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Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway Isolate. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00298-14. [PMID: 24723723 PMCID: PMC3983312 DOI: 10.1128/genomea.00298-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Burkholderia cepacia complex (BCC) is a group of related bacterial species that are commonly isolated from environmental samples. Members of the BCC can cause respiratory infections in cystic fibrosis patients and immunocompromised individuals. We report here the genome sequence of Burkholderia cenocepacia H111, a well-studied model strain of the BCC.
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102
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Draghi WO, Peeters C, Cnockaert M, Snauwaert C, Wall LG, Zorreguieta A, Vandamme P. Burkholderia cordobensis sp. nov., from agricultural soils. Int J Syst Evol Microbiol 2014; 64:2003-2008. [PMID: 24623656 DOI: 10.1099/ijs.0.059667-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-negative, rod-shaped bacteria were isolated from agricultural soils in Córdoba province in central Argentina. Their 16S rRNA gene sequences demonstrated that they belong to the genus Burkholderia, with Burkholderia zhejiangensis as most closely related formally named species; this relationship was confirmed through comparative gyrB sequence analysis. Whole-cell fatty acid analysis supported their assignment to the genus Burkholderia. Burkholderia sp. strain YI23, for which a whole-genome sequence is available, represents the same taxon, as demonstrated by its highly similar 16S rRNA (100% similarity) and gyrB (99.1-99.7%) gene sequences. The results of DNA-DNA hybridization experiments and physiological and biochemical characterization further substantiated the genotypic and phenotypic distinctiveness of the Argentinian soil isolates, for which the name Burkholderia cordobensis sp. nov. is proposed, with strain MMP81(T) ( = LMG 27620(T) = CCUG 64368(T)) as the type strain.
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Affiliation(s)
- Walter O Draghi
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Fundación Instituto Leloir and IIBA - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Cindy Snauwaert
- BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luis G Wall
- Science and Technology Department, National University of Quilmes, Roque Sáenz Peña 352, Bernal, B1876BXD Buenos Aires, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir and IIBA - Consejo Nacional de Investigaciones Científicas y Tecnológicas, Patricias Argentinas 435, C1405BWE Buenos Aires, Argentina
| | - 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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Tümmler B, Wiehlmann L, Klockgether J, Cramer N. Advances in understanding Pseudomonas. F1000PRIME REPORTS 2014; 6:9. [PMID: 24592321 PMCID: PMC3913036 DOI: 10.12703/p6-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas aeruginosa, the type species of pseudomonads, is an opportunistic pathogen that colonizes a wide range of niches. Current genome sequencing projects are producing previously inconceivable detail about the population biology and evolution of P. aeruginosa. Its pan-genome has a larger genetic repertoire than the human genome, which explains the broad metabolic capabilities of P. aeruginosa and its ubiquitous distribution in aquatic habitats. P. aeruginosa may persist in the airways of individuals with cystic fibrosis for decades. The ongoing whole-genome analyses of serial isolates from cystic fibrosis patients provide the so far singular opportunity to monitor the microevolution of a bacterial pathogen during chronic infection over thousands of generations. Although the evolution in cystic fibrosis lungs is neutral overall, some pathoadaptive mutations are selected during the within-host evolutionary process. Even a single mutation may be sufficient to generate novel complex traits provided that predisposing mutational events have previously occurred in the clonal lineage.
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104
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology. Clin Microbiol Rev 2014; 26:547-603. [PMID: 23824373 DOI: 10.1128/cmr.00072-12] [Citation(s) in RCA: 524] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.
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105
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Aubert DF, Hamad MA, Valvano MA. A markerless deletion method for genetic manipulation of Burkholderia cenocepacia and other multidrug-resistant gram-negative bacteria. Methods Mol Biol 2014; 1197:311-327. [PMID: 25172289 DOI: 10.1007/978-1-4939-1261-2_18] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Genetic manipulation of multidrug-resistant bacteria is often difficult and hinders progress in understanding their physiology and pathogenesis. This book chapter highlights advances in genetic manipulation of Burkholderia cenocepacia, which are also applicable to other members of the Burkholderia cepacia complex and multidrug-resistant gram-negative bacteria of other genera. The method detailed here is based on the I-SceI homing endonuclease system, which can be efficiently used for chromosomal integration, deletion, and genetic replacement. This system creates markerless mutations and insertions without leaving a genetic scar and thus can be reused successively to generate multiple modifications in the same strain.
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Affiliation(s)
- Daniel F Aubert
- Department of Microbiology and Immunology, Centre for Human Immunology, University of Western Ontario, London, ON, Canada, N6A 5C1
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106
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The third replicon of members of the Burkholderia cepacia Complex, plasmid pC3, plays a role in stress tolerance. Appl Environ Microbiol 2013; 80:1340-8. [PMID: 24334662 DOI: 10.1128/aem.03330-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The metabolically versatile Burkholderia cepacia complex (Bcc) occupies a variety of niches, including the plant rhizosphere and the cystic fibrosis lung (where it is often fatal to the patient). Bcc members have multipartite genomes, of which the third replicon, pC3 (previously chromosome 3), has been shown to be a nonessential megaplasmid which confers virulence and both antifungal and proteolytic activity on several strains. In this study, pC3 curing was extended to cover strains of 16 of the 17 members of the Bcc, and the phenotypes conferred by pC3 were determined. B. cenocepacia strains H111, MCO-3, and HI2424 were previously cured of pC3; however, this had not proved possible in the epidemic strain K56-2. Here, we investigated the mechanism of this unexpected stability and found that efficient toxin-antitoxin systems are responsible for maintaining pC3 of strain K56-2. Identification of these systems allowed neutralization of the toxins and the subsequent deletion of K56-2pC3. The cured strain was found to exhibit reduced antifungal activity and was attenuated in both the zebrafish and the Caenorhabditis elegans model of infection. We used a PCR screening method to examine the prevalence of pC3 within 110 Bcc isolates and found that this replicon was absent in only four cases, suggesting evolutionary fixation. It is shown that plasmid pC3 increases the resistance of B. cenocepacia H111 to various stresses (oxidative, osmotic, high-temperature, and chlorhexidine-induced stresses), explaining the prevalence of this replicon within the Bcc.
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107
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Cordova-Kreylos AL, Fernandez LE, Koivunen M, Yang A, Flor-Weiler L, Marrone PG. Isolation and characterization of Burkholderia rinojensis sp. nov., a non-Burkholderia cepacia complex soil bacterium with insecticidal and miticidal activities. Appl Environ Microbiol 2013; 79:7669-78. [PMID: 24096416 PMCID: PMC3837800 DOI: 10.1128/aem.02365-13] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/14/2013] [Indexed: 02/05/2023] Open
Abstract
Isolate A396, a bacterium isolated from a Japanese soil sample demonstrated strong insecticidal and miticidal activities in laboratory bioassays. The isolate was characterized through biochemical methods, fatty acid methyl ester (FAME) analysis, sequencing of 16S rRNA, multilocus sequence typing and analysis, and DNA-DNA hybridization. FAME analysis matched A396 to Burkholderia cenocepacia, but this result was not confirmed by 16S rRNA or DNA-DNA hybridization. 16S rRNA sequencing indicated closest matches with B. glumae and B. plantarii. DNA-DNA hybridization experiments with B. plantarii, B. glumae, B. multivorans, and B. cenocepacia confirmed the low genetic similarity (11.5 to 37.4%) with known members of the genus. PCR-based screening showed that A396 lacks markers associated with members of the B. cepacia complex. Bioassay results indicated two mechanisms of action: through ingestion and contact. The isolate effectively controlled beet armyworms (Spodoptera exigua; BAW) and two-spotted spider mites (Tetranychus urticae; TSSM). In diet overlay bioassays with BAW, 1% to 4% (vol/vol) dilution of the whole-cell broth caused 97% to 100% mortality 4 days postexposure, and leaf disc treatment bioassays attained 75% ± 22% mortality 3 days postexposure. Contact bioassays led to 50% larval mortality, as well as discoloration, stunting, and failure to molt. TSSM mortality reached 93% in treated leaf discs. Activity was maintained in cell-free supernatants and after heat treatment (60°C for 2 h), indicating that a secondary metabolite or excreted thermostable enzyme might be responsible for the activity. Based on these results, we describe the novel species Burkholderia rinojensis, a good candidate for the development of a biocontrol product against insect and mite pests.
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108
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Li GX, Wu XQ, Ye JR. Biosafety and colonization of Burkholderia multivorans WS-FJ9 and its growth-promoting effects on poplars. Appl Microbiol Biotechnol 2013; 97:10489-98. [PMID: 24092012 DOI: 10.1007/s00253-013-5276-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 11/28/2022]
Abstract
Burkholderia cepacia complex (Bcc) is a group of bacteria with conflicting biological characteristics, which make them simultaneously beneficial and harmful to humans. They have been exploited for biocontrol, bioremediation, and plant growth promotion. However, their capacity as opportunistic bacteria that infect humans restricts their biotechnological applications. Therefore, the risks of using these bacteria should be assessed. In this study, Burkholderia multivorans WS-FJ9 originally isolated from pine rhizosphere, which was shown to be efficient in solubilizing phosphate, was evaluated with respect to its biosafety, colonization in poplar rhizosphere, and growth-promoting effects on poplar seedlings. Pathogenicity of B. multivorans WS-FJ9 on plants was determined experimentally using onion and tobacco as model plants. Onion bulb inoculated with B. multivorans WS-FJ9 showed slight hypersensitive responses around the inoculation points, but effects were not detectable based on the inner color and odor of the onion. Tobacco leaves inoculated with B. multivorans WS-FJ9 exhibited slightly water-soaked spots around the inoculation points, which did not expand or develop into lesions even with repeated incubation. Pathogenicity of the strain in alfalfa, which has been suggested as an alternative Bcc model for mice, was not detectable. Results from gene-specific polymerase chain reactions showed that the tested B. multivorans WS-FJ9 strain did not possess the BCESM and cblA virulence genes. Scanning electron microscopy revealed that the colonization of the WS-FJ9 strain reached 1.4 × 10(4) colony forming units (cfu) g(-1) rhizosphere soil on day 77 post-inoculation. The B. multivorans WS-FJ9 strain could colonize the rhizosphere as well as the root tissues and cells of poplars. Greenhouse evaluations in both sterilized and non-sterilized soils indicated that B. multivorans WS-FJ9 significantly promoted growth in height, root collar diameter, and plant biomass of inoculated poplar seedlings compared with controls. Phosphorus contents of roots and stems of treated seedlings were 0.57 and 0.55 mg g(-1) higher than those of the controls, respectively. Phosphorus content was lower in the rhizosphere soils by an average of 1.03 mg g(-1) compared with controls. The results demonstrated that B. multivorans WS-FJ9 is a nonpathogenic strain that could colonize the roots and significantly promote the growth of poplar seedlings.
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Affiliation(s)
- Guan-Xi Li
- College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China
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109
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Khodai-Kalaki M, Aubert DF, Valvano MA. Characterization of the AtsR hybrid sensor kinase phosphorelay pathway and identification of its response regulator in Burkholderia cenocepacia. J Biol Chem 2013; 288:30473-30484. [PMID: 24014026 DOI: 10.1074/jbc.m113.489914] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AtsR is a membrane-bound hybrid sensor kinase of Burkholderia cenocepacia that negatively regulates quorum sensing and virulence factors such as biofilm production, type 6-secretion, and protease secretion. Here we elucidate the mechanism of AtsR phosphorelay by site-directed mutagenesis of predicted histidine and aspartic acid phosphoacceptor residues. We demonstrate by in vitro phosphorylation that histidine 245 and aspartic acid 536 are conserved sites of phosphorylation in AtsR, and we also identify the cytosolic response regulator AtsT (BCAM0381) as a key component of the AtsR phosphorelay pathway. Monitoring the function of AtsR and its derivatives in vivo by measuring extracellular protease activity and swarming motility confirmed the in vitro phosphorylation results. Together we find that the AtsR receiver domain plays a fine-tuning role in determining the levels of phosphotransfer from its sensor kinase domain to the AtsT response regulator.
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Affiliation(s)
- Maryam Khodai-Kalaki
- From the Centre for Human Immunology, Department of Microbiology and Immunology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada and
| | - Daniel F Aubert
- From the Centre for Human Immunology, Department of Microbiology and Immunology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada and
| | - Miguel A Valvano
- From the Centre for Human Immunology, Department of Microbiology and Immunology, Schulich School of Medicine, University of Western Ontario, London, Ontario N6A 5C1, Canada and; the Centre for Infection and Immunity, Queen's University Belfast, BT9 5GZ Belfast, United Kingdom.
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110
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De Smet B, Veng C, Kruy L, Kham C, van Griensven J, Peeters C, Ieng S, Phe T, Vlieghe E, Vandamme P, Jacobs J. Outbreak of Burkholderia cepacia bloodstream infections traced to the use of Ringer lactate solution as multiple-dose vial for catheter flushing, Phnom Penh, Cambodia. Clin Microbiol Infect 2013; 19:832-7. [DOI: 10.1111/1469-0691.12047] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 09/12/2012] [Accepted: 09/12/2012] [Indexed: 12/20/2022]
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111
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Li D, March J, Bills T, Holt B, Wilson C, Lowe W, Tolley H, Lee M, Robison R. Gas chromatography-mass spectrometry method for rapid identification and differentiation of Burkholderia pseudomallei
and Burkholderia mallei
from each other, Burkholderia thailandensis
and several members of the Burkholderia cepacia
complex. J Appl Microbiol 2013; 115:1159-71. [DOI: 10.1111/jam.12310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/07/2013] [Accepted: 07/18/2013] [Indexed: 10/26/2022]
Affiliation(s)
- D. Li
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - J.K. March
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - T.M. Bills
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - B.C. Holt
- Department of Statistics; Brigham Young University; Provo UT USA
| | - C.E. Wilson
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - W. Lowe
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
| | - H.D. Tolley
- Department of Statistics; Brigham Young University; Provo UT USA
| | - M.L. Lee
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - R.A. Robison
- Department of Microbiology and Molecular Biology; Brigham Young University; Provo UT USA
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112
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Righi E, Girardis M, Marchegiano P, Venturelli C, Tagliazucchi S, Pecorari M, Borsari L, Carluccio E, Codeluppi M, Mussini C, Aggazzotti G. Characteristics and outcome predictors of patients involved in an outbreak of Burkholderia cepacia complex. J Hosp Infect 2013; 85:73-5. [PMID: 23927925 DOI: 10.1016/j.jhin.2013.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/30/2013] [Indexed: 11/25/2022]
Abstract
A Burkholderia cepacia complex outbreak occurred among ventilated non-cystic fibrosis patients in an intensive care unit (ICU) in Italy: 33 colonized and 13 infected patients were included in a retrospective study aimed at investigating factors related to clinical infection and mortality. Demographic/clinical conditions and mortality did not vary significantly between colonized and infected patients, both groups showing high mortality rates compared with the overall ICU population and similar to that observed in patients with other infections. In multivariate regression analysis, disease severity (defined by the Simplified Acute Physiology Score II) and age were the only independent predictors of early mortality (odds ratio: 1.12; 95% confidence interval: 1.02-1.26; and 1.07; 1.01-1.15, respectively).
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Affiliation(s)
- E Righi
- Department of Diagnostic, Clinical and Public Health Medicine, University of Modena and Reggio Emilia, Italy.
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113
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Ali SW, Yu FB, Haider MS, Yan X, Li SP. Phenotypic and phylogenetic characterization of an abamectin-degrading bacterial strain isolated from a citrus orchard. J GEN APPL MICROBIOL 2013; 59:215-25. [PMID: 23863292 DOI: 10.2323/jgam.59.215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Bacterial strain GB-01 was isolated from abamectin-contaminated soils by continuous enrichment culture. The preliminary identification of strain GB-01 as a Burkholderia species was based mainly on simple biochemical and substrate utilization tests; however, these tests alone cannot accurately differentiate all the species within the genus Burkholderia. The strain GB-01 was subjected to taxonomic analysis through a polyphasic approach, in which phenotypic, genotypic, and phylogenetic information was gathered to conclude the classification of this microbe. Phenotypic information comes from basic bacteriological tests and substrate utilization patterns using the Biolog GN2 MicroPlating system and automated miniature biochemical test kits, i.e. API 20 NE, ID 32 GN and API 50 CH, as well as analyzing the whole cell fatty acid profile. Genotypic information was gathered from whole genome DNA base composition (G+C mol%), and DNA-DNA hybridization with its closest species, while phylogenetic information was collected from the comparative analysis of 16S rRNA and recA gene sequences. The results of polyphasic analysis concluded that strain GB-01 is an atypical strain of the Burkholderia diffusa species.
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Affiliation(s)
- Shinawar Waseem Ali
- Key Lab of Microbiological Engineering of Agricultural Environment, Nanjing Agricultural University, Nanjing, China
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114
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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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115
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Perrin E, Fondi M, Papaleo MC, Maida I, Emiliani G, Buroni S, Pasca MR, Riccardi G, Fani R. A census of RND superfamily proteins in the Burkholderia genus. Future Microbiol 2013; 8:923-37. [DOI: 10.2217/fmb.13.50] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: The aim of this work was to analyze the eight resistance–nodulation–cell division (RND) families (a group of proteins mainly involved in multidrug resistance of Gram-negative bacteria) in 26 Burkholderia genomes in order to gain knowledge regarding their presence and distribution, to obtain a platform for future experimental tests aimed to identify new molecular targets to be used in antimicrobial therapy against Burkholderia species and to refine the annotation of RND-like sequences in these genomes. Materials & methods: A total of 417 coding sequences were retrieved and analyzed using different bioinformatics tools. Results & conclusion: A complex pattern of RND presence and distribution in the different Burkholderia species was disclosed and a core of proteins represented in all 26 genomes was identified. These ‘core’ proteins might represent useful targets of new synthetic antimicrobial compounds. Furthermore, the annotation of RND-like sequences in Burkholderia was refined.
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Affiliation(s)
- Elena Perrin
- Laboratory of Molecular & Microbial Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy
| | - Marco Fondi
- Laboratory of Molecular & Microbial Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy
- Computer Laboratory, University of Cambridge, Cambridge, UK
| | - Maria Cristiana Papaleo
- Laboratory of Molecular & Microbial Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy
| | - Isabel Maida
- Laboratory of Molecular & Microbial Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy
| | - Giovanni Emiliani
- Trees & Timber Institute, National Research Council, via Madonna del Piano, 10, 50019 Florence, Italy
| | - Silvia Buroni
- Department of Biology & Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Maria Rosalia Pasca
- Department of Biology & Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Giovanna Riccardi
- Department of Biology & Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Via Ferrata 9, 27100 Pavia, Italy
| | - Renato Fani
- Laboratory of Molecular & Microbial Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino (Fi), Italy.
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116
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Reliability of automated biochemical identification of Burkholderia pseudomallei is regionally dependent. J Clin Microbiol 2013; 51:3076-8. [PMID: 23784129 DOI: 10.1128/jcm.01290-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Misidentifications of Burkholderia pseudomallei as Burkholderia cepacia by Vitek 2 have occurred. Multidimensional scaling ordination of biochemical profiles of 217 Malaysian and Australian B. pseudomallei isolates found clustering of misidentified B. pseudomallei isolates from Malaysian Borneo. Specificity of B. pseudomallei identification in Vitek 2 and potentially other automated identification systems is regionally dependent.
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117
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Regulon studies and in planta role of the BraI/R quorum-sensing system in the plant-beneficial Burkholderia cluster. Appl Environ Microbiol 2013; 79:4421-32. [PMID: 23686262 DOI: 10.1128/aem.00635-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genus Burkholderia is composed of functionally diverse species, and it can be divided into several clusters. One of these, designated the plant-beneficial-environmental (PBE) Burkholderia cluster, is formed by nonpathogenic species, which in most cases have been found to be associated with plants. It was previously established that members of the PBE group share an N-acyl-homoserine lactone (AHL) quorum-sensing (QS) system, designated BraI/R, that produces and responds to 3-oxo-C14-HSL (OC14-HSL). Moreover, some of them also possess a second AHL QS system, designated XenI2/R2, producing and responding to 3-hydroxy-C8-HSL (OHC8-HSL). In the present study, we performed liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis to determine which AHL molecules are produced by each QS system of this group of bacteria. The results showed that XenI2/R2 is mainly responsible for the production of OHC8-HSL and that the BraI/R system is involved in the production of several different AHLs. This analysis also revealed that Burkholderia phymatum STM815 produces greater amounts of AHLs than the other species tested. Further studies showed that the BraR protein of B. phymatum is more promiscuous than other BraR proteins, responding equally well to several different AHL molecules, even at low concentrations. Transcriptome studies with Burkholderia xenovorans LB400 and B. phymatum STM815 revealed that the BraI/R regulon is species specific, with exopolysaccharide production being the only common phenotype regulated by this system in the PBE cluster. In addition, BraI/R was shown not to be important for plant nodulation by B. phymatum strains or for endophytic colonization and growth promotion of maize by B. phytofirmans PsJN.
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Papp-Wallace KM, Taracila MA, Gatta JA, Ohuchi N, Bonomo RA, Nukaga M. Insights into β-lactamases from Burkholderia species, two phylogenetically related yet distinct resistance determinants. J Biol Chem 2013; 288:19090-102. [PMID: 23658015 DOI: 10.1074/jbc.m113.458315] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Burkholderia cepacia complex and Burkholderia pseudomallei are opportunistic human pathogens. Resistance to β-lactams among Burkholderia spp. is attributable to expression of β-lactamases (e.g. PenA in B. cepacia complex and PenI in B. pseudomallei). Phylogenetic comparisons reveal that PenA and PenI are highly related. However, the analyses presented here reveal that PenA is an inhibitor-resistant carbapenemase, most similar to KPC-2 (the most clinically significant serine carbapenemase), whereas PenI is an extended spectrum β-lactamase. PenA hydrolyzes β-lactams with k(cat) values ranging from 0.38 ± 0.04 to 460 ± 46 s(-1) and possesses high k(cat)/k(inact) values of 2000, 1500, and 75 for β-lactamase inhibitors. PenI demonstrates the highest kcat value for cefotaxime of 9.0 ± 0.9 s(-1). Crystal structure determination of PenA and PenI reveals important differences that aid in understanding their contrasting phenotypes. Changes in the positioning of conserved catalytic residues (e.g. Lys-73, Ser-130, and Tyr-105) as well as altered anchoring and decreased occupancy of the deacylation water explain the lower k(cat) values of PenI. The crystal structure of PenA with imipenem docked into the active site suggests why this carbapenem is hydrolyzed and the important role of Arg-220, which was functionally confirmed by mutagenesis and biochemical characterization. Conversely, the conformation of Tyr-105 hindered docking of imipenem into the active site of PenI. The structural and biochemical analyses of PenA and PenI provide key insights into the hydrolytic mechanisms of β-lactamases, which can lead to the rational design of novel agents against these pathogens.
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Affiliation(s)
- Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs, Cleveland, Ohio 44106, USA
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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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120
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van Duin D, van Delden C. Multidrug-resistant gram-negative bacteria infections in solid organ transplantation. Am J Transplant 2013; 13 Suppl 4:31-41. [PMID: 23464996 DOI: 10.1111/ajt.12096] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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121
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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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Bloodworth RAM, Gislason AS, Cardona ST. Burkholderia cenocepacia conditional growth mutant library created by random promoter replacement of essential genes. Microbiologyopen 2013; 2:243-58. [PMID: 23389959 PMCID: PMC3633349 DOI: 10.1002/mbo3.71] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/24/2012] [Accepted: 01/08/2013] [Indexed: 01/05/2023] Open
Abstract
Identification of essential genes by construction of conditional knockouts with inducible promoters allows the identification of essential genes and creation of conditional growth (CG) mutants that are then available as genetic tools for further studies. We used large-scale transposon delivery of the rhamnose-inducible promoter, PrhaB followed by robotic screening of rhamnose-dependent growth to construct a genomic library of 106 Burkholderia cenocepacia CG mutants. Transposon insertions were found where PrhaB was in the same orientation of widely conserved, well-characterized essential genes as well as genes with no previous records of essentiality in other microorganisms. Using previously reported global gene-expression analyses, we demonstrate that PrhaB can achieve the wide dynamic range of expression levels required for essential genes when the promoter is delivered randomly and mutants with rhamnose-dependent growth are selected. We also show specific detection of the target of an antibiotic, novobiocin, by enhanced sensitivity of the corresponding CG mutant (PrhaB controlling gyrB expression) within the library. Modulation of gene expression to achieve 30-60% of wild-type growth created conditions for specific hypersensitivity demonstrating the value of the CG mutant library for chemogenomic experiments. In summary, CG mutants can be obtained on a large scale by random delivery of a tightly regulated inducible promoter into the bacterial chromosome followed by a simple screening for the CG phenotype, without previous information on gene essentiality.
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Affiliation(s)
- Ruhi A M Bloodworth
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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Chapalain A, Vial L, Laprade N, Dekimpe V, Perreault J, Déziel E. Identification of quorum sensing-controlled genes in Burkholderia ambifaria. Microbiologyopen 2013; 2:226-42. [PMID: 23382083 PMCID: PMC3633348 DOI: 10.1002/mbo3.67] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 12/18/2012] [Accepted: 12/26/2012] [Indexed: 01/23/2023] Open
Abstract
The Burkholderia cepacia complex (Bcc) comprises strains with a virulence potential toward immunocompromised patients as well as plant growth-promoting rhizobacteria (PGPR). Owing to the link between quorum sensing (QS) and virulence, most studies among Bcc species have been directed toward QS of pathogenic bacteria. We have investigated the QS of B. ambifaria, a PGPR only infrequently recovered from patients. The cepI gene, responsible for the synthesis of the main signaling molecule N-octanoylhomoserine lactone (C8 -HSL), was inactivated. Phenotypes of the B. ambifaria cepI mutant we observed, such as increased production of siderophores and decreased proteolytic and antifungal activities, are in agreement with those of other Bcc cepI mutants. The cepI mutant was then used as background strain for a whole-genome transposon-insertion mutagenesis strategy, allowing the identification of 20 QS-controlled genes, corresponding to 17 loci. The main functions identified are linked to antifungal and antimicrobial properties, as we have identified QS-controlled genes implicated in the production of pyrrolnitrin, burkholdines (occidiofungin-like molecules), and enacyloxins. This study provides insights in the QS-regulated functions of a PGPR, which could lead to beneficial potential biotechnological applications.
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Affiliation(s)
- Annelise Chapalain
- INRS-Institut Armand-Frappier, 531 bd des Prairies, Laval, Quebec H7V 1B7, Canada
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Ligeour C, Audfray A, Gillon E, Meyer A, Galanos N, Vidal S, Vasseur JJ, Imberty A, Morvan F. Synthesis of branched-phosphodiester and mannose-centered fucosylated glycoclusters and their binding studies with Burkholderia ambifaria lectin (BambL). RSC Adv 2013. [DOI: 10.1039/c3ra43807d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Zhang YM, Tian CF, Sui XH, Chen WF, Chen WX. Robust markers reflecting phylogeny and taxonomy of rhizobia. PLoS One 2012; 7:e44936. [PMID: 23028691 PMCID: PMC3444505 DOI: 10.1371/journal.pone.0044936] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 08/10/2012] [Indexed: 12/17/2022] Open
Abstract
Genomic ANI (Average Nucleotide Identity) has been found to be able to replace DNA-DNA hybridization in prokaryote taxonomy. The ANI of each of the core genes that has a phylogeny congruent with the reference species tree of rhizobia was compared to the genomic ANI. This allowed us to identify three housekeeping genes (SMc00019-truA-thrA) whose ANI reflected the intraspecies and interspecies genomic ANI among rhizobial strains, revealing an ANI gap (≥2%) between the inter- and intra-species comparisons. The intraspecies (96%) and interspecies (94%) ANI boundaries calculated from three genes (SMc00019-truA-thrA) provided a criterion for bacterial species definition and confirmed 621/629 of known interspecies relationships within Bradyrhizobium, Mesorhizobium, Sinorhizobium and Rhizobium. Some widely studied strains should be renamed. The SMc00019-truA-thrA ANI also correlates well with the genomic ANI of strains in Agrobacterium, Methylobacterium, Ralstonia, Rhodopseudomonas, Cupriavidus and Burkholderia, suggesting their wide applicability in other bacteria.
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Affiliation(s)
- Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
- * E-mail:
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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Aubert DF, O'Grady EP, Hamad MA, Sokol PA, Valvano MA. The Burkholderia cenocepacia sensor kinase hybrid AtsR is a global regulator modulating quorum-sensing signalling. Environ Microbiol 2012; 15:372-85. [PMID: 22830644 DOI: 10.1111/j.1462-2920.2012.02828.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Burkholderia cenocepacia is commonly found in the environment and also as an important opportunistic pathogen infecting patients with cystic fibrosis. Successful infection by this bacterium requires coordinated expression of virulence factors, which is achieved through different quorum sensing (QS) regulatory systems. Biofilm formation and Type 6 secretion system (T6SS) expression in B. cenocepacia K56-2 are positively regulated by QS and negatively regulated by the sensor kinase hybrid AtsR. This study reveals that in addition to affecting biofilm and T6SS activity, the deletion of atsR in B. cenocepacia leads to overproduction of other QS-regulated virulence determinants including proteases and swarming motility. Expression of the QS genes, cepIR and cciIR, was upregulated in the ΔatsR mutant and resulted in early and increased N-acylhomoserine lactone (AHL) production, suggesting that AtsR plays a role in controlling the timing and fine-tuning of virulence gene expression by modulating QS signalling. Furthermore, a ΔatsRΔcepIΔcciI mutant could partially upregulate the same virulence determinants indicating that AtsR also modulates the expression of virulence genes by a second mechanism, independently of any AHL production. Together, our results strongly suggest that AtsR is a global virulence regulator in B. cenocepacia.
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Affiliation(s)
- Daniel F Aubert
- Centre for Human Immunology, Department of Microbiology, University of Western Ontario, London, Ontario, Canada
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Rosales-Reyes R, Aubert DF, Tolman JS, Amer AO, Valvano MA. Burkholderia cenocepacia type VI secretion system mediates escape of type II secreted proteins into the cytoplasm of infected macrophages. PLoS One 2012; 7:e41726. [PMID: 22848580 PMCID: PMC3405007 DOI: 10.1371/journal.pone.0041726] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/27/2012] [Indexed: 11/18/2022] Open
Abstract
Burkholderia cenocepacia is an opportunistic pathogen that survives intracellularly in macrophages and causes serious respiratory infections in patients with cystic fibrosis. We have previously shown that bacterial survival occurs in bacteria-containing membrane vacuoles (BcCVs) resembling arrested autophagosomes. Intracellular bacteria stimulate IL-1β secretion in a caspase-1-dependent manner and induce dramatic changes to the actin cytoskeleton and the assembly of the NADPH oxidase complex onto the BcCV membrane. A Type 6 secretion system (T6SS) is required for these phenotypes but surprisingly it is not required for the maturation arrest of the BcCV. Here, we show that macrophages infected with B. cenocepacia employ the NLRP3 inflammasome to induce IL-1β secretion and pyroptosis. Moreover, IL-1β secretion by B. cenocepacia-infected macrophages is suppressed in deletion mutants unable to produce functional Type VI, Type IV, and Type 2 secretion systems (SS). We provide evidence that the T6SS mediates the disruption of the BcCV membrane, which allows the escape of proteins secreted by the T2SS into the macrophage cytoplasm. This was demonstrated by the activity of fusion derivatives of the T2SS-secreted metalloproteases ZmpA and ZmpB with adenylcyclase. Supporting this notion, ZmpA and ZmpB are required for efficient IL-1β secretion in a T6SS dependent manner. ZmpA and ZmpB are also required for the maturation arrest of the BcCVs and bacterial intra-macrophage survival in a T6SS-independent fashion. Our results uncover a novel mechanism for inflammasome activation that involves cooperation between two bacterial secretory pathways, and an unanticipated role for T2SS-secreted proteins in intracellular bacterial survival.
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Affiliation(s)
- Roberto Rosales-Reyes
- Centre for Human Immunology, Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
- Laboratorio de Infectología, Microbiología e Inmunología Clínicas, Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, México
| | - Daniel F. Aubert
- Centre for Human Immunology, Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Jennifer S. Tolman
- Centre for Human Immunology, Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Amal O. Amer
- Centre for Microbial Interface Biology, Department of Microbial Infection and Immunity and the Department of Internal Medicine, Ohio State University, Columbus, Ohio, United States of America
| | - Miguel A. Valvano
- Centre for Human Immunology, Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
- * E-mail:
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Hamad MA, Di Lorenzo F, Molinaro A, Valvano MA. Aminoarabinose is essential for lipopolysaccharide export and intrinsic antimicrobial peptide resistance inBurkholderia cenocepacia†. Mol Microbiol 2012; 85:962-74. [DOI: 10.1111/j.1365-2958.2012.08154.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Juhas M, Stark M, von Mering C, Lumjiaktase P, Crook DW, Valvano MA, Eberl L. High confidence prediction of essential genes in Burkholderia cenocepacia. PLoS One 2012; 7:e40064. [PMID: 22768221 PMCID: PMC3386938 DOI: 10.1371/journal.pone.0040064] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 05/31/2012] [Indexed: 01/01/2023] Open
Abstract
Background Essential genes are absolutely required for the survival of an organism. The identification of essential genes, besides being one of the most fundamental questions in biology, is also of interest for the emerging science of synthetic biology and for the development of novel antimicrobials. New antimicrobial therapies are desperately needed to treat multidrug-resistant pathogens, such as members of the Burkholderia cepacia complex. Methodology/Principal Findings We hypothesize that essential genes may be highly conserved within a group of evolutionary closely related organisms. Using a bioinformatics approach we determined that the core genome of the order Burkholderiales consists of 649 genes. All but two of these identified genes were located on chromosome 1 of Burkholderia cenocepacia. Although many of the 649 core genes of Burkholderiales have been shown to be essential in other bacteria, we were also able to identify a number of novel essential genes present mainly, or exclusively, within this order. The essentiality of some of the core genes, including the known essential genes infB, gyrB, ubiB, and valS, as well as the so far uncharacterized genes BCAL1882, BCAL2769, BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia. Conclusions/Significance We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and experimental evidence that the large majority of the identified genes are indeed essential. The essential genes identified here may represent valuable targets for the development of novel antimicrobials and their detailed study may shed new light on the functions required to support life.
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Affiliation(s)
- Mario Juhas
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (MJ); (LE)
| | - Manuel Stark
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Christian von Mering
- Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Derrick W. Crook
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Miguel A. Valvano
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Leo Eberl
- Department of Microbiology, Institute of Plant Biology, University of Zurich, Zurich, Switzerland
- * E-mail: (MJ); (LE)
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Kuzumoto K, Kubota N, Ishii K, Yumoto K, Ogiso Y, Nakamura T, Katsuyama T, Oana K, Kawakami Y. Successful cessation of transmitting healthcare -- associated infections due to Burkholderia cepacia complex in a neonatal intensive care unit in a Japanese children's hospital. Eur J Med Res 2012; 16:537-42. [PMID: 22112360 PMCID: PMC3351897 DOI: 10.1186/2047-783x-16-12-537] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Burkholderia cepacia strains have been known to possess the capability to cause serious infections especially in neonatal intensive care units (NICUs), and their multi-drug resistances become a severe threat in hospital settings. The aim of this investigation was to evaluate the B. cepacia complex infections in the NICU in Nagano Children's Hospital, Azumino 399-8288, Japan, and to report the intervention leading to the successful cessation of the outbreak. Methodology The incidence of isolation and antimicrobial susceptibilities of nosocomial Burkholderia cepacia complex strains during a four-year period were retrospectively examined by clinical microbiological records, and by pulsed-field gel electrophoresis analyses along with the bacteriological verification of disinfectant device itself and procedures for its maintenance routinely used in the NICU. Results During the period surveyed between 2007 and 2009, only an isolate per respective year of B. cepacia complex was recovered from each neonate in the NICU. However, in 2010, the successive 6 B. cepacia complex isolates were recovered from different hospitalized neonates. Among them, an isolate was originated from peripheral blood of a neonate, apparently giving rise to systemic infection. In addition, the hospitalized neonate with bacteremia due to B. cepacia complex also exhibited positive cultures from repeated catheterized urine samples together with tracheal aspirate secretions. However other 5 isolates were considered as the transients or contaminants having little to do with infections. Moreover, the 5 isolates between July and October in 2010 revealed completely the same electrophoresis patterns by means of pulsed-field gel electrophoresis analyses, strongly indicating that they were infected through the same medical practices, or by transmission of the same contaminant. Conclusions A small outbreak due to B. cepacia complex was brought about in the NICU in 2010, which appeared to be associated with the same genomovar of B. cepacia complex. The source or the rout of infection was unknown in spite of the repeated epidemiological investigation. It is noteworthy that no outbreak due to B. cepacia complex was noted in the NICU after extensive surveillance intervention.
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Affiliation(s)
- K Kuzumoto
- Department of Laboratory Medicine, Nagano Children's Hospital, Azumino, Japan
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da Silva K, Cassetari ADS, Lima AS, De Brandt E, Pinnock E, Vandamme P, Moreira FMDS. Diazotrophic Burkholderia species isolated from the Amazon region exhibit phenotypical, functional and genetic diversity. Syst Appl Microbiol 2012; 35:253-62. [PMID: 22609342 DOI: 10.1016/j.syapm.2012.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/21/2012] [Accepted: 04/24/2012] [Indexed: 11/24/2022]
Abstract
Forty-eight Burkholderia isolates from different land use systems in the Amazon region were compared to type strains of Burkholderia species for phenotypic and functional characteristics that can be used to promote plant growth. Most of these isolates (n=46) were obtained by using siratro (Macroptilium atropurpureum - 44) and common bean (Phaseolus vulgaris - 2) as the trap plant species; two isolates were obtained from nodules collected in the field from Indigofera suffruticosa and Pithecellobium sp. The evaluated characteristics were the following: colony characterisation on "79" medium, assimilation of different carbon sources, enzymatic activities, solubilisation of phosphates, nitrogenase activity and antifungal activity against Fusarium oxysporium f. sp. phaseoli. Whole cell protein profiles, 16S rRNA, gyrB, and recA gene sequencing and multilocus sequence typing were used to identify the isolates. The isolates showed different cultural and biochemical characteristics depending on the legume species from which they were obtained. Except for one isolate from I. suffruticosa, all isolates were able to solubilise calcium phosphate and present nitrogenase activity under free-living conditions. Only one isolate from common beans, showed antifungal activity. The forty four isolates from siratro nodules were identified as B. fungorum; isolates UFLA02-27 and UFLA02-28, obtained from common bean plants, were identified as B. contaminans; isolate INPA89A, isolated from Indigofera suffruticosa, was a close relative of B. caribensis but could not be assigned to an established species; isolate INPA42B, isolated from Pithecellobium sp., was identified as B. lata. This is the first report of nitrogenase activity in B. fungorum, B. lata and B. contaminans.
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Affiliation(s)
- Krisle da Silva
- Departamento de Biologia, Universidade Federal de Lavras, Campus UFLA, Lavras, Minas Gerais, Brazil.
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Tegos GP, Haynes MK, Schweizer HP. Dissecting novel virulent determinants in the Burkholderia cepacia complex. Virulence 2012; 3:234-7. [PMID: 22546904 DOI: 10.4161/viru.19844] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Prevention and control of infectious diseases remains a major public health challenge and a number of highly virulent pathogens are emerging both in and beyond the hospital setting. Despite beneficial aspects such as use in biocontrol and bioremediation exhibited by members of the Burkholderia cepacia complex (Bcc) some members of this group have recently gained attention as significant bacterial pathogens due to their high levels of intrinsic antibiotic resistance, transmissibility in nosocomial settings, persistence in the presence of antimicrobials and intracellular survival capabilities. The Bcc are opportunistic pathogens and their arsenal of virulence factors includes proteases, lipases and other secreted exoproducts, including secretion system-associated effectors. Deciphering the function of virulence factors and assessment of novel therapeutic strategies has been facilitated by use of diverse non-vertebrate hosts (the fly Drosophila melanogaster, the microscopic nematode Caenorhabditis elegans, the zebrafish and the greater Galleria mellonella wax moth caterpillar larvae). Researchers are now employing sophisticated approaches to dissect the virulence determinants of Bcc with the ultimate goal being the development of novel anti-infective countermeasures. This editorial will highlight selected recent research endeavors aimed at dissecting adaptive responses and the virulence factor portfolio of Burkholderia species.
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Affiliation(s)
- George P Tegos
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA.
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Martínez-Aguilar L, Caballero-Mellado J, Estrada-de Los Santos P. Transfer of Wautersia numazuensis to the genus Cupriavidus as Cupriavidus numazuensis comb. nov. Int J Syst Evol Microbiol 2012; 63:208-211. [PMID: 22389284 DOI: 10.1099/ijs.0.038729-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of the 16S rRNA gene sequences of strains TE26(T) and K6 belonging to Wautersia numazuensis Kageyama et al. 2005 showed the strains to be deeply intermingled among the species of the genus Cupriavidus. The comparison showed that strain TE26(T) was closely related to the type strains of Cupriavidus pinatubonensis (99.1 % 16S rRNA gene sequence similarity), C. basilensis (98.7 %), C. necator (98.7 %) and C. gilardii (98.0 %). However, DNA-DNA hybridization experiments (less than 20 % relatedness) demonstrated that strain TE26(T) is different from these Cupriavidus species. A comparative phenotypic and chemotaxonomic analysis (based on fatty acid profiles) in combination with the 16S rRNA gene sequence phylogenetic analysis and the DNA-DNA hybridization results supported the incorporation of Wautersia numazuensis into the genus Cupriavidus as Cupriavidus numazuensis comb. nov.; the type strain is TE26(T) (=LMG 26411(T) =DSM 15562(T) = CIP 108892(T)).
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Affiliation(s)
- Lourdes Martínez-Aguilar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Jesús Caballero-Mellado
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
| | - Paulina Estrada-de Los Santos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico
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Lynch KH, Dennis JJ. Cangene Gold Medal Award Lecture — Genomic analysis and modification ofBurkholderia cepaciacomplex bacteriophages1This article is based on a presentation by Dr. Karlene Lynch at the 61st Annual Meeting of the Canadian Society of Microbiologists in St. John’s, Newfoundland and Labrador, on 21 June 2011. Dr. Lynch was the recipient of the 2011 Cangene Gold Medal as the Canadian Graduate Student Microbiologist of the Year, an annual award sponsored by Cangene Corporation intended to recognize excellence in graduate research. Can J Microbiol 2012; 58:221-35. [DOI: 10.1139/w11-135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of 17 Gram-negative predominantly environmental bacterial species that cause potentially fatal opportunistic infections in cystic fibrosis (CF) patients. Although its prevalence in these individuals is lower than that of Staphylococcus aureus and Pseudomonas aeruginosa , the Bcc remains a serious problem in the CF community because of the pathogenicity, transmissibility, and inherent antibiotic resistance of these organisms. An alternative treatment for Bcc infections that is currently being developed is phage therapy, the clinical use of viruses that infect bacteria. To assess the suitability of individual phage isolates for therapeutic use, the complete genome sequences of a panel of Bcc‐specific phages were determined and analyzed. These sequences encode a broad range of proteins with a gradient of relatedness to phage and bacterial gene products from Burkholderia and other genera. The majority of these phages were found not to encode virulence factors, and despite their predominantly temperate nature, a proof-of-principle experiment has shown that they may be modified to a lytic form. Both the genomic characterization and subsequent engineering of Bcc‐specific phages are fundamental to the development of an effective phage therapy strategy for these bacteria.
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Affiliation(s)
- Karlene H. Lynch
- 6-008 Centennial Centre for Interdisciplinary Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Jonathan J. Dennis
- 6-008 Centennial Centre for Interdisciplinary Science, Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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Agnoli K, Schwager S, Uehlinger S, Vergunst A, Viteri DF, Nguyen DT, Sokol PA, Carlier A, Eberl L. Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid. Mol Microbiol 2011; 83:362-78. [PMID: 22171913 DOI: 10.1111/j.1365-2958.2011.07937.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Burkholderia cepacia complex (Bcc) consists of 17 closely related species of opportunistic bacterial pathogens, which are particularly problematic for cystic fibrosis patients and immunocompromised individuals. Bcc genomes consist of multiple replicons, and each strain sequenced to date has three chromosomes. In addition to genes thought to be essential for survival, each chromosome carries at least one rRNA operon. We isolated three mutants during a transposon mutagenesis screen that were non-pathogenic in a Caenorhabditis elegans infection model. It was demonstrated that these mutants had lost chromosome 3 (c3), and that the observed attenuation of virulence was a consequence of this. We constructed a c3 mini-replicon and used it to cure c3 from strains of several Bcc species by plasmid incompatibility, resulting in nine c3-null strains covering seven Bcc species. Phenotypic characterization of c3-null mutants revealed that they were attenuated in virulence in multiple infection hosts (rat, zebrafish, C. elegans, Galleria mellonella and Drosophila melanogaster), that they exhibited greatly diminished antifungal activity, and that c3 was required for d-xylose, fatty acid and pyrimidine utilization, as well as for exopolysaccharide production and proteolytic activity in some strains. In conclusion, we show that c3 is not an essential chromosomal element, rather a large plasmid that encodes virulence, secondary metabolism and other accessory functions in Bcc bacteria.
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Affiliation(s)
- K Agnoli
- Department of Microbiology, Institute of Plant Biology, University of Zürich, Zollikerstrasse 107. CH-8008 Zürich, Switzerland
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136
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Abstract
Bcep22-like phages are a recently described group of podoviruses that infect strains of Burkholderia cenocepacia. We have isolated and characterized a novel member of this group named DC1. This podovirus shows many genomic similarities to BcepIL02 and Bcep22, but it infects strains belonging to multiple Burkholderia cepacia complex (BCC) species.
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137
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Ibrahim M, Wang F, Lou MM, Xie GL, Li B, Bo Z, Zhang GQ, Liu H, Wareth A. Copper as an antibacterial agent for human pathogenic multidrug resistant Burkholderia cepacia complex bacteria. J Biosci Bioeng 2011; 112:570-6. [DOI: 10.1016/j.jbiosc.2011.08.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 10/17/2022]
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138
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Bevivino A, Costa B, Cantale C, Cesarini S, Chiarini L, Tabacchioni S, Caballero-Mellado J, Dalmastri C. Genetic relationships among Italian and Mexican maize-rhizosphere Burkholderia cepacia complex (BCC) populations belonging to Burkholderia cenocepacia IIIB and BCC6 group. BMC Microbiol 2011; 11:228. [PMID: 21995705 PMCID: PMC3377929 DOI: 10.1186/1471-2180-11-228] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/13/2011] [Indexed: 11/25/2022] Open
Abstract
Background A close association between maize roots and Burkholderia cepacia complex (BCC) bacteria has been observed in different locations globally. In this study we investigated by MultiLocus Restriction Typing (MLRT) the genetic diversity and relationships among Burkholderia cenocepacia IIIB and BCC6 populations associated with roots of maize plants cultivated in geographically distant countries (Italy and Mexico), in order to provide new insights into their population structure, evolution and ecology. Results The 31 B. cenocepacia IIIB and 65 BCC6 isolates gave rise to 29 and 39 different restriction types (RTs), respectively. Two pairs of isolates of B. cenocepacia IIIB and BCC6, recovered from both Italian and Mexican maize rhizospheres, were found to share the same RT. The eBURST (Based Upon Related Sequence Types) analysis of MLRT data grouped all the B. cenocepacia IIIB isolates into four clonal complexes, with the RT-4-complex including the 42% of them, while the majority of the BCC6 isolates (94%) were grouped into the RT-104-complex. These two main clonal complexes included RTs shared by both Italian and Mexican maize rhizospheres and a clear relationship between grouping and maize variety was also found. Grouping established by eBURST correlated well with the assessment using unweighted-pair group method with arithmetic mean (UPGMA). The standardized index of association values obtained in both B. cenocepacia IIIB and BCC6 suggests an epidemic population structure in which occasional clones emerge and spread. Conclusions Taken together our data demonstrate a wide dispersal of certain B. cenocepacia IIIB and BCC6 isolates in Mexican and Italian maize rhizospheres. Despite the clear relationship found between the geographic origin of isolates and grouping, identical RTs and closely related isolates were observed in geographically distant regions. Ecological factors and selective pressure may preferably promote some genotypes within each local microbial population, favouring the spread of a single clone above the rest of the recombinant population.
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Affiliation(s)
- Annamaria Bevivino
- ENEA (Italian National Agency for New Technologies, Energy and Sustainable Development) Casaccia Research Center-Technical Unit for Sustainable Development and Innovation of Agro-Industrial System, Via Anguillarese 301, 00123 S, Maria di Galeria, Rome, Italy.
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Genomes and characterization of phages Bcep22 and BcepIL02, founders of a novel phage type in Burkholderia cenocepacia. J Bacteriol 2011; 193:5300-13. [PMID: 21804006 DOI: 10.1128/jb.05287-11] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Within the Burkholderia cepacia complex, B. cenocepacia is the most common species associated with aggressive infections in the lungs of cystic fibrosis patients, causing disease that is often refractive to treatment by antibiotics. Phage therapy may be a potential alternative form of treatment for these infections. Here we describe the genome of the previously described therapeutic B. cenocepacia podophage BcepIL02 and its close relative, Bcep22. Phage Bcep22 was found to contain a circularly permuted genome of 63,882 bp containing 77 genes; BcepIL02 was found to be 62,714 bp and contains 76 predicted genes. Major virion-associated proteins were identified by proteomic analysis. We propose that these phages comprise the founding members of a novel podophage lineage, the Bcep22-like phages. Among the interesting features of these phages are a series of tandemly repeated putative tail fiber genes that are similar to each other and also to one or more such genes in the other phages. Both phages also contain an extremely large (ca. 4,600-amino-acid), virion-associated, multidomain protein that accounts for over 20% of the phages' coding capacity, is widely distributed among other bacterial and phage genomes, and may be involved in facilitating DNA entry in both phage and other mobile DNA elements. The phages, which were previously presumed to be virulent, show evidence of a temperate lifestyle but are apparently unable to form stable lysogens in their hosts. This ambiguity complicates determination of a phage lifestyle, a key consideration in the selection of therapeutic phages.
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