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De Luca E, Álvarez-Narváez S, Maboni G, Baptista RP, Nemeth NM, Niedringhaus KD, Ladner JT, Lorch JM, Koroleva G, Lovett S, Palacios GF, Sanchez S. Comparative Genomics Analyses Support the Reclassification of Bisgaard Taxon 40 as Mergibacter gen. nov., With Mergibacter septicus sp. nov. as Type Species: Novel Insights Into the Phylogeny and Virulence Factors of a Pasteurellaceae Family Member Associated With Mortality Events in Seabirds. Front Microbiol 2021; 12:667356. [PMID: 34880834 PMCID: PMC8645869 DOI: 10.3389/fmicb.2021.667356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022] Open
Abstract
The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA, ompH) and colonization (exbD, fur, galU, galE, lpxA, lpxC, and kdsA) of the host and a cytolethal distending toxin (cdt), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201T (=DSM 112696).
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Affiliation(s)
- Eliana De Luca
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Sonsiray Álvarez-Narváez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Grazieli Maboni
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Rodrigo P Baptista
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study, Departments of Pathology and Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Kevin D Niedringhaus
- Southeastern Cooperative Wildlife Disease Study, Departments of Pathology and Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Veterinary Medical Teaching Hospital, University of California, Davis, Davis, CA, United States
| | - Jason T Ladner
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States.,U.S. Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI, United States
| | - Galina Koroleva
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Sean Lovett
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Gustavo F Palacios
- Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases, Frederick, MD, United States
| | - Susan Sanchez
- Athens Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, United States.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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Sandmeier F, Leonard K, Tracy C, Drake K, Esque T, Nussear K, Germano J. Tools to understand seasonality in health: quantification of microbe loads and analyses of compositional ecoimmunological data reveal complex patterns in Mojave Desert Tortoise (Gopherus agassizii) populations. CAN J ZOOL 2019. [DOI: 10.1139/cjz-2018-0255] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using data from six wild Mojave Desert Tortoise (Gopherus agassizii (Cooper, 1861)) populations, we quantified seasonal differences in immune system measurements and microbial load in the respiratory tract, pertinent to this species’ susceptibility to upper respiratory tract disease. We quantified bacteria-killing activity of blood plasma and differential leukocyte counts to detect trends in temporal variation in immune function. We used centered log-ratio (clr) transformations of leukocyte counts and stress that such transformations are necessary for compositional data. We tested animals for the potential pathogen Pasteurella testudinis Snipes and Biberstein, 1982 with a newly created quantitative polymerase chain reaction (qPCR) assay, as well as for the known respiratory pathogens Mycoplasma agassizii Brown et al., 2001 and Mycoplasma testudineum Brown et al., 2004. We found very little disease and suggest that P. testudinis is a prevalent, commensal microbe in these Mojave Desert Tortoise populations, and its quantification may be a tool to study natural fluctuations in microbe levels in Mojave Desert Tortoise respiratory tracts. Our analyses showed that both the potential for inflammatory responses and microbe levels are highest in the spring for healthy Mojave Desert Tortoises, when lymphocyte levels are lowest. The genetic and statistical tools that we used are easily applicable to other wildlife systems and provide the necessary data to quantify species-wide trends in health and test hypotheses pertinent to host–microbe dynamics.
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Affiliation(s)
- F.C. Sandmeier
- Biology Department, Colorado State University–Pueblo, 2200 Bonforte Boulevard, Pueblo, CO 81001, USA
| | - K.L. Leonard
- Biology Department, Colorado State University–Pueblo, 2200 Bonforte Boulevard, Pueblo, CO 81001, USA
| | - C.R. Tracy
- Biology Department, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557, USA
| | - K.K. Drake
- U.S. Geological Survey, 160 North Stephanie Street, Henderson, NV 89074, USA
| | - T.E. Esque
- U.S. Geological Survey, 160 North Stephanie Street, Henderson, NV 89074, USA
| | - K. Nussear
- Geography Department, University of Nevada, Reno, 1664 North Virginia Street, Reno, NV 89557, USA
| | - J.M. Germano
- New Zealand Department of Conservation, 18 Manners Street, Wellington 6011, New Zealand
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3
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Weitzman CL, Sandmeier FC, Tracy CR. Host species, pathogens and disease associated with divergent nasal microbial communities in tortoises. ROYAL SOCIETY OPEN SCIENCE 2018; 5:181068. [PMID: 30473851 PMCID: PMC6227988 DOI: 10.1098/rsos.181068] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
Diverse bacterial communities are found on every surface of macro-organisms, and they play important roles in maintaining normal physiological functions in their hosts. While the study of microbiomes has expanded with the influx of data enabled by recent technological advances, microbiome research in reptiles lags behind other organisms. We sequenced the nasal microbiomes in a sample of four North American tortoise species, and we found differing community compositions among tortoise species and sampling sites, with higher richness and diversity in Texas and Sonoran desert tortoises. Using these data, we investigated the prevalence and operational taxonomic unit (OTU) diversity of the potential pathogen Pasteurella testudinis and found it to be common, abundant and highly diverse. However, the presence of this bacterium was not associated with differences in bacterial community composition within host species. We also found that the presence of nasal discharge from tortoises at the time of sampling was associated with a decline in diversity and a change in microbiome composition, which we posit is due to the harsh epithelial environment associated with immune responses. Repeated sampling across seasons, and at different points of pathogen colonization, should contribute to our understanding of the causes and consequences of different bacterial communities in these long-lived hosts.
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Affiliation(s)
- Chava L. Weitzman
- Department of Biology, University of Nevada, Reno, NV 89557, USA
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV 89557, USA
| | | | - C. Richard Tracy
- Department of Biology, University of Nevada, Reno, NV 89557, USA
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4
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Meng L, Li X, Wang X, Ma K, Liu G, Zhang J. Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system. J Environ Sci (China) 2017; 61:110-117. [PMID: 29191308 DOI: 10.1016/j.jes.2017.09.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 09/16/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
This study aimed to reveal how amoxicillin (AMX) affected the microbial community and the spread mechanism of antibiotic resistance genes (ARGs) in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed (EGSB) reactor was designed and run for 241days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA-1, OXA-2, OXA-10, TEM-1, CTX-M-1, class I integrons (intI1) and 16S rRNA genes were also examined in sludge samples. The results showed that the genera Ignavibacterium, Phocoenobacter, Spirochaeta, Aminobacterium and Cloacibacillus contributed to the degradation of different organic compounds (such as various sugars and amines). And the relative quantification of each β-lactam resistance gene in the study was changed with the increasing of AMX concentration. Furthermore the vertical gene transfer was the main driver for the spread of ARGs rather than horizontal transfer pathways in the system.
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Affiliation(s)
- Lingwei Meng
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Xiangkun Li
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
| | - Xinran Wang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Kaili Ma
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Gaige Liu
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Zhang
- School of Municipal and Environmental Engineering, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China
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5
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Yew WC, Pearce DA, Dunn MJ, Samah AA, Convey P. Bacterial community composition in Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarctica) Penguin stomach contents from Signy Island, South Orkney Islands. Polar Biol 2017. [DOI: 10.1007/s00300-017-2162-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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6
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Adhikary S, Nicklas W, Bisgaard M, Boot R, Kuhnert P, Waberschek T, Aalbæk B, Korczak B, Christensen H. Rodentibacter gen. nov. including Rodentibacter pneumotropicus comb. nov., Rodentibacter heylii sp. nov., Rodentibacter myodis sp. nov., Rodentibacter ratti sp. nov., Rodentibacter heidelbergensis sp. nov., Rodentibacter trehalosifermentans sp. nov., Rodentibacter rarus sp. nov., Rodentibacter mrazii and two genomospecies. Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001866] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sadhana Adhikary
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, Viby Sjælland, Denmark
| | - Ron Boot
- Mr. Tripkade 51, 3571 SW, Utrecht, The Netherlands
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Torsten Waberschek
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Bent Aalbæk
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Bozena Korczak
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Henrik Christensen
- Department of Veterinary Disease Biology, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
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7
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Heidemann Olsen R, Bisgaard M, Christensen JP, Kabell S, Christensen H. Pathology and Molecular Characterization of Escherichia Coli Associated With the Avian Salpingitis-Peritonitis Disease Syndrome. Avian Dis 2016; 60:1-7. [PMID: 26953937 DOI: 10.1637/11237-071715-reg.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Outbreaks of salpingitis and peritonitis cause major economic losses due to high mortality, reduced egg-production, and culling. The aim of the present study was to characterize, in detail, lesions associated with increased mortality in layers due to avianpathogenic Escherichia coli (APEC) and to investigate the population structure of the E. coli involved, which is important for selection of optimal treatment and prophylactic strategies. Among 322 layers received from eight farms with increased mortality due to E. coli, three lesion types were observed; sepsis-like lesions, chronic salpingitis and peritonitis, and chronic salpingitis and peritonitis associated with sepsis-like lesions. One hundred isolates of E. coli obtained in pure culture from the different lesion types were selected for genetic characterization. Six out of 10 submissions (two farms with two submissions) were considered clonal as defined by more than 85% of the typed isolates of E. coli belonging to the same sequence-type (ST). B2 was the most-prevalent phylogroup, including the clonal complex of ST95. The most-important virulence genes of E. coli were demonstrated from both clonal and nonclonal outbreaks, and major differences as to phylogeny and virulence genes were not observed between the lesion types. Cannibalism was more-often observed during polyclonal outbreaks. A new pathotype of APEC is suggested based upon lesions and route of infection, high similarity of virulence genes including plasmid-associated genes, and high frequency of ST95 and other isolates belonging to phylogroup B2. Compared to the best-known pathotypes of E. coli, this needs further investigations, including infection experiments to show if single virulence factors can be pointed out that are specific for the salpingitis-peritonitis pathotype and possibly not found in other pathotypes of E. coli.
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Affiliation(s)
- Rikke Heidemann Olsen
- A University of Copenhagen, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Stigbøjen 4, DK-1870 Frederiksberg C, Denmark
| | | | - Jens Peter Christensen
- A University of Copenhagen, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Stigbøjen 4, DK-1870 Frederiksberg C, Denmark
| | - Susanne Kabell
- C Knowledge Centre for Agriculture, Agro Food Park 15, DK-8200 Aarhus N, Denmark
| | - Henrik Christensen
- A University of Copenhagen, Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Stigbøjen 4, DK-1870 Frederiksberg C, Denmark
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8
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Testudinibacter aquarius gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of freshwater turtles. Int J Syst Evol Microbiol 2016; 66:567-573. [DOI: 10.1099/ijsem.0.000759] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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9
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Nicklas W, Bisgaard M, Aalbæk B, Kuhnert P, Christensen H. Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov. Int J Syst Evol Microbiol 2015; 65:3344-3351. [DOI: 10.1099/ijsem.0.000417] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).
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Affiliation(s)
- Werner Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - Magne Bisgaard
- Professor emeritus, Horsevænget 40, DK-4130 Viby Sjælland, Denmark
| | - Bent Aalbæk
- Department of Veterinary Disease Biology, VetSchool, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Laenggass-Strasse 122, CH-3001 Bern, Switzerland
| | - Henrik Christensen
- Department of Veterinary Disease Biology, VetSchool, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
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Johanne Hansen M, Strøm Braaten M, Miki Bojesen A, Christensen H, Sonne C, Dietz R, Frost Bertelsen M. Ursidibacter maritimus gen. nov., sp. nov. and Ursidibacter arcticus sp. nov., two new members of the family Pasteurellaceae isolated from the oral cavity of bears. Int J Syst Evol Microbiol 2015. [DOI: 10.1099/ijsem.0.000476] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirty-three suspected strains of the family Pasteurellaceae isolated from the oral cavity of polar and brown bears were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA gene and rpoB sequences showed that the investigated isolates formed two closely related monophyletic groups, representing two novel species of a new genus. Based on 16S rRNA gene sequence comparison Bibersteinia trehalosi was the closest related species with a validly published name, with 95.4 % similarity to the polar bear group and 94.4 % similarity to the brown bear group. Otariodibacter oris was the closest related species based on rpoB sequence comparison with a similarity of 89.8 % with the polar bear group and 90 % with the brown bear group. The new genus could be separated from existing genera of the family Pasteurellaceae by three to ten phenotypic characters, and the two novel species could be separated from each other by two phenotypic characters. It is proposed that the strains should be classified as representatives of a new genus, Ursidibacter gen. nov., with two novel species: the type species Ursidibacter maritimus sp. nov., isolated from polar bears (type strain Pb43106T = CCUG 65144T = DSM 28137T, DNA G+C content 39.3 mol%), and Ursidibacter arcticus sp. nov., isolated from brown bears (type strain Bamse61T = CCUG 65145T = DSM 28138T).
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Affiliation(s)
- Mie Johanne Hansen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Mira Strøm Braaten
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
| | - Anders Miki Bojesen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Henrik Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
| | - Christian Sonne
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Faculty of Science and Technology, Arctic Research Centre, Frederiksborgvej 399, PO Box 358, Aarhus University, 4000 Roskilde, Denmark
| | - Mads Frost Bertelsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigboejlen 4, 1870 Frederiksberg C, Denmark
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark
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Draft Genome Sequence of Chelonobacter oris Strain 1662T, Associated with Respiratory Disease in Hermann's Tortoises. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01322-14. [PMID: 25523777 PMCID: PMC4271167 DOI: 10.1128/genomea.01322-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chelonobacter oris 1662T is a type strain of the recently described species of the Pasteurellaceae family. The strain was isolated from the choanae of a captive tortoise with signs of respiratory tract infection. The genome reported here is approximately 2.6 Mb in size and has a G+C content of 47.1%.
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12
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Christensen H, Nicklas W, Bisgaard M. Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov. Int J Syst Evol Microbiol 2014; 64:3636-3643. [DOI: 10.1099/ijs.0.067470-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause’s groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family
Pasteurellaceae
. The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family
Pasteurellaceae
. Partial rpoB sequencing as well as published data on DNA–DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family
Pasteurellaceae
. A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0. The two genera are clearly separated by phenotype from each other and from existing genera of the family
Pasteurellaceae
. The type strain of Mesocricetibacter intestinalis is HIM 933/7T ( = Kunstyr 246/85T = CCUG 28030T = DSM 28403T) while the type strain of Cricetibacter osteomyelitidis is HIM943/7T ( = Kunstyr 507/85T = CCUG 36451T = DSM 28404T).
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Affiliation(s)
- H. Christensen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, 4 Stigbøjlen, DK-1870 Frederiksberg C, Denmark
| | - W. Nicklas
- Microbiological Diagnostics, German Cancer Research Centre, D-69120 Heidelberg, Germany
| | - M. Bisgaard
- Horsevænget 40, DK-4130 Viby Sjælland, Denmark
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Mühldorfer K, Speck S, Wibbelt G. Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats. Int J Syst Evol Microbiol 2014; 64:2424-2430. [PMID: 24776530 DOI: 10.1099/ijs.0.062786-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae. Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3-99.9%) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96% sequence similarity to known members of the Pasteurellaceae. The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6-100% sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8-96% similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08(T) is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08(T) ( = CCUG 64585(T) = DSM 27238(T)). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.
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Affiliation(s)
- Kristin Mühldorfer
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stephanie Speck
- Institute for Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Gudrun Wibbelt
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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Korczak BM, Bisgaard M, Christensen H, Kuhnert P. Frederiksenia canicola gen. nov., sp. nov. isolated from dogs and human dog-bite wounds. Antonie van Leeuwenhoek 2014; 105:731-41. [DOI: 10.1007/s10482-014-0129-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 01/28/2014] [Indexed: 11/28/2022]
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Otariodibacter oris gen. nov., sp. nov., a member of the family
Pasteurellaceae
isolated from the oral cavity of pinnipeds. Int J Syst Evol Microbiol 2012; 62:2572-2578. [DOI: 10.1099/ijs.0.039586-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family
Pasteurellaceae
was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was
Bisgaardia hudsonensis
and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family
Pasteurellaceae
. Members of Bisgaard taxon 57 can be separated from existing genera of the
Pasteurellaceae
by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the
Pasteurellaceae
. The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the
Pasteurellaceae
. The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family
Pasteurellaceae
. On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.
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Kuhnert P, Bisgaard M, Korczak BM, Schwendener S, Christensen H, Frey J. Identification of animal Pasteurellaceae by MALDI-TOF mass spectrometry. J Microbiol Methods 2012; 89:1-7. [PMID: 22343217 DOI: 10.1016/j.mimet.2012.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 10/14/2022]
Abstract
Species of the family Pasteurellaceae play an important role as primary or opportunistic animal pathogens. In veterinary diagnostic laboratories identification of this group of bacteria is mainly done by phenotypic assays while genetic identification based on housekeeping genes is mostly used for research and particularly important diagnostic samples. MALDI-TOF MS seems to represent a promising alternative to the currently practiced cumbersome, phenotypic diagnostics carried out in many veterinary diagnostic laboratories. We therefore assessed its application for animal associated members of the family Pasteurellaceae. The Bruker Biotyper 3.0 database was complemented with reference spectra of clinically relevant as well as commensal animal Pasteurellaceae species using generally five strains per species or subspecies and tested for its diagnostic potential with additional, well characterized field isolates. About 250 strains comprising 15 genera and more than 40 species and subspecies were included in the study, covering most representatives of the family. A high discrimination at the genus and species level was observed. Problematic discrimination was only observed with some closely related species and subspecies. MALDI-TOF MS was shown to represent a highly potent method for the diagnosis of this group of animal pathogens, combining speed, precision and low running costs.
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Affiliation(s)
- Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
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Proposal of Bisgaardia hudsonensis gen. nov., sp. nov. and an additional genomospecies, isolated from seals, as new members of the family Pasteurellaceae. Int J Syst Evol Microbiol 2011; 61:3016-3022. [DOI: 10.1099/ijs.0.028027-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phenotypic and phylogenetic studies were performed on eight Gram-negative-staining, rod-shaped bacteria isolated from seals. Biochemical and physiological studies showed identical profiles for all of the isolates and indicated that they were related to the family Pasteurellaceae. 16S rRNA gene sequencing demonstrated that the organism represented a distinct cluster with two sublines within the family Pasteurellaceae with <96 % sequence similarity to any recognized species. Multilocus sequence analysis (MLSA) including rpoB, infB and recN genes further confirmed these findings with the eight isolates forming a genus-like cluster with two branches. Genome relatedness as deduced from recN gene sequences suggested that the isolates represented a new genus with two species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that these bacteria from seals are classified as Bisgaardia hudsonensis gen. nov., sp. nov. (the type species) and Bisgaardia genomospecies 1. The G+C content of the DNA was 39.5 mol%. The type strain of Bisgaardia hudsonensis gen. nov., sp. nov. is M327/99/2T ( = CCUG 43067T = NCTC 13475T = 98-D-690BT) and the reference strain of Bisgaardia genomospecies 1 is M1765/96/5 ( = CCUG 59551 = NCTC 13474).
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Janda WM. Update on Family Pasteurellaceae and the Status of Genus Pasteurella and Genus Actinobacillus. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.clinmicnews.2011.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Classification of organisms previously reported as the SP and Stewart–Letscher groups, with descriptions of Necropsobacter gen. nov. and of Necropsobacter rosorum sp. nov. for organisms of the SP group. Int J Syst Evol Microbiol 2011; 61:1829-1836. [DOI: 10.1099/ijs.0.024174-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To allow classification of bacteria previously reported as the SP group and the Stewart–Letscher group, 35 isolates from rodents (21), rabbits (eight), a dog and humans (five) were phenotypically and genotypically characterized. Comparison of partial rpoB sequences showed that 34 of the isolates were closely related, demonstrating at least 97.4 % similarity. 16S rRNA gene sequence comparison of 20 selected isolates confirmed the monophyly of the SP group and revealed 98.5 %–100 % similarity between isolates. A blast search using the 16S rRNA gene sequences showed that the highest similarity outside the SP group was 95.5 % to an unclassified rat isolate. The single strain, P625, representing the Stewart–Letscher group showed the highest 16S rRNA gene similarity (94.9–95.5 %) to members of the SP group. recN gene sequence analysis of 11 representative strains resulted in similarities of 97–100 % among the SP group strains, which showed 80 % sequence similarity to the Stewart–Letscher group strain. Sequence similarity values based on the recN gene, indicative for whole genome similarity, showed the SP group being clearly separated from established genera, whereas the Stewart–Letscher group strain was associated with the SP group. A new genus, Necropsobacter gen. nov., with only one species, Necropsobacter rosorum sp. nov., is proposed to include all members of the SP group. The new genus can be separated from existing genera of the family Pasteurellaceae by at least three phenotypic characters. The most characteristic properties of the new genus are that haemolysis is not observed on bovine blood agar, positive reactions are observed in the porphyrin test, acid is produced from (+)-l-arabinose, (+)-d-xylose, dulcitol, (+)-d-galactose, (+)-d-mannose, maltose and melibiose, and negative reactions are observed for symbiotic growth, urease, ornithine decarboxylase and indole. Previous publications have documented that both ubiquinones and demethylmenaquinone were produced by the proposed type strain of the new genus, Michel A/76T, and that the major polyamine of representative strains (type strain not included) of the genus is 1,3-diaminopropane, spermidine is present in moderate amounts and putrescine and spermine are detectable only in minor amounts. The major fatty acids of strain Michel A/76T are C14 : 0, C16 : 0, C16:1ω7c and summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is typical for members of the family Pasteurellaceae. The G+C content of DNA of strain Michel A/76T was estimated to be 52.5 mol% in a previous investigation. The type strain is P709T ( = Michel A/76T = CCUG 28028T = CIP 110147T = CCM 7802T).
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