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Almuzara M, Cittadini R, Traglia G, Haim MS, De Belder D, Alvarez C, de Lourdes Reynal O'Connor Z, Ocampo CV, Barberis C, Prieto M, Campos J, Vay C. Phytobacter spp: the emergence of a new genus of healthcare-associated Enterobacterales encoding carbapenemases in Argentina: a case series. Infect Prev Pract 2024; 6:100379. [PMID: 39006243 PMCID: PMC11245914 DOI: 10.1016/j.infpip.2024.100379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/02/2024] [Indexed: 07/16/2024] Open
Abstract
Members of the genus Phytobacter (order Enterobacterales) are isolated from the natural environment and clinical settings. Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories. In this study we describe the first three clinical cases associated with Phytobacter spp. reported in Argentina. We describe the identification, the molecular analysis using whole genome sequencing and the potential clinical relevance.
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Affiliation(s)
- Marisa Almuzara
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | | | - Germán Traglia
- Unidad de Genómica y Bioinformática, Departamento de Ciencias Biológicas, CENUR Salto, Universidad de La República, Uruguay
| | - María Sol Haim
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Denise De Belder
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Carla Alvarez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | | | | | - Claudia Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
| | - Mónica Prieto
- Laboratorio de Bacteriología Especial, ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Josefina Campos
- Unidad Operativa Centro Nacional de Genómica y Bioinformática ANLIS "Dr Carlos G. Malbrán", CABA, Argentina
| | - Carlos Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Bioquímica Clínica, Cátedra Microbiología Clínica, Hospital de Clínicas “José de San Martín”, CABA, Argentina
- Sanatorio Mater Dei, CABA, Argentina
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2
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Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R, Kvitko BH, Smits THM, Venter SN, Coutinho TA, Heath LS, Palmer M, Vinatzer BA. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999. [PMID: 38029109 PMCID: PMC10665919 DOI: 10.3389/fmicb.2023.1254999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
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Affiliation(s)
- Katherine C. Crosby
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mariah Rojas
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Theo H. M. Smits
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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3
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Susanto M, Dunning J, Chew R. Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review. Clin Case Rep 2023; 11:e7351. [PMID: 37215972 PMCID: PMC10196424 DOI: 10.1002/ccr3.7351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/11/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.
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Affiliation(s)
- Maja Susanto
- Infectious Diseases UnitRedcliffe HospitalRedcliffeQueenslandAustralia
| | - Jacki Dunning
- Department of SurgeryAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
| | - Rusheng Chew
- Infectious Diseases UnitAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
- Centre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
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4
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Smits THM, Arend LNVS, Cardew S, Tång-Hallbäck E, Mira MT, Moore ERB, Sampaio JLM, Rezzonico F, Pillonetto M. Resolving taxonomic confusion: establishing the genus Phytobacter on the list of clinically relevant Enterobacteriaceae. Eur J Clin Microbiol Infect Dis 2022; 41:547-558. [PMID: 35169969 PMCID: PMC8934334 DOI: 10.1007/s10096-022-04413-8] [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: 11/02/2021] [Accepted: 01/25/2022] [Indexed: 11/30/2022]
Abstract
Although many clinically significant strains belonging to the family Enterobacteriaceae fall into a restricted number of genera and species, there is still a substantial number of isolates that elude this classification and for which proper identification remains challenging. With the current improvements in the field of genomics, it is not only possible to generate high-quality data to accurately identify individual nosocomial isolates at the species level and understand their pathogenic potential but also to analyse retrospectively the genome sequence databases to identify past recurrences of a specific organism, particularly those originally published under an incorrect or outdated taxonomy. We propose a general use of this approach to classify further clinically relevant taxa, i.e., Phytobacter spp., that have so far gone unrecognised due to unsatisfactory identification procedures in clinical diagnostics. Here, we present a genomics and literature-based approach to establish the importance of the genus Phytobacter as a clinically relevant member of the Enterobacteriaceae family.
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Affiliation(s)
- Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.
| | - Lavinia N V S Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil
| | - Sofia Cardew
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Erika Tång-Hallbäck
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil
| | - Edward R B Moore
- Culture Collection University of Gothenburg (CCUG), Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.,Department of Infectious Disease, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jorge L M Sampaio
- Faculdade de Ciências Farmacêuticas - University of São Paulo and Fleury Medicina Diagnóstica, São Paulo, SP, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo Pillonetto
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, PR, Brazil. .,Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, PR, Brazil.
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Molecular Network and Culture Media Variation Reveal a Complex Metabolic Profile in Pantoea cf. eucrina D2 Associated with an Acidified Marine Sponge. Int J Mol Sci 2020; 21:ijms21176307. [PMID: 32878176 PMCID: PMC7504411 DOI: 10.3390/ijms21176307] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 01/07/2023] Open
Abstract
The Gram-negative Pantoea eucrina D2 was isolated from the marine sponge Chondrosia reniformis. Sponges were collected in a shallow volcanic vents system in Ischia island (South Italy), influenced by CO2 emissions and lowered pH. The chemical diversity of the secondary metabolites produced by this strain, under different culture conditions, was explored by a combined approach including molecular networking, pure compound isolation and NMR spectroscopy. The metabolome of Pantoea cf. eucrina D2 yielded a very complex molecular network, allowing the annotation of several metabolites, among them two biosurfactant clusters: lipoamino acids and surfactins. The production of each class of metabolites was highly dependent on the culture conditions, in particular, the production of unusual surfactins derivatives was reported for the first time from this genus; interestingly the production of these metabolites only arises by utilizing inorganic nitrogen as a sole nitrogen source. Major components of the extract obtained under standard medium culture conditions were isolated and identified as N-lipoamino acids by a combination of 1D and 2D NMR spectroscopy and HRESI-MS analysis. Assessment of the antimicrobial activity of the pure compounds towards some human pathogens, indicated a moderate activity of leucine containing N-lipoamino acids towards Staphylococcus aureus, Staphylococcus epidermidis and a clinical isolate of the emerging food pathogen Listeria monocytogenes.
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Soutar CD, Stavrinides J. Molecular validation of clinical Pantoea isolates identified by MALDI-TOF. PLoS One 2019; 14:e0224731. [PMID: 31682625 PMCID: PMC6827907 DOI: 10.1371/journal.pone.0224731] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/20/2019] [Indexed: 12/13/2022] Open
Abstract
The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.
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Affiliation(s)
- Craig D. Soutar
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- * E-mail:
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7
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Pillonetto M, Arend L, Gomes SMT, Oliveira MAA, Timm LN, Martins AF, Barth AL, Mazzetti A, Hersemann L, Smits THM, Mira MT, Rezzonico F. Molecular investigation of isolates from a multistate polymicrobial outbreak associated with contaminated total parenteral nutrition in Brazil. BMC Infect Dis 2018; 18:397. [PMID: 30103698 PMCID: PMC6090600 DOI: 10.1186/s12879-018-3287-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 07/31/2018] [Indexed: 12/14/2022] Open
Abstract
Background Between November 2013 and June 2014, 56 cases of bacteremia (15 deaths) associated with the use of Total Parenteral Nutrition (TPN) and/or calcium gluconate (CG) were reported in four Brazilian states. Methods We analyzed 73 bacterial isolates from four states: 45 from blood, 25 from TPN and three from CG, originally identified as Acinetobacter baumannii, Rhizobium radiobacter, Pantoea sp. or Enterobacteriaceae using molecular methods. Results The first two bacterial species were confirmed while the third group of species could not be identified using standard identification protocols. These isolates were subsequently identified by Multi-Locus Sequence Analysis as Phytobacter diazotrophicus, a species related to strains from similar outbreaks in the United States in the 1970’s. Within each species, TPN and blood isolates proved to be clonal, whereas the R. radiobacter isolates retrieved from CG were found to be unrelated. Conclusion This is the first report of a three-species outbreak caused by TPN contaminated with A. baumannii, R. radiobacter and P. diazotrophicus. The concomitant presence of clonal A. baumannii and P. diazotrophicus isolates in several TPN and blood samples, as well as the case of one patient, where all three different species were isolated simultaneously, suggest that the outbreak may be ascribed to a discrete contamination of TPN. In addition, this study highlights the clinical relevance of P. diazotrophicus, which has been involved in outbreaks in the past, but was often misidentified as P. agglomerans. Electronic supplementary material The online version of this article (10.1186/s12879-018-3287-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marcelo Pillonetto
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil. .,Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil.
| | - Lavinia Arend
- Central Public Health Laboratory - State of Paraná - LACEN/PR, Molecular Bacteriology Division, São José dos Pinhais, PR, Brazil
| | - Suzie M T Gomes
- Brazilian Health Surveillance Agency - ANVISA, Brasília, DF, Brazil
| | - Marluce A A Oliveira
- Ezequiel Dias Foundation, Central Public Health Laboratory - State of Minas Gerais, Bacteriology Division, Belo Horizonte, MG, Brazil
| | - Loeci N Timm
- Central Public Health Laboratory - State of Rio Grande do Sul, Bacteriology Division, Porto Alegre, RS, Brazil
| | - Andreza F Martins
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Afonso L Barth
- Research Laboratory on Bacterial Resistance (LABRESIS), Federal University of Rio Grande do Sul, Hospital de Clínicas, Porto Alegre, RS, Brazil
| | - Alana Mazzetti
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Lena Hersemann
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland.,Present Address: Scientific Computing Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, PR, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
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Pillonetto M, Arend LN, Faoro H, D'Espindula HRS, Blom J, Smits THM, Mira MT, Rezzonico F. Emended description of the genus Phytobacter, its type species Phytobacter diazotrophicus (Zhang 2008) and description of Phytobacter ursingii sp. nov. Int J Syst Evol Microbiol 2017; 68:176-184. [PMID: 29125457 DOI: 10.1099/ijsem.0.002477] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Phytobacter diazotrophicus and the associated genus Phytobacter were originally described by Zhanget al. [Arch Microbiol189 (2008), 431-439] on the basis of few endophytic nitrogen-fixing bacteria isolated from wild rice (Oryza rufipogon) in China. In this study, we demonstrate that a number of clinical isolates that were either described in the literature, preserved in culture collections, or obtained during a 2013 multi-state sepsis outbreak in Brazil also belong to the same genus. 16S rRNA gene sequencing, multilocus sequence analysis based on gyrB, rpoB, atpD and infB genes, as well as digital DNA-DNA hybridization support the existence of a second species within the genus Phytobacter. All isolates from the recent Brazilian outbreak, along with some older American clinical strains, were found to belong to the already described species Phytobacterdiazotrophicus, whereas three clinical strains retrieved in the USA over a time span of almost four decades, could be assigned to a new Phytobacter species. Implementation of an extended set of biochemical tests showed that the two Phytobacter species could phenotypically be discriminated from each other by the ability to utilize l-sorbose and d-serine. This feature was limited to the strains of the novel species described herein, for which the name Phytobacter ursingii sp. nov. is proposed, with ATCC 27989T (=CNCTC 5729T) as the designated type strain. An emended description of the species Phytobacter diazotrophicus and of the genus Phytobacter is also provided.
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Affiliation(s)
- Marcelo Pillonetto
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil.,Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | - Lavinia N Arend
- Molecular Bacteriology Division, Central Public Health Laboratory, State of Paraná, São José dos Pinhais-PR, Brazil
| | | | - Helena R S D'Espindula
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Marcelo T Mira
- Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba-PR, Brazil
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
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Rezzonico F, Smits THM, Born Y, Blom J, Frey JE, Goesmann A, Cleenwerck I, de Vos P, Bonaterra A, Duffy B, Montesinos E. Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. Int J Syst Evol Microbiol 2016; 66:1583-1592. [PMID: 26813696 DOI: 10.1099/ijsem.0.000920] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A survey to obtain potential antagonists of pome fruit tree diseases yielded two yellow epiphytic bacterial isolates morphologically similar to Pantoea agglomerans, but showing no biocontrol activity. Whole-cell MALDI-TOF mass spectrometry and analysis of 16S rRNA gene and gyrB sequences suggested the possibility of a novel species with a phylogenetic position in either the genus Pantoea or the genus Erwinia. Multi-locus sequence analysis (MLSA) placed the two strains in the genus Erwinia and supported their classification as a novel species. The strains showed general phenotypic characteristics typical of this genus and results of DNA-DNA hybridizations confirmed that they represent a single novel species. Both strains showed a DNA G+C content, as determined by HPLC, of 54.5 mol% and could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, potassium 2-ketogluconate, maltose, melibiose and raffinose. Whole-genome sequencing of strain EM595T revealed the presence of a chromosomal carotenoid biosynthesis gene cluster similar to those found in species of the genera Cronobacter and Pantoea that explains the pigmentation of the strain, which is atypical for the genus Erwinia. Additional strains belonging to the same species were recovered from different plant hosts in three different continents, revealing the cosmopolitan nature of this epiphyte. The name Erwinia gerundensis sp. nov. is proposed, with EM595T ( = LMG 28990T = CCOS 903T) as the designated type strain.
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Affiliation(s)
- Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland.,Department of Plant Protection and Extension Fruits and Vegetables, Institute for Plant Production Sciences, Agroscope, CH-8820 Wädenswil, Switzerland
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland.,Department of Plant Protection and Extension Fruits and Vegetables, Institute for Plant Production Sciences, Agroscope, CH-8820 Wädenswil, Switzerland
| | - Yannick Born
- Department of Plant Protection and Extension Fruits and Vegetables, Institute for Plant Production Sciences, Agroscope, CH-8820 Wädenswil, Switzerland
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, D-35390 Giessen, Germany
| | - Jürg E Frey
- Department of Diagnostics and Risk Assessment Plant Protection, Institute for Plant Production Sciences, Agroscope, CH-8820 Wädenswil, Switzerland
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität, D-35390 Giessen, Germany
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Paul de Vos
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Anna Bonaterra
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, E-17071 Girona, Spain
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), CH-8820 Wädenswil, Switzerland.,Department of Plant Protection and Extension Fruits and Vegetables, Institute for Plant Production Sciences, Agroscope, CH-8820 Wädenswil, Switzerland
| | - Emilio Montesinos
- Institute of Food and Agricultural Technology-CIDSAV-XaRTA, University of Girona, E-17071 Girona, Spain
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10
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Walterson AM, Stavrinides J. Pantoea:insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol Rev 2015; 39:968-84. [DOI: 10.1093/femsre/fuv027] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/31/2022] Open
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11
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Braun-Kiewnick A, Lehmann A, Rezzonico F, Wend C, Smits THM, Duffy B. Development of species-, strain- and antibiotic biosynthesis-specific quantitative PCR assays for Pantoea agglomerans as tools for biocontrol monitoring. J Microbiol Methods 2012; 90:315-20. [PMID: 22705381 DOI: 10.1016/j.mimet.2012.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/04/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
Pantoea agglomerans is a cosmopolitan plant epiphytic bacterium that includes some of the most effective biological antagonists against the fire blight pathogen Erwinia amylovora, a major threat to pome fruit production worldwide. Strain E325 is commercially available as Bloomtime Biological™ in the USA and Canada. New quantitative PCR (qPCR) assays were developed for species- and strain -specific detection in the environment, and for detection of indigenous strains carrying the biocontrol antibacterial peptide biosynthesis gene paaA. The qPCR assays were highly specific, efficient and sensitive, detecting fewer than three cells per reaction or 700 colony forming units per flower, respectively. The qPCR assays were tested on field samples, giving first indications to the incidence of P. agglomerans E325 related strains, total P. agglomerans and pantocin A producing bacteria in commercial orchards. These assays will facilitate monitoring the environmental behavior of biocontrol P. agglomerans after orchard application for disease protection, proprietary strain-tracking, and streamlined screening for discovery of new biocontrol strains.
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Affiliation(s)
- Andrea Braun-Kiewnick
- Agroscope Changins-Wädenswil ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland
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