture of the tissue associated microbial population structure in R. decussatus and R. philippinarum clams, which, ultimately, allowed the identification of specific tissue-related taxa.
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Affiliation(s)
- Diego Gerpe
- Departamento de Microbiología Y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Aide Lasa
- Departamento de Microbiología Y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Alberto Lema
- Departamento de Microbiología Y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología Y Parasitología, CRETUS & CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Campus Vida s/n, 15782, Santiago de Compostela, Spain.
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15
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Polo D, Lois M, Fernández-Núñez MT, Romalde JL. Detection of SARS-CoV-2 RNA in bivalve mollusks and marine sediments. Sci Total Environ 2021; 786:147534. [PMID: 33984699 PMCID: PMC8099584 DOI: 10.1016/j.scitotenv.2021.147534] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 05/04/2023]
Abstract
The presence of SARS-CoV-2 in wastewater pose the question of whether this new pandemic virus could be released into watercourses and potentially continue to finally reach coastal waters. In this study, we employed two bivalve molluscan species from the genus Ruditapes as sentinel organisms to investigate the presence of SARS-CoV-2 signals in the marine coastal environment. Estuarine sediments from the natural clam banks were also analyzed. Viral RNA was detected by RT-qPCR, targeting IP4, E and N1 genomic regions. Positive samples were also subjected to a PMAxx-triton viability RT-qPCR assay in order to discriminate between intact and altered capsids, obtaining indirect information about the viability of the virus. SARS-CoV-2 RNA traces were detected in 9/12 clam samples by RT-qPCR, from which 4 were positive for two different target regions. Viral quantification ranged from <LoQ to 4.48 Log genomic copies/g of digestive tissue. Regarding the sediment samples, 3/12 were positive by RT-qPCR, but only IP4 region was successfully amplificated. Quantification values for sediment samples ranged from <LoQ to 3.60 Log genomic copies/g of sediment. RNA signals disappeared in the PMAxx-triton viability RT-qPCR assay, indicating non-infectious potential. In addition, the recently discovered human-specific gut associated bacteriophage crAssphage was also quantified as a biomarker for the presence of human-derived wastewater contamination on the study area. CrAssphage was detected in 100% of both types of samples with quantification values ranging from <LoQ to 5.94 Log gc/g digestive tissue and from <LoQ to 4.71 Log gc/g sediment. Statistical analysis also showed that quantification levels for the crAssphage in clams are significantly higher than in sediments. These findings represent the first detection of SARS-CoV-2 RNA in the marine environment, demonstrating that it can reach these habitats and make contact with the marine life.
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Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Marta Lois
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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16
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Carcereny A, Martínez-Velázquez A, Bosch A, Allende A, Truchado P, Cascales J, Romalde JL, Lois M, Polo D, Sánchez G, Pérez-Cataluña A, Díaz-Reolid A, Antón A, Gregori J, Garcia-Cehic D, Quer J, Palau M, Ruano CG, Pintó RM, Guix S. Monitoring Emergence of the SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). Environ Sci Technol 2021; 55:11756-11766. [PMID: 34397216 PMCID: PMC8404293 DOI: 10.1021/acs.est.1c03589] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 05/03/2023]
Abstract
Since its first identification in the United Kingdom in late 2020, the highly transmissible B.1.1.7 variant of SARS-CoV-2 has become dominant in several countries raising great concern. We developed a duplex real-time RT-qPCR assay to detect, discriminate, and quantitate SARS-CoV-2 variants containing one of its mutation signatures, the ΔHV69/70 deletion, and used it to trace the community circulation of the B.1.1.7 variant in Spain through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19). The B.1.1.7 variant was detected earlier than clinical epidemiological reporting by the local authorities, first in the southern city of Málaga (Andalucía) in week 20_52 (year_week), and multiple introductions during Christmas holidays were inferred in different parts of the country. Wastewater-based B.1.1.7 tracking showed a good correlation with clinical data and provided information at the local level. Data from wastewater treatment plants, which reached B.1.1.7 prevalences higher than 90% for ≥2 consecutive weeks showed that 8.1 ± 2.0 weeks were required for B.1.1.7 to become dominant. The study highlights the applicability of RT-qPCR-based strategies to track specific mutations of variants of concern as soon as they are identified by clinical sequencing and their integration into existing wastewater surveillance programs, as a cost-effective approach to complement clinical testing during the COVID-19 pandemic.
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Affiliation(s)
- Albert Carcereny
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Adán Martínez-Velázquez
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Albert Bosch
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Ana Allende
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Pilar Truchado
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jenifer Cascales
- Research
Group on Microbiology and Quality of Fruit and Vegetables, CEBAS-CSIC, Murcia 30100, Spain
| | - Jesús L Romalde
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Marta Lois
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - David Polo
- Department
of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute
CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Gloria Sánchez
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Alba Pérez-Cataluña
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Azahara Díaz-Reolid
- Department
of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology, IATA-CSIC, Paterna 46980, Spain
| | - Andrés Antón
- Microbiology
Department, Vall d’Hebron Institut
de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital
Campus, Barcelona 08035, Spain
| | - Josep Gregori
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Damir Garcia-Cehic
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Josep Quer
- Liver
Unit, Liver Diseases - Viral Hepatitis, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona 08035, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), Instituto de Salud
Carlos III, Madrid 28029, Spain
| | - Margarita Palau
- General
Directorate of Public Health, Ministry of Health, Madrid 28014, Spain
| | - Cristina González Ruano
- Subdirección
General de Protección de las Aguas y Gestión de Riesgos,
Ministerio para la Transición Ecológica y el Reto Demográfico, Madrid 28071, Spain
| | - Rosa M Pintó
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
| | - Susana Guix
- Enteric
Virus laboratory, Department of Genetics, Microbiology and Statistics,
Section of Microbiology, Virology and Biotechnology, School of Biology, University of Barcelona, Barcelona 08028, Spain
- Research
Institute of Nutrition and Food Safety (INSA), University of Barcelona, Santa
Coloma de Gramenet 08921, Spain
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17
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Polo D, Lema A, Gándara E, Romalde JL. Prevalence of human bocavirus infections in Europe. A systematic review and meta-analysis. Transbound Emerg Dis 2021; 69:2451-2461. [PMID: 34250765 DOI: 10.1111/tbed.14233] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/18/2021] [Accepted: 07/09/2021] [Indexed: 11/29/2022]
Abstract
Human bocaviruses (HBoVs) are recently described as human emergent viruses, especially in young children. In this study, we undertook a systematic review and meta-analysis to estimate their prevalence in Europe. PubMed, Web of Science and Scopus databases were systematically screened for clinical studies, up to October 2020. Study eligibility criteria were primary full-text articles from clinical studies, conducted using valid screening test methods and published in peer-reviewed journals, in English or Spanish and from European countries. The overall pooled prevalence, prevalence by country as well as the prevalence of HBoV as a single or co-pathogen were estimated using a random-effects model. Sub-group and meta-regression analyses explored potential sources of heterogeneity in the data. A total of 35 studies involving 32,656 subjects from 16 European countries met the inclusion criteria. Heterogeneity (I2 = 97.0%, p < .01) was seen among studies; HBoV prevalence varied from 2.0 to 45.69% with a pooled estimate of 9.57% (95%CI 7.66-11.91%). The HBoV prevalence both as a single infection (3.99%; 95%CI 2.99-5.31%) or as co-infection with other viruses (5.06%; 95%CI 3.88-6.58%) was also analysed. On a geographic level, prevalence by country did not show statistical differences, ranging from 3.24% (Greece) to 21.05% (Denmark). An odds ratio analysis was also included in order to evaluate the relevance of the variable 'age' as a risk factor of HBoV infection in children <5 years old. The OR value of 1.77 (95%CI 1.13-2.77; p < .01) indicated that being <5 years old is a risk factor for HBoV infection. This study showed that HBoV has a moderate prevalence among European countries.
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Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alberto Lema
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Enia Gándara
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Li L, Nesme J, Quintela-Baluja M, Balboa S, Hashsham S, Williams MR, Yu Z, Sørensen SJ, Graham DW, Romalde JL, Dechesne A, Smets BF. Extended-Spectrum β-Lactamase and Carbapenemase Genes are Substantially and Sequentially Reduced during Conveyance and Treatment of Urban Sewage. Environ Sci Technol 2021; 55:5939-5949. [PMID: 33886308 DOI: 10.1021/acs.est.0c08548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Urban wastewater systems (UWSs) are a main receptacle of excreted antibiotic resistance genes (ARGs) and their host microorganisms. However, we lack integrated and quantitative observations of the occurrence of ARGs in the UWS to characterize the sources and identify processes that contribute to their fate. We sampled the UWSs from three medium-size cities in Denmark, Spain, and the United Kingdom and quantified 70 clinically important extended-spectrum β-lactamase and carbapenemase genes along with the mobile genetic elements and microbial communities. Results from all three countries showed that sewage-especially from hospitals-carried substantial loads of ARGs (106-107 copies per person equivalent), but these loads progressively declined along sewers and through sewage treatment plants, resulting in minimal emissions (101-104 copies per person equivalent). Removal was primarily during sewage conveyance (65 ± 36%) rather than within sewage treatment (34 ± 23%). The extended-spectrum β-lactamase and carbapenemase genes were clustered in groups based on their persistence in the UWS compartments. The less-persistent groups were associated to putative host taxa (especially Enterobacteriaceae and Moraxellaceae), while the more persistent groups appeared horizontally transferred and correlated significantly with total cell numbers and mobile genetic elements. This documentation of a substantial ARG reduction during sewage conveyance provides opportunities for antibiotic resistance management and a caution for sewage-based antibiotic resistance surveillance.
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Affiliation(s)
- Liguan Li
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Joseph Nesme
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | | | - Sabela Balboa
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Syed Hashsham
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing 48824, Michigan, USA
| | - Maggie R Williams
- School of Engineering and Technology, Central Michigan University, Mt. Pleasant 48859, Michigan, USA
| | - Zhuofeng Yu
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, U.K
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Arnaud Dechesne
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Lyngby 2800, DK
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Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain.
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20
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Hassoun-Kheir N, Stabholz Y, Kreft JU, de la Cruz R, Romalde JL, Nesme J, Sørensen SJ, Smets BF, Graham D, Paul M. Comparison of antibiotic-resistant bacteria and antibiotic resistance genes abundance in hospital and community wastewater: A systematic review. Sci Total Environ 2020; 743:140804. [PMID: 32758846 DOI: 10.1016/j.scitotenv.2020.140804] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/04/2020] [Accepted: 07/05/2020] [Indexed: 05/10/2023]
Abstract
Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) are constantly shed into the aquatic environment, with hospital wastewater potentially acting as an important source for resistance spread into the environment. A systematic review was conducted aiming to investigate the role of hospital wastewater on dissemination of antimicrobial resistance in the aquatic environment. Studies included in the review compared the prevalence of ARB and/or ARGs in hospital versus community wastewater. Data were extracted on ARB and/or ARG prevalence. Data on sampling techniques, microbiological methodology and risk of bias of included studies were recorded. Thirty-seven studies were included. Higher frequencies of antibiotic resistance determinants were found in hospital wastewater compared to community sources in 30/37 (81%) of included studies. However, trends for specific multi-drug-resistant bacteria differed. Antibiotic-resistant Gram-negative were more prevalent in hospital compared to community wastewaters, with higher concentrations of extended-spectrum-beta-lactamase-producing pathogens and carbapenemase-producing Enterobacteriaceae in hospital sources in 9/9 studies and 6/7 studies, respectively. Hospitals did not contribute consistently to the abundance of vancomycin-resistant Enterococci (VRE); 5/10 studies found higher abundance of VRE in hospital compared to community wastewaters. Reporting on sampling methods, wastewater treatment processes and statistical analysis were at high risk of bias. Extreme heterogeneity in study methods and outcome reporting precluded meta-analysis. Current evidence concurs that hospital wastewater is an important source for antibiotic resistance in aquatic environments, mainly multidrug-resistant Gram-negative bacteria. Future research is needed to assess the effect of wastewater treatment processes on overall antibiotic resistance in the aquatic environment.
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Affiliation(s)
- Nasreen Hassoun-Kheir
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel.
| | - Yoav Stabholz
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection & Centre for Computational Biology & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roberto de la Cruz
- Institute of Microbiology and Infection & Centre for Computational Biology & School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Barth F Smets
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - David Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Mical Paul
- Infectious Diseases Institute, Rambam Health Care Campus, Haifa, Israel, HaAliya HaShniya St 8, Haifa 3109601, Israel; The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Efron St 1, Haifa 3109601, Israel
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21
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López Cabo M, Romalde JL, Simal-Gandara J, Gago Martínez A, Giráldez Fernández J, Bernárdez Costas M, Pascual del Hierro S, Pousa Ortega Á, Manaia CM, Abreu Silva J, Rodríguez Herrera J. Identification of Emerging Hazards in Mussels by the Galician Emerging Food Safety Risks Network (RISEGAL). A First Approach. Foods 2020; 9:foods9111641. [PMID: 33182842 PMCID: PMC7697966 DOI: 10.3390/foods9111641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 01/04/2023] Open
Abstract
Emerging risk identification is a priority for the European Food Safety Authority (EFSA). The goal of the Galician Emerging Food Safety Risks Network (RISEGAL) is the identification of emerging risks in foods produced and commercialized in Galicia (northwest Spain) in order to propose prevention plans and mitigation strategies. In this work, RISEGAL applied a systematic approach for the identification of emerging food safety risks potentially affecting bivalve shellfish. First, a comprehensive review of scientific databases was carried out to identify hazards most quoted as emerging in bivalves in the period 2016–2018. Then, identified hazards were semiquantitatively assessed by a panel of food safety experts, who scored them accordingly with the five evaluation criteria proposed by EFSA: novelty, soundness, imminence, scale, and severity. Scores determined that perfluorinated compounds, antimicrobial resistance, Vibrio parahaemolyticus, hepatitis E virus (HEV), and antimicrobial residues are the emerging hazards that are considered most imminent and severe and that could cause safety problems of the highest scale in the bivalve value chain by the majority of the experts consulted (75%). Finally, in a preliminary way, an exploratory study carried out in the Galician Rías highlighted the presence of HEV in mussels cultivated in class B production areas.
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Affiliation(s)
- Marta López Cabo
- Seafood Microbiology and Technology Section, Instituto de Investigacións Mariñas, Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.B.C.); (S.P.d.H.); (J.R.H.)
- Correspondence: ; Tel.: +34-986231930-860261
| | - Jesús L. Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology & Institute CRETUS, Universidade de Santiago de Compostela, E15782 Santiago de Compostela, Spain;
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, Universidade de Vigo–Ourense Campus, E32004 Ourense, Spain;
| | - Ana Gago Martínez
- Department Analytical and Food Chemistry, Universidade de Vigo, 36310 Vigo, Spain; (A.G.M.); (J.G.F.)
| | - Jorge Giráldez Fernández
- Department Analytical and Food Chemistry, Universidade de Vigo, 36310 Vigo, Spain; (A.G.M.); (J.G.F.)
| | - Marta Bernárdez Costas
- Seafood Microbiology and Technology Section, Instituto de Investigacións Mariñas, Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.B.C.); (S.P.d.H.); (J.R.H.)
| | - Santiago Pascual del Hierro
- Seafood Microbiology and Technology Section, Instituto de Investigacións Mariñas, Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.B.C.); (S.P.d.H.); (J.R.H.)
| | - Ánxela Pousa Ortega
- Direccion Xeral de Innovación e Xestión da Saúde Pública, Consellería de Sanidade, Xunta de Galicia, 15781 Santiago de Compostela, Spain;
| | - Célia M. Manaia
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (C.M.M.); (J.A.S.)
| | - Joana Abreu Silva
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal; (C.M.M.); (J.A.S.)
| | - Juan Rodríguez Herrera
- Seafood Microbiology and Technology Section, Instituto de Investigacións Mariñas, Spanish National Research Council (CSIC), 36208 Vigo, Spain; (M.B.C.); (S.P.d.H.); (J.R.H.)
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22
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Polo D, Quintela-Baluja M, Corbishley A, Jones DL, Singer AC, Graham DW, Romalde JL. Making waves: Wastewater-based epidemiology for COVID-19 - approaches and challenges for surveillance and prediction. Water Res 2020; 186:116404. [PMID: 32942178 PMCID: PMC7480445 DOI: 10.1016/j.watres.2020.116404] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/13/2020] [Accepted: 09/06/2020] [Indexed: 05/17/2023]
Abstract
The presence of SARS-CoV-2 in the feces of infected patients and wastewater has drawn attention, not only to the possibility of fecal-oral transmission but also to the use of wastewater as an epidemiological tool. The COVID-19 pandemic has highlighted problems in evaluating the epidemiological scope of the disease using classical surveillance approaches, due to a lack of diagnostic capacity, and their application to only a small proportion of the population. As in previous pandemics, statistics, particularly the proportion of the population infected, are believed to be widely underestimated. Furthermore, analysis of only clinical samples cannot predict outbreaks in a timely manner or easily capture asymptomatic carriers. Threfore, community-scale surveillance, including wastewater-based epidemiology, can bridge the broader community and the clinic, becoming a valuable indirect epidemiological prediction tool for SARS-CoV-2 and other pandemic viruses. This article summarizes current knowledge and discusses the critical factors for implementing wastewater-based epidemiology of COVID-19.
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Affiliation(s)
- David Polo
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
| | - Marcos Quintela-Baluja
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, United Kingdom
| | - Davey L Jones
- Environment Centre Wales, Bangor University, Bangor, Gwynedd, LL57 2UW, United Kingdom; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew C Singer
- UK Centre for Ecology & Hydrology. Wallingford, Oxfordshire, OX10 8BB, United Kingdom
| | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Facultade de Bioloxía & Institute CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, 15782, Spain.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abstract
Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.
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Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago, Spain.
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Corrigendum (2): Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos. Front Microbiol 2019; 10:2253. [PMID: 31611866 PMCID: PMC6779803 DOI: 10.3389/fmicb.2019.02253] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/17/2019] [Indexed: 11/13/2022] Open
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
| | - María 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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26
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Romalde JL, Balboa S, Ventosa A. Editorial: Microbial Taxonomy, Phylogeny and Biodiversity. Front Microbiol 2019; 10:1324. [PMID: 31275263 PMCID: PMC6593068 DOI: 10.3389/fmicb.2019.01324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/28/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Sabela Balboa
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
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27
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Rivadulla E, Varela MF, Mesquita JR, Nascimento MSJ, Romalde JL. Detection of Hepatitis E Virus in Shellfish Harvesting Areas from Galicia (Northwestern Spain). Viruses 2019; 11:v11070618. [PMID: 31284466 PMCID: PMC6669863 DOI: 10.3390/v11070618] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/01/2019] [Accepted: 07/03/2019] [Indexed: 12/23/2022] Open
Abstract
The hepatitis E virus (HEV) affects almost 20 million individuals annually, causing approximately 3.3 million acute liver injuries, 56,600 deaths, and huge healthcare-associated economic losses. Shellfish produced close to urban and livestock areas can bioaccumulate this virus and transmit it to the human population. The aim of this study was to evaluate the presence of HEV in molluscan shellfish, in order to deepen the knowledge about HEV prevalence in Galicia (northwestern Spain), and to investigate this as a possible route of HEV transmission to humans. A total of 168 shellfish samples was obtained from two different Galician rías (Ría de Ares-Betanzos and Ría de Vigo). The samples were analyzed by reverse transcription-quantitative PCR (RT-qPCR). RT-nested PCR and sequencing were used for further genotyping and phylogenetic analysis of positive samples. HEV was detected in 41 (24.4%) samples, at quantification levels ranging from non-quantifiable (<102 copies of the RNA genome (RNAc)/g tissue) to 1.1 × 105 RNAc/g tissue. Phylogenetic analysis based on the open reading frame (ORF)2 region showed that all sequenced isolates belonged to genotype 3, and were closely related to strains of sub-genotype e, which is of swine origin. The obtained results demonstrate a significant prevalence of HEV in bivalve molluscs from Galician rías, reinforcing the hypothesis that shellfish may be a potential route for HEV transmission to humans.
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Affiliation(s)
- Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miguel F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - João R Mesquita
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal
| | - Maria S J Nascimento
- Epidemiology Research Unit (EPIUnit), Instituto de Saúde Pública da Universidade do Porto, 4050-600 Porto, Portugal
- Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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López-Goñi I, Giner-Lamia J, Álvarez-Ordoñez A, Benitez-Páez A, Claessen D, Cortesao M, de Toro M, García-Ruano D, Granato ET, Kovács ÁT, Romalde JL, Sana TG, Sánchez-Angulo M, Sangari FJ, Smits WK, Sturm T, Thomassin JL, Valdehuesa KNG, Zapotoczna M. #EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide. FEMS Microbiol Lett 2019; 366:5521206. [DOI: 10.1093/femsle/fnz141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/19/2019] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Twitter is one of the most popular social media networks that, in recent years, has been increasingly used by researchers as a platform to share science and discuss ongoing work. Despite its popularity, Twitter is not commonly used as a medium to teach science. Here, we summarize the results of #EUROmicroMOOC: the first worldwide Microbiology Massive Open Online Course taught in English using Twitter. Content analytics indicated that more than 3 million users saw posts with the hashtag #EUROmicroMOOC, which resulted in over 42 million Twitter impressions worldwide. These analyses demonstrate that free Microbiology MOOCs shared on Twitter are valuable educational tools that reach broad audiences throughout the world. We also describe our experience teaching an entire Microbiology course using Twitter and provide recommendations when using social media to communicate science to a broad audience.
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Affiliation(s)
- I López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, E-31080 Pamplona, Spain
| | - J Giner-Lamia
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Campus Montegancedo-UPM, E-28223 Pozuelo de Alarcón, Madrid,Spain
- Departamento de Biotecnología-Biología Vegetal, ETSIAAB, UPM, Ciudad Universitaria, E-28040 Madrid, Spain
| | - A Álvarez-Ordoñez
- Departamento de Higiene y Tecnología de los Alimentos, Instituto de Ciencia y Tecnología de los Alimentos, Universidad de León, E-24071 León, Spain
| | - Alfonso Benitez-Páez
- Institute of Agrochemistry and Food Technology IATA-CSIC. C/Catedràtic Agustín Escardino Benlloch, 7, E-46980 Paterna-Valencia, Spain
| | - D Claessen
- Intitute of Biology, Leiden University, NL-2333 Leiden, the Netherlands
| | - M Cortesao
- German Aerospace Center (DLR), D-51147 Cologne, Germany
| | - M de Toro
- Fundacion Rioja Salud, E-26006 Logroño, Spain
| | - D García-Ruano
- Institute of Functional Biology and Genomics, USAL–CSIC, University of Salamanca, E-37002 Salamanca, Spain
| | - E T Granato
- Department of Zoology, University of Oxford, OX1 3SZ Oxford, United Kingdom
| | - Á T Kovács
- DTU Bioengineering, Bacterial Interactions and Evolution group,1 Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - J L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - T G Sana
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - M Sánchez-Angulo
- Departamento de Producción Vegetal y Microbiología, University of Miguel Hernández, E-03202 Elche, Spain
| | - F J Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC) CSIC-University of Cantabria and Department of Molecular Biology, University of Cantabria, E-39011 Santander, Spain
| | - W K Smits
- Department of Medical Microbiology, Leiden University Medical Center, NL-2300 RC Leiden, the Netherlands
| | - T Sturm
- Cabrillo College, Aptos, CA 95003, USA
| | - J L Thomassin
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, 28 rue du Dr. Roux, Paris F-75724 France
| | - K N G Valdehuesa
- Department of Energy Science and Technology, Myongji University, 03674 South Korea
| | - M Zapotoczna
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
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29
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Pérez-Cataluña A, Salas-Massó N, Diéguez AL, Balboa S, Lema A, Romalde JL, Figueras MJ. Corrigendum: Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Caos. Front Microbiol 2018; 9:3123. [PMID: 30622519 PMCID: PMC6308300 DOI: 10.3389/fmicb.2018.03123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/03/2018] [Indexed: 12/05/2022] Open
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 José 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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Varela MF, Monteiro S, Rivadulla E, Santos R, Romalde JL. Development of a novel digital RT-PCR method for detection of human sapovirus in different matrices. J Virol Methods 2018; 254:21-24. [PMID: 29407209 DOI: 10.1016/j.jviromet.2018.01.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/27/2022]
Abstract
A new nanofluidic digital RT-PCR method was developed for sapovirus (SaV) using control material obtained according to standards for enteric viruses. Primers employed amplify a fragment of 112 bp of the polymerase capsid junction, allowing the detection of human genogroups I, II and IV. Analytical validation was performed in clinical, shellfish and environmental water samples. This novel protocol rendered great effectiveness and repetitiveness, as well as higher sensitivity than real time RT-PCR assay, with differences in quantification ranging from 0.1 to 2.6 log-units. The method described here can constitute a promising tool for standardizing SaV quantification.
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Affiliation(s)
- Miguel F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Silvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001, Lisboa, Portugal
| | - Enrique Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001, Lisboa, Portugal
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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31
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Lasa A, Mira A, Camelo-Castillo A, Belda-Ferre P, Romalde JL. Characterization of the microbiota associated to Pecten maximus gonads using 454-pyrosequencing. Int Microbiol 2018; 19:93-99. [PMID: 27845496 DOI: 10.2436/20.1501.01.267] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/03/2016] [Indexed: 11/15/2022]
Abstract
A next-generation sequencing (NGS) approach was used to study the microbiota associated to Pecten maximus broodstock, applying pyrosequencing of PCR-amplified V1-V4 16S rRNA gene regions. We analysed the resident bacterial communities in female and male scallop gonads before and after spawning. DNA samples were amplified and quality-filtered reads were assigned to family and genus taxonomic levels using the Ribosomal Database Project classifier. A total of 18,520 sequences were detected, belonging to 13 phyla, including Proteobacteria (55%), Bacteroidetes (11,7%), Firmicutes (3%), Actinobacteria (2%) and Spirochaetes (1,2%), and 110 genera. The major fraction of the sequences detected corresponded to Proteobacteria, Beta- and Gammaprotebacteria being the most abundant classes. The microbiota of P. maximus gonad harbour a wide diversity, however differences on male and female samples were observed, where female gonad samples show a larger number of genera and families. The dominant bacterial genera appeared to be Delftia, Acinetobacter, Hydrotalea, Aquabacterium, Bacillus, Sediminibacterium, Sphingomonas, and Pseudomonas that were present among the four analysed samples. This next generation sequencing technique, applied for the first time in P. maximus (great scallop) gonads was useful for the study of the bacterial communities in this mollusc, unravelling the great bacterial diversity in its microbiota. [Int Microbiol 19(2): 93-99(2016)].
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Affiliation(s)
- Aide Lasa
- Department of Microbiology and Parasitology, CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alex Mira
- Department of Genomics and Health, Foundation FISABIO, High Research Center of Public Health, Valencia, Spain
| | - Anny Camelo-Castillo
- Department of Genomics and Health, Foundation FISABIO, High Research Center of Public Health, Valencia, Spain
| | - Pedro Belda-Ferre
- Department of Genomics and Health, Foundation FISABIO, High Research Center of Public Health, Valencia, Spain
| | - Jesús L Romalde
- Department of Microbiology and Parasitology, CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abdel-Moneim AS, Varma A, Pujol FH, Lewis GK, Paweska JT, Romalde JL, Söderlund-Venermo M, Moore MD, Nevels MM, Vakharia VN, Joshi V, Malik YS, Shi Z, Memish ZA. Launching a Global Network of Virologists: The World Society for Virology (WSV). Intervirology 2018; 60:276-277. [PMID: 29874676 DOI: 10.1159/000488762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/26/2018] [Indexed: 01/14/2023] Open
Affiliation(s)
- Ahmed S Abdel-Moneim
- Microbiology Department, College of Medicine, Taif University, Taif, Saudi Arabia.,Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef, Egypt
| | - Anupam Varma
- Advanced Centre for Plant Virology, Indian Agricultural Research Institute, New Delhi, India
| | - Flor H Pujol
- Laboratorio de Virología Molecular, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
| | - George K Lewis
- Division of Vaccine Research, Institute of Human Virology, Maryland University, Baltimore, Maryland, USA
| | - Janusz T Paweska
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Sandringham, South Africa
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Matthew D Moore
- Department of Food Science, University of Massachusetts, Amherst, Massachusetts, USA
| | - Michael M Nevels
- Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, United Kingdom.,Institute for Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Vikram N Vakharia
- Institute of Marine and Environmental Technology, University of Maryland, Baltimore, Maryland, USA
| | - Vinod Joshi
- Amity Institute of Virology and Immunology, Amity University, Sector-125, Uttar Pradesh, India
| | | | - Zhengli Shi
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ziad A Memish
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Research Department and Division of Infectious Diseases, Department of Medicine, Prince Mohamed Bin Abdulaziz Hospital, Ministry of Health, Riyadh, Saudi Arabia
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Polo D, García-Fernández I, Fernández-Ibañez P, Romalde JL. Hepatitis A Virus Disinfection in Water by Solar Photo-Fenton Systems. Food Environ Virol 2018; 10:159-166. [PMID: 29468537 DOI: 10.1007/s12560-018-9339-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/15/2018] [Indexed: 05/29/2023]
Abstract
This study evaluates and compares the effectiveness of solar photo-Fenton systems for the inactivation of hepatitis A virus (HAV) in water. The effect of solar irradiance, dark- Fenton reaction and three different reactant concentrations (2.5/5, 5/10 and 10/20 mg/L of Fe2+/H2O2) on the photo-Fenton process were tested in glass bottle reactors (200 mL) during 6 h under natural sunlight. Disinfection kinetics were determined both by RT-qPCR and infectivity assays. Mean water temperatures ranged from 25 to 27.3 °C, with a maximum local noon UV irradiances of 22.36 W/m2. Photo-Fenton systems yielded increased viral reduction rates in comparison with the isolated effect under the Fenton reaction in darkness (negligible viral reduction) or the solar radiation (0.25 Log of RNA reduction). With the highest concentration employed (10-20 mg/L Fe2+-H2O2), an average RNA reduction rate of ~ 1.8 Log (initial concentration of 105 pfu/mL) and a reduction of 80% in the infectivity capacity were reached. Results showed a strong synergistic effect between Fe2+/H2O2 and sunlight, demonstrating that significant disinfection rates of HAV under photo-Fenton systems may occur with relatively higher efficiency at middle environmental temperatures and without the need for an energy-intensive light source.
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Affiliation(s)
- David Polo
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | | | - Pilar Fernández-Ibañez
- Plataforma Solar de Almería, CIEMAT, Tabernas, Spain
- Engineering Research Institute ERI, Ulster University, Antrim, UK
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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Buján N, Balboa S, L Romalde J, E Toranzo A, Magariños B. Population genetic and evolution analysis of controversial genus Edwardsiella by multilocus sequence typing. Mol Phylogenet Evol 2018; 127:513-521. [PMID: 29751087 DOI: 10.1016/j.ympev.2018.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/19/2018] [Accepted: 05/07/2018] [Indexed: 10/17/2022]
Abstract
At present, the genus Edwardsiella compiles five species: E. tarda, E. hoshinae, E. ictaluri, E. piscicida and E. anguillarum. Some species of this genus such us E. ictaluri and E. piscicida are important pathogens of numerous fish species. With the description of the two latter species, the phylogeny of Edwardsiella became more complicated. With the aim to clarify the relationships among all species in the genus, a multilocus sequence typing (MLST) approach was developed and applied to characterize 56 isolates and 6 reference strains belonging to the five Edwardsiella species. Moreover, several analyses based on the MLST scheme were performed to investigate the evolution within the genus, as well as the influence of recombination and mutation in the speciation. Edwardsiella isolates presented a high genetic variability reflected in the fourteen sequence types (ST) represented by a single isolates out of eighteen total ST. Mutation events were considerably more frequent than recombination, although both approximately equal influenced the genetic diversification. However, the speciation among species occurred mostly by recombination. Edwardsiella genus displays a non-clonal population structure with some degree of geographical isolation followed by a population expansion of E. piscicida. A database from this study was created and hosted on pubmlst.org (http://pubmlst.org/edwardsiella/).
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Affiliation(s)
- Noemí Buján
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
| | - Sabela Balboa
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alicia E Toranzo
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Beatriz Magariños
- Departamento de Microbioloxía e Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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37
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Vercauteren M, De Swaef E, Declercq A, Bosseler L, Gulla S, Balboa S, Romalde JL, Devriese L, Polet H, Boyen F, Chiers K, Decostere A. First isolation of Vibrio tapetis and an atypical strain of Aeromonas salmonicida from skin ulcerations in common dab (Limanda limanda) in the North Sea. J Fish Dis 2018; 41:329-335. [PMID: 29148593 DOI: 10.1111/jfd.12729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/15/2017] [Indexed: 06/07/2023]
Abstract
Skin ulcerations rank amongst the most prevalent lesions affecting wild common dab (Limanda limanda) with an increase in prevalence of up to 3.5% in the Belgian part of the North Sea. A complex aetiology of these ulcerations is suspected, and many questions remain on the exact factors contributing to these lesions. To construct the aetiological spectrum of skin ulcerations in flatfish, a one-day monitoring campaign was undertaken in the North Sea. Fifteen fish presented with one or more ulcerations on the pigmented and/or non-pigmented side. Pathological features revealed various stages of ulcerations with loss of epidermal and dermal tissue, inflammatory infiltrates and degeneration of the myofibers bordering the ulceration, albeit in varying degrees. Upon bacteriological examination, pure cultures of Vibrio tapetis were retrieved in high numbers from five fish and of Aeromonas salmonicida in one fish. The V. tapetis isolates showed cross-reactivity with the sera against the representative strain of serotype O2 originating form a carpet-shell clam (Ruditapes descussatus). Moreover, the A. salmonicida isolates displayed a previously undescribed vapA gene sequence (A-layer type) with possible specificity towards common dab. Further research is necessary to pinpoint the exact role of these agents in the development of skin ulcerations in common dab.
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Affiliation(s)
- M Vercauteren
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - E De Swaef
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - A Declercq
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - L Bosseler
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - S Gulla
- Norwegian Veterinary Institute, Oslo, Norway
| | - S Balboa
- Department of Microbiology and Parasitology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J L Romalde
- Department of Microbiology and Parasitology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - L Devriese
- Animal Sciences Unit - Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Ostend, Belgium
- Department of Environment and Health, Vrije Universiteit, Amsterdam, The Netherlands
| | - H Polet
- Animal Sciences Unit - Aquatic Environment and Quality, Institute for Agricultural and Fisheries Research (ILVO), Ostend, Belgium
| | - F Boyen
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - K Chiers
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - A Decostere
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Romalde JL, Rivadulla E, Varela MF, Barja JL. An overview of 20 years of studies on the prevalence of human enteric viruses in shellfish from Galicia, Spain. J Appl Microbiol 2017; 124:943-957. [PMID: 29094428 DOI: 10.1111/jam.13614] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022]
Abstract
Galicia (NW Spain) has 1490 km of coastline, and its particular topography, characterized by the presence of fiord-like inlets, called rías, with an important primary production, makes this region very favourable for shellfish growth and culture. In fact, Galicia is one of the most important mussel producers in the world. Due to its proximity to cities and villages and the anthropogenic activities in these estuaries, and despite the routine official controls on the bivalve harvesting areas, contamination with material of faecal origin is sometimes possible but, current regulation based on Escherichia coli as an indicator micro-organism has been revealed as useful for bacterial contaminants, this is not the case for enteric viruses. The aim of this review is to offer a picture on the situation of different harvesting areas in Galicia, from a virological standpoint. A recompilation of results obtained in the last 20 years is presented, including not only the data for the well-known agents norovirus (NoV) and hepatitis A virus (HAV) but also data on emerging viral hazards, including sapovirus (SaV), hepatitis E virus (HEV) and aichivirus (AiV). Epidemiological differences related to diverse characteristics of the harvesting areas, viral genotype distribution or epidemiological links between environmental and clinical strains will also be presented and discussed. The presentation of these historical data all together could be useful for future decisions by competent authorities for a better management of shellfish growing areas.
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Affiliation(s)
- J L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - E Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J L Barja
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Buján N, Mohammed H, Balboa S, Romalde JL, Toranzo AE, Arias CR, Magariños B. Genetic studies to re-affiliate Edwardsiella tarda fish isolates to Edwardsiella piscicida and Edwardsiella anguillarum species. Syst Appl Microbiol 2017; 41:30-37. [PMID: 29150173 DOI: 10.1016/j.syapm.2017.09.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 08/30/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022]
Abstract
Until 2012, the genus Edwardsiella was composed by three species Edwardsiella tarda, Edwardsiella hoshinae and Edwardsiella ictaluri. In 2013, Edwardsiella piscicida, compiling fish pathogenic strains previously identified as E. tarda was described, and more recently a new species isolated from diseased eel was reported, namely Edwardsiella anguillarum. The incorporation of these species into the genus makes necessary a revision of the taxonomic position of the isolates previously identified as E. tarda. Using AFLP technique, MLSA studies and in silico DNA-DNA hybridization, 46 of 49 E. tarda isolates were re-assigned as E. piscicida and 2 as E. anguillarum, whereas it was confirmed previous classification of the Edwardsiella types and reference strains used. The study of the taxonomic resolution of the genes 16S rRNA, adk, atpD, dnaJ, glnA, hsp60, tuf as well as the possible combinations among housekeeping genes, showed that the gene dnaJ was the more resolutive. In conclusion, the use of molecular techniques is necessary to accurately identify Edwardsiella isolates, especially when differentiating new species from E. tarda.
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Affiliation(s)
- Noemí Buján
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
| | - Haitham Mohammed
- Aquatic Microbiology Laboratory, SFAAS, Center for Advanced Science, Innovation, and Commerce, Auburn University, Auburn, AL 36849, USA; Department of Animal Medicine, Faculty of Veterinary Medicine, Assiut University, Assiut 71526, Egypt
| | - Sabela Balboa
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jesús L Romalde
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Alicia E Toranzo
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Cova R Arias
- Aquatic Microbiology Laboratory, SFAAS, Center for Advanced Science, Innovation, and Commerce, Auburn University, Auburn, AL 36849, USA
| | - Beatriz Magariños
- Departamento de Microbioloxía y Parasitoloxía, CIBUS-Facultade de Bioloxía and Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
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Diéguez AL, Pichon P, Balboa S, Magnesen T, Romalde JL. Complete characterization of new isolates of Neptunomonas phycophila leads to emend its description and opens possibilities of biotechnological applications. Microbiologyopen 2017; 6. [PMID: 28925024 PMCID: PMC5727359 DOI: 10.1002/mbo3.519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 11/29/2022] Open
Abstract
Five strains were isolated from gonad of Great scallop (Pecten maximus) broodstock in a Norwegian hatchery. The study of 16S rRNA gene sequences showed that these isolates belong to Neptunomonas phycophila, a bacterium originally isolated from a symbiont of the anemone Aiptasia tagetes from Puerto Rico. The gyrB and rpoB genes sequences confirmed the affiliation of the scallop isolates to this species. Phenotypic characterization was performed and some differences between the Norwegian isolates and the type strain of N. phycophila were detected, such as ranges of temperature, pH, and tolerance to salinity or the use of several substrates as sole carbon source which lead to an emended description of the species. The strain 3CM2.5 showed phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The whole genomes of the scallop strain 3CM2.5 and type strain of the species CECT 8716T were obtained and the annotation of these genomes revealed the presence of genes involved in degradation of aromatic compounds in both strains. Results obtained not only widen the geographical and host ranges of N. phycophila, but also point out possible biotechnological applications for this bacterial species.
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Affiliation(s)
- Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, Santiago de Compostela, Spain
| | - Phillip Pichon
- Institute of Marine Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, Santiago de Compostela, Spain
| | - Thorolf Magnesen
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, Santiago de Compostela, Spain
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Gulla S, Rønneseth A, Sørum H, Vågnes Ø, Balboa S, Romalde JL, Colquhoun DJ. Vibrio tapetis from wrasse used for ectoparasite bio-control in salmon farming: phylogenetic analysis and serotyping. Dis Aquat Organ 2017; 125:189-197. [PMID: 28792417 DOI: 10.3354/dao03140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
So-called 'cleaner fish', including various wrasse (Labridae) species, have become increasingly popular in Norwegian salmon farming in recent years for biocontrol of the salmon louse Lepeophtheirus salmonis. Cleaner fish mortalities in salmon farms are, however, often high. Various bacterial agents are frequently associated with episodes of increased cleaner fish mortality, and Vibrio tapetis is regularly cultured from diseased wrasse. In the present study, we investigated the genetic relationships among 54 V. tapetis isolates (34 from wrasse species) by multilocus sequence analysis (MLSA; rpoD, ftsZ, pyrH, rpoA and atpA). In the resulting phylogenetic tree, all wrasse isolates belonged to sub-clusters within V. tapetis subsp. tapetis. Slide agglutination testing further confirmed the complete dominance amongst these isolates of 4 O-antigen serotypes, designated here as V. tapetis subsp. tapetis serotypes O1, O3, O4 and O5, respectively. A pilot challenge trial using serotypes O3, O4 and O5 did not indicate high pathogenicity towards ballan wrasse Labrus bergylta, thus questioning the role of V. tapetis as a primary pathogen of this fish species.
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Affiliation(s)
- Snorre Gulla
- Norwegian Veterinary Institute, Pb 750 Sentrum, 0106 Oslo, Norway
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Diéguez AL, Balboa S, Magnesen T, Romalde JL. Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery. Int J Syst Evol Microbiol 2017; 67:1327-1332. [PMID: 28109200 DOI: 10.1099/ijsem.0.001809] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four bacterial strains, LFT 1.7T, LT2C 2.5, LT4C 2.8 and TM 4.6, were isolated from great scallop (Pecten maximus) larvae and tank seawater in a Norwegian hatchery and characterized by a polyphasic approach including determination of phenotypic, chemotaxonomic and genomic traits. All were Gram-stain-negative, motile rods, oxidase- and catalase-positive and required sea salts for growth. Major fatty acids present were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0, C14 : 0, summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I), C12 : 0 3-OH and C12 : 0. Strain LFT 1.7T contained menaquinone MK-6 as the sole respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that all strains formed a distinct lineage within the genus Arcobacter with a low similarity to known species (94.77-95.32 %). The DNA G+C content was 28.7 mol%. Results of in silico DNA-DNA hybridization and average nucleotide identity confirmed that the isolates constitute a novel species of Arcobacter, for which the name Arcobacter lekithochrous sp. nov. is proposed. The type strain is LFT 1.7T (=CECT 8942T=DSM 100870T).
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Affiliation(s)
- Ana L Diéguez
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, 15782 Santiago de Compostela, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, 15782 Santiago de Compostela, Spain
| | - Thorolf Magnesen
- Department of Biology, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago, 15782 Santiago de Compostela, Spain
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Dubert J, Barja JL, Romalde JL. New Insights into Pathogenic Vibrios Affecting Bivalves in Hatcheries: Present and Future Prospects. Front Microbiol 2017; 8:762. [PMID: 28515714 PMCID: PMC5413579 DOI: 10.3389/fmicb.2017.00762] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/12/2017] [Indexed: 12/15/2022] Open
Abstract
Hatcheries constitute nowadays the only viable solution to support the husbandry of bivalve molluscs due to the depletion and/or overexploitation of their natural beds. Hatchery activities include the broodstock conditioning and spawning, rearing larvae and spat, and the production of microalgae to feed all stages of the production cycle. However, outbreaks of disease continue to be the main bottleneck for successful larval and spat production, most of them caused by different representatives of the genus Vibrio. Therefore, attention must be paid on preventive and management measures that allow the control of such undesirable bacterial populations. The present review provides an updated picture of the recently characterized Vibrio species associated with disease of bivalve molluscs during early stages of development, including the controversial taxonomic affiliation of some of them and relevant advances in the knowledge of their virulence determinants. The problematic use of antibiotics, as well as its eco-friendly alternatives are also critically discussed.
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Affiliation(s)
- Javier Dubert
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Juan L Barja
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
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Levican A, Lasa A, Irgang R, Romalde JL, Poblete-Morales M, Avendaño-Herrera R. Isolation of Vibrio tapetis from two native fish species (Genypterus chilensis and Paralichthys adspersus) reared in Chile and description of Vibrio tapetis subsp. quintayensis subsp. nov. Int J Syst Evol Microbiol 2017; 67:716-723. [DOI: 10.1099/ijsem.0.001705] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Arturo Levican
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
- Escuela de Tecnología Médica, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Rute Irgang
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Matías Poblete-Morales
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
| | - Ruben Avendaño-Herrera
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andres Bello, Valparaíso, Chile
- Laboratorio de Patología de Organismos Acuáticos y Biotecnología Acuícola, Universidad Andrés Bello, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile
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Lasa A, Romalde JL. Genome sequence of three Psychrobacter sp. strains with potential applications in bioremediation. Genom Data 2017; 12:7-10. [PMID: 28229046 PMCID: PMC5312645 DOI: 10.1016/j.gdata.2017.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/03/2017] [Accepted: 01/25/2017] [Indexed: 11/04/2022]
Abstract
To date, the genus Psychrobacter consists of 37 recognized species isolated from different sources, however they are more frequently found in cold and other non-polar environments of low water activity. Some strains belonging to the genus have shown different enzymatic activities with potential applications in bioremediation or food industry. In the present study, the whole genome sequences of three Psychrobacter-like strains (C 20.9, Cmf 22.2 and Rd 27.2) isolated from reared clams in Galicia (Spain) are described. The sequenced genomes resulted in an assembly size of 3,143,782 bp for C 20.9 isolate, 3,168,467 bp for Cmf 22.2 isolate and 3,028,386 bp for Rd 27.2 isolate. Among the identified coding sequences of the genomes, mercury detoxification and biogeochemistry genes were found, as well as genes related to heavy metals and antibiotic resistance. Also virulence-related features were identified such as the siderophore vibrioferrin or an aerobactin-like siderophore. The phylogenetic analysis of the 16S rRNA gene suggested that these strains may represent novel species of the Psychrobacter genus. The genome sequences of the Psychrobacter sp. strains have been deposited at DDBJ/EMBL/GenBank under the accession numbers MRYA00000000 (Cmf 22.2), MRYB00000000 (Rd 27.2) and MRYC00000000 (C 20.9), and the sequences could be found at the site https://www.ncbi.nlm.nih.gov/bioproject/PRJNA353858.
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Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología. Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología. Universidade de Santiago de Compostela, Campus Vida s/n. 15782, Santiago de Compostela, Spain
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Lasa A, Gibas CJ, Romalde JL. Comparative Genomic Analysis of Two Vibrio toranzoniae Strains with Different Virulence Capacity Reveals Clues on Its Pathogenicity for Fish. Front Microbiol 2017; 8:86. [PMID: 28194141 PMCID: PMC5277001 DOI: 10.3389/fmicb.2017.00086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/12/2017] [Indexed: 11/30/2022] Open
Abstract
Vibrio toranzoniae is a Gram-negative bacterium of the Splendidus clade within the Vibrio genus. V. toranzoniae was first isolated from healthy clams in Galicia (Spain) but recently was also identified associated to disease outbreaks of red conger eel in Chile. Experimental challenges showed that the Chilean isolates were able to produce fish mortalities but not the strains isolated from clams. The aim of the present study was to determine the differences at the genomic level between the type strain of the species (CECT 7225T) and the strain R17, isolated from red conger eel in Chile, which could explain their different virulent capacity. The genome-based comparison showed high homology between both strains but differences were observed in certain gene clusters that include some virulence factors. Among these, we found that iron acquisition systems and capsule synthesis genes were the main differential features between both genomes that could explain the differences in the pathogenicity of the strains. Besides, the studied genomes presented genomic islands and toxins, and the R17 strain presented CRISPR sequences that are absent on the type strain. Taken together, this analysis provided important insights into virulence factors of V. toranzoniae that will lead to a better understanding of the pathogenic process.
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Affiliation(s)
- Aide Lasa
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Cynthia J Gibas
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte Charlotte, NC, USA
| | - Jesús L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela Santiago de Compostela, Spain
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Rivadulla E, Varela MF, Romalde JL. Low prevalence of Aichi virus in molluscan shellfish samples from Galicia (NW Spain). J Appl Microbiol 2016; 122:516-521. [PMID: 27891729 DOI: 10.1111/jam.13363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/19/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022]
Abstract
AIMS The aim of this study was to detect and quantify Aichi virus (AiV) in shellfish from three estuaries in Galicia, the main producer of molluscs in Europe. METHODS AND RESULTS A total of 249 shellfish samples were analysed using a reverse transcription-quantitative PCR procedure. AiV was detected in 15 of 249 (6·02%) samples. Ría de Ares-Betanzos showed the highest prevalence (11·1%), followed by Ría do Burgo (3·7%) and Ría de Vigo, (2·56%). AiV quantifications ranged from nonquantifiable (under the limit of quantification of the method) to 6·9 × 103 RNAc per g DT, with a mean value of 1·9 × 102 RNAc per g DT. CONCLUSION Results obtained indicated that the prevalence of this enteric virus in the studied area is considerably lower than those of other enteric viruses, such as Norovirus, Sapovirus, HAV or HEV. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study that detects the presence of AiV in shellfish from authorized harvesting areas in Spain. Further studies with clinical samples are needed to determine the potential risk of AiV for human health in Galicia.
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Affiliation(s)
- E Rivadulla
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - M F Varela
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - J L Romalde
- Departamento de Microbiología y Parasitología, CIBUS-Facultad de Biología, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Pereira C, Moreirinha C, Rocha RJ, Calado R, Romalde JL, Nunes ML, Almeida A. Application of bacteriophages during depuration reduces the load of Salmonella Typhimurium in cockles. Food Res Int 2016; 90:73-84. [DOI: 10.1016/j.foodres.2016.10.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/07/2016] [Accepted: 10/22/2016] [Indexed: 01/02/2023]
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López-Goñi I, Martínez-Viñas MJ, Antón J, Cid VJ, González AM, Brown-Jaque M, García-Lobo JM, Sánchez M, Vilchez JI, Robledo-Mahón T, Seder-Colomina M, Tapia-Paniagua ST, de Rojas AH, Mira A, Gallego-Parrilla JJ, Díaz TML, Maicas S, Villalobo E, Quindós G, Balboa S, Romalde JL, Aguilar-Pérez C, Tomás A, Linares M, Zaragoza Ó, Gil-Serna J, Ferrer-Espada R, Camacho AI, Vinué L, García-Lara J. Twitter as a Tool for Teaching and Communicating Microbiology: The #microMOOCSEM Initiative. J Microbiol Biol Educ 2016; 17:492-494. [PMID: 28101285 PMCID: PMC5134962 DOI: 10.1128/jmbe.v17i3.1200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Online social networks are increasingly used by the population on a daily basis. They are considered a powerful tool for science communication and their potential as educational tools is emerging. However, their usefulness in academic practice is still a matter of debate. Here, we present the results of our pioneering experience teaching a full Basic Microbiology course via Twitter (#microMOOCSEM), consisting of 28 lessons of 40-45 minutes duration each, at a tweet per minute rate during 10 weeks. Lessons were prepared by 30 different lecturers, covering most basic areas in Microbiology and some monographic topics of general interest (malaria, HIV, tuberculosis, etc.). Data analysis on the impact and acceptance of the course were largely affirmative, promoting a 330% enhancement in the followers and a >350-fold increase of the number of visits per month to the Twitter account of the host institution, the Spanish Society for Microbiology. Almost one third of the course followers were located overseas. Our study indicates that Massive Online Open Courses (MOOC) via Twitter are highly dynamic, interactive, and accessible to great audiences, providing a valuable tool for social learning and communicating science. This strategy attracts the interest of students towards particular topics in the field, efficiently complementing customary academic activities, especially in multidisciplinary areas like Microbiology.
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Affiliation(s)
- Ignacio López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | | | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Víctor J. Cid
- Departamento de Microbiología II, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana Martín González
- Departamento de Microbiología III, Universidad Complutense de Madrid, Madrid, Spain
| | - Maryury Brown-Jaque
- Departamento de Genética, Microbiología y Estadística, Universitat de Barcelona, Barcelona, Spain
| | | | - Manuel Sánchez
- Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, Elche, Spain
| | | | | | | | | | | | - Alejandro Mira
- Centro Superior de Investigación en Salud Pública, Fundación FISABIO, Valencia, Spain
| | | | | | - Sergi Maicas
- Departament de Microbiologia i Ecologia, Universitat de València, Valencia, Spain
| | - Eduardo Villalobo
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
| | - Guillermo Quindós
- Departamento de Inmunología, Microbiología y Parasitología, Facultad de Medicina y Enfermería, Universidad País Vasco, Bilbao, Spain
| | - Sabela Balboa
- Departamento de Microbiología y Parasitología, Universidad Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesús L. Romalde
- Departamento de Microbiología y Parasitología, Universidad Santiago de Compostela, Santiago de Compostela, Spain
| | - Clara Aguilar-Pérez
- Departamento de Microbiología, Medicina Preventiva y Salud Publica, Universidad de Zaragoza, Zaragoza, Spain
| | - Anna Tomás
- Departamento de Microbiología, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Óscar Zaragoza
- Servicio de Micología, Centro Nacional de Microbiología, ISCIII, Madrid, Spain
| | - Jéssica Gil-Serna
- Departamento de Microbiología III, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Ferrer-Espada
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ana I. Camacho
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Laura Vinué
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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Pereira C, Moreirinha C, Lewicka M, Almeida P, Clemente C, Romalde JL, Nunes ML, Almeida A. Characterization and in vitro evaluation of new bacteriophages for the biocontrol of Escherichia coli. Virus Res 2016; 227:171-182. [PMID: 27756632 DOI: 10.1016/j.virusres.2016.09.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/28/2016] [Indexed: 01/21/2023]
Abstract
In the present study two new phages (phT4A and ECA2) were characterized and their efficacy was evaluated separately and in cocktail (phT4A/ECA2) to control Escherichia coli. The isolated phages, phT4A and ECA2, belonged to the Myoviridae and Podoviridae family, respectively and both are safe (no integrase and toxin codifying genes) to be used in bacterial control. In general, the increase of multiplicity of infection (MOI) from 1 to 100 promoted a significant increase in the efficiency of phage phT4A and phage cocktail phT4A/ECA2. Both phages were effective against E. coli, but phage phT4A (reduction of 5.8 log CFU/mL after 8h treatment) was more effective than phage ECA2 phage (reduction of 4.7 log CFU/mL after 8h treatment). The use of a cocktail phT4A/ECA2 was significantly more effective (reductions of 6.2 log CFU/mL after 6h treatment) than the use single phage suspensions of phT4A and ECA2 (reductions 5.3 log CFU/mL and 4.9 log CFU/mL, respectively, after 6h treatment). The rate of emergence of phage-resistant mutants was lower for phage phT4A when compared with phage ECA2 and phage cocktail phT4A/ECA2.The results indicate that in addition to the efficacy, the potential development of phage-resistant mutants must also be considered in the design of phage cocktails.
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Affiliation(s)
- Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Catarina Moreirinha
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Magdalena Lewicka
- STAB VIDA-Investigação e Serviços em Ciências Biológicas, Madan Parque, 2825-182 Caparica, Portugal
| | - Paulo Almeida
- STAB VIDA-Investigação e Serviços em Ciências Biológicas, Madan Parque, 2825-182 Caparica, Portugal
| | - Carla Clemente
- STAB VIDA-Investigação e Serviços em Ciências Biológicas, Madan Parque, 2825-182 Caparica, Portugal
| | - Jesús L Romalde
- Departamento de Microbiología e Parasitología, CIBUS-Facultad de Biologia, Universidade de Santiago de Compostela, Campus Vida s/n., 15782 Santiago de Compostela, Spain
| | - Maria L Nunes
- Portuguese Institute for Sea and Atmosphere (IPMA IP), Av. Brasília, 1449-006 Lisbon, Portugal
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
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