101
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Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules. Int J Syst Evol Microbiol 2013; 63:3950-3957. [DOI: 10.1099/ijs.0.048777-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus
Burkholderia
, with the representative strain WSM5005T being most closely related to
Burkholderia tuberum
(98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus
Burkholderia
. Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus
Burkholderia
with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.
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102
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De Meyer SE, Cnockaert M, Ardley JK, Trengove RD, Garau G, Howieson JG, Vandamme P. Burkholderia rhynchosiae sp. nov., isolated from Rhynchosia ferulifolia root nodules. Int J Syst Evol Microbiol 2013; 63:3944-3949. [DOI: 10.1099/ijs.0.048751-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-negative, rod-shaped bacteria were isolated from root nodules of the South African legume Rhynchosia ferulifolia and authenticated on this host. Based on phylogenetic analysis of the 16S rRNA gene, strains WSM3930 and WSM3937T belonged to the genus
Burkholderia
, with the highest degree of sequence similarity to
Burkholderia terricola
(98.84 %). Additionally, the housekeeping genes gyrB and recA were analysed since 16S rRNA gene sequences are highly similar between closely related species of the genus
Burkholderia
. The results obtained for both housekeeping genes, gyrB and recA, showed the highest degree of sequence similarity of the novel strains towards
Burkholderia caledonica
LMG 19076T (94.2 % and 94.5 %, respectively). Chemotaxonomic data, including fatty acid profiles and respiratory quinone data supported the assignment of strains WSM3930 and WSM3937T to the genus
Burkholderia
. DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains WSM3930 and WSM3937T from the most closely related species of the genus
Burkholderia
with validly published names. We conclude, therefore, that these strains represent a novel species for which the name Burkholderia rhynchosiae sp. nov. is proposed, with strain WSM3937T ( = LMG 27174T = HAMBI 3354T) as the type strain.
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Affiliation(s)
- Sofie E. De Meyer
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Julie K. Ardley
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Robert D. Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Giovanni Garau
- Dipartimento di Scienze Ambientali Agrarie e Biotecnologie Agro-Alimentari (DiSAABA), University of Sassari, Italy
| | - John G. Howieson
- Centre for Rhizobium Studies, Murdoch University, Western Australia 6150, Australia
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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103
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Inhaled aztreonam for chronic Burkholderia infection in cystic fibrosis: a placebo-controlled trial. J Cyst Fibros 2013; 13:296-305. [PMID: 24176390 DOI: 10.1016/j.jcf.2013.08.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/28/2013] [Accepted: 08/30/2013] [Indexed: 11/24/2022]
Abstract
BACKGROUND Individuals with Burkholderia spp. infection have historically been excluded from efficacy trials of inhaled antibiotics, including aztreonam for inhalation solution (AZLI). METHODS A double-blind, placebo-controlled, 24-week trial of continuous AZLI/placebo treatment was undertaken in individuals with cystic fibrosis (CF) and chronic Burkholderia spp. infection. All subjects also received usual medical care (determined by their physicians). Additional antibiotic use was not restricted. RESULTS Baseline FEV1% predicted values ranged from 15.8% to 114.6%. No significant treatment differences (AZLI vs. placebo) were observed at week 24 for any endpoints, including FEV1% predicted, number of respiratory exacerbations requiring systemic/inhaled antibiotics, or hospitalizations. Continuous AZLI administration was well tolerated. Burkholderia spp. susceptibility to antibiotics commonly used in CF therapy showed little change. CONCLUSIONS 24-weeks of continuous AZLI treatment did not significantly improve lung function in CF subjects with chronic Burkholderia spp. infection. Non-study antibiotic use may have confounded any potential AZLI effects.
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104
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Factors influencing acquisition of Burkholderia cepacia complex organisms in patients with cystic fibrosis. J Clin Microbiol 2013; 51:3975-80. [PMID: 24048536 DOI: 10.1128/jcm.01360-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia cepacia complex organisms are important transmissible pathogens found in cystic fibrosis (CF) patients. In recent years, the rates of cross-infection of epidemic strains have declined due to effective infection control efforts. However, cases of sporadic B. cepacia complex infection continue to occur in some centers. The acquisition pathways and clinical outcomes of sporadic B. cepacia complex infection are unclear. We sought to determine the patient clinical characteristics, outcomes, incidence, and genotypic relatedness for all cases of B. cepacia complex infection at two CF centers. We also sought to study the external conditions that influence the acquisition of infection. From 2001 to 2011, 67 individual organisms were cultured from the respiratory samples of 64 patients. Sixty-five percent of the patients were adults, in whom chronic infections were more common (68%) (P = 0.006). The incidence of B. cepacia complex infection increased by a mean of 12% (95% confidence interval [CI], 3 to 23%) per year. The rates of transplantation and death were similar in the incident cases who developed chronic infection compared to those in patients with chronic Pseudomonas aeruginosa infection. Multilocus sequence typing revealed 50 individual strains from 65 isolates. Overall, 85% of the patients were infected with unique strains, suggesting sporadic acquisition of infection. The yearly incidence of nonepidemic B. cepacia complex infection was positively correlated with the amount of rainfall in the two sites examined: subtropical Brisbane (r = 0.65, P = 0.031) and tropical Townsville (r = 0.82, P = 0.002). This study demonstrates that despite strict cohort segregation, new cases of unrelated B. cepacia complex infection continue to occur. These data also support an environmental origin of infection and suggest that climate conditions may be associated with the acquisition of B. cepacia complex infections.
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105
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Vandamme P, De Brandt E, Houf K, Salles JF, Dirk van Elsas J, Spilker T, LiPuma JJ. Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil. Int J Syst Evol Microbiol 2013; 63:4707-4718. [PMID: 23959831 DOI: 10.1099/ijs.0.048900-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Analysis of partial gyrB gene sequences revealed six taxa in a group of 17 Burkholderia glathei-like isolates which were further examined by (GTG)5-PCR fingerprinting, 16S rRNA gene sequence analysis, DNA-DNA hybridizations, determination of the DNA G+C content, whole-cell fatty acid analysis and an analysis of cell and colony morphology and more than 180 biochemical characteristics. The results demonstrated that one taxon consisting of three human clinical isolates represented Burkholderia zhejiangensis, a recently described methyl-parathion-degrading bacterium isolated from a wastewater-treatment system in China. The remaining taxa represented five novel species isolated from soil or rhizosphere soil samples, and could be distinguished by both genotypic and phenotypic characteristics. We therefore propose to formally classify these bacteria as Burkholderia humi sp. nov. (type strain, LMG 22934(T) = CCUG 63059(T)), Burkholderia choica sp. nov. (type strain, LMG 22940(T) = CCUG 63063(T)), Burkholderia telluris sp. nov. (type strain, LMG 22936(T) = CCUG 63060(T)), Burkholderia udeis sp. nov. (type strain, LMG 27134(T) = CCUG 63061(T)) and Burkholderia terrestris sp. nov. (type strain, LMG 22937(T) = CCUG 63062(T)).
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Affiliation(s)
- Peter Vandamme
- Laboratorium voor Microbiologie, Vakgroep Biochemie en microbiologie, Faculteit Wetenschappen, Universiteit Gent, Gent, Belgium
| | - Evie De Brandt
- Laboratorium voor Microbiologie, Vakgroep Biochemie en microbiologie, Faculteit Wetenschappen, Universiteit Gent, Gent, Belgium
| | - Kurt Houf
- Vakgroep Veterinaire Volksgezondheid en Voedselveiligheid, Faculteit Diergeneeskunde, Universiteit Gent, Gent, Belgium
| | - Joana Falcão Salles
- Department of Microbial Ecology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Center for Life Sciences, University of Groningen, The Netherlands
| | - Theodore Spilker
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John J LiPuma
- Department of Pediatrics and Communicable Disease, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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106
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Peeters C, Zlosnik JEA, Spilker T, Hird TJ, LiPuma JJ, Vandamme P. Burkholderia pseudomultivorans sp. nov., a novel Burkholderia cepacia complex species from human respiratory samples and the rhizosphere. Syst Appl Microbiol 2013; 36:483-9. [PMID: 23867250 DOI: 10.1016/j.syapm.2013.06.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/11/2013] [Accepted: 06/14/2013] [Indexed: 11/24/2022]
Abstract
Eleven Burkholderia cepacia-like isolates of human clinical and environmental origin were examined by a polyphasic approach including recA and 16S rRNA sequence analysis, multilocus sequence analysis (MLSA), DNA base content determination, fatty acid methyl ester analysis, and biochemical characterization. The results of this study demonstrate that these isolates represent a novel species within the B. cepacia complex (Bcc) for which we propose the name Burkholderia pseudomultivorans. The type strain is strain LMG 26883(T) (=CCUG 62895(T)). B. pseudomultivorans can be differentiated from other Bcc species by recA gene sequence analysis, MLSA, and several biochemical tests including growth at 42°C, acidification of sucrose and adonitol, lysine decarboxylase and β-galactosidase activity, and esculin hydrolysis.
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107
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SNaPBcen: a novel and practical tool for genotyping Burkholderia cenocepacia. J Clin Microbiol 2013; 51:2646-53. [PMID: 23761147 DOI: 10.1128/jcm.01019-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Burkholderia cenocepacia is the most prevalent and feared member of the Burkholderia cepacia complex in lung infections of cystic fibrosis (CF). Genotyping and monitoring of long-term colonization are critical at clinical units; however, the differentiation of specific lineages performed by multilocus sequence typing (MLST) is still limited to a small number of isolates due to the high cost and time-consuming procedure. The aim of this study was to optimize a protocol (the SNaPBcen assay) for extensive bacterial population studies. The strategy used for the SNaPBcen assay is based on targeting single nucleotide polymorphisms (SNPs) located in MLST genes instead of sequencing full MLST sequences. Nonpolymorphic and redundant MLST positions were eliminated, and a set of 24 polymorphisms included in the SNaPBcen assay ensures a high-resolution genomic characterization. These polymorphisms were identified based on the comparative analysis of 137 B. cenocepacia MLST profiles available online (http://pubmlst.org/bcc/). The group of 81 clinical isolates of B. cenocepacia examined in this study using the SNaPBcen assay revealed 51 distinct profiles, and a final discriminatory power of 0.9997 compared with MLST was determined. The SNaPBcen assay was able to reveal isolates with microvariations and the presence of multiple clonal variants in patients chronically colonized with B. cenocepacia. Main phylogenetic subgroups IIIA, IIIB, and IIIC of B. cenocepacia could be separated by the Gl94R polymorphism included in the panel. The SNaPBcen assay proved to be a rapid and robust alternative to the standard MLST for B. cenocepacia, allowing the simultaneous analysis of multiple polymorphisms following amplification and mini-sequencing reactions.
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108
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Voronina OL, Chernukha MY, Shaginyan IA, Kunda MS, Avetisyan LR, Orlova AA, Lunin VG, Avakyan LV, Kapranov NI, Amelina EL, Chuchalin AG, Gintsburg AL. Characterization of genotypes for Burkholderia cepacia complex strains isolated from patients in hospitals of the Russian federation. MOLECULAR GENETICS, MICROBIOLOGY AND VIROLOGY 2013. [DOI: 10.3103/s0891416813020079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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109
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Phylogenetic analysis of burkholderia species by multilocus sequence analysis. Curr Microbiol 2013; 67:51-60. [PMID: 23404651 DOI: 10.1007/s00284-013-0330-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 01/21/2013] [Indexed: 01/16/2023]
Abstract
Burkholderia comprises more than 60 species of environmental, clinical, and agro-biotechnological relevance. Previous phylogenetic analyses of 16S rRNA, recA, gyrB, rpoB, and acdS gene sequences as well as genome sequence comparisons of different Burkholderia species have revealed two major species clusters. In this study, we undertook a multilocus sequence analysis of 77 type and reference strains of Burkholderia using atpD, gltB, lepA, and recA genes in combination with the 16S rRNA gene sequence and employed maximum likelihood and neighbor-joining criteria to test this further. The phylogenetic analysis revealed, with high supporting values, distinct lineages within the genus Burkholderia. The two large groups were named A and B, whereas the B. rhizoxinica/B. endofungorum, and B. andropogonis groups consisted of two and one species, respectively. The group A encompasses several plant-associated and saprophytic bacterial species. The group B comprises the B. cepacia complex (opportunistic human pathogens), the B. pseudomallei subgroup, which includes both human and animal pathogens, and an assemblage of plant pathogenic species. The distinct lineages present in Burkholderia suggest that each group might represent a different genus. However, it will be necessary to analyze the full set of Burkholderia species and explore whether enough phenotypic features exist among the different clusters to propose that these groups should be considered separate genera.
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110
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Dedeckova K, Kalferstova L, Strnad H, Vavrova J, Drevinek P. Novel diagnostic PCR assay for Burkholderia cenocepacia epidemic strain ST32 and its utility in monitoring infection in cystic fibrosis patients. J Cyst Fibros 2013; 12:475-81. [PMID: 23317764 DOI: 10.1016/j.jcf.2012.12.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/30/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND A highly transmissible Burkholderia cenocepacia sequence type (ST) 32 strain caused a major outbreak at the Prague Cystic Fibrosis (CF) Centre in the late 1990s and early 2000s. Because a large number of CF patients were affected by ST32, a rapid and easy-to-use diagnostic tool for ST32 infection was urgently needed for the detection of new cases as well as for long-term surveillance. The present study sought to identify unique DNA sequences within the ST32 genome to develop an ST32 strain-specific PCR assay. METHODS Genomic subtractive hybridisation between B. cenocepacia ST32 and the closely related genome-sequenced strain B. cenocepacia ST28 identified a 325 bp long region that was absent in all but one Burkholderia strain, as demonstrated by our newly designed PCR. RESULTS Out of 57 strains, only B. cenocepacia ST33 cross-reacted with ST32, resulting in a PCR specificity of 98.2%. This specificity was further tested by various genotyping methods, which revealed the practical indistinguishibility of ST32 and ST33. The PCR sensitivity, checked on a panel of 50 ST32 clinical isolates, was 100%. A closer examination of the ST32-specific sequence revealed no significant homology apart from a fragment of the ISBmu3 transposase. CONCLUSIONS This novel ST32-specific PCR assay allows the rapid and reliable detection of a globally distributed B. cenocepacia epidemic strain. Its routine use is especially well suited to infection surveillance programs for CF populations with a high rate of ST32 infection. This PCR method can also be used to detect ST33, a clonal variant of ST32.
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Affiliation(s)
- Klara Dedeckova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, V Uvalu 84, Prague 5, 150 06, Czech Republic
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111
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Almeida LA, Araujo R. Highlights on molecular identification of closely related species. INFECTION GENETICS AND EVOLUTION 2012; 13:67-75. [PMID: 22982158 DOI: 10.1016/j.meegid.2012.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 10/27/2022]
Abstract
The term "complex" emerged in the literature at the beginning of the genomic era associated to taxonomy and grouping organisms that belong to different species but exhibited similar patterns according to their morphological, physiological and/or other phenotypic features. DNA-DNA hybridization values ~70% and high identity on 16S rRNA gene sequences were recommended for species delineation. Electrophoretic methods showed in some cases to be useful for species identification and population structure but the reproducibility was questionable. Later, the implementation of polyphasic approaches involving phenotypic and molecular methods brought new insights into the analysis of population structure and phylogeny of several "species complexes", allowing the identification of new closely related species. Likewise, the introduction of multilocus sequence typing and sequencing analysis of several genes offered an evolutionary perspective to the term "species complex". Several centres worldwide have recently released increasing genetic information on distinct microbial species. A brief review will be presented to highlight the definition of "species complex" for selected microorganisms, mainly the prokaryotic Acinetobacter calcoaceticus -Acinetobacter baumannii, Borrelia burgdorferi sensu lato, Burkholderia cepacia, Mycobacterium tuberculosis and Nocardia asteroides complexes, and the eukaryotic Aspergillus fumigatus, Leishmania donovani and Saccharomyces sensu stricto complexes. The members of these complexes may show distinct epidemiology, pathogenicity and susceptibility, turning critical their correct identification. Dynamics of prokaryotic and eukaryotic genomes can be very distinct and the term "species complex" should be carefully extended.
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Affiliation(s)
- Lígia A Almeida
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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112
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification of Burkholderia pseudomallei: importance of expanding databases with pathogens endemic to different localities. J Clin Microbiol 2012; 50:3142-3. [PMID: 22718946 DOI: 10.1128/jcm.01349-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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113
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Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK, Venturi V. Common features of environmental and potentially beneficial plant-associated Burkholderia. MICROBIAL ECOLOGY 2012; 63:249-266. [PMID: 21850446 DOI: 10.1007/s00248-011-9929-1] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 08/01/2011] [Indexed: 05/31/2023]
Abstract
The genus Burkholderia comprises more than 60 species isolated from a wide range of niches. Although they have been shown to be diverse and ubiquitously distributed, most studies have thus far focused on the pathogenic species due to their clinical importance. However, the increasing number of recently described Burkholderia species associated with plants or with the environment has highlighted the division of the genus into two main clusters, as suggested by phylogenetical analyses. The first cluster includes human, animal, and plant pathogens, such as Burkholderia glumae, Burkholderia pseudomallei, and Burkholderia mallei, as well as the 17 defined species of the Burkholderia cepacia complex, while the other, more recently established cluster comprises more than 30 non-pathogenic species, which in most cases have been found to be associated with plants, and thus might be considered to be potentially beneficial. Several species from the latter group share characteristics that are of use when associating with plants, such as a quorum sensing system, the presence of nitrogen fixation and/or nodulation genes, and the ability to degrade aromatic compounds. This review examines the commonalities in this growing subgroup of Burkholderia species and discusses their prospective biotechnological applications.
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Affiliation(s)
- Zulma Rocío Suárez-Moreno
- Bacteriology Group, International Centre for Genetic Engineering & Biotechnology, Padriciano 99, 34149 Trieste, Italy
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114
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Lemaire B, Van Oevelen S, De Block P, Verstraete B, Smets E, Prinsen E, Dessein S. Identification of the bacterial endosymbionts in leaf nodules of Pavetta (Rubiaceae). Int J Syst Evol Microbiol 2012; 62:202-209. [DOI: 10.1099/ijs.0.028019-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three genera in the Rubiaceae (Pavetta, Psychotria and Sericanthe) harbour bacterial endosymbionts within leaf nodules or galls. The present paper identifies the bacterial endophytes in three leaf-nodulating Pavetta species. In order to reveal their identity and assess their phylogenetic position, 16S rRNA, recA and gyrB genes were sequenced from an extensive sampling of Burkholderia strains. This multigene approach results in a robust phylogeny, which places the bacterial endosymbionts of Pavetta at two distinct positions within the genus Burkholderia (class Betaproteobacteria), suggesting that leaf-nodulating endosymbionts within Pavetta have different origins. The endophytes of nodulated Psychotria species were recognized as the closest relatives to the Pavetta endosymbionts. Our results suggest that the endosymbionts of Pavetta represent novel species, which can be classified as ‘Candidatus Burkholderia hispidae’, ‘Candidatus Burkholderia rigidae’ and ‘Candidatus Burkholderia schumannianae’.
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Affiliation(s)
- Benny Lemaire
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
| | - Sandra Van Oevelen
- Laboratory of Plant Growth and Development, University of Antwerp, Department of Biology, Groenenborgerlaan 171, BE-2020 Antwerp, Belgium
| | - Petra De Block
- National Botanic Garden of Belgium, Domein van Bouchout, BE-1860 Meise, Belgium
| | - Brecht Verstraete
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
| | - Erik Smets
- National Herbarium of The Netherlands, Leiden University, PO Box 9514, 2300 RA Leiden, The Netherlands
- Netherlands Centre for Biodiversity Naturalis, PO Box 9517, 2300 RA Leiden, The Netherlands
- Laboratory of Plant Systematics, K.U. Leuven, Kasteelpark Arenberg 31, PO Box 2437, BE-3001 Leuven, Belgium
| | - Els Prinsen
- Laboratory of Plant Growth and Development, University of Antwerp, Department of Biology, Groenenborgerlaan 171, BE-2020 Antwerp, Belgium
| | - Steven Dessein
- National Botanic Garden of Belgium, Domein van Bouchout, BE-1860 Meise, Belgium
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115
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Lemaire B, Vandamme P, Merckx V, Smets E, Dessein S. Bacterial leaf symbiosis in angiosperms: host specificity without co-speciation. PLoS One 2011; 6:e24430. [PMID: 21915326 PMCID: PMC3168474 DOI: 10.1371/journal.pone.0024430] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 08/09/2011] [Indexed: 11/25/2022] Open
Abstract
Bacterial leaf symbiosis is a unique and intimate interaction between bacteria and flowering plants, in which endosymbionts are organized in specialized leaf structures. Previously, bacterial leaf symbiosis has been described as a cyclic and obligate interaction in which the endosymbionts are vertically transmitted between plant generations and lack autonomous growth. Theoretically this allows for co-speciation between leaf nodulated plants and their endosymbionts. We sequenced the nodulated Burkholderia endosymbionts of 54 plant species from known leaf nodulated angiosperm genera, i.e. Ardisia, Pavetta, Psychotria and Sericanthe. Phylogenetic reconstruction of bacterial leaf symbionts and closely related free-living bacteria indicates the occurrence of multiple horizontal transfers of bacteria from the environment to leaf nodulated plant species. This rejects the hypothesis of a long co-speciation process between the bacterial endosymbionts and their host plants. Our results indicate a recent evolutionary process towards a stable and host specific interaction confirming the proposed maternal transmission mode of the endosymbionts through the seeds. Divergence estimates provide evidence for a relatively recent origin of bacterial leaf symbiosis, dating back to the Miocene (5-23 Mya). This geological epoch was characterized by cool and arid conditions, which may have triggered the origin of bacterial leaf symbiosis.
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Affiliation(s)
- Benny Lemaire
- Laboratory of Plant Systematics, K.U.Leuven, Leuven, Belgium.
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116
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Bacterial leaf symbiosis in Ardisia (Myrsinoideae, Primulaceae): molecular evidence for host specificity. Res Microbiol 2011; 162:528-34. [DOI: 10.1016/j.resmic.2011.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 03/14/2011] [Indexed: 11/18/2022]
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117
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Gautam V, Singhal L, Ray P. Burkholderia cepacia complex: beyond pseudomonas and acinetobacter. Indian J Med Microbiol 2011; 29:4-12. [PMID: 21304187 DOI: 10.4103/0255-0857.76516] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Burkholderia cepacia complex (BCC) is an important nosocomial pathogen in hospitalised patients, particularly those with prior broad-spectrum antibacterial therapy. BCC causes infections that include bacteraemia, urinary tract infection, septic arthritis, peritonitis and respiratory tract infection. Due to high intrinsic resistance and being one of the most antimicrobial-resistant organisms encountered in the clinical laboratory, these infections can prove very difficult to treat and, in some cases, result in death. Patients with cystic fibrosis (CF) and those with chronic granulomatous disease are predisposed to infection by BCC bacteria. BCC survives and multiplies in aqueous hospital environments, including disinfectant agents and intravenous fluids, where it may persist for long periods. Outbreaks and pseudo-outbreaks of BCC septicaemia have been documented in intensive care units, oncology units and renal failure patients. BCC is phenotypically unremarkable, and the complex exhibits an extensive diversity of genotypes. BCC is of increasing importance for agriculture and bioremediation because of their antinematodal and antifungal properties as well as their capability to degrade a wide range of toxic compounds. It has always been a tedious task for a routine microbiological laboratory to identify the nonfermenting gram-negative bacilli, and poor laboratory proficiency in identification of this nonfermenter worldwide still prevails. In India, there are no precise reports of the prevalence of BCC infection, and in most cases, these bacteria have been ambiguously reported as nonfermenting gram-negative bacilli or simply Pseudomonas spp. The International Burkholderia cepacia Working Group is open to clinicians and scientists interested in advancing knowledge of BCC infection/colonisation in persons with CF through the collegial exchange of information and promotion of coordinated approaches to research.
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Affiliation(s)
- V Gautam
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
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Verstraete B, Van Elst D, Steyn H, Van Wyk B, Lemaire B, Smets E, Dessein S. Endophytic bacteria in toxic South African plants: identification, phylogeny and possible involvement in gousiekte. PLoS One 2011; 6:e19265. [PMID: 21541284 PMCID: PMC3082559 DOI: 10.1371/journal.pone.0019265] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 03/24/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND South African plant species of the genera Fadogia, Pavetta and Vangueria (all belonging to Rubiaceae) are known to cause gousiekte (literally 'quick disease'), a fatal cardiotoxicosis of ruminants characterised by acute heart failure four to eight weeks after ingestion. Noteworthy is that all these plants harbour endophytes in their leaves: nodulating bacteria in specialized nodules in Pavetta and non-nodulating bacteria in the intercellular spaces between mesophyll cells in Fadogia and Vangueria. PRINCIPAL FINDINGS Isolation and analyses of these endophytes reveal the presence of Burkholderia bacteria in all the plant species implicated in gousiekte. Although the nodulating and non-nodulating bacteria belong to the same genus, they are phylogenetically not closely related and even fall in different bacterial clades. Pavetta harborii and Pavetta schumanniana have their own specific endophyte--Candidatus Burkholderia harborii and Candidatus Burkholderia schumanniana--while the non-nodulating bacteria found in the other gousiekte-inducing plants show high similarity to Burkholderia caledonica. In this group, the bacteria are host specific at population level. Investigation of gousiekte-inducing plants from other African countries resulted in the discovery of the same endophytes. Several other plants of the genera Afrocanthium, Canthium, Keetia, Psydrax, Pygmaeothamnus and Pyrostria were tested and were found to lack bacterial endophytes. CONCLUSIONS The discovery and identification of Burkholderia bacteria in gousiekte-inducing plants open new perspectives and opportunities for research not only into the cause of this economically important disease, but also into the evolution and functional significance of bacterial endosymbiosis in Rubiaceae. Other South African Rubiaceae that grow in the same area as the gousiekte-inducing plants were found to lack bacterial endophytes which suggests a link between bacteria and gousiekte. The same bacteria are consistently found in gousiekte-inducing plants from different regions indicating that these plants will also be toxic to ruminants in other African countries.
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Affiliation(s)
- Brecht Verstraete
- Laboratory of Plant Systematics, Katholieke Universiteit Leuven, Leuven, Belgium.
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Vandamme P, Dawyndt P. Classification and identification of the Burkholderia cepacia complex: Past, present and future. Syst Appl Microbiol 2011; 34:87-95. [DOI: 10.1016/j.syapm.2010.10.002] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2010] [Revised: 10/20/2010] [Accepted: 10/24/2010] [Indexed: 11/24/2022]
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Novel pan-genomic analysis approach in target selection for multiplex PCR identification and detection of Burkholderia pseudomallei, Burkholderia thailandensis, and Burkholderia cepacia complex species: a proof-of-concept study. J Clin Microbiol 2010; 49:814-21. [PMID: 21177905 DOI: 10.1128/jcm.01702-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Burkholderia pseudomallei, Burkholderia thailandensis, and the Burkholderia cepacia complex differ greatly in pathogenicity and epidemiology. Yet, they are occasionally misidentified by biochemical profiling, and even 16S rRNA gene sequencing may not offer adequate discrimination between certain species groups. Using the 23 B. pseudomallei, four B. thailandensis, and 16 B. cepacia complex genome sequences available, we identified gene targets specific to each of them (a Tat domain protein, a 70-kDa protein, and a 12-kDa protein for B. pseudomallei, B. thailandensis, and the B. cepacia complex, respectively), with an in-house developed algorithm. Using these targets, we designed a robust multiplex PCR assay useful for their identification and detection from soil and simulated sputum samples. For all 43 B. pseudomallei, seven B. thailandensis, and 20 B. cepacia complex (B. multivorans, n = 6; B. cenocepacia, n = 3; B. cepacia, n = 4; B. arboris, n = 2; B. contaminans, B. anthina, and B. pyrrocinia, n = 1 each; other unnamed members, n = 2) isolates, the assay produced specific products of predicted size without false positives or negatives. Of the 60 soil samples screened, 19 (31.6%) and 29 (48.3%) were positive for B. pseudomallei and the B. cepacia complex, respectively, and in four (6.7%) soil samples, the organisms were codetected. DNA sequencing confirmed that all PCR products originated from their targeted loci. This novel pan-genomic analysis approach in target selection is simple, computationally efficient, and potentially applicable to any species that harbors species-specific genes. A multiplex PCR assay for rapid and accurate identification and detection of B. pseudomallei, B. thailandensis, and the B. cepacia complex was developed and verified.
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Pope CE, Short P, Carter PE. Species distribution of Burkholderia cepacia complex isolates in cystic fibrosis and non-cystic fibrosis patients in New Zealand. J Cyst Fibros 2010; 9:442-6. [DOI: 10.1016/j.jcf.2010.08.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 08/12/2010] [Accepted: 08/15/2010] [Indexed: 10/19/2022]
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Abstract
Infection of the airways remains the primary cause of morbidity and mortality in persons with cystic fibrosis (CF). This review describes salient features of the epidemiologies of microbial species that are involved in respiratory tract infection in CF. The apparently expanding spectrum of species causing infection in CF and recent changes in the incidences and prevalences of infection due to specific bacterial, fungal, and viral species are described. The challenges inherent in tracking and interpreting rates of infection in this patient population are discussed.
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Direct culture-independent Strain typing of Burkholderia cepacia complex in sputum samples from patients with cystic fibrosis. J Clin Microbiol 2010; 48:1888-91. [PMID: 20181898 DOI: 10.1128/jcm.02359-09] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined if multilocus sequence typing (MLST), a method for genotyping and species identification of Burkholderia cepacia complex bacteria, could be applied directly to cystic fibrosis sputum. The redesigned nested-PCR MLST format was successfully used to accurately identify strains in 23 sputum samples, of which 8 were culture negative.
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