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PeerJ 2015In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair...
In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.
PubMed: 26336650
DOI: 10.7717/peerj.1225 -
Infection and Drug Resistance 2019(), an emerging pathogen, is able to trigger a pronounced pro-inflammatory response that results in lung dysfunction in cystic fibrosis (CF) patients. All previous...
(), an emerging pathogen, is able to trigger a pronounced pro-inflammatory response that results in lung dysfunction in cystic fibrosis (CF) patients. All previous isolates have been obtained from the respiratory samples of CF patients, with no reported cases of bacteremia. For the first time, we report isolates recovered twice from the blood cultures of a patient with liver cancer who had undergone allogeneic liver transplantation. These isolates were successfully identified by combining mass spectrometry and molecular techniques based on 16S rRNA sequencing methods. At the onset of the bacteremia, the patient's peripheral T, B and NK cell counts were 181.68/μL, 59.57/μL and 70.66/μL, respectively. The serum procalcitonin level, C-reactive protein level and peripheral neutrophil granulocyte percentage were 0.56 ng/mL, 61.00 mg/L and 96.8%, respectively. We found these isolates to be susceptible to ciprofloxacin and piperacillin/tazobactam and to be intermediate to amikacin. Previous studies have found isolates to be resistant. All of the data combined showed that compromised immune function from allogeneic liver transplantation plus immunosuppressive therapy contributes to the occurrence of bacteremia. Furthermore, the isolates demonstrated characteristic resistance profiles.
PubMed: 31695454
DOI: 10.2147/IDR.S227643 -
Transplantation Dec 2021Uncontrolled donation after circulatory death (DCD) donors are an extraordinary resource to increase the number of lungs available for transplantation. However, the risk...
BACKGROUND
Uncontrolled donation after circulatory death (DCD) donors are an extraordinary resource to increase the number of lungs available for transplantation. However, the risk of the warm ischemia resulting from cardiac arrest to irreversibly damage the organs is considerable. Moreover, graft preservation issues and organizational problems often worsen the dangerous effects of warm ischemia. Ex vivo lung perfusion (EVLP) enables us to evaluate and recondition lungs whose functionality is doubtful, as well as to overcome the difficulties related to time and logistics.
METHODS
We report the case of uncontrolled DCD lungs successfully treated with an exceptionally prolonged EVLP. Because the donor's blood count and liver biopsy showed signs of possible leukemia, EVLP was protracted up to 17 h while waiting for immunohistochemical analyses to rule out this diagnosis; eventually, the results came back negative, and the lungs were judged suitable for transplantation.
RESULTS
The recipient was a 32-y-old male individual with cystic fibrosis, colonized by Pandoraea pnomenusa. Bilateral transplantation required central extracorporeal membrane oxygenation. The patient was extubated after 36 h and was discharged 21 d after the operation. Despite early recolonization by Pandoraea pnomenusa and airway complications requiring pneumatic dilatation, he is alive and has a satisfactory respiratory function 15 mo after transplantation.
CONCLUSIONS
Uncontrolled DCD represents a challenge due to both logistical issues and the complexity of graft evaluation before procurement. EVLP with cellular perfusate could be a valuable tool to overcome these limits. Nonetheless, caution should be exercised when interpreting the effects of this technique on airway healing.
Topics: Extracorporeal Circulation; Humans; Lung; Lung Transplantation; Male; Organ Preservation; Perfusion; Tissue Donors; Warm Ischemia
PubMed: 33496562
DOI: 10.1097/TP.0000000000003646 -
Frontiers in Microbiology 2023The root rot disease causes a great economic loss, and the disease severity usually increases as ginseng ages. However, it is still unclear whether the disease severity...
The root rot disease causes a great economic loss, and the disease severity usually increases as ginseng ages. However, it is still unclear whether the disease severity is related to changes in microorganisms during the entire growing stage of American ginseng. The present study examined the microbial community in the rhizosphere and the chemical properties of the soil in 1-4-year-old ginseng plants grown in different seasons at two different sites. Additionally, the study investigated ginseng plants' root rot disease index (DI). The results showed that the DI of ginseng increased 2.2 times in one sampling site and 4.7 times in another during the 4 years. With respect to the microbial community, the bacterial diversity increased with the seasons in the first, third, and fourth years but remained steady in the second year. The seasonal changing of relative abundances of bacteria and fungi showed the same trend in the first, third, and fourth years but not in the second year. Linear models revealed that the relative abundances of and spp. were negatively correlated with DI, while the relative abundance of spp. were positively correlated with DI ( < 0.05). The Mantel test showed that soil chemical properties, including available nitrogen, phosphorus, potassium, calcium, magnesium, organic matter, and pH, were significantly correlated to microbial composition. The contents of available potassium and nitrogen were positively correlated with DI, while pH and organic matter were negatively correlated with DI. In summary, we can deduce that the second year is the key period for the shift of the American ginseng rhizosphere microbial community. Disease aggravation after the third year is related to the deterioration of the rhizosphere microecosystem.
PubMed: 36865777
DOI: 10.3389/fmicb.2023.1097742 -
Bioprocess and Biosystems Engineering Dec 2013Kraft lignin (KL) is the major pollutant in black liquor. The bacterial strain Pandoraea sp. B-6 was able to degrade KL without any co-substrate under high alkaline...
Kraft lignin (KL) is the major pollutant in black liquor. The bacterial strain Pandoraea sp. B-6 was able to degrade KL without any co-substrate under high alkaline conditions. At least 38.2 % of chemical oxygen demand and 41.6 % of color were removed in 7 days at concentrations from 1 to 6 g L(-1). The optimum pH for KL degradation was 10 and the optimum temperature was 30 °C. The greatest activities of 2,249.2 U L(-1) for manganese peroxidase and 1,120.6 U L(-1) for laccase were detected on the third and fifth day at pH 10, respectively. Many small molecules, such as cinnamic acid, ferulic acid, 2-hydroxy benzyl alcohol, and vanillyl methyl ketone, were formed during the period of KL degradation based on GC-MS analysis. These results indicate that this strain has great potential for biotreatment of black liquor.
Topics: Bambusa; Biological Assay; Biological Oxygen Demand Analysis; Burkholderia; Color; Gas Chromatography-Mass Spectrometry; Hydrogen-Ion Concentration; Hydrolysis; Lignin; Temperature
PubMed: 23877715
DOI: 10.1007/s00449-013-0972-9 -
Journal of Clinical Microbiology Nov 2009The identification of microbial species from respiratory specimens and their susceptibility to antimicrobial agents are among the most important diagnostic measures of...
The identification of microbial species from respiratory specimens and their susceptibility to antimicrobial agents are among the most important diagnostic measures of care for patients with cystic fibrosis (CF). Under the umbrella of EuroCareCF, two quality assurance trials of CF microbiology were performed in 2007 and 2008. Nine formulations with CF bacterial isolates were dispatched. A total of 31/37 laboratories from 18/21 European countries participated in the 2007 and 2008 trials. The common CF pathogens Pseudomonas aeruginosa and Staphylococcus aureus were correctly identified by almost all participants in both trials, even if the strains presented uncommon phenotypes. Burkholderia cenocepacia IIIB and Burkholderia vietnamensis CF isolates, however, were correctly assigned to the species level by only 26% and 27% of the laboratories, respectively. Emerging pathogens such as Achromobacter xylosoxidans, Inquilinus limosus, and Pandoraea pnomenusa were also not detected or were misclassified by many laboratories. One participant correctly identified all CF isolates in both trials. The percentages of correct classifications (susceptible, intermediate, resistant) by antimicrobial susceptibility testing ranged from 55 to 100% (median, 96%) per isolate and drug. The shortcomings in the diagnostics of rare and emerging pathogens point to the need for continuing education in CF microbiology and suggest the establishment of CF microbiology reference laboratories.
Topics: Bacteria; Bacterial Infections; Bacteriological Techniques; Bronchopneumonia; Cystic Fibrosis; Diagnostic Errors; Europe; Health Services Research; Humans; Microbial Sensitivity Tests; Quality Control
PubMed: 19741077
DOI: 10.1128/JCM.01182-09 -
Journal of Global Antimicrobial... Mar 2024Gram-negative pathogens causing respiratory infection in people with cystic fibrosis and bronchiectasis are becoming progressively more resistant to conventional...
OBJECTIVES
Gram-negative pathogens causing respiratory infection in people with cystic fibrosis and bronchiectasis are becoming progressively more resistant to conventional antibiotics. Although cefiderocol is licenced for the treatment of infections due to Gram-negative organisms, there are limited data on the activity of cefiderocol against pathogens associated with chronic respiratory diseases. The aim of this study was to determine the susceptibility of Gram-negative pathogens from cystic fibrosis and bronchiectasis to cefiderocol and comparator antibiotics.
METHODS
Minimal inhibitory concentrations (MICs) of cefiderocol and 15 comparator antibiotics were determined by broth microdilution against 300 respiratory isolates: Burkholderia spp., Stenotrophomonas spp., Achromobacter spp., Ralstonia spp. and Pandoraea spp., and used to calculate the MIC of each antibiotic required to inhibit 50% (MIC) and 90% (MIC) of isolates.
RESULTS
The MIC and MIC of cefiderocol for all 300 isolates tested was 0.25 and 32 mg/L, with 232 (77.3%) isolates having an MIC value ≤2 mg/L. In addition, cefiderocol demonstrated excellent activity against Stenotrophomonas spp. and Achromobacter spp. isolates, with 86.7% and 87.2%, respectively, exhibiting an MIC of 2 mg/L. Tigecycline also demonstrated good activity against all isolates with an MIC of <0.5 mg/L.
CONCLUSIONS
These in vitro data demonstrated that cefiderocol had greater activity than most comparator antibiotics and could be an alternative treatment option for respiratory infection caused by these pathogens that has not responded to first-line therapy.
Topics: Humans; Cefiderocol; Cephalosporins; Cystic Fibrosis; Gram-Negative Bacteria; Drug Resistance, Multiple, Bacterial; Anti-Bacterial Agents; Bronchiectasis; Respiratory Tract Infections
PubMed: 38336228
DOI: 10.1016/j.jgar.2024.01.023 -
Journal of Bacteriology Aug 2007Biphenyl dioxygenase (BPDO) catalyzes the aerobic transformation of biphenyl and various polychlorinated biphenyls (PCBs). In three different assays, BPDO(B356) from... (Comparative Study)
Comparative Study
Biphenyl dioxygenase (BPDO) catalyzes the aerobic transformation of biphenyl and various polychlorinated biphenyls (PCBs). In three different assays, BPDO(B356) from Pandoraea pnomenusa B-356 was a more potent PCB-degrading enzyme than BPDO(LB400) from Burkholderia xenovorans LB400 (75% amino acid sequence identity), transforming nine congeners in the following order of preference: 2,3',4-trichloro approximately 2,3,4'-trichloro > 3,3'-dichloro > 2,4,4'-trichloro > 4,4'-dichloro approximately 2,2'-dichloro > 2,6-dichloro > 2,2',3,3'-tetrachloro approximately 2,2',5,5'-tetrachloro. Except for 2,2',5,5'-tetrachlorobiphenyl, BPDO(B356) transformed each congener at a higher rate than BPDO(LB400). The assays used either whole cells or purified enzymes and either individual congeners or mixtures of congeners. Product analyses established previously unrecognized BPDO(B356) activities, including the 3,4-dihydroxylation of 2,6-dichlorobiphenyl. BPDO(LB400) had a greater apparent specificity for biphenyl than BPDO(B356) (k(cat)/K(m) = 2.4 x 10(6) +/- 0.7 x 10(6) M(-1) s(-1) versus k(cat)/K(m) = 0.21 x 10(6) +/- 0.04 x 10(6) M(-1) s(-1)). However, the latter transformed biphenyl at a higher maximal rate (k(cat) = 4.1 +/- 0.2 s(-1) versus k(cat) = 0.4 +/- 0.1 s(-1)). A variant of BPDO(LB400) containing four active site residues of BPDO(B356) transformed para-substituted congeners better than BPDO(LB400). Interestingly, a substitution remote from the active site, A267S, increased the enzyme's preference for meta-substituted congeners. Moreover, this substitution had a greater effect on the kinetics of biphenyl utilization than substitutions in the substrate-binding pocket. In all variants, the degree of coupling between congener depletion and O(2) consumption was approximately proportional to congener depletion. At 2.4-A resolution, the crystal structure of the BPDO(B356)-2,6-dichlorobiphenyl complex, the first crystal structure of a BPDO-PCB complex, provided additional insight into the reactivity of this isozyme with this congener, as well as into the differences in congener preferences of the BPDOs.
Topics: Amino Acid Substitution; Biotransformation; Burkholderiaceae; Crystallography, X-Ray; Gas Chromatography-Mass Spectrometry; Iron-Sulfur Proteins; Kinetics; Magnetic Resonance Spectroscopy; Models, Molecular; Oxygenases; Polychlorinated Biphenyls; Protein Structure, Tertiary; Substrate Specificity
PubMed: 17526697
DOI: 10.1128/JB.01476-06 -
Journal of Clinical Microbiology May 2003A 30-year-old man died with Pandoraea pnomenusa sepsis after lung transplantation. Pandoraea species are gram-negative rods, closely related to, and commonly...
A 30-year-old man died with Pandoraea pnomenusa sepsis after lung transplantation. Pandoraea species are gram-negative rods, closely related to, and commonly misidentified as, Burkholderia cepacia complex or Ralstonia species. Heretofore considered soil bacteria and colonizers that infect patients with chronic lung diseases, Pandoraea species can produce severe infections.
Topics: Adult; Bacteremia; Betaproteobacteria; Fatal Outcome; Gram-Negative Bacterial Infections; Humans; Lung Transplantation; Male; Multiple Organ Failure; Sepsis
PubMed: 12734295
DOI: 10.1128/JCM.41.5.2255-2257.2003 -
Journal of Clinical Microbiology Oct 2003Burkholderia pseudomallei and B. mallei, the causative agents of melioidosis and glanders, respectively, are designated category B biothreat agents. Current methods for...
Burkholderia pseudomallei and B. mallei, the causative agents of melioidosis and glanders, respectively, are designated category B biothreat agents. Current methods for identifying these organisms rely on their phenotypic characteristics and an extensive set of biochemical reactions. We evaluated the use of 16S rRNA gene sequencing to rapidly identify these two species and differentiate them from each other as well as from closely related species and genera such as Pandoraea spp., Ralstonia spp., Burkholderia gladioli, Burkholderia cepacia, Burkholderia thailandensis, and Pseudomonas aeruginosa. We sequenced the 1.5-kb 16S rRNA gene of 56 B. pseudomallei and 23 B. mallei isolates selected to represent a wide range of temporal, geographic, and origin diversity. Among all 79 isolates, a total of 11 16S types were found based on eight positions of difference. Nine 16S types were identified in B. pseudomallei isolates based on six positions of difference, with differences ranging from 0.5 to 1.5 bp. Twenty-two of 23 B. mallei isolates showed 16S rRNA gene sequence identity and were designated 16S type 10, whereas the remaining isolate was designated type 11. This report provides a basis for rapidly identifying and differentiating B. pseudomallei and B. mallei by molecular methods.
Topics: Animals; Bacterial Typing Techniques; Burkholderia; Burkholderia Infections; Burkholderia pseudomallei; DNA, Ribosomal; Environmental Microbiology; Genes, rRNA; Humans; Melioidosis; Molecular Sequence Data; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 14532197
DOI: 10.1128/JCM.41.10.4647-4654.2003