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Dosi A, Meziti A, Tounta E, Koemtzopoulos K, Komnenou A, Dendrinos P, Kormas K. Fecal and skin microbiota of two rescued Mediterranean monk seal pups during rehabilitation. Microbiol Spectr 2024; 12:e0280523. [PMID: 38084980 PMCID: PMC10783143 DOI: 10.1128/spectrum.02805-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 11/15/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE This study showed that during the rehabilitation of two rescued Mediterranean monk seal pups (Monachus monachus), the skin and fecal bacterial communities showed similar succession patterns between the two individuals. This finding means that co-housed pups share their microbiomes, and this needs to be considered in cases of infection outbreaks and their treatment. The housing conditions, along with the feeding scheme and care protocols, including the admission of antibiotics as prophylaxis, probiotics, and essential food supplements, resulted in bacterial communities with no apparent pathogenic bacteria. This is the first contribution to the microbiome of the protected seal species of M. monachus and contributes to the animal's conservation practices through its microbiome.
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Affiliation(s)
- Aggeliki Dosi
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Alexandra Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Eleni Tounta
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Kimon Koemtzopoulos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Anastasia Komnenou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Dendrinos
- MOm/Hellenic Society for the Study and Protection of the Monk Seal, Athens, Greece
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
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An L, Chan JL, Nguyen M, Yang S, Deville JG. Case Report: Disseminated Edwardsiella tarda infection in an immunocompromised patient. Front Cell Infect Microbiol 2023; 13:1292768. [PMID: 38053529 PMCID: PMC10694257 DOI: 10.3389/fcimb.2023.1292768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
Human infection caused by bacteria of the Edwardsiella genus is rare and most often presents with gastroenteritis that rarely requires antibiotics. Our case report describes a medically complex patient with chronic steroid use contributing to an immunocompromised state, who presented with fever and abdominal pain. The patient was later found to have Edwardsiella tarda (E. tarda) bacteremia and underwent paracentesis confirming E. tarda bacterial peritonitis requiring a prolonged antibiotic course. This case report aims to illustrate the presentation, diagnosis, and management of an uncommon infection that can have severe complications especially among immunocompromised patients.
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Affiliation(s)
- Lucia An
- University of California, Los Angeles (UCLA) Mattel Children’s Hospital, Department of Pediatrics, Division of Pediatric Hospital Medicine, Los Angeles, CA, United States
| | - June L. Chan
- University of California, Los Angeles (UCLA) Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, Los Angeles, CA, United States
| | - Margaret Nguyen
- University of California, Los Angeles (UCLA) Mattel Children’s Hospital, Department of Pediatrics, Division of Pediatric Hospital Medicine, Los Angeles, CA, United States
| | - Shangxin Yang
- University of California, Los Angeles (UCLA) Clinical Microbiology Laboratory, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, Los Angeles, CA, United States
| | - Jaime G. Deville
- University of California, Los Angeles (UCLA) Mattel Children’s Hospital, Department of Pediatrics, Division of Pediatric Infectious Disease, Los Angeles, CA, United States
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Rehman MNU, Dawar FU, Zeng J, Fan L, Feng W, Wang M, Yang N, Guo G, Zheng J. Complete genome sequence analysis of Edwardsiella tarda SC002 from hatchlings of Siamese crocodile. Front Vet Sci 2023; 10:1140655. [PMID: 36968469 PMCID: PMC10034365 DOI: 10.3389/fvets.2023.1140655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/08/2023] [Indexed: 03/11/2023] Open
Abstract
Edwardsiella tarda is a Gram-negative, facultative anaerobic rod-shaped bacterium and the causative agent of the systemic disease “Edwardsiellosis”. It is commonly prevalent in aquatic organisms with subsequent economic loss and hence has attracted increasing attention from researchers. In this study, we investigated the complete genome sequence of a highly virulent isolate Edwardsiella tarda SC002 isolated from hatchlings of the Siamese crocodile. The genome of SC002 consisted of one circular chromosome of length 3,662,469 bp with a 57.29% G+C content and four novel plasmids. A total of 3,734 protein-coding genes, 12 genomic islands (GIs), 7 prophages, 48 interspersed repeat sequences, 248 tandem repeat sequences, a CRISPR component with a total length of 175 bp, and 171 ncRNAs (tRNA = 106, sRNA = 37, and rRNA = 28) were predicted. In addition, the coding genes of assembled genome were successfully annotated against eight general databases (NR = 3,618/3,734, COG = 2,947/3,734, KEGG = 3,485/3,734, SWISS-PROT = 2,787/3,734, GO = 2,648/3,734, Pfam = 2,648/3,734, CAZy = 130/3,734, and TCDB = 637/3,734) and four pathogenicity-related databases (ARDB = 11/3,734, CARD = 142/3,734, PHI = 538/3,734, and VFDB = 315/3,734). Pan-genome and comparative genome analyses of the complete sequenced genomes confirmed their evolutionary relationships. The present study confirmed that E. tarda SC002 is a potential pathogen bearing a bulk amount of antibiotic resistance, virulence, and pathogenic genes and its open pan-genome may enhance its host range in the future.
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Affiliation(s)
- Muhammad Nafees Ur Rehman
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Farman Ullah Dawar
- Department of Zoology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Jifeng Zeng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
| | - Lixia Fan
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Wei Feng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Mengqi Wang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Nuo Yang
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Guiying Guo
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
| | - Jiping Zheng
- Laboratory of Microbiological Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, China
- One Health Institute, Hainan University, Haikou, China
- *Correspondence: Jiping Zheng
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Guo M, Zhang L, Ye J, He X, Cao P, Zhou Z, Liu X. Characterization of the pathogenesis and immune response to a highly virulent Edwardsiella tarda strain responsible for mass mortality in the hybrid snakehead (Channa maculate ♀ × Channa argus ♂). Microb Pathog 2022; 170:105689. [PMID: 35917990 DOI: 10.1016/j.micpath.2022.105689] [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: 04/22/2022] [Revised: 07/11/2022] [Accepted: 07/19/2022] [Indexed: 11/28/2022]
Abstract
Edwardsiella tarda is reported as the causative agent of the systemic disease Edwardsiellosis in fish, which lead to huge economic losses in aquaculture. The pathogenicity and immune response to a highly virulent E. tarda isolate responsible for mass mortality in hybrid snakehead were performed. After species identification, morphology and virulence gene detection of Edwardsiella isolated from hybrid snakehead, the pathogenicity of the strain and histopathological changes in infected fish were analyzed. The infected fish exhibited typical acute hemorrhagic symptoms and enlarged internal organs. Histopathology revealed that the liver, spleen, kidney and intestinal tissues of diseased fish exhibited marked inflammatory with vacuolar degeneration and cell necrosis. Subsequently, humoral immune factors such as superoxide dismutase, lysozyme and acid phosphatase activities were detected as serum indicators, and real-time quantitative PCR was used to investigate immune-related genes (STAT1, HSP70, IgM, IL-6, IL-8, TRAF2, CD40, HLA-DMA and LCK) expression patterns in liver, spleen and head kidney. The results showed that these enzyme activity indicators and immune-related gene expression were significantly activated compared with healthy fish. These data provide insight into the pathogenic mechanisms and host immune responses of E. tarda, which could be useful for the future prevention and treatment of Edwardsiellosis in fish.
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Affiliation(s)
- Mengya Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Liwen Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jiaxin Ye
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiao He
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Pan Cao
- Institute of Surface Engineering, Yangzhou University, Yangzhou, 225127, China
| | - Zicheng Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaodan Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
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da Costa AR, Chideroli RT, Lanes GC, Ferrari NA, Chicoski LM, Batista CE, Pandolfi VCF, Ware C, Griffin MJ, Dos Santos AR, de Carvalho Azevedo VA, da Costa MM, de Pádua Pereira U. Multiplex PCR assay for correct identification of the fish pathogenic species of Edwardsiella genus reveals the presence of E. anguillarum in South America in strains previously characterized as E. tarda. J Appl Microbiol 2022; 132:4225-4235. [PMID: 35332638 DOI: 10.1111/jam.15538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022]
Abstract
AIMS Develop a species-specific multiplex PCR to correctly identify Edwardsiella species in routine diagnostic for fish bacterial diseases. METHODS AND RESULTS The genomes of 62 Edwardsiella spp. isolates available from the National Center for Biotechnology Information (NCBI) database were subjected to taxonomic and pan-genomic analyses to identify unique regions that could be exploited by species-specific PCR. The designed primers were tested against isolated Edwardsiella spp. strains, revealing errors in commercial biochemical tests for bacterial classification regarding Edwardsiella species. CONCLUSION Some of the genomes of Edwardsiella spp. in the NCBI platform were incorrectly classified, which can lead to errors in some research. A functional mPCR was developed to differentiate between phenotypically and genetically ambiguous Edwardsiella, with which, we detected the presence of Edwardsiella anguillarum affecting fish in Brazil. SIGNIFICANCE AND IMPACT OF THE STUDY This study shows that the misclassification of Edwardsiella spp in Brazil concealed the presence of E. anguillarum in South America. Also, this review of the taxonomic classification of the Edwardsiella genus is a contribution to the field to help researchers with their sequencing and identification of genomes, showing some misclassifications in online databases that must be corrected, as well as developing an easy assay to characterize Edwardsiella species in an end-point mPCR.
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Affiliation(s)
- Arthur Roberto da Costa
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Roberta Torres Chideroli
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil.,Microbiology and Immunology Laboratory, Department of Zootechnics, Federal University of São Francisco Valley, Petrolina, Brazil
| | - Gabriel Chagas Lanes
- Faculty of Computer Science, Federal University of Uberlândia, Uberlândia, Brazil
| | - Natália Amoroso Ferrari
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Larissa Melo Chicoski
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Catiane Estefani Batista
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Victor César Freitas Pandolfi
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
| | - Cynthia Ware
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, USA
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, MS, USA
| | | | - Vasco Ariston de Carvalho Azevedo
- Laboratory of Molecular and Cellular Genetics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Mateus Matiuzzi da Costa
- Microbiology and Immunology Laboratory, Department of Zootechnics, Federal University of São Francisco Valley, Petrolina, Brazil
| | - Ulisses de Pádua Pereira
- Laboratory of Fish Bacteriology, Department of Preventive Veterinary Medicine, State University of Londrina, Londrina, Brazil
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Glaeser SP, Silva LMR, Prieto R, Silva MA, Franco A, Kämpfer P, Hermosilla C, Taubert A, Eisenberg T. A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales. MICROBIAL ECOLOGY 2022; 83:18-33. [PMID: 33745062 PMCID: PMC8881428 DOI: 10.1007/s00248-021-01729-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/03/2021] [Indexed: 05/08/2023]
Abstract
Large baleen and toothed whales play crucial ecological roles in oceans; nonetheless, very little is known about their intestinal microbiomes. Based on striking differences in natural history and thus in feeding behaviours, it can be expected that intestinal microbiomes of large baleen whales and toothed whales are different. To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea. Faecal samples from free-ranging large whales collected off the Azores Archipelago (Portugal) were used, comprising 13 individual baleen whales (one sei, two blue and ten fin whales) and four sperm whales. The phylogenetic composition of the Bacteria faecal microbiomes of baleen and toothed whales showed no significant differences at the phylum level. However, significant differences were detected at the family and genus levels. Most abundant phyla were Firmicutes, Bacteroidetes, Proteobacteria, Tenericutes and Spirochaeta. Few highly abundant bacterial genera were identified as key taxa with a high contribution to differences among baleen and toothed whales microbiomes. Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea. This is the first study that directly compares the faecal bacterial and archaeal microbiomes of free-ranging baleen and toothed whales which represent the two parvorders of Cetacea which members are fully aquatic large mammals which were evolutionary split millions of years ago.
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Affiliation(s)
- Stefanie P Glaeser
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Liliana M R Silva
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Rui Prieto
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
- MARE-Marine and Environmental Sciences Centre, Lisbon, Portugal
| | - Mónica A Silva
- Institute of Marine Research (IMAR) and Okeanos R&D Centre, University of the Azores, Horta, Portugal
| | - Angel Franco
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Peter Kämpfer
- Institute of Applied Microbiology, Justus Liebig University Giessen, IFZ-Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Carlos Hermosilla
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Anja Taubert
- Institute of Parasitology, Justus Liebig University, Giessen, Germany
| | - Tobias Eisenberg
- Department of Veterinary Medicine, Hessian State Laboratory (LHL), Giessen, Germany
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Kim SG, Giri SS, Yun S, Kim HJ, Kim SW, Kang JW, Han SJ, Kwon J, Jun JW, Oh WT, Park SC. Genomic characterization of bacteriophage pEt-SU, a novel phiKZ-related virus infecting Edwardsiella tarda. Arch Virol 2019; 165:219-222. [PMID: 31630274 DOI: 10.1007/s00705-019-04432-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/11/2019] [Indexed: 11/29/2022]
Abstract
A bacteriophage infecting Edwardsiella tarda (named pEt-SU) was isolated from freshwater collected in Chung-ju, South Korea. The whole genome of pEt-SU was 276,734 bp in length, representing the first giant phage infecting Edwardsiella reported to date. A total of 284 putative open reading frames were predicted and annotated. Morphology and genome analyses verified that pEt-SU may be distantly related to the phiKZ-like phages, a well-known giant myovirus. The findings in this study provide new insights into the phages infecting E. tarda ads well as fundamental data for the study of giant phages.
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Affiliation(s)
- Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Saekil Yun
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jung Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Se Jin Han
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, Republic of Korea
| | - Woo Taek Oh
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, 08826, Republic of Korea.
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