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BMC Pulmonary Medicine Feb 2017Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These...
BACKGROUND
Pandoraea species are considered emerging pathogens in the context of cystic fibrosis (CF) and are difficult to identify by conventional biochemical methods. These multidrug resistant bacteria remain poorly understood particularly in terms of natural resistance, mechanisms of acquired resistance and impact on the prognosis of the disease and the lung function. Among them, Pandoraea sputorum has been previously described in few cases of CF patients from Spain, Australia, France and United States, underlining the need of more clinical data for a better knowledge of its pathogenicity. This is the first report relating to P. sputorum in a CF patient in Argentina.
CASE PRESENTATION
Pandoraea sputorum was identified in a nine-year-old cystic fibrosis patient from Argentina, after treatment failure during an exacerbation. The isolates were successfully identified by combining molecular techniques based on 16S rRNA sequencing and mass spectrometry (MS) methods, after reassessing previous misidentified isolates by conventional methods. After first isolation of P. sputorum, patient's clinical condition worsened but later improved after a change in the treatment. Although isolates showed susceptibility to trimethoprim-sulfamethoxazole and imipenem, in our case, the antibiotic treatment failed in the eradication of P. sputorum.
CONCLUSIONS
All combined data showed a chronic colonization with P. sputorum associated to a deterioration of lung function. We noted that the presence of P. sputorum can be underestimated in CF patients and MALDI-TOF MS appears to be a promising means of accurate identification of Pandoraea species.
Topics: Argentina; Burkholderiaceae; Child; Cystic Fibrosis; Humans; Male; RNA, Ribosomal, 16S; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Sputum
PubMed: 28173787
DOI: 10.1186/s12890-017-0373-y -
Genome Announcements Nov 2015Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant pathogens in persons with cystic fibrosis (CF). To aid in understanding the...
Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant pathogens in persons with cystic fibrosis (CF). To aid in understanding the role of P. apista in CF lung disease, we used Illumina MiSeq and nanopore MinION technology to sequence the whole genome of the P. apista LMG 16407(T).
PubMed: 26564037
DOI: 10.1128/genomeA.01300-15 -
Journal of Biotechnology Jun 2015Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete...
Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete genome sequence of P. vervacti DSM 23571(T). A complete pathway for degradation of oxalate was revealed from the genome analysis. These data are important to path new opportunities for genetic engineering in the field of biotechnology.
Topics: Base Composition; Base Sequence; Burkholderiaceae; Gene Components; Genome, Bacterial; Industrial Microbiology; Metabolic Networks and Pathways; Molecular Sequence Data; Oxalates; Sequence Analysis, DNA; Soil Microbiology; Turkey
PubMed: 25848988
DOI: 10.1016/j.jbiotec.2015.03.020 -
Journal of Applied Microbiology Oct 2007To isolate and characterize an oxalate-degrading Pandoraea sp. OXJ-11.
AIMS
To isolate and characterize an oxalate-degrading Pandoraea sp. OXJ-11.
METHODS AND RESULTS
A new bacterium Pandoraea sp. OXJ-11 was isolated from soil samples, which can grow in the medium with oxalate as the sole carbon and energy source. The isolate OXJ-11 is Gram-negative straight rod. It occurs singly and is motile by means of a double polar flagellum. Catalase is positive and nitrate is not reduced. It grows aerobically and the optimum growth temperature and the optimum pH are at 30 degrees C and pH 6.0, respectively. The polyphasic taxonomic data along with 16S rRNA sequence comparison demonstrate that the isolate OXJ-11 should belong to the genus Pandoraea and represent a new member in this family.
CONCLUSIONS
Oxalate could be degraded and the oxalate-degrading enzyme activity was detected when the isolate OXJ-11 grew in the medium with oxalate as carbon source.
SIGNIFICANCE AND IMPACT OF THE STUDY
Oxalate-degrading Pandoraea sp. OXJ-11 would be beneficial to the potential application in the control of sclerotinia stem rot in economically important plants caused by fungus Sclerotinia sclerotiorum, and in making plants resistant to the white mold disease by oxalate-degrading enzyme transgene.
Topics: Biomass; Burkholderia; Culture Media; Hydrogen-Ion Concentration; Oxalates; Phenotype; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Soil Microbiology; Temperature
PubMed: 17897211
DOI: 10.1111/j.1365-2672.2007.03363.x -
Parasitology Sep 2018Parasitic trypanosomatids diverged from free-living kinetoplastid ancestors several hundred million years ago. These parasites are relatively well known, due in part to... (Review)
Review
Parasitic trypanosomatids diverged from free-living kinetoplastid ancestors several hundred million years ago. These parasites are relatively well known, due in part to several unusual cell biological and molecular traits and in part to the significance of a few - pathogenic Leishmania and Trypanosoma species - as aetiological agents of serious neglected tropical diseases. However, the majority of trypanosomatid biodiversity is represented by osmotrophic monoxenous parasites of insects. In two lineages, novymonads and strigomonads, osmotrophic lifestyles are supported by cytoplasmic endosymbionts, providing hosts with macromolecular precursors and vitamins. Here we discuss the two independent origins of endosymbiosis within trypanosomatids and subsequently different evolutionary trajectories that see entrainment vs tolerance of symbiont cell divisions cycles within those of the host. With the potential to inform on the transition to obligate parasitism in the trypanosomatids, interest in the biology and ecology of free-living, phagotrophic kinetoplastids is beginning to enjoy a renaissance. Thus, we take the opportunity to additionally consider the wider relevance of endosymbiosis during kinetoplastid evolution, including the indulged lifestyle and reductive evolution of basal kinetoplastid Perkinsela.
Topics: Biodiversity; Biological Evolution; Evolution, Molecular; Genome, Protozoan; Kinetoplastida; Leishmania; Symbiosis; Trypanosoma; Trypanosomatina
PubMed: 29895336
DOI: 10.1017/S0031182018000781 -
PloS One 2013The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a...
The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs) is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356)). BPDO(B356), a heterohexameric (αβ)(3) Rieske oxygenase (RO), catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356) with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II) has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDO(B356) and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments.
Topics: Biphenyl Compounds; Burkholderiaceae; Catalytic Domain; Crystallography, X-Ray; Dioxygenases; Models, Molecular; Mutagenesis; Phylogeny; Polychlorinated Biphenyls; Protein Conformation; Protein Subunits; Substrate Specificity
PubMed: 23308114
DOI: 10.1371/journal.pone.0052550 -
Acta Crystallographica. Section F,... Nov 2010cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of biphenyl and polychlorinated biphenyls. BphB from Pandoraea pnomenusa...
cis-Biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is involved in the aerobic biodegradation of biphenyl and polychlorinated biphenyls. BphB from Pandoraea pnomenusa strain B-356 was overexpressed in Escherichia coli, purified to homogeneity and crystallized. Crystals were obtained by the sitting-drop vapour-diffusion method using polyethylene glycol 3350 and 0.2 M sodium malonate. A BphB crystal diffracted to 2.8 Å resolution and belonged to space group P4(3)2(1)2, with unit-cell parameters a = b = 75.2, c = 180.4 Å. Preliminary crystallographic analysis indicated the presence of two molecules in the asymmetric unit, giving a Matthews coefficient of 2.2 Å(3) Da(-1) and a solvent content of 44%.
Topics: Burkholderiaceae; Crystallization; Crystallography, X-Ray; Gene Expression; Oxidoreductases
PubMed: 21045310
DOI: 10.1107/S1744309110036894 -
International Journal of Systematic and... Sep 2016A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells...
A Gram-staining-negative, facultatively aerobic, white-colony-forming bacterium, designated strain SE-S21T, was isolated from forest soil of Jeju Island in Korea. Cells were motile rods with a single polar flagellum, showing catalase- and oxidase-positive reactions. Growth was observed at 10-40 °C (optimum, 30 °C), pH 4.0-10.0 (optimum, pH 7.0-7.5) and with 0-4.0 % (w/v) NaCl (optimum, 0-2 %). Only ubiquinone-8 was detected as the isoprenoid quinone, and C16 : 0, C17 : 0 cyclo, C19 : 1ω8c cyclo and summed feature 2 (comprising C12 : 0 aldehyde and/or unknown) were found to be the major fatty acids. Phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown aminophospholipid, an unknown aminolipid and an unknown lipid were detected as the major polar lipids. Putrescine and 2-hydroxyputrescine were the predominant polyamines. The DNA G+C content was 61.0 mol%. Phylogenetic analyses based on 16S rRNA and DNA gyrase B gene sequences revealed that strain SE-S21T formed a phyletic lineage within the genus Pandoraea. Strain SE-S21T was most closely related to Pandoraea faecigallinarum KOxT and Pandoraea pnomenusa CCUG 38742T with 98.8 % and 98.7 % 16S rRNA gene sequence similarities, respectively. However, the DNA-DNA relatedness values between strain SE-S21T and the type strains of P. faecigallinarum and P. pnomenusa were 26.6±5.7 % and 20.5±3.7 %, respectively. On the basis of phenotypic, chemotaxonomic and molecular features, strain SE-S21T clearly represents a novel species of the genus Pandoraea, for which the name Pandoraea terrae sp. nov. is proposed. The type strain is SE-S21T (=KACC 18127T=JCM 30137T). An emended description of the genus Pandoraea is also proposed.
Topics: Bacterial Typing Techniques; Base Composition; Burkholderiaceae; DNA, Bacterial; Fatty Acids; Forests; Islands; Nucleic Acid Hybridization; Phospholipids; Phylogeny; Putrescine; RNA, Ribosomal, 16S; Republic of Korea; Sequence Analysis, DNA; Soil Microbiology; Ubiquinone
PubMed: 27267599
DOI: 10.1099/ijsem.0.001229 -
Microorganisms May 2023The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in... (Review)
Review
The respiratory tract of lung transplant recipients (LTR) is likely to be colonized with non-fermentative Gram-negative rods. As a consequence of the improvements in molecular sequencing and taxonomy, an increasing number of bacterial species have been described. We performed a review of the literature of bacterial infections in LTR involving non-fermentative Gram-negative rods with exclusion of , , spp. and spp. Overall, non-fermenting GNR were recovered from 17 LTR involving the following genera: , , , , , and . We then discuss the issues raised by these bacteria, including detection and identification, antimicrobial resistance, pathogenesis, and cross-transmission.
PubMed: 37374970
DOI: 10.3390/microorganisms11061468 -
ACS Omega Dec 2017The present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain sp....
The present study investigates polyhydroxyalkanoate (PHA) production from lignin and its derivatives by a previously reported lignin-degrading bacterial strain sp. ISTKB. PHA production was screened by fluorescence microscopy and flow cytometry using a Nile red stain. PHA and biomass accumulation, while screening, was found to be maximum on 4-hydroxybenzoic acid followed by -coumaric acid, vanillic acid, 2,6-dimethoxyphenol, and kraft lignin after 96 h. Monomer composition was analyzed by gas chromatography-mass spectrometry (GC-MS) and was followed by Fourier transform infrared and H NMR analysis, indicating PHA to be a copolymer of P(hydroxybutyrate--hydroxyvalerate). Genomic analysis of sp. ISTKB also complemented the results of GC-MS and NMR, and the relevant genes responsible for the synthesis of small chain length PHA were discovered in the genome. Process parameters were optimized by response surface methodology for enhanced production of PHA and biomass on 4-hydroxybenzoate. Optimization results showed 30 and 66% increase in the biomass and PHA production, respectively. The results obtained were promising and indicated that if lignin is depolymerized into low-molecular-weight intermediates, then it can easily be utilized and converted into value-added products like PHA by microbes.
PubMed: 30023602
DOI: 10.1021/acsomega.7b01615