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Methodological tools to study species of the genus Burkholderia. Appl Microbiol Biotechnol 2021; 105:9019-9034. [PMID: 34755214 PMCID: PMC8578011 DOI: 10.1007/s00253-021-11667-3] [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: 09/13/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022]
Abstract
Bacteria belonging to the Burkholderia genus are extremely versatile and diverse. They can be environmental isolates, opportunistic pathogens in cystic fibrosis, immunocompromised or chronic granulomatous disease patients, or cause disease in healthy people (e.g., Burkholderia pseudomallei) or animals (as in the case of Burkholderia mallei). Since the genus was separated from the Pseudomonas one in the 1990s, the methodological tools to study and characterize these bacteria are evolving fast. Here we reviewed the techniques used in the last few years to update the taxonomy of the genus, to study gene functions and regulations, to deepen the knowledge on the drug resistance which characterizes these bacteria, and to elucidate their mechanisms to establish infections. The availability of these tools significantly impacts the quality of research on Burkholderia and the choice of the most appropriated is fundamental for a precise characterization of the species of interest. Key points • Updated techniques to study the genus Burkholderia were reviewed. • Taxonomy, genomics, assays, and animal models were described. • A comprehensive overview on recent advances in Burkholderia studies was made.
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You M, Fang S, MacDonald J, Xu J, Yuan ZC. Isolation and characterization of Burkholderia cenocepacia CR318, a phosphate solubilizing bacterium promoting corn growth. Microbiol Res 2019; 233:126395. [PMID: 31865096 DOI: 10.1016/j.micres.2019.126395] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/06/2019] [Accepted: 12/13/2019] [Indexed: 12/20/2022]
Abstract
Plant-growth promoting rhizobacteria benefit crop health and growth through various mechanisms including phosphate and potassium solubilisation, and antimicrobial activity. Previously, we sequenced the genome of bacterial strain Burkholderia cenocepacia CR318, which was isolated from the roots of the starch corn (Zea mays L.) in London, Ontario, Canada. In this work, the species identity of this isolate is confirmed by recA phylogeny and in silico DNA-DNA hybridization (isDDH), and its plant-growth promoting characteristics are described. B. cenocepacia CR318 exhibited strong activity of inorganic phosphate and potassium solubilization. It significantly promoted the growth of corn plants and roots by solubilizing inorganic tricalcium phosphate under greenhouse conditions. Functional analysis of the complete B. cenocepacia CR318 genome revealed genes associated with phosphate metabolism such as pstSCAB encoding a high affinity inorganic phosphate-specific transporter, and the pqqABCDE gene cluster involved in the biosynthesis of pyrroloquinoline quinone (PQQ), which is a required cofactor for quinoprotein glucose dehydrogenase (Gdh). However, it appears that B. cenocepacia CR318 lacks the quinoprotein Gdh which can produce gluconic acid to solubilize inorganic phosphate. Overall, these findings provide an important step in understanding the molecular mechanisms underlying the plant growth promotion trait of B. cenocepacia CR318.
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Affiliation(s)
- Man You
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada; Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Shumei Fang
- Life Science and Technology College, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang, 163319, China
| | - Jacqueline MacDonald
- Department of Microbiology and Immunology, University of Western Ontario, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada; Department of Microbiology and Immunology, University of Western Ontario, Canada.
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Chewapreecha C, Mather AE, Harris SR, Hunt M, Holden MTG, Chaichana C, Wuthiekanun V, Dougan G, Day NPJ, Limmathurotsakul D, Parkhill J, Peacock SJ. Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei. Commun Biol 2019; 2:428. [PMID: 31799430 PMCID: PMC6874650 DOI: 10.1038/s42003-019-0678-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
The environmental bacterium Burkholderia pseudomallei causes melioidosis, an important endemic human disease in tropical and sub-tropical countries. This bacterium occupies broad ecological niches including soil, contaminated water, single-cell microbes, plants and infection in a range of animal species. Here, we performed genome-wide association studies for genetic determinants of environmental and human adaptation using a combined dataset of 1,010 whole genome sequences of B. pseudomallei from Northeast Thailand and Australia, representing two major disease hotspots. With these data, we identified 47 genes from 26 distinct loci associated with clinical or environmental isolates from Thailand and replicated 12 genes in an independent Australian cohort. We next outlined the selective pressures on the genetic loci (dN/dS) and the frequency at which they had been gained or lost throughout their evolutionary history, reflecting the bacterial adaptability to a wide range of ecological niches. Finally, we highlighted loci likely implicated in human disease.
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Affiliation(s)
- Claire Chewapreecha
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Bioinformatics and Systems Biology Program, School of Bioresource and Technology, King Mongkut’s University of Technology Thonburi, Bangkok, 10150 Thailand
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich, NR4 7UQ UK
- Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ UK
| | | | - Martin Hunt
- Wellcome Sanger Institute, Hinxton, CB10 1SA UK
| | | | - Chutima Chaichana
- Department of Mathematics, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok, 10140 Thailand
| | - Vanaporn Wuthiekanun
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
| | - Nicholas P. J. Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Direk Limmathurotsakul
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400 Thailand
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES UK
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ UK
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Lung Diseases: Chronic Respiratory Infections. Int J Mol Sci 2018; 19:ijms19103051. [PMID: 30301242 PMCID: PMC6213170 DOI: 10.3390/ijms19103051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
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Rossi E, Paroni M, Landini P. Biofilm and motility in response to environmental and host-related signals in Gram negative opportunistic pathogens. J Appl Microbiol 2018; 125:1587-1602. [PMID: 30153375 DOI: 10.1111/jam.14089] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/30/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022]
Abstract
Most bacteria can switch between a planktonic, sometimes motile, form and a biofilm mode, in which bacterial cells can aggregate and attach to a solid surface. The transition between these two forms represents an example of bacterial adaptation to environmental signals and stresses. In 'environmental pathogens', namely, environmental bacteria that are also able to cause disease in animals and humans, signals associated either with the host or with the external environment, such as temperature, oxygen availability, nutrient concentrations etc., play a major role in triggering the switch between the motile and the biofilm mode, via complex regulatory mechanisms that control flagellar synthesis and motility, and production of adhesion factors. In this review article, we present examples of how environmental signals can impact biofilm formation and cell motility in the Gram negative bacteria Pseudomonas aeruginosa, Escherichia coli and in the Burkholderia genus, and how the switch between motile and biofilm mode can be an essential part of a more general process of adaptation either to the host or to the external environment.
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Affiliation(s)
- E Rossi
- Department of Clinical Microbiology, Rigshospitalet, København, Denmark
| | - M Paroni
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - P Landini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
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McCarron A, Donnelley M, Parsons D. Airway disease phenotypes in animal models of cystic fibrosis. Respir Res 2018; 19:54. [PMID: 29609604 PMCID: PMC5879563 DOI: 10.1186/s12931-018-0750-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/13/2018] [Indexed: 12/20/2022] Open
Abstract
In humans, cystic fibrosis (CF) lung disease is characterised by chronic infection, inflammation, airway remodelling, and mucus obstruction. A lack of pulmonary manifestations in CF mouse models has hindered investigations of airway disease pathogenesis, as well as the development and testing of potential therapeutics. However, recently generated CF animal models including rat, ferret and pig models demonstrate a range of well characterised lung disease phenotypes with varying degrees of severity. This review discusses the airway phenotypes of currently available CF animal models and presents potential applications of each model in airway-related CF research.
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Affiliation(s)
- Alexandra McCarron
- Adelaide Medical School, Discipline of Paediatrics, University of Adelaide, Adelaide, SA, Australia. .,Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, SA, Australia. .,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia.
| | - Martin Donnelley
- Adelaide Medical School, Discipline of Paediatrics, University of Adelaide, Adelaide, SA, Australia.,Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - David Parsons
- Adelaide Medical School, Discipline of Paediatrics, University of Adelaide, Adelaide, SA, Australia.,Department of Respiratory and Sleep Medicine, Women's and Children's Hospital, Adelaide, SA, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
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Bodilis J, Denet E, Brothier E, Graindorge A, Favre-Bonté S, Nazaret S. Comparative Genomics of Environmental and Clinical Burkholderia cenocepacia Strains Closely Related to the Highly Transmissible Epidemic ET12 Lineage. Front Microbiol 2018; 9:383. [PMID: 29559964 PMCID: PMC5845691 DOI: 10.3389/fmicb.2018.00383] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 02/20/2018] [Indexed: 01/14/2023] Open
Abstract
The Burkholderia cenocepacia epidemic ET12 lineage belongs to the genomovar IIIA including the reference strain J2315, a highly transmissible epidemic B. cenocepacia lineage. Members of this lineage are able to cause lung infections in immunocompromised and cystic fibrosis patients. In this study, we describe the genome of F01, an environmental B. cenocepacia strain isolated from soil in Burkina Faso that is, to our knowledge, the most closely related strain to this epidemic lineage. A comparative genomic analysis was performed on this new isolate, in association with five clinical and one environmental B. cenocepacia strains whose genomes were previously sequenced. Antibiotic resistances, virulence phenotype, and genomic contents were compared and discussed with an emphasis on virulent and antibiotic determinants. Surprisingly, no significant differences in antibiotic resistance and virulence were found between clinical and environmental strains, while the most important genomic differences were related to the number of prophages identified in their genomes. The ET12 lineage strains showed a noticeable greater number of prophages (partial or full-length), especially compared to the phylogenetically related environmental F01 strain (i.e., 5–6 and 3 prophages, respectively). Data obtained suggest possible involvements of prophages in the clinical success of opportunistic pathogens.
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Affiliation(s)
- Josselin Bodilis
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France.,EA 4312 Laboratoire de Microbiologie Signaux et Microenvironnement, Université de Rouen, Mont-Saint-Aignan, France
| | - Elodie Denet
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France
| | - Elisabeth Brothier
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France
| | - Arnault Graindorge
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France
| | - Sabine Favre-Bonté
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France
| | - Sylvie Nazaret
- Research Group on Environmental Multi-Resistance and Efflux Pump, INRA 1418, UMR CNRS 5557, Laboratoire Ecologie Microbienne, Ecole Nationale Vétérinaire de Lyon, Université de Lyon 1, Villeurbanne, France
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