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Capasso C, Supuran CT. Bacterial ι-CAs. Enzymes 2024; 55:121-142. [PMID: 39222989 DOI: 10.1016/bs.enz.2024.05.003] [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] [Indexed: 09/04/2024]
Abstract
Recent research has identified a novel class of carbonic anhydrases (CAs), designated ι-CA, predominantly found in marine diatoms, eukaryotic algae, cyanobacteria, bacteria, and archaea genomes. This class has garnered attention owing to its unique biochemical properties and evolutionary significance. Through bioinformatic analyses, LCIP63, a protein initially annotated with an unknown function, was identified as a potential ι-CA in the marine diatom Thalassiosira pseudonana. Subsequent biochemical characterization revealed that LCIP63 has CA activity and its preference for manganese ions over zinc, indicative of evolutionary adaptation to marine environments. Further exploration of bacterial ι-CAs, exemplified by Burkholderia territorii ι-CA (BteCAι), demonstrated catalytic efficiency and sensitivity to sulfonamide and inorganic anion inhibitors, the classical CA inhibitors (CAIs). The classification of ι-CAs into two variant types based on their sequences, distinguished by the COG4875 and COG4337 domains, marks a significant advancement in our understanding of these enzymes. Structural analyses of COG4337 ι-CAs from eukaryotic microalgae and cyanobacteria thereafter revealed a distinctive structural arrangement and a novel catalytic mechanism involving specific residues facilitating CO2 hydration in the absence of metal ion cofactors, deviating from canonical CA behavior. These findings underscore the biochemical diversity within the ι-CA class and highlight its potential as a target for novel antimicrobial agents. Overall, the elucidation of ι-CA properties and mechanisms advances our knowledge of carbon metabolism in diverse organisms and underscores the complexity of CA evolution and function.
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Affiliation(s)
- Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy.
| | - Claudiu T Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Firenze, italy
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2
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Guerrero-Egido G, Pintado A, Bretscher KM, Arias-Giraldo LM, Paulson JN, Spaink HP, Claessen D, Ramos C, Cazorla FM, Medema MH, Raaijmakers JM, Carrión VJ. bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria. Nat Commun 2024; 15:2072. [PMID: 38453959 PMCID: PMC10920822 DOI: 10.1038/s41467-024-46302-y] [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: 07/13/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.com/Carrion-lab/bacLIFE ) a streamlined computational workflow for genome annotation, large-scale comparative genomics, and prediction of lifestyle-associated genes (LAGs). As a proof of concept, we analyzed 16,846 genomes from the Burkholderia/Paraburkholderia and Pseudomonas genera, which led to the identification of hundreds of genes potentially associated with a plant pathogenic lifestyle. Site-directed mutagenesis of 14 of these predicted LAGs of unknown function, followed by plant bioassays, showed that 6 predicted LAGs are indeed involved in the phytopathogenic lifestyle of Burkholderia plantarii and Pseudomonas syringae pv. phaseolicola. These 6 LAGs encompassed a glycosyltransferase, extracellular binding proteins, homoserine dehydrogenases and hypothetical proteins. Collectively, our results highlight bacLIFE as an effective computational tool for prediction of LAGs and the generation of hypotheses for a better understanding of bacteria-host interactions.
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Affiliation(s)
- Guillermo Guerrero-Egido
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Adrian Pintado
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Kevin M Bretscher
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Luisa-Maria Arias-Giraldo
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, N-Power Medicine, Redwood City, CA, 94063, USA
| | - Herman P Spaink
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Dennis Claessen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Cayo Ramos
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
- Área de Genética, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
| | - Francisco M Cazorla
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain
| | - Marnix H Medema
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Víctor J Carrión
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Departamento de Microbiología, Facultad de Ciencias, Campus Universitario de Teatinos s/n, Universidad de Málaga, 29010, Málaga, Spain.
- Departamento de Protección de Cultivos, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Campus Universitario de Teatinos, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), 29010, Málaga, Spain.
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3
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Cacioppo M, De Zorzi R, Syrgiannis Z, Bellich B, Bertoncin P, Jou IA, Brady JW, Rizzo R, Cescutti P. Microscopy and modelling investigations on the morphology of the biofilm exopolysaccharide produced by Burkholderia multivorans strain C1576. Int J Biol Macromol 2023; 253:127294. [PMID: 37813217 PMCID: PMC10872726 DOI: 10.1016/j.ijbiomac.2023.127294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Bacteria form very often biofilms where they embed in a self-synthesized matrix exhibiting a gel-like appearance. Matrices offer several advantages, including defence against external threats and the easiness of intercellular communication. In infections, biofilm formation enhances bacteria resistance against antimicrobials, causing serious clinical problems for patients' treatments. Biofilm matrices are composed of proteins, extracellular DNA, and polysaccharides, the latter being the major responsible for matrix architecture. The repeating unit of the biofilm polysaccharide synthesized by Burkholderia multivorans strain C1576 contains two mannoses and two sequentially linked rhamnoses, one of them 50 % methylated on C-3. Rhamnose, a 6-deoxysugar, has lower polarity than other common monosaccharides and its methylation further reduces polarity. This suggests a possible role of this polysaccharide in the biofilm matrix; in fact, computer modelling and atomic force microscopy studies evidenced intra- and inter-molecular non-polar interactions both within polysaccharides and with aliphatic molecules. In this paper, the polysaccharide three-dimensional morphology was investigated using atomic force microscopy in both solid and solution states. Independent evidence of the polymer conformation was obtained by transmission electron microscopy which confirmed the formation of globular compact structures. Finally, data from computer dynamic simulations were used to model the three-dimensional structure.
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Affiliation(s)
- Michele Cacioppo
- Department of Chemical and Pharmaceutical Sciences, INSTM UdR Trieste, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, INSTM UdR Trieste, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Zois Syrgiannis
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Barbara Bellich
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Paolo Bertoncin
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Ining A Jou
- Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA
| | - John W Brady
- Food Science Department, Cornell University, 101A Stocking Hall, Ithaca, NY 14853, USA
| | - Roberto Rizzo
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy.
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4
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Hameed A, Nguyen DH, Lin SY, Stothard P, Neelakandan P, Young LS, Young CC. Hormesis of glyphosate on ferulic acid metabolism and antifungal volatile production in rice root biocontrol endophyte Burkholderia cepacia LS-044. CHEMOSPHERE 2023; 345:140511. [PMID: 37871874 DOI: 10.1016/j.chemosphere.2023.140511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/04/2023] [Accepted: 10/20/2023] [Indexed: 10/25/2023]
Abstract
Glyphosate (GP, N-phosphonomethyl glycine) is one of the most popular organophosphate herbicides widely used in agricultural practices worldwide. There have been extensive reports on the biohazard attributes and hormetic impacts of GP on plant and animal systems. However, the effects of GP on plant growth-promoting microbes and its ecological relevance remain unknown. Here, we show that GP does exert a hormetic impact on Burkholderia cepacia LS-044, a rice (Oryza sativa ssp. japonica cv. Tainung 71) root endophytic isolate. We used increasing doses of ferulic acid (FA, 1-25 mM) and GP (0.5-5 mM) to test the growth and antifungal volatile production in LS-044 by electrochemical, liquid chromatographic, gas chromatographic and spectrophotometric means. GP treatment at a low dose (0.5 mM) increased FA utilization and significantly (P < 0.0001) enhanced antifungal volatile activity in LS-044. Although FA (1 mM) was rapidly utilized by LS-044, no chromatographically detectable utilization of GP was observed at tested doses (0.5-5 mM). LS-044 emitted predominant amounts of tropone in addition to moderate-to-minor amounts of diverse ketones and/or their derivatives (acetone, acetophenone, 2-butanone, 1-propanone, 1-(2-furanyl-ethanone, 1-phenyl-1-propanone and 1-(3-pyridinyl)-1-propanone), d-menthol, 2-methoxy-3-(1-methylethyl)-pyrazine, dimethyl disulfide, pyridine and ammonium carbamate when grown under GP supplement. GP hormesis on LS-044 induced phenotypic variations in O. sativa ssp. japonica cv. Tainan 11 as evident through seed germination assay. Genes involved in the transformation of FA, and a key gene encoding 5-enolpyruvylshikimate 3-phosphate synthase (EPSPS) with Gly-94 and Tyr-95 residues localized at active site most likely rendering EPSPS sensitivity to GP, were detected in LS-044. This is the first report on the GP hormesis influencing morphological and metabolic aspects including volatile emission in a biocontrol bacterium that could modulate rice plant phenotype.
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Affiliation(s)
- Asif Hameed
- Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to be University), Deralakatte, Mangalore, 575018, India; Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Duc Hai Nguyen
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
| | - Shih-Yao Lin
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada
| | - Poovarasan Neelakandan
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan
| | - Li-Sen Young
- Tetanti AgriBiotech Inc. No. 1, Gongyequ 10th Rd., Xitun Dist., Taichung, 40755, Taiwan
| | - Chiu-Chung Young
- Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 402, Taiwan.
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5
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Bellich B, Terán LC, Fazli MM, Berti F, Rizzo R, Tolker-Nielsen T, Cescutti P. The Bep gene cluster in Burkholderia cenocepacia H111 codes for a water-insoluble exopolysaccharide essential for biofilm formation. Carbohydr Polym 2023; 301:120318. [PMID: 36436859 PMCID: PMC9713610 DOI: 10.1016/j.carbpol.2022.120318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/22/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Burkholderia cenocepacia is an opportunistic pathogen isolated from cystic fibrosis patients where it causes infections that are extremely difficult to treat with antibiotics, and sometimes have a fatal outcome. Biofilm is a virulence trait of B. cenocepacia, and is associated with infection persistence and increased tolerance to antibiotics. In biofilms exopolysaccharides have an important role, conferring mechanical stability and antibiotic tolerance. Two different exopolysaccharides were isolated from B. cenocepacia H111 biofilms: a water-soluble polysaccharide rich in rhamnose and containing an L-Man residue, and a water-insoluble polymer made of glucose, galactose and mannose. In the present work, the product encoded by B. cenocepacia H111 bepA-L gene cluster was identified as the water-insoluble exopolysaccharide, using mutant strains and NMR spectroscopy of the purified polysaccharides. It was also demonstrated that the B. cenocepacia H111 wild type strain produces the water-insoluble exopolysaccharide in pellicles, thus underlining its potential importance in in vivo infections.
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Affiliation(s)
- Barbara Bellich
- Department of Life Sciences, University of Trieste, via L. Giorgieri 1, Bdg. C11, 34127 Trieste, Italy
| | - Lucrecia C Terán
- Department of Life Sciences, University of Trieste, via L. Giorgieri 1, Bdg. C11, 34127 Trieste, Italy
| | - Magnus M Fazli
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | | | - Roberto Rizzo
- Department of Life Sciences, University of Trieste, via L. Giorgieri 1, Bdg. C11, 34127 Trieste, Italy
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Paola Cescutti
- Department of Life Sciences, University of Trieste, via L. Giorgieri 1, Bdg. C11, 34127 Trieste, Italy.
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Vidal JM, Fonseca A, Ruiz P, Sepúlveda D, Carrasco C, Scilipoti S, Barros J, Valenzuela A, Saavedra R, Ruiz-Tagle N, Urrutia H. Genomic features of Pseudomonas sp. RGM2144 correlates with increased survival of rainbow trout infected by Flavobacterium psychrophilum. JOURNAL OF FISH DISEASES 2023; 46:1-15. [PMID: 36130050 DOI: 10.1111/jfd.13713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/21/2022] [Accepted: 08/25/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the probiotic potential of the biofilm formed by the strain Pseudomonas sp. RGM2144 on rainbow trout survival. When challenged with the fish pathogen Flavobacterium psychrophilum, Pseudomonas sp. RGM2144 increased rainbow trout survival to 92.7 ± 1.2% (control: 35.3 ± 9.5%, p < .0001). The draft genome of Pseudomonas sp. RGM2144 is 6.8 Mbp long, with a completeness 100% and a contamination of 0.4%. The genome contains 6122 protein-coding genes of which 3564 (~60%) have known functions. The genome and phylogeny indicate that Pseudomonas sp. RGM2144 is a new species in the Pseudomonas genus, with few virulence factors, plasmids, and genes associated with antimicrobial resistance, suggesting a non-pathogenic bacterium with protective potential. In addition, the genome encodes for 11 secondary metabolite biosynthetic gene clusters that could be involved in the inhibition of F. psychrophilum. We suggest that Pseudomonas sp. RGM2144 may be applied as a probiotic in salmonid fish farming.
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Affiliation(s)
- José M Vidal
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
- Departamento de Investigación y Desarrollo, Ecombio limitada, Concepción, Chile
| | - Alexis Fonseca
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
- Laboratorio de Bentos, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Chile
- Center for Electromicrobiology, Department of Biology, Aarhus University, Denmark
| | - Pamela Ruiz
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andres Bello, Talcahuano, Chile
| | - Daniela Sepúlveda
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Carlos Carrasco
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | | | - Javier Barros
- Departamento de Investigación y Desarrollo, Concepción, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Ricardo Saavedra
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Nathaly Ruiz-Tagle
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Homero Urrutia
- Laboratorio de Biopelículas y Microbiología Ambiental, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
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Surface Motility Favors Codependent Interaction between Pseudomonas aeruginosa and Burkholderia cenocepacia. mSphere 2022; 7:e0015322. [PMID: 35862793 PMCID: PMC9429929 DOI: 10.1128/msphere.00153-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Interactions between different bacterial species shape bacterial communities and their environments. The opportunistic pathogens Pseudomonas aeruginosa and Burkholderia cenocepacia both can colonize the lungs of individuals affected by cystic fibrosis. Using the social surface behavior called swarming motility as a study model, we noticed intricate interactions between B. cenocepacia K56-2 and P. aeruginosa PA14. While strain K56-2 does not swarm under P. aeruginosa favorable swarming conditions, co-inoculation with a nonmotile PA14 flagellum-less ΔfliC mutant restored spreading for both strains. We show that P. aeruginosa provides the wetting agent rhamnolipids allowing K56-2 to perform swarming motility, while aflagellated PA14 appears to “hitchhike” along with K56-2 cells in the swarming colony. IMPORTANCEPseudomonas aeruginosa and Burkholderia cenocepacia are important opportunistic pathogens often found together in the airways of persons with cystic fibrosis. Laboratory cocultures of both species often ends with one taking over the other. We used a surface motility assay to study the social interactions between populations of these bacterial species. Under our conditions, B. cenocepacia cannot swarm without supplementation of the wetting agent produced by P. aeruginosa. In a mixed colony of both species, an aflagellated mutant of P. aeruginosa provides the necessary wetting agent to B. cenocepacia, allowing both bacteria to swarm and colonize a surface. We highlight this peculiar interaction where both bacteria set aside their antagonistic tendencies to travel together.
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De Luca V, Petreni A, Carginale V, Scaloni A, Supuran CT, Capasso C. Effect of amino acids and amines on the activity of the recombinant ι-carbonic anhydrase from the Gram-negative bacterium Burkholderia territorii. J Enzyme Inhib Med Chem 2021; 36:1000-1006. [PMID: 33980103 PMCID: PMC8128165 DOI: 10.1080/14756366.2021.1919891] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 01/10/2023] Open
Abstract
We here report a study on the activation of the ι-class bacterial CA from Burkholderia territorii (BteCAι). This protein was recently characterised as a zinc-dependent enzyme that shows a significant catalytic activity (kcat 3.0 × 105 s-1) for the physiological reaction of CO2 hydration to bicarbonate and protons. Some amino acids and amines, among which some proteinogenic derivatives as well as histamine, dopamine and serotonin, showed efficient activating properties towards BteCAι, with activation constants in the range 3.9-13.3 µM. L-Phe, L-Asn, L-Glu, and some pyridyl-alkylamines, showed a weaker activating effect towards BteCAι, with KA values ranging between 18.4 µM and 45.6 µM. Nowadays, no information is available on active site architecture, metal ion coordination and catalytic mechanism of members of the ι-group of CAs, and this study represents another contribution towards a better understanding of this still uncharacterised class of enzymes.
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Affiliation(s)
- Viviana De Luca
- Department of Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Polo Scientifico, Florence, Italy
- Proteomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, CNR, Naples, Italy
| | - Andrea Petreni
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Vincenzo Carginale
- Department of Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Polo Scientifico, Florence, Italy
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment, CNR, Naples, Italy
| | - Claudiu T. Supuran
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Clemente Capasso
- Department of Neurofarba, Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Polo Scientifico, Florence, Italy
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A Polyclonal Antibody Raised against the Burkholderia cenocepacia OmpA-like Protein BCAL2645 Impairs the Bacterium Adhesion and Invasion of Human Epithelial Cells In Vitro. Biomedicines 2021; 9:biomedicines9121788. [PMID: 34944603 PMCID: PMC8698911 DOI: 10.3390/biomedicines9121788] [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: 11/03/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
Respiratory infections by bacteria of the Burkholderia cepacia complex (Bcc) remain a life threat to cystic fibrosis (CF) patients, due to the faster lung function decline and the absence of effective eradication strategies. Immunotherapies are regarded as an attractive alternative to control and reduce the damages caused by these infections. In this work, we report the cloning and functional characterization of the OmpA-like BCAL2645 protein, previously identified and found to be immunoreactive against sera from CF patients with a record of Bcc infections. The BCAL2645 protein is shown to play a role in biofilm formation, adherence to mucins and invasion of human lung epithelial cells. The expression of the BCAL2645 protein was found to be increased in culture medium, mimicking the lungs of CF patients and microaerophilic conditions characteristic of the CF lung. Moreover, a polyclonal antibody raised against BCAL2645 was found to inhibit, by about 75 and 85%, the ability of B. cenocepacia K56-2 to bind and invade in vitro CFBE41o- human bronchial epithelial cells. These results highlight the potential of anti-BCAL2645 antibodies for the development of passive immunization therapies to protect CF patients against Bcc infections.
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Lauman P, Dennis JJ. Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex. Viruses 2021; 13:1331. [PMID: 34372537 PMCID: PMC8310193 DOI: 10.3390/v13071331] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 01/16/2023] Open
Abstract
The increasing prevalence and worldwide distribution of multidrug-resistant bacterial pathogens is an imminent danger to public health and threatens virtually all aspects of modern medicine. Particularly concerning, yet insufficiently addressed, are the members of the Burkholderia cepacia complex (Bcc), a group of at least twenty opportunistic, hospital-transmitted, and notoriously drug-resistant species, which infect and cause morbidity in patients who are immunocompromised and those afflicted with chronic illnesses, including cystic fibrosis (CF) and chronic granulomatous disease (CGD). One potential solution to the antimicrobial resistance crisis is phage therapy-the use of phages for the treatment of bacterial infections. Although phage therapy has a long and somewhat checkered history, an impressive volume of modern research has been amassed in the past decades to show that when applied through specific, scientifically supported treatment strategies, phage therapy is highly efficacious and is a promising avenue against drug-resistant and difficult-to-treat pathogens, such as the Bcc. In this review, we discuss the clinical significance of the Bcc, the advantages of phage therapy, and the theoretical and clinical advancements made in phage therapy in general over the past decades, and apply these concepts specifically to the nascent, but growing and rapidly developing, field of Bcc phage therapy.
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Affiliation(s)
| | - Jonathan J. Dennis
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada;
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11
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Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species. Microorganisms 2021; 9:microorganisms9061290. [PMID: 34204835 PMCID: PMC8231600 DOI: 10.3390/microorganisms9061290] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner-Doudoroff (ED), pentose-phosphate (PP), and lower Embden-Meyerhoff-Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.
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Burkholderia ubonensis High-Level Tetracycline Resistance Is Due to Efflux Pump Synergy Involving a Novel TetA(64) Resistance Determinant. Antimicrob Agents Chemother 2021; 65:AAC.01767-20. [PMID: 33318011 DOI: 10.1128/aac.01767-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Burkholderia ubonensis, a nonpathogenic soil bacterium belonging to the Burkholderia cepacia complex (Bcc), is highly resistant to some clinically significant antibiotics. The concern is that B. ubonensis may serve as a resistance reservoir for Bcc or B. pseudomallei complex (Bpc) organisms that are opportunistic human pathogens. Using a B. ubonensis strain highly resistant to tetracycline (MIC, ≥256 µg/ml), we identified and characterized tetA(64) that encodes a novel tetracycline-specific efflux pump of the major facilitator superfamily. TetA(64) and associated TetR(64) regulator expression are induced by tetracyclines. Although TetA(64) is the primary tetracycline and doxycycline resistance determinant, maximum tetracycline and doxycycline resistance requires synergy between TetA(64) and the nonspecific AmrAB-OprA resistance nodulation cell division efflux pump. TetA(64) does not efflux minocycline, tigecycline, and eravacycline. Comprehensive screening of genome sequences showed that TetA(64) is unequally distributed in the Bcc and absent from the Bpc. It is present in some major cystic fibrosis pathogens, like Burkholderia cenocepacia, but absent from others like Burkholderia multivorans The tetR(64)-tetA(64) genes are located in a region of chromosome 1 that is highly conserved in Burkholderia sp. Because there is no evidence for transposition, the tetR(64)-tetA(64) genes may have been acquired by homologous recombination after horizontal gene transfer. Although Burkholderia species contain a resident multicomponent efflux pump that allows them to respond to tetracyclines up to a certain concentration, the acquisition of the single-component TetA(64) by some species likely provides the synergy that these bacteria need to defend against high tetracycline concentrations in niche environments.
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13
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Gao ZH, Zhang QM, Lv YY, Wang YQ, Zhao BN, Qiu LH. Paraburkholderia acidiphila sp. nov., Paraburkholderia acidisoli sp. nov. and Burkholderia guangdongensis sp. nov., isolated from forest soil, and reclassification of Burkholderia ultramafica as Paraburkholderia ultramafica comb. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 33555242 DOI: 10.1099/ijsem.0.004690] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-negative, aerobic, motile and rod-shaped bacterial strains, 7Q-K02T, DHF22T and DHOM02T, were isolated from forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, China. Strains 7Q-K02T, DHF22T and DHOM02T grew at 4-37, 4-42 and 12-37 °C, pH 3.0-8.5, 3.5-8.5 and 5.0-8.0, and in the presence of 0-3.0, 0-3.5 and 0-2.5 % (w/v) NaCl; with optima at 28-33, 28 and 28-33 °C, pH 3.5-6.5, 4.0-5.5 and 6.5-7.0, and 0-1.5, 0-1.5 and 0.5-1.5 % (w/v) NaCl, respectively. Strains 7Q-K02T and DHF22T have the highest 16S rRNA gene sequence similarities of 99.0 and 98.0 % to Paraburkholderia sacchari LMG 19450T and 97.7 % between themselves, while strain DHOM02T shares the highest similarity of 98.4 % to 'Burkholderia rinojensis' A396T followed by 98.3 % to Burkholderia plantarii ATCC 43733T. In the 16S rRNA gene sequence phylogram, strain 7Q-K02T formed a sister branch with Paraburkholderia sacchari, Paraburkholderia oxyphila and Paraburkholderia paradisi, and strain DHF22T was separated from all other species within the genus Paraburkholderia, while strain DHOM02T formed a separated clade with members of the genus Burkholderia. The DNA G+C contents of strains 7Q-K02T, DHF22T and DHOM02T wwe 64.3, 65.4 and 66.6 %, respectively. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values of strains 7Q-K02T, DHF22T and closely related Paraburkholderia strains were in the ranges of 25.5-43.7 % and 81.5-91.3 %, respectively. While dDDH and ANI values between strain DHOM02T and Burkholderia strains with genome sequence data were in the ranges of 22.4-31.0 % and 78.2-86.1 %, respectively. These three strains have the same major respiratory quinone: ubiquinone-8. Strains 7Q-K02T, DHF22T and DHOM02T have C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c) as their major fatty acid compositions. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of phenotypic, phylogenetic, genomic analyses and chemotaxonomic data, strains 7Q-K02T and DHF22T represent two novel species of the genus Paraburkholderia, for which the names Paraburkholderia acidiphila sp. nov. (type strain 7Q-K02T=CGMCC 1.15433T=KCTC 62472T=LMG 29209T) and Paraburkholderia acidisoli sp. nov. (type strain DHF22T=GDMCC 1.1448T=LMG 30262T) are proposed, while strain DHOM02T represents a novel species in the genus Burkholderia, for which the name Burkholderia guangdongensis sp. nov. (type strain DHOM02T=KCTC 42625T=LMG 28843T) is proposed. We also propose to transfer Burkholderia ultramafica to the genus Paraburkholderia as Paraburkholderia ultramafica comb. nov. based mainly on the results of phylogenomic analysis.
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Affiliation(s)
- Zeng-Hong Gao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qiu-Mei Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Ying-Ying Lv
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - You-Qi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Bing-Nan Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Li-Hong Qiu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
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De Luca V, Petreni A, Nocentini A, Scaloni A, Supuran CT, Capasso C. Effect of Sulfonamides and Their Structurally Related Derivatives on the Activity of ι-Carbonic Anhydrase from Burkholderia territorii. Int J Mol Sci 2021; 22:ijms22020571. [PMID: 33430028 PMCID: PMC7827628 DOI: 10.3390/ijms22020571] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Carbonic anhydrases (CAs) are essential metalloenzymes in nature, catalyzing the carbon dioxide reversible hydration into bicarbonate and proton. In humans, breathing and many other critical physiological processes depend on this enzymatic activity. The CA superfamily function and inhibition in pathogenic bacteria has recently been the object of significant advances, being demonstrated to affect microbial survival/virulence. Targeting bacterial CAs may thus be a valid alternative to expand the pharmacological arsenal against the emergence of widespread antibiotic resistance. Here, we report an extensive study on the inhibition profile of the recently discovered ι-CA class present in some bacteria, including Burkholderia territorii, namely BteCAι, using substituted benzene-sulfonamides and clinically licensed sulfonamide-, sulfamate- and sulfamide-type drugs. The BteCAι inhibition profile showed: (i) several benzene-sulfonamides with an inhibition constant lower than 100 nM; (ii) a different behavior with respect to other α, β and γ-CAs; (iii) clinically used drugs having a micromolar affinity. This prototype study contributes to the initial recognition of compounds which efficiently and selectively inhibit a bacterial member of the ι-CA class, for which such a selective inhibition with respect to other protein isoforms present in the host is highly desired and may contribute to the development of novel antimicrobials.
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Affiliation(s)
- Viviana De Luca
- Institute of Biosciences and Bioresources, CNR, via Pietro Castellino 111, 80131 Napoli, Italy;
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, CNR, via Argine 1085, 80147 Napoli, Italy;
| | - Andrea Petreni
- Section of Pharmaceutical and Nutraceutical Sciences, Department of Neurofarba, University of Florence, via U. Schiff 6, 50019 Florence, Italy; (A.P.); (A.N.)
| | - Alessio Nocentini
- Section of Pharmaceutical and Nutraceutical Sciences, Department of Neurofarba, University of Florence, via U. Schiff 6, 50019 Florence, Italy; (A.P.); (A.N.)
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, CNR, via Argine 1085, 80147 Napoli, Italy;
| | - Claudiu T. Supuran
- Section of Pharmaceutical and Nutraceutical Sciences, Department of Neurofarba, University of Florence, via U. Schiff 6, 50019 Florence, Italy; (A.P.); (A.N.)
- Correspondence: (C.T.S.); (C.C.); Tel.: +39-055-4573729 (C.T.S.); +39-081-613-2559 (C.C.)
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, CNR, via Pietro Castellino 111, 80131 Napoli, Italy;
- Correspondence: (C.T.S.); (C.C.); Tel.: +39-055-4573729 (C.T.S.); +39-081-613-2559 (C.C.)
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15
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Wang G, Zarodkiewicz P, Valvano MA. Current Advances in Burkholderia Vaccines Development. Cells 2020; 9:E2671. [PMID: 33322641 PMCID: PMC7762980 DOI: 10.3390/cells9122671] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
The genus Burkholderia includes a wide range of Gram-negative bacterial species some of which are pathogenic to humans and other vertebrates. The most pathogenic species are Burkholderia mallei, Burkholderia pseudomallei, and the members of the Burkholderia cepacia complex (Bcc). B. mallei and B. pseudomallei, the cause of glanders and melioidosis, respectively, are considered potential bioweapons. The Bcc comprises a subset of Burkholderia species associated with respiratory infections in people with chronic granulomatous disease and cystic fibrosis. Antimicrobial treatment of Burkholderia infections is difficult due to the intrinsic multidrug antibiotic resistance of these bacteria; prophylactic vaccines provide an attractive alternative to counteract these infections. Although commercial vaccines against Burkholderia infections are still unavailable, substantial progress has been made over recent years in the development of vaccines against B. pseudomallei and B. mallei. This review critically discusses the current advances in vaccine development against B. mallei, B. pseudomallei, and the Bcc.
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Affiliation(s)
| | | | - Miguel A. Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast BT9 7BL, UK; (G.W.); (P.Z.)
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16
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Del Prete S, Nocentini A, Supuran CT, Capasso C. Bacterial ι-carbonic anhydrase: a new active class of carbonic anhydrase identified in the genome of the Gram-negative bacterium Burkholderia territorii. J Enzyme Inhib Med Chem 2020; 35:1060-1068. [PMID: 32314608 PMCID: PMC7191908 DOI: 10.1080/14756366.2020.1755852] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/05/2020] [Indexed: 01/30/2023] Open
Abstract
The carbonic anhydrases (CAs, EC 4.2.1.1) catalyse a simple but physiologically crucial reversible reaction, the carbon dioxide hydration with the production of bicarbonate and protons. In the last years, and especially, to the rapid emergence of the bacterial antibiotic resistance that is occurring worldwide, the understanding of the function of bacterial CAs has increased significantly. Recently, a new CA-class (ι-CA) was discovered in the marine diatom T. pseudonana. It has been reported that bacterial genomes may contain genes with relevant homology to the diatom ι-class CA. Still, the catalytic activity of the enzyme encoded by the gene was not investigated. Thus, herein, for the first time, we cloned, expressed, and purified the recombinant bacterial ι-CA (acronym BteCAι) identified in the genome of Burkholderia territorii. The recombinant BteCAι resulted in a good catalyst for the hydration of CO2 to bicarbonate and protons, with a kcat of 3.0 × 105 s -1 and kcat/KM of 3.9 × 107 M -1 s -1, and is also sensitive to inhibition by the sulphonamide acetazolamide. Furthermore, with the aid of the protonography, it has been demonstrated that BteCAι can be present as a dimer. This result is corroborated by the construction of a molecular model of BteCAι, which showed that the enzyme is formed by two equivalent monomers having a structure similar to a butterfly.
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Affiliation(s)
- Sonia Del Prete
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
| | - Alessio Nocentini
- Department of NEUROFARBA, University of Florence, Section of Pharmaceutical and Nutraceutical Sciences, Firenze, Italy
| | - Claudiu T. Supuran
- Department of NEUROFARBA, University of Florence, Section of Pharmaceutical and Nutraceutical Sciences, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
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17
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Amiss AS, Webb JR, Mayo M, Currie BJ, Craik DJ, Henriques ST, Lawrence N. Safer In Vitro Drug Screening Models for Melioidosis Therapy Development. Am J Trop Med Hyg 2020; 103:1846-1851. [PMID: 32975176 DOI: 10.4269/ajtmh.20-0248] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Melioidosis is a neglected tropical disease caused by the Gram-negative soil bacterium Burkholderia pseudomallei. Current antibiotic regimens used to treat melioidosis are prolonged and expensive, and often ineffective because of intrinsic and acquired antimicrobial resistance. Efforts to develop new treatments for melioidosis are limited by the risks associated with handling pathogenic B. pseudomallei, which restricts research to facilities with biosafety level three containment. Closely related nonpathogenic Burkholderia can be investigated under less stringent biosafety level two containment, and we hypothesized that they could be used as model organisms for developing therapies that would also be effective against B. pseudomallei. We used microbroth dilution assays to compare drug susceptibility profiles of three B. pseudomallei strains and five nonpathogenic Burkholderia strains. Burkholderia humptydooensis, Burkholderia thailandensis, and Burkholderia territorii had similar susceptibility profiles to pathogenic B. pseudomallei that support their potential as safer in vitro models for developing new melioidosis therapies.
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Affiliation(s)
- Anna S Amiss
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jessica R Webb
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Mark Mayo
- Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - Bart J Currie
- Northern Territory Medical Program, Department of Infectious Diseases, Royal Darwin Hospital, Darwin, Australia.,Global and Tropical Health Division, Menzies School of Health Research, Darwin, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Sónia Troeira Henriques
- Queensland University of Technology, School of Biomedical Sciences, Institute of Healthy and Biomedical Innovation, and Translational Research Institute, Brisbane, Queensland, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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18
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Terán LC, Distefano M, Bellich B, Petrosino S, Bertoncin P, Cescutti P, Sblattero D. Proteomic Studies of the Biofilm Matrix including Outer Membrane Vesicles of Burkholderia multivorans C1576, a Strain of Clinical Importance for Cystic Fibrosis. Microorganisms 2020; 8:E1826. [PMID: 33228110 PMCID: PMC7699398 DOI: 10.3390/microorganisms8111826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/28/2022] Open
Abstract
Biofilms are aggregates of microbial cells encased in a highly hydrated matrix made up of self-produced extracellular polymeric substances (EPS) which consist of polysaccharides, proteins, nucleic acids, and lipids. While biofilm matrix polysaccharides are unraveled, there is still poor knowledge about the identity and function of matrix-associated proteins. With this work, we performed a comprehensive proteomic approach to disclose the identity of proteins associated with the matrix of biofilm-growing Burkholderia multivorans C1576 reference strain, a cystic fibrosis clinical isolate. Transmission electron microscopy showed that B. multivorans C1576 also releases outer membrane vesicles (OMVs) in the biofilm matrix, as already demonstrated for other Gram-negative species. The proteomic analysis revealed that cytoplasmic and membrane-bound proteins are widely represented in the matrix, while OMVs are highly enriched in outer membrane proteins and siderophores. Our data suggest that cell lysis and OMVs production are the most important sources of proteins for the B. multivorans C1576 biofilm matrix. Of note, some of the identified proteins are lytic enzymes, siderophores, and proteins involved in reactive oxygen species (ROS) scavenging. These proteins might help B. multivorans C1576 in host tissue invasion and defense towards immune system assaults.
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Affiliation(s)
| | | | | | | | | | | | - Daniele Sblattero
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.C.T.); (M.D.); (B.B.); (S.P.); (P.B.); (P.C.)
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19
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De Volder AL, Teves S, Isasmendi A, Pinheiro JL, Ibarra L, Breglia N, Herrera T, Vazquez M, Hernandez C, Degrossi J. Distribution of Burkholderia cepacia complex species isolated from industrial processes and contaminated products in Argentina. Int Microbiol 2020; 24:157-167. [PMID: 33184776 DOI: 10.1007/s10123-020-00151-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/21/2020] [Accepted: 10/29/2020] [Indexed: 01/03/2023]
Abstract
Burkholderia cepacia complex (Bcc) members have clinical relevance as opportunistic pathogens in patients with cystic fibrosis and are responsible of numerous nosocomial infections. These closely related bacteria are also reported as frequent contaminants of industrial products. In this retrospective study, we use PCR and recA gene sequence analysis to identify at species level Bcc isolates recovered from massive consumption products and industrial processes in Argentina during the last 25 years. The sequences obtained were also compared with recA sequences from clinical Bcc isolates deposited in GenBank database. We detected Bcc in purified water and preserved products from pharmaceutics, cosmetics, household cleaning articles, and beverages industries. B. contaminans (which is prevalent among people with cystic fibrosis in Argentina) was the most frequent Bcc species identified (42% of the Bcc isolates studied). B. cepacia (10%), B. cenocepacia (5%), B. vietnamiensis (16%), B. arboris (3%), and the recently defined B. aenigmatica (24%) were also detected. Rec A sequences from all B. cepacia and most B. contaminans industrial isolates obtained in this study displayed 100% identity with recA sequences from isolates infecting Argentinean patients. This information brings evidence for considering industrial massive consumption products as a potential source of Bcc infections. In addition, identification at species level in industrial microbiological laboratories is necessary for a better epidemiological surveillance. Particularly in Argentina, more studies are required in order to reveal the role of these products in the acquisition of B. contaminans infections.
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Affiliation(s)
- A López De Volder
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - S Teves
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - A Isasmendi
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - J L Pinheiro
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - L Ibarra
- Servicio de Bacteriología Clínica, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - N Breglia
- Cátedra de Microbiología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - T Herrera
- Facultad de Ciencias Exactas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M Vazquez
- Servicio de Bacteriología Clínica, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - C Hernandez
- Servicio de Microbiología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - José Degrossi
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina. .,Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 4° Floor, Ciudad Autónoma de Buenos Aires, Argentina.
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20
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Murugesan M, Ranjan J, Devanga Ragupathi NK, Michael JS, Viggeswarpu S, Wilson BP, Veeraraghavan B. Diagnostic methods and identification challenges experienced in a Burkholderia contaminans outbreak occurred in a tertiary care centre. Indian J Med Microbiol 2020; 39:192-195. [PMID: 33966861 DOI: 10.1016/j.ijmmb.2020.10.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Recently, a novel species contaminans belonging to the family Burkholderia cepacia complex (Bcc) is rising as a hospital pathogen. Detection of Burkholderia contaminans, a member of Bcc can be done only by MALDI TOF and sequencing techniques. We report the diagnostic challenges faced in an outbreak of bacteremia due to B. contaminans grown in diltiazem vials. METHOD The department of microbiology notified the infection control team about a cluster of eleven patients with B. contaminans isolated from blood culture. An outbreak investigation was initiated by performing environmental surveillance and sterility testing of solutions given for the patients. Routine phenotypical methods for identification of species followed by MALDI-TOF and sequencing was performed to identify the pathogen. RESULTS All the patients detected with B. contaminans were having cardiac disease and received diltiazem. Sterility testing of diltiazem vials given for the patient and an unopened vial of same batch has grown B. contaminans. Clonal typing has confirmed the sequence similarities between patient and solution isolates. CONCLUSION Due to diagnostic challenge in identifying the species of Bcc, MALDI TOF and clonal typing remains the key diagnostic tools available to detect Bcc species at an earliest especially in an outbreak.
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Affiliation(s)
- Malathi Murugesan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jai Ranjan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | | | - Joy Sarojini Michael
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India; Hospital Infection Control Committee, Christian Medical College, Vellore, Tamil Nadu, India
| | - Surekha Viggeswarpu
- Department of Geriatrics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Benny Paul Wilson
- Department of Geriatrics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India.
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A Phylogeny-Informed Proteomics Approach for Species Identification within the Burkholderia cepacia Complex. J Clin Microbiol 2020; 58:JCM.01741-20. [PMID: 32878952 DOI: 10.1128/jcm.01741-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/26/2020] [Indexed: 01/17/2023] Open
Abstract
Ancestral genetic exchange between members of many important bacterial pathogen groups has resulted in phylogenetic relationships better described as networks than as bifurcating trees. In certain cases, these reticulated phylogenies have resulted in phenotypic and molecular overlap that challenges the construction of practical approaches for species identification in the clinical microbiology laboratory. Burkholderia cepacia complex (Bcc), a betaproteobacteria species group responsible for significant morbidity in persons with cystic fibrosis and chronic granulomatous disease, represents one such group where network-structured phylogeny has hampered the development of diagnostic methods for species-level discrimination. Here, we present a phylogeny-informed proteomics approach to facilitate diagnostic classification of pathogen groups with reticulated phylogenies, using Bcc as an example. Starting with a set of more than 800 Bcc and Burkholderia gladioli whole-genome assemblies, we constructed phylogenies with explicit representation of inferred interspecies recombination. Sixteen highly discriminatory peptides were chosen to distinguish B. cepacia, Burkholderia cenocepacia, Burkholderia multivorans, and B. gladioli and multiplexed into a single, rapid liquid chromatography-tandem mass spectrometry multiple reaction monitoring (LC-MS/MS MRM) assay. Testing of a blinded set of isolates containing these four Burkholderia species demonstrated 50/50 correct automatic negative calls (100% accuracy with a 95% confidence interval [CI] of 92.9 to 100%), and 70/70 correct automatic species-level positive identifications (100% accuracy with 95% CI 94.9 to 100%) after accounting for a single initial incorrect identification due to a preanalytic error, correctly identified on retesting. The approach to analysis described here is applicable to other pathogen groups for which development of diagnostic classification methods is complicated by interspecies recombination.
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Kurakin GF, Samoukina AM, Potapova NA. Bacterial and Protozoan Lipoxygenases Could be Involved in Cell-to-Cell Signaling and Immune Response Suppression. BIOCHEMISTRY (MOSCOW) 2020; 85:1048-1071. [PMID: 33050851 DOI: 10.1134/s0006297920090059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipoxygenases are found in animals, plants, and fungi, where they are involved in a wide range of cell-to-cell signaling processes. The presence of lipoxygenases in a number of bacteria and protozoa has been also established, but their biological significance remains poorly understood. Several hypothetical functions of lipoxygenases in bacteria and protozoa have been suggested without experimental validation. The objective of our study was evaluating the functions of bacterial and protozoan lipoxygenases by evolutionary and taxonomic analysis using bioinformatics tools. Lipoxygenase sequences were identified and examined using BLAST, followed by analysis of constructed phylogenetic trees and networks. Our results support the theory on the involvement of lipoxygenases in the formation of multicellular structures by microorganisms and their possible evolutionary significance in the emergence of multicellularity. Furthermore, we observed association of lipoxygenases with the suppression of host immune response by parasitic and symbiotic bacteria including dangerous opportunistic pathogens.
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Affiliation(s)
- G F Kurakin
- Department of Biochemistry and Laboratory Medicine, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia.
| | - A M Samoukina
- Department of Microbiology, Virology, and Immunology, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia
| | - N A Potapova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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Hassan AA, dos Santos SC, Cooper VS, Sá-Correia I. Comparative Evolutionary Patterns of Burkholderia cenocepacia and B. multivorans During Chronic Co-infection of a Cystic Fibrosis Patient Lung. Front Microbiol 2020; 11:574626. [PMID: 33101250 PMCID: PMC7545829 DOI: 10.3389/fmicb.2020.574626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
During chronic respiratory infections of cystic fibrosis (CF) patients, bacteria adaptively evolve in response to the nutritional and immune environment as well as influence other infecting microbes. The present study was designed to gain insights into the genetic mechanisms underlying adaptation and diversification by the two most prevalent pathogenic species of the Burkholderia cepacia complex (Bcc), B. cenocepacia and B. multivorans. Herein, we study the evolution of both of these species during coinfection of a CF patient for 4.4 years using genome sequences of 9 B. multivorans and 11 B. cenocepacia. This co-infection spanned at least 3 years following initial infection by B. multivorans and ultimately ended in the patient's death by cepacia syndrome. Both species acquired several mutations with accumulation rates of 2.08 (B. cenocepacia) and 2.27 (B. multivorans) SNPs/year. Many of the mutated genes are associated with oxidative stress response, transition metal metabolism, defense mechanisms against antibiotics, and other metabolic alterations consistent with the idea that positive selection might be driven by the action of the host immune system, antibiotic therapy and low oxygen and iron concentrations. Two orthologous genes shared by B. cenocepacia and B. multivorans were found to be under strong selection and accumulated mutations associated with lineage diversification. One gene encodes a nucleotide sugar dehydratase involved in lipopolysaccharide O-antigen (OAg) biosynthesis (wbiI). The other gene encodes a putative two-component regulatory sensor kinase protein required to sense and adapt to oxidative- and heavy metal- inducing stresses. This study contributes to understanding of shared and species-specific evolutionary patterns of B. cenocepacia and B. multivorans evolving in the same CF lung environment.
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Affiliation(s)
- A. Amir Hassan
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra C. dos Santos
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Sousa SA, Seixas AM, Mandal M, Rodríguez-Ortega MJ, Leitão JH. Characterization of the Burkholderia cenocepacia J2315 Surface-Exposed Immunoproteome. Vaccines (Basel) 2020; 8:vaccines8030509. [PMID: 32899969 PMCID: PMC7565204 DOI: 10.3390/vaccines8030509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/27/2020] [Accepted: 09/03/2020] [Indexed: 11/16/2022] Open
Abstract
Infections by the Burkholderia cepacia complex (Bcc) remain seriously life threatening to cystic fibrosis (CF) patients, and no effective eradication is available. A vaccine to protect patients against Bcc infections is a highly attractive therapeutic option, but none is available. A strategy combining the bioinformatics identification of putative surface-exposed proteins with an experimental approach encompassing the “shaving” of surface-exposed proteins with trypsin followed by peptide identification by liquid chromatography and mass spectrometry is here reported. The methodology allowed the bioinformatics identification of 263 potentially surface-exposed proteins, 16 of them also experimentally identified by the “shaving” approach. Of the proteins identified, 143 have a high probability of containing B-cell epitopes that are surface-exposed. The immunogenicity of three of these proteins was demonstrated using serum samples from Bcc-infected CF patients and Western blotting, validating the usefulness of this methodology in identifying potentially immunogenic surface-exposed proteins that might be used for the development of Bcc-protective vaccines.
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Affiliation(s)
- Sílvia A. Sousa
- iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; (A.M.M.S.); (M.M.)
- Correspondence: (S.A.S.); (J.H.L.); Tel.: +351-2184-19986 (S.A.S.); +351-2184-17688 (J.H.L.)
| | - António M.M. Seixas
- iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; (A.M.M.S.); (M.M.)
| | - Manoj Mandal
- iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; (A.M.M.S.); (M.M.)
| | | | - Jorge H. Leitão
- iBB–Institute for Bioengineering and Biosciences, 1049-001 Lisbon, Portugal; (A.M.M.S.); (M.M.)
- Correspondence: (S.A.S.); (J.H.L.); Tel.: +351-2184-19986 (S.A.S.); +351-2184-17688 (J.H.L.)
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Wong KSK, Dhaliwal S, Bilawka J, Srigley JA, Champagne S, Romney MG, Tilley P, Sadarangani M, Zlosnik JEA, Chilvers MA. Matrix-assisted laser desorption/ionization time-of-flight MS for the accurate identification of Burkholderia cepacia complex and Burkholderia gladioli in the clinical microbiology laboratory. J Med Microbiol 2020; 69:1105-1113. [PMID: 32597748 PMCID: PMC7642978 DOI: 10.1099/jmm.0.001223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/09/2020] [Indexed: 12/22/2022] Open
Abstract
Introduction. Burkholderia cepacia complex (Bcc) bacteria, currently consisting of 23 closely related species, and Burkholderia gladioli, can cause serious and difficult-to-treat infections in people with cystic fibrosis. Identifying Burkholderia bacteria to the species level is considered important for understanding epidemiology and infection control, and predicting clinical outcomes. Matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF) is a rapid method recently introduced in clinical laboratories for bacterial species-level identification. However, reports on the ability of MALDI-TOF to accurately identify Bcc to the species level are mixed.Aim. The aim of this project was to evaluate the accuracy of MALDI-TOF using the Biotyper and VITEK MS systems in identifying isolates from 22 different Bcc species and B. gladioli compared to recA gene sequencing, which is considered the current gold standard for Bcc.Methodology. To capture maximum intra-species variation, phylogenetic trees were constructed from concatenated multi-locus sequence typing alleles and clustered with a novel k-medoids approach. One hundred isolates representing 22 Bcc species, plus B. gladioli, were assessed for bacterial identifications using the two MALDI-TOF systems.Results. At the genus level, 100 and 97.0 % of isolates were confidently identified as Burkholderia by the Biotyper and VITEK MS systems, respectively; moreover, 26.0 and 67.0 % of the isolates were correctly identified to the species level, respectively. In many, but not all, cases of species misidentification or failed identification, a representative library for that species was lacking.Conclusion. Currently available MALDI-TOF systems frequently do not accurately identify Bcc bacteria to the species level.
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Affiliation(s)
- Kendrew S. K. Wong
- Division of Respiratory Medicine, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Suk Dhaliwal
- Microbiology, BC Children’s Hospital, Vancouver, BC, Canada
| | - Jennifer Bilawka
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
| | - Jocelyn A. Srigley
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sylvie Champagne
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marc G. Romney
- Pathology and Laboratory Medicine, Providence Health Care, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Manish Sadarangani
- Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Vaccine Evaluation Centre, BC Children’s Hospital, Vancouver, BC, Canada
| | - James E. A. Zlosnik
- Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Mark A. Chilvers
- Division of Respiratory Medicine, Department of Pediatrics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
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Depoorter E, De Canck E, Peeters C, Wieme AD, Cnockaert M, Zlosnik JEA, LiPuma JJ, Coenye T, Vandamme P. Burkholderia cepacia Complex Taxon K: Where to Split? Front Microbiol 2020; 11:1594. [PMID: 32760373 PMCID: PMC7372133 DOI: 10.3389/fmicb.2020.01594] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
The objective of the present study was to provide an updated classification for Burkholderia cepacia complex (Bcc) taxon K isolates. A representative set of 39 taxon K isolates were analyzed through multilocus sequence typing (MLST) and phylogenomic analyses. MLST analysis revealed the presence of at least six clusters of sequence types (STs) within taxon K, two of which contain the type strains of Burkholderia contaminans (ST-102) and Burkholderia lata (ST-101), and four corresponding to the previously defined taxa Other Bcc groups C, G, H and M. This clustering was largely supported by a phylogenomic tree which revealed three main clades. Isolates of B. contaminans and of Other Bcc groups C, G, and H represented a first clade which generally shared average nucleotide identity (ANI) and average digital DNA-DNA hybridization (dDDH) values at or above the 95-96% ANI and 70% dDDH thresholds for species delineation. A second clade consisted of Other Bcc group M bacteria and of four B. lata isolates and was supported by average ANI and dDDH values of 97.2 and 76.1% within this clade and average ANI and dDDH values of 94.5 and 57.2% toward the remaining B. lata isolates (including the type strain), which represented a third clade. We therefore concluded that isolates known as Other Bcc groups C, G, and H should be classified as B. contaminans, and propose a novel species, Burkholderia aenigmatica sp. nov., to accommodate Other Bcc M and B. lata ST-98, ST-103, and ST-119 isolates. Optimized MALDI-TOF MS databases for the identification of clinical Burkholderia isolates may provide correct species-level identification for some of these bacteria but would identify most of them as B. cepacia complex. MLST facilitates species-level identification of many taxon K strains but some may require comparative genomics for accurate species-level assignment. Finally, the inclusion of Other Bcc groups C, G, and H into B. contaminans affects the phenotype of this species minimally and the proposal to classify Other Bcc group M and B. lata ST-98, ST-103, and ST-119 strains as a novel Burkholderia species is supported by a distinctive phenotype, i.e., growth at 42°C and lysine decarboxylase activity.
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Affiliation(s)
- Eliza Depoorter
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - James E A Zlosnik
- Division of Infectious Diseases, Department of Pediatrics, The University of British Columbia, Vancouver, BC, Canada
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
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27
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Kong P, Hong C. Complete genome sequence of a boxwood endophyte Burkholderia sp. SSG with broad biotechnological application potential. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 26:e00455. [PMID: 32368513 PMCID: PMC7184123 DOI: 10.1016/j.btre.2020.e00455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 03/09/2020] [Accepted: 04/08/2020] [Indexed: 11/20/2022]
Abstract
Burkholderia sp. strain SSG is a boxwood endophyte with potent antagonistic activities against a variety of plant pathogens. Here we present its complete genome sequence that is 8.6 Mb long with a GC content of 66.9%, 10,209 predicted protein-coding sequences, and 866 secondary metabolism gene clusters. Many of these genes and clusters involve antibiosis and other antagonistic activities against plant pathogens and insect pests as well as plant growth promoting traits but none for the Burkholderia cepacia epidemic strain marker. This genome sequence supports SSG as a potent biocontrol agent and source of other biotechnological applications.
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Affiliation(s)
- Ping Kong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA
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28
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Sýkorová P, Novotná J, Demo G, Pompidor G, Dubská E, Komárek J, Fujdiarová E, Houser J, Hároníková L, Varrot A, Shilova N, Imberty A, Bovin N, Pokorná M, Wimmerová M. Characterization of novel lectins from Burkholderia pseudomallei and Chromobacterium violaceum with seven-bladed β-propeller fold. Int J Biol Macromol 2020; 152:1113-1124. [DOI: 10.1016/j.ijbiomac.2019.10.200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/08/2023]
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Del Prete S, De Luca V, Nocentini A, Scaloni A, Mastrolorenzo MD, Supuran CT, Capasso C. Anion Inhibition Studies of the Beta-Carbonic Anhydrase from Escherichia coli. Molecules 2020; 25:E2564. [PMID: 32486444 PMCID: PMC7321114 DOI: 10.3390/molecules25112564] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/15/2022] Open
Abstract
The interconversion of CO2 and HCO3- is catalyzed by a superfamily of metalloenzymes, known as carbonic anhydrases (CAs, EC 4.2.1.1), which maintain the equilibrium between dissolved inorganic CO2 and HCO3-. In the genome of Escherichia coli, a Gram-negative bacterium typically colonizing the lower intestine of warm-blooded organisms, the cyn operon gene includes the CynT gene, encoding for a β-CA, and CynS gene, encoding for the cyanase. CynT (β-CA) prevents the depletion of the cellular bicarbonate, which is further used in the reaction catalyzed by cyanase. A second β-CA (CynT2 or Can or yadF), as well as a γ and ι-CAs were also identified in the E. coli genome. CynT2 is essential for bacterial growth at atmospheric CO2 concentration. Here, we characterized the kinetic properties and the anion inhibition profiles of recombinant CynT2. The enzyme showed a good activity for the physiological CO2 hydratase reaction with the following parameters: kcat = 5.3 × 105 s-1 and kcat/KM = of 4.1 × 107 M-1 s-1. Sulfamide, sulfamate, phenylboronic acid, phenylarsonic acid, and diethyldithiocarbamate were the most effective CynT2 inhibitors (KI = 2.5 to 84 µM). The anions allowed for a detailed understanding of the interaction of inhibitors with the amino acid residues surrounding the catalytic pocket of the enzyme and may be used as leads for the design of more efficient and specific inhibitors.
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Affiliation(s)
- Sonia Del Prete
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; (S.D.P.); (V.D.L.)
| | - Viviana De Luca
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; (S.D.P.); (V.D.L.)
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, CNR, Via Argine 1085, 80147 Naples, Italy,
| | - Alessio Nocentini
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.N.); (M.D.M.)
| | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, CNR, Via Argine 1085, 80147 Naples, Italy,
| | - Margaret D. Mastrolorenzo
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.N.); (M.D.M.)
- University of California, San Diego (UCSD), 3425 Lebon Drive, Unit 918, San Diego, CA 92122, USA
| | - Claudiu T. Supuran
- Department of Neurofarba, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Via U. Schiff 6, Sesto Fiorentino, 50019 Florence, Italy; (A.N.); (M.D.M.)
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131 Napoli, Italy; (S.D.P.); (V.D.L.)
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Gautam V, Kumar S, Patil PP, Meletiadis J, Patil PB, Mouton JW, Sharma M, Daswal A, Singhal L, Ray P, Singh M. Exploring the Interplay of Resistance Nodulation Division Efflux Pumps, AmpC and OprD in Antimicrobial Resistance of Burkholderia cepacia Complex in Clinical Isolates. Microb Drug Resist 2020; 26:1144-1152. [PMID: 32354297 DOI: 10.1089/mdr.2019.0102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aim: This study aimed at investigating the association of gene expression of multidrug efflux pumps (MexA, MexC, MexE, and MexX), the outer membrane porin OprD, and the β-lactamase AmpC with the antimicrobial susceptibility among 44 clinical isolates of Burkholderia cepacia complex (Bcc). Results: Increased expression of ampC gene showed significant association with reduced susceptibility to chloramphenicol. In fact, reduced susceptibility to chloramphenicol was correlated with overexpression of most genes (ampC, mexC, mexE, and mexX) studied here in majority (>95%) of the Bcc isolates. Increased mexA expression showed significant association with reduced susceptibility to β-lactam antimicrobials (ceftazidime, piperacillin-tazobactam, and meropenem) and co-trimoxazole. Reduced susceptibility to meropenem also showed significant correlation with overexpression of mexC and mexX, whereas reduced susceptibility to ceftazidime was also associated with mexE overexpression. Reduced susceptibility to levofloxacin was significantly associated with overexpression of mexX. The involvement of the efflux pumps in levofloxacin and ceftazidime resistance was further inferred from the finding that the efflux pump inhibitor, carbonyl cyanide m-chlorophenylhydrazone reduced minimum inhibitory concentrations for both the antimicrobials. Conclusions: To conclude, this study explored the high-level expression of mexC, mexE, and mexX efflux pumps genes and ampC in the clinical isolates of Bcc, which can be targeted at treating infections caused by Bcc.
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Affiliation(s)
- Vikas Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Kumar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prashant P Patil
- Laboratory of Bacterial Genomics and Evolution, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Joseph Meletiadis
- Clinical Microbiology Laboratory, Attikon University Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Prabhu B Patil
- Laboratory of Bacterial Genomics and Evolution, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Johan W Mouton
- Department of Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands
| | - Megha Sharma
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anmol Daswal
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Lipika Singhal
- Department of Microbiology, Government Medical College and Hospital, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Meenu Singh
- Department of Pediatrics, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Burkholderia cepacia Complex Bacteria: a Feared Contamination Risk in Water-Based Pharmaceutical Products. Clin Microbiol Rev 2020; 33:33/3/e00139-19. [PMID: 32295766 DOI: 10.1128/cmr.00139-19] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Burkholderia cepacia (formerly Pseudomonas cepacia) was once thought to be a single bacterial species but has expanded to the Burkholderia cepacia complex (Bcc), comprising 24 closely related opportunistic pathogenic species. These bacteria have a widespread environmental distribution, an extraordinary metabolic versatility, a complex genome with three chromosomes, and a high capacity for rapid mutation and adaptation. Additionally, they present an inherent resistance to antibiotics and antiseptics, as well as the abilities to survive under nutrient-limited conditions and to metabolize the organic matter present in oligotrophic aquatic environments, even using certain antimicrobials as carbon sources. These traits constitute the reason that Bcc bacteria are considered feared contaminants of aqueous pharmaceutical and personal care products and the frequent reason behind nonsterile product recalls. Contamination with Bcc has caused numerous nosocomial outbreaks in health care facilities, presenting a health threat, particularly for patients with cystic fibrosis and chronic granulomatous disease and for immunocompromised individuals. This review addresses the role of Bcc bacteria as a potential public health problem, the mechanisms behind their success as contaminants of pharmaceutical products, particularly in the presence of biocides, the difficulties encountered in their detection, and the preventive measures applied during manufacturing processes to control contamination with these objectionable microorganisms. A summary of Bcc-related outbreaks in different clinical settings, due to contamination of diverse types of pharmaceutical products, is provided.
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32
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Scoffone VC, Barbieri G, Buroni S, Scarselli M, Pizza M, Rappuoli R, Riccardi G. Vaccines to Overcome Antibiotic Resistance: The Challenge of Burkholderia cenocepacia. Trends Microbiol 2020; 28:315-326. [DOI: 10.1016/j.tim.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022]
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Jin Y, Zhou J, Zhou J, Hu M, Zhang Q, Kong N, Ren H, Liang L, Yue J. Genome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status. Biol Direct 2020; 15:6. [PMID: 32131884 PMCID: PMC7057466 DOI: 10.1186/s13062-020-0258-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 02/06/2023] Open
Abstract
Background Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed. Methods We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering. Results We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species. Conclusions This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species. Reviewer This article was reviewed by Dr. Xianwen Ren.
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Affiliation(s)
- Yuan Jin
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jianglin Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Jing Zhou
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Mingda Hu
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Qi Zhang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China
| | - Na Kong
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.,Anhui University, Hefei, 230039, Anhui, China
| | - Hongguang Ren
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
| | - Long Liang
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,Anhui University, Hefei, 230039, Anhui, China.
| | - Junjie Yue
- Beijing Institute of Biotechnology, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, No. 20, DongDaJie Street, Fengtai, Beijing, 100071, China.
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Oppy CC, Jebeli L, Kuba M, Oates CV, Strugnell R, Edgington-Mitchell LE, Valvano MA, Hartland EL, Newton HJ, Scott NE. Loss of O-Linked Protein Glycosylation in Burkholderia cenocepacia Impairs Biofilm Formation and Siderophore Activity and Alters Transcriptional Regulators. mSphere 2019; 4:e00660-19. [PMID: 31722994 PMCID: PMC6854043 DOI: 10.1128/msphere.00660-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
O-linked protein glycosylation is a conserved feature of the Burkholderia genus. The addition of the trisaccharide β-Gal-(1,3)-α-GalNAc-(1,3)-β-GalNAc to membrane exported proteins in Burkholderia cenocepacia is required for bacterial fitness and resistance to environmental stress. However, the underlying causes of the defects observed in the absence of glycosylation are unclear. Using proteomics, luciferase reporter assays, and DNA cross-linking, we demonstrate the loss of glycosylation leads to changes in transcriptional regulation of multiple proteins, including the repression of the master quorum CepR/I. These proteomic and transcriptional alterations lead to the abolition of biofilm formation and defects in siderophore activity. Surprisingly, the abundance of most of the known glycosylated proteins did not significantly change in the glycosylation-defective mutants, except for BCAL1086 and BCAL2974, which were found in reduced amounts, suggesting they could be degraded. However, the loss of these two proteins was not responsible for driving the proteomic alterations, biofilm formation, or siderophore activity. Together, our results show that loss of glycosylation in B. cenocepacia results in a global cell reprogramming via alteration of the transcriptional regulatory systems, which cannot be explained by the abundance changes in known B. cenocepacia glycoproteins.IMPORTANCE Protein glycosylation is increasingly recognized as a common posttranslational protein modification in bacterial species. Despite this commonality, our understanding of the role of most glycosylation systems in bacterial physiology and pathogenesis is incomplete. In this work, we investigated the effect of the disruption of O-linked glycosylation in the opportunistic pathogen Burkholderia cenocepacia using a combination of proteomic, molecular, and phenotypic assays. We find that in contrast to recent findings on the N-linked glycosylation systems of Campylobacter jejuni, O-linked glycosylation does not appear to play a role in proteome stabilization of most glycoproteins. Our results reveal that loss of glycosylation in B. cenocepacia strains leads to global proteome and transcriptional changes, including the repression of the quorum-sensing regulator cepR (BCAM1868) gene. These alterations lead to dramatic phenotypic changes in glycosylation-null strains, which are paralleled by both global proteomic and transcriptional alterations, which do not appear to directly result from the loss of glycosylation per se. This research unravels the pleiotropic effects of O-linked glycosylation in B. cenocepacia, demonstrating that its loss does not simply affect the stability of the glycoproteome, but also interferes with transcription and the broader proteome.
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Affiliation(s)
- Cameron C Oppy
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Miku Kuba
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Clare V Oates
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Richard Strugnell
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Laura E Edgington-Mitchell
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, Bluestone Center for Clinical Research, New York, New York, USA
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Elizabeth L Hartland
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Hayley J Newton
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Savi D, Quattrucci S, Trancassini M, Dalmastri C, De Biase RV, Maggisano M, Palange P, Bevivino A. Impact of clonally-related Burkholderia contaminans strains in two patients attending an Italian cystic fibrosis centre: a case report. BMC Pulm Med 2019; 19:164. [PMID: 31464603 PMCID: PMC6714384 DOI: 10.1186/s12890-019-0923-6] [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: 04/13/2019] [Accepted: 08/19/2019] [Indexed: 11/11/2022] Open
Abstract
Background Burkholderia contaminans is one of the 20 closely related bacterial of the Burkholderia cepacia complex, a group of bacteria that are ubiquitous in the environment and capable of infecting people with cystic fibrosis (CF). This species is an emerging pathogen and it has been widely isolated from CF patients in Argentina, Spain, Portugal, Australia, Canada, USA with a low prevalence in Ireland, France, Russia, Switzerland, Czech Republic, and Italy. This is the first report of B. contaminans affecting two Italian CF patients attending the same CF Centre. We correlate B. contaminans colonisation with lung function decline and co-infection with other clinically relevant CF pathogens. Case presentation B. contaminans was identified by Multi Locus Sequence Typing in routine sputum analysis of two Caucasian CF women homozygous for Phe508del CFTR mutation. Sequence Type 102 was detected in both strains. It is known that B. contaminans ST102 was isolated both from CF and non-CF patients, with an intercontinental spread across the world. Random Amplified Polymorphic DNA analysis revealed the genetic relatedness between the two strains. We examined their susceptibility to antimicrobial agents, comparing the latter with that recorded for other B. contaminans isolated from different countries. We also described key virulence factors possibly linked with a clinical outcome. Specifically, we attempted to correlate colonization with the incidence of acute exacerbation of symptoms and lung function decline. Conclusions This case presentation suggests that acquisition of B. contaminans ST102 is not directly associated with a lung function decline. We retain that the presence of other CF pathogens (i.e. MRSA and Trichosporon) along with B. contaminans ST102 might have contributed to the worsening of clinical conditions in our CF patients. The circumstances leading to the establishment of B. contaminans ST102 infections are still unknown. We highlight the importance to proper detect and typing bacteria implicated in CF infection by using molecular techniques.
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Affiliation(s)
- Daniela Savi
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy. .,Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, Rome, Italy.
| | - Serena Quattrucci
- Dipartimento Materno Infantile e Scienze Urologiche, Sapienza University of Rome, Rome, Italy
| | - Maria Trancassini
- Department of Public Health and Infectious Diseases, Laboratory of Microbiology, Policlinico Umberto I Hospital, Rome, Italy
| | - Claudia Dalmastri
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
| | | | - Marta Maggisano
- Sant'Andrea Hospital, Sapienza University of Rome, Rome, Italy
| | - Paolo Palange
- Department of Public Health and Infectious Diseases, Adult Cystic Fibrosis Centre, "Sapienza" University of Rome, V.le Universita' 37, 00185, Rome, Italy
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, ENEA C.R Casaccia, 00123, Rome, Italy
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Hassan AA, Coutinho CP, Sá-Correia I. Burkholderia cepacia Complex Species Differ in the Frequency of Variation of the Lipopolysaccharide O-Antigen Expression During Cystic Fibrosis Chronic Respiratory Infection. Front Cell Infect Microbiol 2019; 9:273. [PMID: 31417878 PMCID: PMC6686744 DOI: 10.3389/fcimb.2019.00273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/17/2019] [Indexed: 11/13/2022] Open
Abstract
Burkholderia cepacia complex (Bcc) bacteria can adapt to the lung environment of cystic fibrosis (CF) patients resulting in the emergence of a very difficult to eradicate heterogeneous population leading to chronic infections associated with rapid lung function loss and increased mortality. Among the important phenotypic modifications is the variation of the lipopolysaccharide (LPS) structure at level of the O-antigen (OAg) presence, influencing adherence, colonization and the ability to evade the host defense mechanisms. The present study was performed to understand whether the loss of OAg expression during CF infection can be considered a general phenomenon in different Bcc species favoring its chronicity. In fact, it is still not clear why different Bcc species/strains differ in their ability to persist in the CF lung and pathogenic potential. The systematic two-decade-retrospective-longitudinal-screening conducted covered 357 isolates retrieved from 19 chronically infected patients receiving care at a central hospital in Lisbon. The study involved 21 Bcc strains of six/seven Bcc species/lineages, frequently or rarely isolated from CF patients worldwide. Different strains/clonal variants obtained during infection gave rise to characteristic OAg-banding patterns. The two most prevalent and feared species, B. cenocepacia and B. multivorans, showed a tendency to lose the OAg along chronic infection. B. cenocepacia recA lineage IIIA strains known to lead to particularly destructive infections exhibit the most frequent OAg loss, compared with lineage IIIB. The switch frequency increased with the duration of infection and the level of lung function deterioration. For the first time, it is shown that the rarely found B. cepacia and B. contaminans, whose representation in the cohort of patients examined is abnormally high, keep the OAg even during 10- or 15-year infections. Data from co-infections with different Bcc species reinforced these conclusions. Concerning the two other rarely found species examined, B. stabilis exhibited a stable OAg expression phenotype over the infection period while for the single clone of the more distantly related B. dolosa species, the OAg-chain was absent from the beginning of the 5.5-year infection until the patient dead. This work reinforces the relevance attributed to the OAg-expression switch suggesting marked differences in the various Bcc species.
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Affiliation(s)
- A. Amir Hassan
- iBB - Institute for Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Carla P. Coutinho
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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Cloutier M, Muru K, Ravicoularamin G, Gauthier C. Polysaccharides from Burkholderia species as targets for vaccine development, immunomodulation and chemical synthesis. Nat Prod Rep 2019; 35:1251-1293. [PMID: 30023998 DOI: 10.1039/c8np00046h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2018 Burkholderia species are a vast group of human pathogenic, phytopathogenic, and plant- or environment-associated bacteria. B. pseudomallei, B. mallei, and B. cepacia complex are the causative agents of melioidosis, glanders, and cystic fibrosis-related infections, respectively, which are fatal diseases in humans and animals. Due to their high resistance to antibiotics, high mortality rates, and increased infectivity via the respiratory tract, B. pseudomallei and B. mallei have been listed as potential bioterrorism agents by the Centers for Disease Control and Prevention. Burkholderia species are able to produce a large network of surface-exposed polysaccharides, i.e., lipopolysaccharides, capsular polysaccharides, and exopolysaccharides, which are virulence factors, immunomodulators, major biofilm components, and protective antigens, and have crucial implications in the pathogenicity of Burkholderia-associated diseases. This review provides a comprehensive and up-to-date account regarding the structural elucidation and biological activities of surface polysaccharides produced by Burkholderia species. The chemical synthesis of oligosaccharides mimicking Burkholderia polysaccharides is described in detail. Emphasis is placed on the recent research efforts toward the development of glycoconjugate vaccines against melioidosis and glanders based on synthetic or native Burkholderia oligo/polysaccharides.
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Affiliation(s)
- Maude Cloutier
- INRS-Institut Armand-Frappier, Université du Québec, 531, boul. des Prairies, Laval, Québec H7V 1B7, Canada.
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Quorum Sensing as Antivirulence Target in Cystic Fibrosis Pathogens. Int J Mol Sci 2019; 20:ijms20081838. [PMID: 31013936 PMCID: PMC6515091 DOI: 10.3390/ijms20081838] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive genetic disorder which leads to the secretion of a viscous mucus layer on the respiratory epithelium that facilitates colonization by various bacterial pathogens. The problem of drug resistance has been reported for all the species able to colonize the lung of CF patients, so alternative treatments are urgently needed. In this context, a valid approach is to investigate new natural and synthetic molecules for their ability to counteract alternative pathways, such as virulence regulating quorum sensing (QS). In this review we describe the pathogens most commonly associated with CF lung infections: Staphylococcus aureus, Pseudomonas aeruginosa, species of the Burkholderia cepacia complex and the emerging pathogens Stenotrophomonas maltophilia, Haemophilus influenzae and non-tuberculous Mycobacteria. For each bacterium, the QS system(s) and the molecules targeting the different components of this pathway are described. The amount of investigations published in the last five years clearly indicate the interest and the expectations on antivirulence therapy as an alternative to classical antibiotics.
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Degrossi JJ, Merino C, Isasmendi AM, Ibarra LM, Collins C, Bo NE, Papalia M, Fernandez JS, Hernandez CM, Papp-Wallace KM, Bonomo RA, Vazquez MS, Power P, Ramirez MS. Whole Genome Sequence Analysis of Burkholderia contaminans FFH2055 Strain Reveals the Presence of Putative β-Lactamases. Curr Microbiol 2019; 76:485-494. [PMID: 30783798 DOI: 10.1007/s00284-019-01653-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Burkholderia contaminans is a member of the Burkholderia cepacia complex (Bcc), a pathogen with increasing prevalence among cystic fibrosis (CF) patients and the cause of numerous outbreaks due to the use of contaminated commercial products. The antibiotic resistance determinants, particularly β-lactamases, have been poorly studied in this species. In this work, we explored the whole genome sequence (WGS) of a B. contaminans isolate (FFH 2055) and detected four putative β-lactamase-encoding genes. In general, these genes have more than 93% identity with β-lactamase genes found in other Bcc species. Two β-lactamases, a class A (Pen-like, suggested name PenO) and a class D (OXA-like), were further analyzed and characterized. Amino acid sequence comparison showed that Pen-like has 82% and 67% identity with B. multivorans PenA and B. pseudomallei PenI, respectively, while OXA-like displayed strong homology with class D enzymes within the Bcc, but only 22-44% identity with available structures from the OXA family. PCR reactions designed to study the presence of these two genes revealed a heterogeneous distribution among clinical and industrial B. contaminans isolates. Lastly, blaPenO gene was cloned and expressed into E. coli to investigate the antibiotic resistance profile and confers an extended-spectrum β-lactamase (ESBL) phenotype. These results provide insight into the presence of β-lactamases in B. contaminans, suggesting they play a role in antibiotic resistance of these bacteria.
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Affiliation(s)
- José J Degrossi
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Cindy Merino
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Adela M Isasmendi
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Lorena M Ibarra
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Chelsea Collins
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Nicolás E Bo
- Cátedra de Salud Pública e Higiene Ambiental, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Papalia
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jennifer S Fernandez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA
| | - Claudia M Hernandez
- Servicio de Bacteriología, Hospital de Pediatría Juan P. Garrahan, Buenos Aires, Argentina
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, OH, 44106, USA
- Department of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
- Departments of Microbiology and Molecular Biology, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miryam S Vazquez
- Servicio de Bacteriología, Hospital de Niños Ricardo Gutierrez, Buenos Aires, Argentina
| | - Pablo Power
- Cátedra de Microbiología, Laboratorio de Resistencia Bacteriana, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María S Ramirez
- Department of Biological Science, California State University Fullerton, 800 N State College Blvd, Fullerton, CA, 92831, USA.
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Furlan JPR, Pitondo-Silva A, Braz VS, Gallo IFL, Stehling EG. Evaluation of different molecular and phenotypic methods for identification of environmental Burkholderia cepacia complex. World J Microbiol Biotechnol 2019; 35:39. [PMID: 30739255 DOI: 10.1007/s11274-019-2614-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/05/2019] [Indexed: 12/01/2022]
Abstract
The correct identification of different genera and bacterial species is essential, especially when these bacteria cause infections and appropriate therapies need to be chosen. Bacteria belonging to the Burkholderia cepacia complex are considered important opportunistic pathogens, causing different types of infections in immunocompromised, principally in patients with cystic fibrosis. Twenty-one isolates were obtained from different soil samples and identified by sequencing of 16S rRNA, 23S rRNA, recA gene, MLST and by VITEK 2 and MALDI-TOF MS systems. Then, statistical analyses were performed. VITEK 2 and MALDI-TOF MS systems showed different bacterial genera. Sequencing of the 16S rRNA, 23S rRNA gene and amplification of recA gene showed that all the isolates belong to the B. cepacia complex. Sequencing of the recA gene showed a predominance of B. cenocepacia. The PCR of the recA gene showed a high specificity when it is necessary to identify the bacteria belonging to the B. cepacia complex in comparison with 16S and 23S rRNA genes sequencing. MLST analyzes showed a diversity of STs, which have not yet been correlated to the species. Phenotypic identification was not suitable for the identification of these pathogens since in many cases different genera have been reported, including identification by using MALDI-TOF MS.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - André Pitondo-Silva
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.,School of Dentistry, University of Ribeirao Preto (UNAERP), Ribeirão Preto, Brazil
| | - Vânia Santos Braz
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Inara Fernanda Lage Gallo
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analysis, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café S/N. Monte Alegre, Ribeirão Preto, SP, 14040-903, Brazil.
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Gislason AS, Turner K, Domaratzki M, Cardona ST. Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia. Microb Genom 2019; 3. [PMID: 29208119 PMCID: PMC5729917 DOI: 10.1099/mgen.0.000140] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Burkholderia cenocepacia K56-2 belongs to the Burkholderia cepacia complex, a group of Gram-negative opportunistic pathogens that have large and dynamic genomes. In this work, we identified the essential genome of B. cenocepacia K56-2 using high-density transposon mutagenesis and insertion site sequencing (Tn-seq circle). We constructed a library of one million transposon mutants and identified the transposon insertions at an average of one insertion per 27 bp. The probability of gene essentiality was determined by comparing of the insertion density per gene with the variance of neutral datasets generated by Monte Carlo simulations. Five hundred and eight genes were not significantly disrupted, suggesting that these genes are essential for survival in rich, undefined medium. Comparison of the B. cenocepacia K56-2 essential genome with that of the closely related B. cenocepacia J2315 revealed partial overlapping, suggesting that some essential genes are strain-specific. Furthermore, 158 essential genes were conserved in B. cenocepacia and two species belonging to the Burkholderia pseudomallei complex, B. pseudomallei K96243 and Burkholderia thailandensis E264. Porins, including OpcC, a lysophospholipid transporter, LplT, and a protein involved in the modification of lipid A with aminoarabinose were found to be essential in Burkholderia genomes but not in other bacterial essential genomes identified so far. Our results highlight the existence of cell envelope processes that are uniquely essential in species of the genus Burkholderia for which the essential genomes have been identified by Tn-seq.
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Affiliation(s)
- April S Gislason
- 1Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Keith Turner
- 2Monsanto Company, 700 Chesterfield Parkway W, Chesterfield, MO, 63017, USA
| | - Mike Domaratzki
- 3Department of Computer Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Silvia T Cardona
- 4Department of Medical Microbiology & Infectious Diseases, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
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Distinct Modes of Promoter Recognition by Two Iron Starvation σ Factors with Overlapping Promoter Specificities. J Bacteriol 2019; 201:JB.00507-18. [PMID: 30455278 DOI: 10.1128/jb.00507-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023] Open
Abstract
OrbS and PvdS are extracytoplasmic function (ECF) σ factors that regulate transcription of operons required for the biosynthesis of the siderophores ornibactin and pyoverdine in the Burkholderia cepacia complex and Pseudomonas spp., respectively. Here we show that promoter recognition by OrbS requires specific tetrameric -35 and -10 element sequences that are strikingly similar to those of the consensus PvdS-dependent promoter. However, whereas Pseudomonas aeruginosa PvdS can serve OrbS-dependent promoters, OrbS cannot utilize PvdS-dependent promoters. To identify features present at OrbS-dependent promoters that facilitate recognition by OrbS, we carried out a detailed analysis of the nucleotide sequence requirements for promoter recognition by both OrbS and PvdS. This revealed that DNA sequence features located outside the sigma binding elements are required for efficient promoter utilization by OrbS. In particular, the presence of an A-tract extending downstream from the -35 element at OrbS-dependent promoters was shown to be an important contributor to OrbS specificity. Our observations demonstrate that the nature of the spacer sequence can have a major impact on promoter recognition by some ECF σ factors through modulation of the local DNA architecture.IMPORTANCE ECF σ factors regulate subsets of bacterial genes in response to environmental stress signals by directing RNA polymerase to promoter sequences known as the -35 and -10 elements. In this work, we identify the -10 and -35 elements that are recognized by the ECF σ factor OrbS. Furthermore, we demonstrate that efficient promoter utilization by this σ factor also requires a polyadenine tract located downstream of the -35 region. We propose that the unique architecture of A-tract DNA imposes conformational features on the -35 element that facilitates efficient recognition by OrbS. Our results show that sequences located between the core promoter elements can make major contributions to promoter recognition by some ECF σ factors.
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Richter AM, Fazli M, Schmid N, Shilling R, Suppiger A, Givskov M, Eberl L, Tolker-Nielsen T. Key Players and Individualists of Cyclic-di-GMP Signaling in Burkholderia cenocepacia. Front Microbiol 2019; 9:3286. [PMID: 30687272 PMCID: PMC6335245 DOI: 10.3389/fmicb.2018.03286] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Burkholderia cenocepacia H111 is an opportunistic pathogen associated with chronic lung infections in cystic fibrosis patients. Biofilm formation, motility and virulence of B. cenocepacia are regulated by the second messenger cyclic di-guanosine monophosphate (c-di-GMP). In the present study, we analyzed the role of all 25 putative c-di-GMP metabolizing proteins of B. cenocepacia H111 with respect to motility, colony morphology, pellicle formation, biofilm formation, and virulence. We found that RpfR is a key regulator of c-di-GMP signaling in B. cenocepacia, affecting a broad spectrum of phenotypes under various environmental conditions. In addition, we identified Bcal2449 as a regulator of B. cenocepacia virulence in Galleria mellonella larvae. While Bcal2449 consists of protein domains that may catalyze both c-di-GMP synthesis and degradation, only the latter was essential for larvae killing, suggesting that a decreased c-di-GMP level mediated by the Bcal2449 protein is required for virulence of B. cenocepacia. Finally, our work suggests that some individual proteins play a role in regulating exclusively motility (CdpA), biofilm formation (Bcam1160) or both (Bcam2836).
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Affiliation(s)
- Anja M Richter
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mustafa Fazli
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadine Schmid
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Rebecca Shilling
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Angela Suppiger
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Givskov
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Leo Eberl
- Department of Microbiology, University of Zurich, Zurich, Switzerland
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Diaz Caballero J, Clark ST, Wang PW, Donaldson SL, Coburn B, Tullis DE, Yau YCW, Waters VJ, Hwang DM, Guttman DS. A genome-wide association analysis reveals a potential role for recombination in the evolution of antimicrobial resistance in Burkholderia multivorans. PLoS Pathog 2018; 14:e1007453. [PMID: 30532201 PMCID: PMC6300292 DOI: 10.1371/journal.ppat.1007453] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/19/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023] Open
Abstract
Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We performed a population genomics study of 111 B. multivorans sputum isolates from one CF patient through three stages of infection including an early incident isolate, deep sampling of a one-year period of chronic infection occurring weeks before a lung transplant, and deep sampling of a post-transplant infection. We reconstructed the evolutionary history of the population and used a lineage-controlled genome-wide association study (GWAS) approach to identify genetic variants associated with antibiotic resistance. We found the incident isolate was basally related to the rest of the strains and more susceptible to antibiotics from three classes (β-lactams, aminoglycosides, quinolones). The chronic infection isolates diversified into multiple, distinct genetic lineages and showed reduced antimicrobial susceptibility to the same antibiotics. The post-transplant reinfection isolates derived from the same source as the incident isolate and were genetically distinct from the chronic isolates. They also had a level of susceptibility in between that of the incident and chronic isolates. We identified numerous examples of potential parallel pathoadaptation, in which multiple mutations were found in the same locus or even codon. The set of parallel pathoadaptive loci was enriched for functions associated with virulence and resistance. Our GWAS analysis identified statistical associations between a polymorphism in the ampD locus with resistance to β-lactams, and polymorphisms in an araC transcriptional regulator and an outer membrane porin with resistance to both aminoglycosides and quinolones. Additionally, these three loci were independently mutated four, three and two times, respectively, providing further support for parallel pathoadaptation. Finally, we identified a minimum of 14 recombination events, and observed that loci carrying putative parallel pathoadaptations and polymorphisms statistically associated with β-lactam resistance were over-represented in these recombinogenic regions. Cystic fibrosis (CF) is the most common lethal genetic disorder affecting individuals of European descent. Most CF patients die at a young age due to chronic lung infections. Among the organisms involved in these infections are bacteria from the Burkholderia cepacia complex (BCC), which are strongly associated with poor clinical prognosis. This study examines how the most prevalent BCC species among CF patients, B. multivorans, evolves within a single CF patient by studying the first B. multivorans isolate recovered from the patient, one hundred isolates recovered over a one year period during the chronic infection phase, and an additional ten isolates recovered after the reinfection of the transplanted lungs. We found that B. multivorans diversify phenotypically and genetically within the CF lung over the course of the infection, and evolves into a complex population during the chronic infection phase. We found that isolates collected from the post-transplant reinfection were more closely related to descendants of the original isolate rather than those recovered in the chronic infection. We identify genetic variants statistically associated with resistance to the antibiotics, and showed that some of these variants were found in regions that show patterns of recombination (genetic exchange) between strains. We also found that genes which were mutated multiple times during overall infection were more likely to be found in regions showing signals consistent with recombination. The presence of multiple independent mutations in a gene is a very strong signal that the gene helps bacteria adapt to their environment. Overall, this study provides insight into how pathogens adapt to the host during long-term infections, specific genes associated with antibiotic resistance, and the origin of new and recurrent infections.
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Affiliation(s)
- Julio Diaz Caballero
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Shawn T. Clark
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W. Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Sylva L. Donaldson
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Bryan Coburn
- Division of Infectious Diseases, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - D. Elizabeth Tullis
- Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Yvonne C. W. Yau
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Valerie J. Waters
- Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - David M. Hwang
- Latner Thoracic Surgery Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - David S. Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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45
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Gomes MC, Tasrini Y, Subramoni S, Agnoli K, Feliciano JR, Eberl L, Sokol P, O’Callaghan D, Vergunst AC. The afc antifungal activity cluster, which is under tight regulatory control of ShvR, is essential for transition from intracellular persistence of Burkholderia cenocepacia to acute pro-inflammatory infection. PLoS Pathog 2018; 14:e1007473. [PMID: 30513124 PMCID: PMC6301696 DOI: 10.1371/journal.ppat.1007473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/20/2018] [Accepted: 11/19/2018] [Indexed: 01/22/2023] Open
Abstract
The opportunistic pathogen Burkholderia cenocepacia is particularly life-threatening for cystic fibrosis (CF) patients. Chronic lung infections with these bacteria can rapidly develop into fatal pulmonary necrosis and septicaemia. We have recently shown that macrophages are a critical site for replication of B. cenocepacia K56-2 and the induction of fatal pro-inflammatory responses using a zebrafish infection model. Here, we show that ShvR, a LysR-type transcriptional regulator that is important for biofilm formation, rough colony morphotype and inflammation in a rat lung infection model, is also required for the induction of fatal pro-inflammatory responses in zebrafish larvae. ShvR was not essential, however, for bacterial survival and replication in macrophages. Temporal, rhamnose-induced restoration of shvR expression in the shvR mutant during intramacrophage stages unequivocally demonstrated a key role for ShvR in transition from intracellular persistence to acute fatal pro-inflammatory disease. ShvR has been previously shown to tightly control the expression of the adjacent afc gene cluster, which specifies the synthesis of a lipopeptide with antifungal activity. Mutation of afcE, encoding an acyl-CoA dehydrogenase, has been shown to give similar phenotypes as the shvR mutant. We found that, like shvR, afcE is also critical for the switch from intracellular persistence to fatal infection in zebrafish. The closely related B. cenocepacia H111 has been shown to be less virulent than K56-2 in several infection models, including Galleria mellonella and rats. Interestingly, constitutive expression of shvR in H111 increased virulence in zebrafish larvae to almost K56-2 levels in a manner that absolutely required afc. These data confirm a critical role for afc in acute virulence caused by B. cenocepacia that depends on strain-specific regulatory control by ShvR. We propose that ShvR and AFC are important virulence factors of the more virulent Bcc species, either through pro-inflammatory effects of the lipopeptide AFC, or through AFC-dependent membrane properties.
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Affiliation(s)
| | - Yara Tasrini
- VBMI, INSERM, Université de Montpellier, Nîmes, France
| | - Sujatha Subramoni
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Kirsty Agnoli
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | | | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Pamela Sokol
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Canada
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46
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Cullen L, O'Connor A, McCormack S, Owens RA, Holt GS, Collins C, Callaghan M, Doyle S, Smith D, Schaffer K, Fitzpatrick DA, McClean S. The involvement of the low-oxygen-activated locus of Burkholderia cenocepacia in adaptation during cystic fibrosis infection. Sci Rep 2018; 8:13386. [PMID: 30190507 PMCID: PMC6127331 DOI: 10.1038/s41598-018-31556-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Chronic infection with opportunistic pathogens including Burkholderia cepacia complex (Bcc) is a hallmark of cystic fibrosis (CF). We investigated the adaptive mechanisms facilitating chronic lung infection in sequential Bcc isolates from two siblings with CF (P1 and P2), one of whom also experienced intermittent blood-stream infections (P2). We previously showed increased lung cell attachment with colonisation time in both P1 and P2. WGS analysis confirmed that the isolates are closely related. Twelve genes showed three or more mutations, suggesting these were genes under selection. Single nucleotide polymorphisms (SNVs) in 45 regulatory genes were also observed. Proteomic analysis showed that the abundance of 149 proteins increased over 61-months in sputum isolates, and both time- and source-related alterations in protein abundance between the second patient’s isolates. A consistent time-dependent increase in abundance of 19 proteins encoded by a low-oxygen-activated (lxa) locus was observed in both sets of isolates. Attachment was dramatically reduced in a B. cenocepacia K56-2Δlxa-locus deletion mutant, further indicating that it encodes protein(s) involved in host-cell attachment. Time-related changes in virulence in Galleria mellonella or motility were not observed. We conclude that the lxa-locus, associated with anoxic persistence in vitro, plays a role in host-cell attachment and adaptation to chronic colonization in the hypoxic niche of the CF lung.
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Affiliation(s)
- Louise Cullen
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, 24, Ireland
| | - Andrew O'Connor
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, 24, Ireland.,School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Sarah McCormack
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Rebecca A Owens
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Giles S Holt
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, England
| | - Cassandra Collins
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, 24, Ireland
| | - Máire Callaghan
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, 24, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Co. Kildare, Ireland
| | - Darren Smith
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, England
| | - Kirsten Schaffer
- Department of Microbiology, St. Vincent's University Hospital, Elm Park, Dublin, Ireland
| | | | - Siobhán McClean
- Centre of Microbial Host Interactions, Institute of Technology Tallaght, Dublin, 24, Ireland. .,School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland.
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47
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In Vitro Susceptibility of Burkholderia cepacia Complex Isolated from Cystic Fibrosis Patients to Ceftazidime-Avibactam and Ceftolozane-Tazobactam. Antimicrob Agents Chemother 2018; 62:AAC.00590-18. [PMID: 29914964 DOI: 10.1128/aac.00590-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/11/2018] [Indexed: 01/05/2023] Open
Abstract
We tested the in vitro susceptibility of ceftazidime-avibactam and ceftolozane-tazobactam and 13 other antibiotics against 91 Burkholderia cepacia complex (BCC) strains isolated from cystic fibrosis patients since 2012. The highest susceptibility (82%) was found for trimethoprim-sulfamethoxazole. Eighty-one and 63% of all BCC strains were susceptible to ceftazidime-avibactam and ceftolozane-tazobactam, respectively. For temocillin, ceftazidime, piperacillin-tazobactam, and meropenem, at least 50% of the strains were susceptible. B. stabilis seems to be more resistant than other BCC species.
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48
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Vasireddy L, Bingle LEH, Davies MS. Antimicrobial activity of essential oils against multidrug-resistant clinical isolates of the Burkholderia cepacia complex. PLoS One 2018; 13:e0201835. [PMID: 30071118 PMCID: PMC6072103 DOI: 10.1371/journal.pone.0201835] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/22/2018] [Indexed: 12/14/2022] Open
Abstract
Members of the Burkholderia cepacia complex (Bcc) are an important cause of opportunistic or nosocomial infections that may be hard to treat due to a high incidence of multidrug resistance. We characterised a collection of 51 clinical isolates from this complex, assigning them to 18 sequence types using multi-locus sequence type analysis. Resistance to eight commonly used antibiotics was assessed using by using agar-dilution assays to calculate MICs and widespread and heterogeneous multidrug resistance was confirmed, with eight strains proving resistant to all antibiotics tested. Disc diffusion screening of antimicrobial activity of a range of plant essential oils against these Bcc isolates identified six oils with significant activity (lavender, lemongrass, marjoram, peppermint, tea tree and rosewood) and broth microdilution assays indicated that of these lemongrass and rosewood oils had the highest activity, with MIC50 values of 0.5% and MIC90 values of 1%. Comparison of MIC and MBC values showed that four of these six oils, including lemongrass and rosewood, were bacteriocidal rather than bacteriostatic in their effects. Qualitative analysis of the four bacteriocidal essential oils via GC/MS indicated the presence of 55 different component compounds, mostly monoterpenes. We assessed selected essential oil components as anti-Bcc agents and demonstrated that terpinen-4-ol and geraniol were effective with MICs of 0.125-0.5% (v/v) and 0.125-1% (v/v), respectively. Time-kill studies indicate that these two alcohols are effective against non-growing cells in an efflux-dependent manner. Analysis of bacterial leakage of potassium ions and 260 nm UV-absorbing material on treatment with terpinen-4-ol and geraniol suggested that the observed anti-Bcc activity was a consequence of membrane disruption. This finding was supported by a gas chromatography analysis of bacterial fatty acid methyl esters, which indicated changes in membrane fatty acid composition caused by terpinen-4-ol and geraniol. These essential oils or oil components may ultimately prove useful as therapeutic drugs, for example to treat Bcc infections in CF patients.
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Affiliation(s)
- Lakshmi Vasireddy
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Lewis E. H. Bingle
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
| | - Mark S. Davies
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Sunderland, United Kingdom
- * E-mail:
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49
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Bach E, Sant'Anna FH, Magrich Dos Passos JF, Balsanelli E, de Baura VA, Pedrosa FDO, de Souza EM, Passaglia LMP. Detection of misidentifications of species from the Burkholderia cepacia complex and description of a new member, the soil bacterium Burkholderia catarinensis sp. nov. Pathog Dis 2018; 75:3934654. [PMID: 28859310 DOI: 10.1093/femspd/ftx076] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/04/2017] [Indexed: 12/31/2022] Open
Abstract
The correct identification of bacteria from the Burkholderia cepacia complex (Bcc) is crucial for epidemiological studies and treatment of cystic fibrosis infections. However, genome-based identification tools are revealing many controversial Bcc species assignments. The aim of this work is to re-examine the taxonomic position of the soil bacterium B. cepacia 89 through polyphasic and genomic approaches. recA and 16S rRNA gene sequence analysis positioned strain 89 inside the Bcc group. However, based on the divergence score of seven concatenated allele sequences, and values of average nucleotide identity, and digital DNA:DNA hybridization, our results suggest that strain 89 is different from other Bcc species formerly described. Thus, we propose to classify Burkholderia sp. 89 as the novel species Burkholderia catarinensis sp. nov. with strain 89T (=DSM 103188T = BR 10601T) as the type strain. Moreover, our results call the attention to some probable misidentifications of Bcc genomes at the National Center for Biotechnology Information database.
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Affiliation(s)
- Evelise Bach
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | - Fernando Hayashi Sant'Anna
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
| | | | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR 80060-000, Brazil
| | - Luciane Maria Pereira Passaglia
- Laboratório de Microbiologia Agrícola, Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Bento Goncalves 9500, Porto Alegre, RS 91501-970, Brazil
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50
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[The controversial Burkholderia cepacia complex, a group of plant growth promoting species and plant, animals and human pathogens]. Rev Argent Microbiol 2018; 51:84-92. [PMID: 29691107 DOI: 10.1016/j.ram.2018.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 10/10/2017] [Accepted: 01/03/2018] [Indexed: 11/22/2022] Open
Abstract
The Burkholderia cepacia complex is a group of 22 species, which are known as opportunistic pathogens in immunocompromised people, especially those suffering from cystic fibrosis. It is also found in nosocomial infections and is difficult to eradicate due to intrinsic resistance to several antibiotics. The species have large genomes (up to 9 Mbp), distributed into 2-5 replicons. These features significantly contribute to genome plasticity, which makes them thrive in different environments like soil, water, plants or even producing nodules in legume plants. Some B. cepacia complex species are beneficial in bioremediation, biocontrol and plant-growth promotion. However, because the B. cepacia complex is involved in human infection, its use in agriculture is restricted. B. cepacia complex is being constantly studied due to the health problems that it causes and because of its agricultural potential. In this review, the history of B. cepacia complex and the most recently published information related to this complex are revised.
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