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Draghi WO, Degrossi J, Bialer M, Brelles-Mariño G, Abdian P, Soler-Bistué A, Wall L, Zorreguieta A. Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices. PLoS One 2018; 13:e0200651. [PMID: 30001428 PMCID: PMC6042781 DOI: 10.1371/journal.pone.0200651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/29/2018] [Indexed: 11/19/2022] Open
Abstract
No-tillage crop production has revolutionized the agriculture worldwide. In our country more than 30 Mha are currently cultivated under no-till schemes, stressing the importance of this management system for crop production. It is widely recognized that soil microbiota is altered under different soil managements. In this regard the structure of Burkholderia populations is affected by soils management practices such as tillage, fertilization, or crop rotation. The stability of these structures, however, has not been evaluated under sustainable schemes where the impact of land practices could be less deleterious to physicochemical soils characteristics. In order to assess the structure of Burkholderia spp. populations in no-till schemes, culturable Burkholderia spp. strains were quantified and their biodiversity evaluated. Results showed that Burkholderia spp. biodiversity, but not their abundance, clearly displayed a dependence on agricultural managements. We also showed that biodiversity was mainly influenced by two soil factors: Total Organic Carbon and Total Nitrogen. Results showed that no-till schemes are not per se sufficient to maintain a richer Burkholderia spp. soil microbiota, and additional traits should be considered when sustainability of productive soils is a goal to fulfil productive agricultural schemes.
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Affiliation(s)
- Walter Omar Draghi
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- Instituto de Biotecnología y Biología Molecular–CCT La Plata CONICET, Universidad Nacional de La Plata, La Plata, Argentina
- * E-mail: (AZ); (WOD)
| | - Jose Degrossi
- Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Magalí Bialer
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | - Graciela Brelles-Mariño
- Center for Research and Development of Industrial Fermentations, (CINDEFI, CCT-LA PLATA-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Patricia Abdian
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
| | | | - Luis Wall
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, IIBBA CONICET, Buenos Aires, Argentina
- * E-mail: (AZ); (WOD)
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Salloum T, Nassour E, Araj GF, Abboud E, Tokajian S. Insights into the genome diversity and virulence of two clinical isolates of Burkholderia cenocepacia. J Med Microbiol 2018; 67:1157-1167. [PMID: 29897328 DOI: 10.1099/jmm.0.000759] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
PURPOSE Burkholderia cenocepacia is among the most common members of the Burkholderia cepacia complex (Bcc) isolated from patients with cystic fibrosis (CF). The factors triggering the high rates of morbidity and mortality in CF patients are not well elucidated. In this study, we aim to highlight the genome diversity of two clinical isolates of B. cenocepacia through comparative genome analysis. METHODOLOGY The repertoire of virulence factors and resistance genes compared to reference strains J2315 and K56-2 was elucidated. The isolates were screened for the presence of phages and insertion sequences. Two methods were combined to obtain an accurate prediction of genomic islands (GIs): the cumulative GC profile and the IslandViewer web tool. To study evolutionary relatedness, whole genome-based single-nucleotide polymorphism (wgSNP) analysis was also performed with 43 publically available strains of the Bcc of various sequence types.Results/Key findings. Genome-based species identification of the two isolates BC-AUH and BC-BMEH confirmed the species as B. cenocepacia. Both belonged to ST-602, a double-locus variant of ST-32 (CC31), genomovar IIIA, and carried a large number of antibiotic resistance genes. Eighteen GIs were predicted in BC-AUH and BC-BMEH, occupying 9.3 and 6.1 % of the respective genomes. Comparison to J2315 revealed 89 and 85 genes unique to BC-BMEH and BC-AUH, respectively. Additionally, 1823 intergenic SNPs were detected between BC-BMEH and BC-AUH. CONCLUSION This study mapped existing genetic variations in B. cenocepacia associated with notorious outcomes in CF patients, and the data obtained provide comprehensive, genome-inferred insights and multifactorial examination of an important human pathogen.
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Affiliation(s)
- Tamara Salloum
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Elie Nassour
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - George F Araj
- 2Department of Pathology and Laboratory Medicine, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Edmond Abboud
- 3Laboratory Department, the Middle East Institute of Health University Center, Bsalim, Lebanon
| | - Sima Tokajian
- 1Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
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Bruto M, Prigent-Combaret C, Muller D, Moënne-Loccoz Y. Analysis of genes contributing to plant-beneficial functions in Plant Growth-Promoting Rhizobacteria and related Proteobacteria. Sci Rep 2014; 4:6261. [PMID: 25179219 PMCID: PMC4151105 DOI: 10.1038/srep06261] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/11/2014] [Indexed: 01/22/2023] Open
Abstract
The positive effects of root-colonizing bacteria cooperating with plants lead to improved growth and/or health of their eukaryotic hosts. Some of these Plant Growth-Promoting Rhizobacteria (PGPR) display several plant-beneficial properties, suggesting that the accumulation of the corresponding genes could have been selected in these bacteria. Here, this issue was targeted using 23 genes contributing directly or indirectly to established PGPR effects, based on genome sequence analysis of 304 contrasted Alpha- Beta- and Gammaproteobacteria. Most of the 23 genes studied were also found in non-PGPR Proteobacteria and none of them were common to all 25 PGPR genomes studied. However, ancestral character reconstruction indicated that gene transfers -predominantly ancient- resulted in characteristic gene combinations according to taxonomic subgroups of PGPR strains. This suggests that the PGPR-plant cooperation could have established separately in various taxa, yielding PGPR strains that use different gene assortments. The number of genes contributing to plant-beneficial functions increased along the continuum -animal pathogens, phytopathogens, saprophytes, endophytes/symbionts, PGPR- indicating that the accumulation of these genes (and possibly of different plant-beneficial traits) might be an intrinsic PGPR feature. This work uncovered preferential associations occurring between certain genes contributing to phytobeneficial traits and provides new insights into the emergence of PGPR bacteria.
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Affiliation(s)
- Maxime Bruto
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Daniel Muller
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- 1] Université de Lyon, F-69622, Lyon, France [2] Université Lyon 1, Villeurbanne, France [3] CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France
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Zuleta LFG, Cunha CDO, de Carvalho FM, Ciapina LP, Souza RC, Mercante FM, de Faria SM, Baldani JI, Straliotto R, Hungria M, de Vasconcelos ATR. The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes. BMC Genomics 2014; 15:535. [PMID: 24972629 PMCID: PMC4101177 DOI: 10.1186/1471-2164-15-535] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. RESULTS Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a. CONCLUSIONS The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation.
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Characterization of Klebsiella sp. strain 10982, a colonizer of humans that contains novel antibiotic resistance alleles and exhibits genetic similarities to plant and clinical Klebsiella isolates. Antimicrob Agents Chemother 2014; 58:1879-88. [PMID: 24395222 DOI: 10.1128/aac.01605-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A unique Klebsiella species strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit. Klebsiella sp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC β-lactamase designated FOX-10. A novel variant of the LEN β-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in either Klebsiella pneumoniae clinical isolates or Klebsiella nitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis of Klebsiella sp. 10982 and sequenced Klebsiella genomes demonstrated that Klebsiella sp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes and K. pneumoniae clinical isolates. Metabolic features identified in the genome of Klebsiella sp. 10982 distinguish this isolate from other Klebsiella clinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophytic Klebsiella isolates and is absent from Klebsiella clinical isolates. Additionally, the Klebsiella sp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily in K. pneumoniae isolates from liver abscesses. Comparative genomic analysis of Klebsiella sp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body.
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Cescutti P, Cuzzi B, Herasimenka Y, Rizzo R. Structure of a novel exopolysaccharide produced by Burkholderia vietnamiensis, a cystic fibrosis opportunistic pathogen. Carbohydr Polym 2013; 94:253-60. [DOI: 10.1016/j.carbpol.2013.01.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/03/2013] [Accepted: 01/18/2013] [Indexed: 11/29/2022]
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The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia. ISME JOURNAL 2013; 7:1568-81. [PMID: 23486248 PMCID: PMC3721108 DOI: 10.1038/ismej.2013.36] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 12/11/2022]
Abstract
Burkholderia cenocepacia is a Gram-negative aerobic bacterium that belongs to a group of opportunistic pathogens displaying diverse environmental and pathogenic lifestyles. B. cenocepacia is known for its ability to cause lung infections in people with cystic fibrosis and it possesses a large 8 Mb multireplicon genome encoding a wide array of pathogenicity and fitness genes. Transcriptomic profiling across nine growth conditions was performed to identify the global gene expression changes made when B. cenocepacia changes niches from an environmental lifestyle to infection. In comparison to exponential growth, the results demonstrated that B. cenocepacia changes expression of over one-quarter of its genome during conditions of growth arrest, stationary phase and surprisingly, under reduced oxygen concentrations (6% instead of 20.9% normal atmospheric conditions). Multiple virulence factors are upregulated during these growth arrest conditions. A unique discovery from the comparative expression analysis was the identification of a distinct, co-regulated 50-gene cluster that was significantly upregulated during growth under low oxygen conditions. This gene cluster was designated the low-oxygen-activated (lxa) locus and encodes six universal stress proteins and proteins predicted to be involved in metabolism, transport, electron transfer and regulation. Deletion of the lxa locus resulted in B. cenocepacia mutants with aerobic growth deficiencies in minimal medium and compromised viability after prolonged incubation in the absence of oxygen. In summary, transcriptomic profiling of B. cenocepacia revealed an unexpected ability of aerobic Burkholderia to persist in the absence of oxygen and identified the novel lxa locus as key determinant of this important ecophysiological trait.
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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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9
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Graindorge A, Menard A, Monnez C, Cournoyer B. Insertion sequence evolutionary patterns highlight convergent genetic inactivations and recent genomic island acquisitions among epidemic Burkholderia cenocepacia. J Med Microbiol 2011; 61:394-409. [PMID: 21980044 DOI: 10.1099/jmm.0.036822-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Burkholderia cenocepacia B&B clone was found previously to be responsible for an epidemic outbreak within an intensive care unit in France. This clone belongs to the ST32 clonal complex, which is one of the most prevalent among French cystic fibrosis patients and is known to be related to the highly virulent ET12 clonal complex. Genomic repartition biases of insertion sequences (ISs) were investigated to improve our understanding of the evolutionary events leading to B. cenocepacia diversification and the emergence of such epidemic lineages. IS were used for tracking convergent genetic inactivations and recent DNA acquisitions. B. cenocepacia IS families and subgroups were compared in terms of genetic diversity and genomic architecture using fully sequenced genomes, PCR screening and DNA blot analysis. These analyses revealed several features shared by the B&B and ET12 epidemic clones. IS elements showed a frequent localization on genomic islands (GI) and indicated convergent evolution towards inactivation of certain loci. The IS407 subgroup of the IS3 family was identified as a good indicator of recently acquired GIs in clone ET12. Several IS407 elements showed strain-specific or clonal complex-specific localizations. IS407 DNA probing of a DNA library built from the B. cenocepacia B&B epidemic clone led to the identification of a recently acquired IS407-tagged GI likely to be conjugative and integrative. The B&B clone showed significant differences in its IS architecture from that of ST32 strains isolated from Czech cystic fibrosis patients.
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Affiliation(s)
- Arnault Graindorge
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Aymeric Menard
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Claire Monnez
- VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
| | - Benoit Cournoyer
- Environmental Microbiology Lyon, Biological Resource Center, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France.,VetAgro Sup Veterinary School, Lyon, France.,Research Group on Bacterial Opportunistic Pathogens and Environment, Université de Lyon, UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, Lyon, France
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10
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Vial L, Chapalain A, Groleau MC, Déziel E. The various lifestyles of theBurkholderia cepaciacomplex species: a tribute to adaptation. Environ Microbiol 2010; 13:1-12. [DOI: 10.1111/j.1462-2920.2010.02343.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Souza ALF, Invitti AL, Rego FGM, Monteiro RA, Klassen G, Souza EM, Chubatsu LS, Pedrosa FO, Rigo LU. The involvement of the nif-associated ferredoxin-like genes fdxA and fdxN of Herbaspirillum seropedicae in nitrogen fixation. J Microbiol 2010; 48:77-83. [PMID: 20221733 DOI: 10.1007/s12275-009-0077-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 07/26/2009] [Indexed: 10/19/2022]
Abstract
The pathway of electron transport to nitrogenase in the endophytic beta-Proteobacterium Herbaspirillum seropedicae has not been characterized. We have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxA and fdxN. The fdxA gene is part of the operon nifHDKENXorf1orf2fdxAnifQmodABC and is transcribed from the nifH promoter, as revealed by lacZ gene fusion. The fdxN gene is probably cotranscribed with the nifB gene. Mutational analysis suggests that the FdxA protein is essential for maximum nitrogenase activity, since the nitrogenase activity of the fdxA mutant strain was reduced to about 30% of that of the wild-type strain. In addition, the fdxA mutation had no effect on the nitrogenase switch-off in response to ammonium. Nitrogenase activity of a mutant strain lacking the fdxN gene was completely abolished. This phenotype was reverted by complementation with fdxN expressed under lacZ promoter control. The results suggest that the products of both the fdxA and fdxN genes are probably involved in electron transfer during nitrogen fixation.
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Affiliation(s)
- André L F Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Brazil
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12
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Molina-Henares MA, de la Torre J, García-Salamanca A, Molina-Henares AJ, Herrera MC, Ramos JL, Duque E. Identification of conditionally essential genes for growth ofPseudomonas putidaKT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol 2010; 12:1468-85. [DOI: 10.1111/j.1462-2920.2010.02166.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Lavenir R, Sanroma M, Gibert S, Crouzet O, Laurent F, Kravtsoff J, Mazoyer MA, Cournoyer B. Spatio-temporal analysis of infra-specific genetic variations among a Pseudomonas aeruginosa water network hospital population: invasion and selection of clonal complexes. J Appl Microbiol 2010; 105:1491-501. [PMID: 19146487 DOI: 10.1111/j.1365-2672.2008.03907.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To investigate infra-specific spatio-temporal dynamics of a hospital water network Pseudomonas aeruginosa population. To infer the origin of water network isolates and assess their potential health hazard. METHODS AND RESULTS 168 P. aeruginosa strains were isolated from tap waters and swabs of tap nozzle aerators of a hospital unit, over 2 years, and from rectal swabs and nosocomial infections. Genetic diversity among this collection was assessed by pulsed field gel electrophoresis of SpeI restricted genomic DNA. Virulence gene sets, biofilm properties, and hypochlorite resistance were analysed. Exactly 68% of the water samples and 74% of the tap nozzle aerators harboured P. aeruginosa. The strains were divided into 22 clonal lineages, with one dominant clone shown to have been involved in a nosocomial infection. CONCLUSIONS An important turnover among the P. aeruginosa hospital population was observed. Some clonal lineages were found to persist, spread in the unit, and diversify into clonal complexes. Rectal carriage appeared an important source of contamination of the water network. SIGNIFICANCE AND IMPACT OF THE STUDY High P. aeruginosa infra-specific population diversity suggested a broad ability in colonizing water networks but persistence analysis indicated a strong selection leading to the emergence of dominant clones.
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Epidemiology and molecular characterization of a clone of Burkholderia cenocepacia responsible for nosocomial pulmonary tract infections in a French intensive care unit. Diagn Microbiol Infect Dis 2010; 66:29-40. [DOI: 10.1016/j.diagmicrobio.2009.06.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 06/04/2009] [Accepted: 06/08/2009] [Indexed: 11/17/2022]
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15
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Pirone L, Bragonzi A, Farcomeni A, Paroni M, Auriche C, Conese M, Chiarini L, Dalmastri C, Bevivino A, Ascenzioni F. Burkholderia cenocepacia strains isolated from cystic fibrosis patients are apparently more invasive and more virulent than rhizosphere strains. Environ Microbiol 2008; 10:2773-84. [PMID: 18643926 DOI: 10.1111/j.1462-2920.2008.01697.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Given the widespread presence of Burkholderia cenocepacia in the rhizosphere it is important to determine whether rhizosphere strains are pathogenic for cystic fibrosis patients or not. Eighteen B. cenocepacia strains of rhizosphere and clinical origin were typed by multi-locus sequence typing (MLST) analysis and compared for their ability to invade pulmonary epithelial cells and their virulence in a mouse model of airway infection. Although there was great variability, clinical strains were the most invasive in vitro. Almost all the rhizosphere and two clinical strains were defined as non-invasive, six clinical strains as invasive, and two strains of both clinical and environmental origin as indeterminate. Exposure of murine airways to clinical strains caused higher acute mortality than that seen after challenge with rhizosphere strains. Furthermore, both clinical and environmental strains were able to persist in the lungs of infected mice, with no significant differences in bacterial loads and localization 14 days after challenge. DNA dot blot analyses of AHL synthase, porin and amidase genes, which play a role in B. cenocepacia virulence, showed that they were present in B. cenocepacia strains irrespective of their origin. Overall, our results suggest that rhizosphere strains do not differ from clinical strains in some pathogenic traits.
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Affiliation(s)
- Luisa Pirone
- ENEA C.R. Casaccia - Department of Biotechnologies, Agroindustry and Protection of Health, Plant Genetics and Genomics Section, Rome, Italy
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Moisander PH, Beinart RA, Voss M, Zehr JP. Diversity and abundance of diazotrophic microorganisms in the South China Sea during intermonsoon. ISME JOURNAL 2008; 2:954-67. [PMID: 18528417 DOI: 10.1038/ismej.2008.51] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The spatial heterogeneity of diversity and abundance of diazotrophs were investigated off the Vietnamese coast in the South China Sea (SCS). The study area extended from the Mekong River plume to the shelf region and beyond to stations extending to 1700 m depth. The SCS diazotroph community, based on nifH gene diversity, had components closely related to sequences from open ocean, estuarine, saltmarsh and microbial mat communities. Rarefaction analysis suggested that by using a 97% similarity operational taxonomic unit definition, the majority of nifH sequence diversity in the samples was covered by the 384 nifH clones obtained. The majority of the nifH sequences recovered fell into two clusters: one comprised of Trichodesmium sequences and the other an alpha-proteobacterial group. Unicellular cyanobacterial groups A and B, and symbiotic filamentous cyanobacterial diazotrophs were detected sporadically. Trichodesmium was by far the most abundant diazotroph, with up to 6 x 10(5) nifH gene copies per liter. Quantitative PCR probe-primer sets were designed and used to quantify two proteobacterial groups, revealing abundances up to 10(3)-10(4) nifH gene copies per liter, with the highest abundances in the photic zone. Major components of the clone library were also revealed by a nifH microarray and multidimensional scaling (MDS) analysis. MDS showed that samples from the >10 microm size fraction from 0- to 5-m depths clustered separately from the rest of the samples, primarily due to the abundance of Trichodesmium sequences. The SCS diazotroph community has a relatively low diversity and is a mixture of both estuarine and oceanic fingerprints.
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Affiliation(s)
- Pia H Moisander
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
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Menard A, de los Santos PE, Graindorge A, Cournoyer B. Architecture of Burkholderia cepacia complex sigma70 gene family: evidence of alternative primary and clade-specific factors, and genomic instability. BMC Genomics 2007; 8:308. [PMID: 17784948 PMCID: PMC2194791 DOI: 10.1186/1471-2164-8-308] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 09/04/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Burkholderia cepacia complex (Bcc) groups bacterial species with beneficial properties that can improve crop yields or remediate polluted sites but can also lead to dramatic human clinical outcomes among cystic fibrosis (CF) or immuno-compromised individuals. Genome-wide regulatory processes of gene expression could explain parts of this bacterial duality. Transcriptional sigma70 factors are components of these processes. They allow the reversible binding of the DNA-dependent RNA polymerase to form the holoenzyme that will lead to mRNA synthesis from a DNA promoter region. Bcc genome-wide analyses were performed to investigate the major evolutionary trends taking place in the sigma70 family of these bacteria. RESULTS Twenty sigma70 paralogous genes were detected in the Burkholderia cenocepacia strain J2315 (Bcen-J2315) genome, of which 14 were of the ECF (extracytoplasmic function) group. Non-ECF paralogs were related to primary (rpoD), alternative primary, stationary phase (rpoS), flagellin biosynthesis (fliA), and heat shock (rpoH) factors. The number of sigma70 genetic determinants among this genome was of 2,86 per Mb. This number is lower than the one of Pseudomonas aeruginosa, a species found in similar habitats including CF lungs. These two bacterial groups showed strikingly different sigma70 family architectures, with only three ECF paralogs in common (fecI-like, pvdS and algU). Bcen-J2315 sigma70 paralogs showed clade-specific distributions. Some paralogs appeared limited to the ET12 epidemic clone (ecfA2), particular Bcc species (sigI), the Burkholderia genus (ecfJ, ecfF, and sigJ), certain proteobacterial groups (ecfA1, ecfC, ecfD, ecfE, ecfG, ecfL, ecfM and rpoS), or were broadly distributed in the eubacteria (ecfI, ecfK, ecfH, ecfB, and rpoD-, rpoH-, fliA-like genes). Genomic instability of this gene family was driven by chromosomal inversion (ecfA2), recent duplication events (ecfA and RpoD), localized (ecfG) and large scale deletions (sigI, sigJ, ecfC, ecfH, and ecfK), and a phage integration event (ecfE). CONCLUSION The Bcc sigma70 gene family was found to be under strong selective pressures that could lead to acquisition/deletion, and duplication events modifying its architecture. Comparative analysis of Bcc and Pseudomonas aeruginosa sigma70 gene families revealed distinct evolutionary strategies, with the Bcc having selected several alternative primary factors, something not recorded among P. aeruginosa and only previously reported to occur among the actinobacteria.
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Affiliation(s)
- Aymeric Menard
- Université de Lyon, Lyon, France
- Research group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, and Ecole Nationale Vétérinaire de Lyon, France
| | - Paulina Estrada de los Santos
- Université de Lyon, Lyon, France
- Research group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, and Ecole Nationale Vétérinaire de Lyon, France
| | - Arnault Graindorge
- Université de Lyon, Lyon, France
- Research group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, and Ecole Nationale Vétérinaire de Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Lyon, France
- Research group on «Bacterial Opportunistic Pathogens and Environment», UMR5557 Ecologie Microbienne, Université Lyon 1, CNRS, and Ecole Nationale Vétérinaire de Lyon, France
- UMR CNRS 5557 Ecologie Microbienne, Mendel Bldg., 5floor, Université Lyon 1, 69622 Villeurbanne Cedex, France
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