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Saticioglu IB, Duman M, Ajmi N, Altun S, Rochat T, Duchaud E. Phylogenomic characterization of Flavobacterium psychrophilum isolates retrieved from Turkish rainbow trout farms. JOURNAL OF FISH DISEASES 2024:e13961. [PMID: 38773965 DOI: 10.1111/jfd.13961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/09/2024] [Accepted: 04/26/2024] [Indexed: 05/24/2024]
Abstract
Flavobacterium psychrophilum, a devastating fish pathogen, is responsible for bacterial cold-water disease (BCWD), also known as rainbow trout fry syndrome. F. psychrophilum is the main causative agent of outbreaks in rainbow trout farms, especially at early live stages. In the present study, we aimed to characterize F. psychrophilum Turkish isolates. Eighteen isolates were retrieved from BCWD outbreaks between 2014 and 2021. In vitro phenotypic characterization showed gelatin and casein hydrolysis capacities and in vitro adhesion for all isolates, whereas elastinolytic activity was present for 16 of 18 isolates. We used complete genome sequencing to infer MLST-type, serotype and phylogenetic reconstruction. Strikingly, one strain isolated from Coruh trout (FP-369) belongs to ST393, a previously undescribed ST, and is phylogenetically distant from the other isolates. However, all strains retrieved from rainbow trout belong to the well-characterized clonal complex CC-ST10, 12 of 17 were tightly connected in a single cluster. Several serotypes (Types -1, -2 and -3) were represented among isolates, but no correlation was observed with geographic origins. This analysis suggests a regional dissemination of an epidemic, disease-producing bacterial population. This study provides a basis for epidemiological surveillance of isolates circulating in Turkey and phenotypic data for future molecular studies of virulence traits of this important fish pathogen.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Nihed Ajmi
- Graduate School of Health Sciences, Bursa Uludag University, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
| | - Eric Duchaud
- Université Paris-Saclay, INRAE, UVSQ, VIM, Jouy-en-Josas, France
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2
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Buyuk F, Karakaya E, Akar M, Kayman T, Tarhane S, Ozcan HE, Celebi O, Saticioglu IB, Anuk T, Abay S, Otlu S, Aydin F. A comprehensive study of Helicobacter pylori infection: molecular analysis, antibacterial susceptibility, and histopathological examination. Antonie Van Leeuwenhoek 2023; 116:1261-1273. [PMID: 37603113 DOI: 10.1007/s10482-023-01868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Helicobacter pylori is a pathogen associated with gastroduodenal diseases. This study aimed; (i) to investigate H. pylori presence by invasive tests in adult dyspeptic patients, (ii) to determine antibiotic susceptibility and genotypic characteristics of the H. pylori isolates, and (iii) to investigate the relationship between the H. pylori genotypes and the histopathological findings. In this cross-sectional study, gastric biopsy samples from 208 adult dyspeptic patients were used for culture, tissue Polymerase Chain Reaction (PCR), and histopathological analysis. Antibiotic susceptibility of the H. pylori isolates was analyzed by gradient method. Analysis of the virulence genes was performed by monoplex PCR. Genetic profiles (from A to H) were created based on the virulence genes presence. Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR) was used for the genotyping of the H. pylori isolates. The mean age of the patients was 46 (± 15) years and 128 (61.5%) of them were female. H. pylori positivity was detected by culture, tissue PCR and histopathological examination in 59 (28.4%), 114 (54.8%) and 81 (38.9%) patients, respectively. The overall prevalence of H. pylori was found to be 63% (131/208). All H. pylori isolates were susceptible to tetracycline and amoxicillin. The resistance rates for metronidazole, clarithromycin, levofloxacin, and rifampicin were 67.2%, 27.9%, 34.4% and 13.11%, respectively. Multi drug resistance (MDR) was detected at the rate of 45.9% (28/61). While the most common virulence gene was cagA (93.44%), the least common was vacAm1 (23%). The predominant genetic profile was profile A (47.5%). ERIC-PCR results revealed a total of 26 different patterns. A high prevalence of H. pylori was detected in adult dyspeptic patients as in developing countries. It was observed significant genotypic heterogeneity and virulence gene diversity within the isolates. A considerable resistance rate detected against antibiotics such as clarithromycin, metronidazole, and levofloxacin, which are frequently used in the eradication of H. pylori, should be taken into consideration when creating regional empirical treatment regimens.
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Affiliation(s)
- Fatih Buyuk
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye.
| | - Emre Karakaya
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Mustafa Akar
- Department of Gastroenterology, University of Health Sciences, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Türkiye
| | - Tuba Kayman
- Department of Medical Microbiology, Faculty of Medicine, Kırıkkale University, Kırıkkale, Türkiye
| | - Serdal Tarhane
- Veterinary Department, Eldivan Vocational School of Health Services, Çankırı Karatekin University, Çankırı, Türkiye
| | - Hacer Ece Ozcan
- Department of Medical Pathology, Mersin City Hospital, Mersin, Türkiye
| | - Ozgur Celebi
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Uludağ University, Bursa, Türkiye
| | - Turgut Anuk
- Department of General Surgery, Erzurum Faculty of Medicine, University of Health Sciences, Erzurum, Türkiye
| | - Secil Abay
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
| | - Salih Otlu
- Department of Microbiology, Faculty of Veterinary Medicine, Kafkas University, Kars, Türkiye
| | - Fuat Aydin
- Department of Microbiology, Faculty of Veterinary Medicine, Erciyes University, Kayseri, Türkiye
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Knupp C, Loch TP. Immersion challenge of three salmonid species (family Salmonidae) with three multilocus sequence typing variants of Flavobacterium psychrophilum provides evidence of differential host specificity. JOURNAL OF FISH DISEASES 2023. [PMID: 37974459 DOI: 10.1111/jfd.13889] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Bacterial coldwater disease (BCWD), caused by Flavobacterium psychrophilum, results in significant losses among multiple salmonid (family Salmonidae) species. Molecular epidemiology and serotyping studies have suggested that some variants are host specific; however, these associations have not been evaluated by cross-challenging fish species with putatively host-associated F. psychrophilum isolates via more natural (i.e. immersion) exposure routes. To this end, F. psychrophilum isolates US19-COS, US62-ATS and US87-RBT, each originally recovered from diseased coho salmon (Oncorhynchus kisutch), Atlantic salmon (Salmo salar) or rainbow trout (O. mykiss), and belonging to a host-associated multilocus sequence typing clonal complex (e.g. CC-ST9, CC-ST232 or CC-ST10), were PCR-serotyped, evaluated for proteolytic activity, and used to challenge adipose fin-clipped 4-month old Atlantic salmon, coho salmon and rainbow trout via immersion. Findings showed US87-RBT caused disease and mortality only in rainbow trout (e.g. 56.7% survival probability). US19-COS and US62-ATS caused more mortality in coho salmon and Atlantic salmon but also caused disease in both other host species, albeit to a lesser extent. Observed survival differences may be due to variant antigenic/virulence determinants as differences in serotype and proteolytic activity were discovered. Collectively, results highlight the intricacies of F. psychrophilum-host interactions and provide further in vivo evidence that some F. psychrophilum MLST variants are host specific, which may have implications for the development of BCWD prevention and control strategies.
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Affiliation(s)
- Christopher Knupp
- Aquatic Animal Health Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Thomas P Loch
- Aquatic Animal Health Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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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. JOURNAL OF FISH DISEASES 2023. [PMID: 37965781 DOI: 10.1111/jfd.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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Hegde A, Kabra S, Basawa RM, Khile DA, Abbu RUF, Thomas NA, Manickam NB, Raval R. Bacterial diseases in marine fish species: current trends and future prospects in disease management. World J Microbiol Biotechnol 2023; 39:317. [PMID: 37743401 PMCID: PMC10518295 DOI: 10.1007/s11274-023-03755-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 09/26/2023]
Abstract
The fisheries sub-sector of aquaculture-i.e., the pisciculture industry, contributes significantly to a country's economy, employing a sizable proportion of the population. It also makes important contributions to household food security because the current demand for animal protein cannot be fulfilled by harvesting wild fish from riverines, lakes, dams, and oceans. For good pond management techniques and sustaining fish health, the fisherfolk, and the industry require well-established regulatory structures, efficient disease management strategies, and other extended services. In rearing marine fish, infections resulting from disease outbreaks are a weighty concern because they can cause considerable economic loss due to morbidity and mortality. Consequently, to find effective solutions for the prevention and control of the major diseases limiting fish production in aquaculture, multidisciplinary studies on the traits of potential fish pathogens, the biology of the fish as hosts, and an adequate understanding of the global environmental factors are fundamental. This review highlights the various bacterial diseases and their causative pathogens prevalent in the pisciculture industry and the current solutions while emphasising marine fish species. Given that preexisting methods are known to have several disadvantages, other sustainable alternatives like antimicrobial peptides, synthetic peptides, probiotics, and medicinal treatments have emerged to be an enormous potential solution to these challenges.
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Affiliation(s)
- Avani Hegde
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Suhani Kabra
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Renuka Manjunath Basawa
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Dnyanada Anil Khile
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Rahil Ummar Faruk Abbu
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Naomi Ann Thomas
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Nava Bharati Manickam
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- Manipal Biomachines, Manipal Institute of Technology (MIT), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
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Saticioglu IB, Ay H, Altun S, Duman M. Genomic insight into Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2023; 46:126385. [PMID: 36410095 DOI: 10.1016/j.syapm.2022.126385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/15/2022]
Abstract
Four strains, designated as C-2, C-17T, C-39T and Ch-15, were isolated from farmed rainbow trout samples showing clinical signs during an investigation for a fish-health screening study. The pairwise 16S rRNA gene sequence analysis showed that strain C-17T shared the highest identity level of 98.1 % with the type strain of Chryseobacterium piscium LMG 23089T while strains C-2, C-39T and Ch-15 were closely related to Chryseobacterium balustinum DSM 16775T with an identity level of 99.3 %. A polyphasic approach involving phenotypic, chemotaxonomic and genome-based analyses was employed to determine the taxonomic provenance of the strains. The overall genome relatedness indices including dDDH and ANI analyses confirmed that strains C-2, C-17T, C-39T and Ch-15 formed two novel species within the genus Chryseobacterium. Chemotaxonomic analyses showed that strains C-17T and C-39T have typical characteristics of the genus Chryseobacterium by having phosphatidylethanolamine in their polar lipid profile, MK-6 as only isoprenoid quinone and the presence of iso-C15:0 as major fatty acid. The genome size and G + C content of the strains ranged between 4.4 and 5.0 Mb and 33.5 - 33.6 %, respectively. Comprehensive genome analyses revealed that the strains have antimicrobial resistance genes, prophages and horizontally acquired genes in addition to secondary metabolite-coding gene clusters. In conclusion, based on the polyphasic analyses conducted on the present study, strains C-17T and C-39T are representatives of two novel species within the genus Chryseobacterium, for which the names Chryseobacterium turcicum sp. nov. and Chryseobacterium muglaense sp. nov. with the type strains C-17T (=JCM 34190T = KCTC 82250T) and C-39T (=JCM 34191T = KCTC 822251T), respectively, are proposed.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey; Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
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Li S, Chai J, Knupp C, Nicolas P, Wang D, Cao Y, Deng F, Chen F, Lu T, Loch TP. Phenotypic and Genetic Characterization of Flavobacterium psychrophilum Recovered from Diseased Salmonids in China. Microbiol Spectr 2021; 9:e0033021. [PMID: 34523994 PMCID: PMC8557942 DOI: 10.1128/spectrum.00330-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/20/2022] Open
Abstract
Flavobacterium psychrophilum, the etiological agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome, causes great economic losses in salmonid aquaculture worldwide. Recent molecular studies have uncovered important epidemiological and ecological aspects of this pathogen; however, such data are lacking for F. psychrophilum populations affecting aquaculture in China. Herein, F. psychrophilum phenotype, genotype, and virulence were characterized for isolates recovered from epizootics in multiple salmonid aquaculture facilities across China. Thirty-one F. psychrophilum isolates, originating from four provinces and three host fish species, were predominantly homogeneous biochemically but represented 5 sequence types (STs) according to multilocus sequence typing (MLST) that belonged to clonal complex CC-ST10 or 3 newly recognized singleton STs. PCR-based serotyping classified 19 and 12 F. psychrophilum isolates into molecular serotypes 1 and 0, respectively, showing an obvious relationship with host species. Antimicrobial susceptibility analysis via broth microdilution revealed reduced susceptibility to enrofloxacin, flumequine, and oxolinic acid, moderate susceptibility to gentamicin, erythromycin, and florfenicol, and variable susceptibility to ampicillin and oxytetracycline. In vivo challenge experiments confirmed the ability of two representative Chinese F. psychrophilum isolates to induce typical signs of BCWD and mortality in 1-year-old rainbow trout (Oncorhynchus mykiss). Findings collectively demonstrate (i) that BCWD outbreaks in China studied thus far are caused by F. psychrophilum lineages that are common on other continents (e.g., CC-ST10) and others that have not been reported elsewhere (e.g., ST355, ST356, ST357), (ii) that F. psychrophilum molecular serotypes distinguish isolates from different host fish species, even within STs, and (iii) reduced F. psychrophilum antimicrobial susceptibility against compounds used for BCWD control in China. IMPORTANCE Flavobacterium psychrophilum causes substantial economic losses in salmonid aquaculture worldwide. Although this bacterium is also believed to be a disease source in China, published reports of its presence do not yet exist. Herein, F. psychrophilum was linked to multiple disease outbreaks in several salmonid aquaculture facilities within four Chinese provinces, and polyphasic characterization revealed that most isolates were genetically distinct from strains recovered on other continents. Analyses further revealed the predominating molecular serotypes, antimicrobial susceptibility profiles, and pathogenic potential of two representative recovered isolates. Collectively, the results presented here provide important data on the epidemiology and disease ecology of F. psychrophilum in China and pave the way for targeted prevention and control methods to be pursued in the future.
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Affiliation(s)
- Shaowu Li
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Jingru Chai
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Christopher Knupp
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Di Wang
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Yongsheng Cao
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Furong Deng
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Fuguang Chen
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Tongyan Lu
- Department of Aquatic Animal Health, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
- Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, China
| | - Thomas P. Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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8
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Duman M, Ay H, Altun S, Sahin N, Saticioglu IB. Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout. Int J Syst Evol Microbiol 2021; 71. [PMID: 34296991 DOI: 10.1099/ijsem.0.004903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two yellow-pigmented isolates, F-60T and F-392, were isolated from the internal organs of an apparently healthy rainbow trout (Oncorhynchus mykiss). The strains were identified as members of the genus Flavobacterium based on the results of 16S rRNA gene sequence analysis. Strains F-60T and F-392 had the highest 16S rRNA gene sequence identity level of 97.4 % to the type strain of Flavobacterium crassostreae LPB0076T. A polyphasic taxonomic approach including phenotypic, chemotaxonomic and genomic characterization was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity based on blast (ANIb) values for strains F-60T and F-392 were calculated as 100 %. However, dDDH and ANI analyses between the strains and their close neighbours confirmed that both strains represent a novel species in the genus Flavobacterium. The strains shared the highest dDDH and ANIb levels of 23.3 and 77.9%, respectively, with the type strain of Flavobacterium frigidarium DSM 17623T while those values for F. crassostreae LPB0076T were obtained as 21.4-21.5 % and 76.3 %. The DNA G+C content of the strains was 34.5 mol%. Chemotaxonomic and phylogenomic analyses of these isolates confirmed that both strains are representatives of a novel species for which the name Flavobacterium muglaense sp. nov. is proposed, with F-60T as the type strain (=JCM 34196T=KCTC 82256T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, Samsun 55139, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey
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Knupp C, Kiupel M, Brenden TO, Loch TP. Host-specific preference of some Flavobacterium psychrophilum multilocus sequence typing genotypes determines their ability to cause bacterial coldwater disease in coho salmon (Oncorhynchus kisutch). JOURNAL OF FISH DISEASES 2021; 44:521-531. [PMID: 33476403 DOI: 10.1111/jfd.13340] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Flavobacterium psychrophilum causes bacterial coldwater disease (BCWD) in salmonids, resulting in significant losses worldwide. Several serotyping and genetic studies of F. psychrophilum have suggested some geno-/serotypes may be either host-specific or generalistic in nature; however, this association has not been adequately explored in vivo using more natural exposure routes. Herein, F. psychrophilum isolate US19-COS, originally recovered from coho salmon (Oncorhynchus kisutch) and belonging to multilocus sequence typing clonal complex (CC) CC-ST9, and isolate US53-RBT, recovered from rainbow trout (Oncorhynchus mykiss) and belonging to CC-ST10, were serotyped via PCR, evaluated for proteolytic activity and utilized to determine their median lethal dose in immersion-challenged coho salmon fingerlings. US19-COS belonged to serotype 0, hydrolysed casein and gelatin but not elastin, led to fulminant multiorgan infections and elicited severe gross and microscopic pathology. In contrast, US53-RBT, belonging to serotype 2, hydrolysed all three substrates, but did not lead to detectable infections, disease signs or mortality in any exposed coho salmon despite proving virulent to rainbow trout in previous experiments. This study provides in vivo evidence for potential host specificity of some F. psychrophilum genotypes that can also be serologically distinct, a matter of importance towards better understanding F. psychrophilum disease ecology and epidemiology.
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Affiliation(s)
- Christopher Knupp
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
| | - Matti Kiupel
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Travis O Brenden
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
- Quantitative Fisheries Center, Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Thomas P Loch
- Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, USA
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
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10
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Duman M, Mulet M, Altun S, Saticioglu IB, Gomila M, Lalucat J, Garcia-Valdes E. Pseudomonas piscium sp. nov., Pseudomonas pisciculturae sp. nov. , Pseudomonas mucoides sp. nov. and Pseudomonas neuropathica sp. nov. isolated from rainbow trout. Int J Syst Evol Microbiol 2021; 71. [PMID: 33629945 DOI: 10.1099/ijsem.0.004714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six Gram negative, motile bacteria were isolated from rainbow trout (Oncorhynchus mykiss). The 16S rRNA sequence similarity values grouped them in the Pseudomonas mandelii (strains P49, P50T, 154aT and P154b), Pseudomonas fluorescens (strain P115T) and Pseudomonas koreensis (strain P155T) phylogenetic subgroups in the genus Pseudomonas. The DNA G+C content ranged from 58.5 to 60 mol%. The strains were characterized phenotypically using API 20NE and Biolog GENIII tests, and chemotaxonomically by their whole-cell MALDI-TOF MS protein profiles and fatty acid contents. Multi-locus sequence analysis with four housekeeping gene sequences (rpoD, rpoB, gyrB and 16S rRNA) together with genome comparisons by average nucleotide identity and genome-to-genome distance calculations were performed. Results showed that the similarity values of these strains to known species type strains were lower than the thresholds established for species in the genus Pseudomonas. Based on these data, we concluded that strains P49, P50T, P115T, P154aT, P154b and P155T belonged to four novel species. The names proposed are: Pseudomonas piscium sp. nov. for strains P49 and P50T with P50T (=CECT 30175T=CCUG 74871T) as the type strain; Pseudomonas pisciculturae sp. nov. for strain P115T (CECT 30173T=CCUG 74873T); Pseudomonas mucoides sp. nov. for strains P154aT and P154b with P154aT (=CECT 30177T=CCUG 74874T) as the type strain; and Pseudomonas neuropathica sp. nov. for strain P155T (=CECT 30178T=CCUG 74875T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Soner Altun
- Department of Aquatic Animal Diseases, Bursa Uludag University, Faculty of Veterinary Medicine, 16059 Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.,Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena Garcia-Valdes
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain.,Institut Mediterrani d'Estudis Avançats (IMEDEA CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
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11
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Saticioglu IB, Ay H, Altun S, Duman M, Sahin N. Flavobacterium turcicum sp. nov. and Flavobacterium kayseriense sp. nov. isolated from farmed rainbow trout in Turkey. Syst Appl Microbiol 2021; 44:126186. [PMID: 33647765 DOI: 10.1016/j.syapm.2021.126186] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
During a study on culturable microorganisms from fish farms, four yellow-pigmented gram negative, rod shaped isolates, F-47T, F-339T, F-380 and F-400, were recovered from rainbow trout samples exhibiting clinical signs. Based on 16S rRNA gene sequence analysis, the strains were identified as members of the genus Flavobacterium. Strains F-47T and F-380 shared the highest 16S rRNA gene sequence identity level of 97.6% with the type strain of Flavobacterium frigoris DSM 15719T while strains F-339T and F-400 shared the highest identity level of 97.6% with the type strain of F. caseinilyticum AT-3-2T. A polyphasic taxonomic approach including phenotypic and genomic characterization as well as whole-cell MALDI-TOF mass spectrometry analyses was employed to ascertain the taxonomic position of the strains within the genus Flavobacterium. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses between strains F-47T, F-339T and their close neighbours F. frigoris DSM 15719T and F. caseinilyticum AT-3-2T, respectively, confirmed that both strains represent novel species in the genus Flavobacterium. The DNA G+C contents of the strains F-47T and F-339T are 34.3% and 35.3%, respectively. It can be concluded on the basis of polyphasic characterization as well as pairwise genome comparisons that the strains F-47T and F-339T represent two novel species within the genus Flavobacterium, for which Flavobacterium kayseriense sp. nov. F-47T (=JCM 34195T=KCTC 82255T) and Flavobacterium turcicum sp. nov. F-339T (=JCM 34202T=KCTC 82262T) are proposed, respectively.
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Affiliation(s)
- Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280, Kayseri, Turkey.
| | - Hilal Ay
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
| | - Soner Altun
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Muhammed Duman
- Department of Aquatic Animal Diseases, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa 16059, Turkey
| | - Nevzat Sahin
- Department of Molecular Biology and Genetics, Faculty of Science and Arts, Ondokuz Mayis University, 55139 Samsun, Turkey
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12
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Einarsdottir T, Guttormsdottir G, Connaghan D, Hjartardottir S. Longitudinal survey of Flavobacterium species in Icelandic salmonid fish farms. DISEASES OF AQUATIC ORGANISMS 2020; 141:15-24. [PMID: 32940247 DOI: 10.3354/dao03508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Flavobacterium species cause significant disease in salmonid farming worldwide, typically seen as mortality in sac fry and later as necrosis and ulceration in fingerlings and fry. In this study, we sampled Atlantic salmon Salmo salar and Arctic char Salvelinus alpinus from 5 Icelandic fish farms in 2014 and 2017, where flavobacteria were suspected to cause disease. The objective of the study was to identify and characterise the bacteria by sequencing the 16S rRNA gene and multilocus sequence type housekeeping genes. We found 5 distinct groups of flavobacteria: 3 that were homogeneous and appeared to persist in the fish farms between 2014 and 2017 and 2 that were heterogeneous and transient. Flavobacterium psychrophilum could be isolated from diseased Arctic char from all 5 fish farms in both 2014 and 2017. However, while the other 4 Flavobacterium sp. groups were isolated from Atlantic salmon, water and roe, F. psychrophilum could not be isolated from these samples. This indicates that flavobacteria other than F. psychrophilum may be the primary cause of fin and tail rot in Icelandic Atlantic salmon fry.
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13
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Avendaño-Herrera R, Tapia-Cammas D, Duchaud E, Irgang R. Serological diversity in Flavobacterium psychrophilum: A critical update using isolates retrieved from Chilean salmon farms. JOURNAL OF FISH DISEASES 2020; 43:877-888. [PMID: 32567047 DOI: 10.1111/jfd.13199] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
Chile is currently the second largest producer of farmed salmon worldwide, but Flavobacterium psychrophilum, as one of the most detrimental pathogens, is responsible for major losses during the freshwater culturing step in salmonid fish farms. An antigenic study conducted 10 years ago reported four serological groups using 20 F. psychrophilum Chilean strains. To reduce disease outbreaks and to develop vaccine candidates, antigenic knowledge needs to be regularly updated using a significant number of additional recent F. psychrophilum isolates. The present study aimed at investigating the serological diversity of 118 F. psychrophilum isolates collected between 2006 and 2018 from farmed Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and coho salmon (Oncorhynchus kisutch). The current study supports an expansion of the known antigenic groups in Chile from 4 to 14. However, the use of the slide-agglutination technique for serotyping is costly, is labour-intensive and requires significant technical expertise. Addressing these points, the mPCR-based procedure was a very useful tool for serotyping the collected Chilean F. psychrophilum isolates. This technique revealed the presence of diverse mPCR serotypes (i.e. types 0, 1, 2 and 4). Therefore, mPCR should be employed to select the bacterial strain(s) for vaccine development and to conduct follow-up, selective breeding or epidemiological surveillance in Chilean fish farms. Given the presented findings, changes to Chilean fish-farming practices are vital for ensuring the continued productivity and well-being of farmed salmonids.
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Affiliation(s)
- Ruben Avendaño-Herrera
- Universidad Andrés Bello, Laboratorio de Patología de Organismos Acuáticosy Biotecnología Acuícolas, Facultad de Ciencias de la Vida, Viña del Mar, Chile
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
- Centro de Investigación Marina Quintay (CIMARQ), Universidad Andrés Bello, Valparaíso, Chile
| | - Diana Tapia-Cammas
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
| | - Eric Duchaud
- Université Paris-Saclay, INRAE, UVSQ, Jouy-en-Josas, France
| | - Rute Irgang
- Interdisciplinary Center for Aquaculture Research (INCAR), Viña del Mar, Chile
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14
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Duman M, Mulet M, Saticioglu IB, Altun S, Gomila M, Lalucat J, García-Valdés E. Pseudomonas sivasensis sp. nov. isolated from farm fisheries in Turkey. Syst Appl Microbiol 2020; 43:126103. [PMID: 32690194 DOI: 10.1016/j.syapm.2020.126103] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 10/24/2022]
Abstract
A study of 91 isolates from fish farms in Turkey showed that isolates P7T, P11, P24b, P29, P72, P73 and P158 belonged to the genus Pseudomonas according to 16S rRNA nucleotide sequence analysis. The analysis of the sequences of the RNA polymerase sigma factor gene (rpoD) located these strains in the Pseudomonas fluorescens lineage of species within the P. fluorescens subgroup, close to the cluster composed of the species Pseudomonas grimontii, Pseudomonas marginalis and Pseudomonas panacis. Based on similarities in the 16S rRNA and rpoD gene sequences of three previously isolated strains from other origins (CCUG 57209, CCUG 62357 and W5.2-93) linked them to the same cluster. A polyphasic taxonomic approach including phenotypic characterization, fatty acid composition, and multilocus sequence analysis, together with whole-cell MALDI-TOF data, corroborated this assumption. The genome G+C mol% contents were 59.48 and 59.71, respectively. The average nucleotide indices based on BLAST analysis and the genome-to-genome distance calculation for the P7T and CCUG 57209 strains with their closest relative, P. grimontii, were 88.16-88.29% and 38.10-38.20%, respectively. These data confirm that isolates P7T, P11, P24b, P29, P72, P73, P158, CCUG 57209, CCUG 62357 and W5.2-93 represent a new species for which the name Pseudomonas sivasensis is proposed, with P7T as a type strain (=CCUG 74260T= and CECT30107T).
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animals Disease, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Magdalena Mulet
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Erciyes University, 38280 Kayseri, Turkey
| | - Soner Altun
- Department of Aquatic Animals Disease, Faculty of Veterinary Medicine, Bursa Uludag University, 16059 Bursa, Turkey
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain
| | - Elena García-Valdés
- Microbiologia, Departament de Biologia, Edifici Guillem Colom, Universitat de les Illes Balears, Campus UIB, 07122 Palma de Mallorca, Spain; Institut Mediterrani d'Estudis Avançats (IMEDEA, CSIC-UIB), Campus UIB, 07122 Palma de Mallorca, Spain.
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