scholarly journals FluorescenceIn SituHybridization (FISH) and Peptide Nucleic Acid Probe-Based FISH for Diagnosis of Q Fever Endocarditis and Vascular Infections

2018 ◽  
Vol 56 (9) ◽  
Author(s):  
Elsa Prudent ◽  
Hubert Lepidi ◽  
Emmanouil Angelakis ◽  
Didier Raoult
Keyword(s):  
Peptide Nucleic Acid ◽  
Q Fever ◽  
Immunohistochemical Analysis ◽  
Content Type ◽  
Peptide Nucleic Acid Probe ◽  
Vascular Infections ◽  
Pna Fish ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACTEndocarditis and vascular infections are common manifestations of persistent localized infection due toCoxiella burnetii, and recently, fluorescencein situhybridization (FISH) was proposed as an alternative tool for their diagnosis. In this study, we evaluated the efficiency of FISH in a series of valve and vascular samples infected byC. burnetii. We tested 23C. burnetii-positive valves and thrombus samples obtained from patients with Q fever endocarditis. Seven aneurysms and thrombus specimens were retrieved from patients with Q fever vascular infections. Samples were analyzed by culture, immunochemistry, and FISH with oligonucleotide and PNA probes targetingC. burnetii-specific 16S rRNA sequences. The immunohistochemical analysis was positive for five (17%) samples with significantly more copies ofC. burnetiiDNA than the negative ones (P= 0.02). FISH was positive for 13 (43%) samples and presented 43% and 40% sensitivity compared to that for quantitative PCR (qPCR) and culture, respectively. PNA FISH detectedC. burnetiiin 18 (60%) samples and presented 60% and 55% sensitivity compared to that for qPCR and culture, respectively. Immunohistochemistry had 38% and 28% sensitivity compared to that for FISH and PNA FISH, respectively. Samples found positive by both immunohistochemistry and PNA FISH contained significantly more copies ofC. burnetiiDNA than the negative ones (P= 0.03). Finally, PNA FISH was more sensitive than FISH (60% versus 43%, respectively) for the detection ofC. burnetii. We provide evidence that PNA FISH and FISH are important assays for the diagnosis ofC. burnetiiendocarditis and vascular infections.

scholarly journals Draft Genome Sequence of Psychrobacter okhotskensis Strain 5179-1A, Isolated from a Raw Cured Ham Storage Crate

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
Joseph Wambui ◽  
Marina Morach ◽  
Nicole Cernela ◽  
Marc J. A. Stevens ◽  
Giovanni Ghielmetti ◽  
...  
Keyword(s):  
16S Rrna ◽  
Genome Sequence ◽  
Draft Genome ◽  
Gc Content ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT We present the draft genome sequence of Psychrobacter okhotskensis strain 5179-1A, which was isolated from a raw cured ham storage crate. Its size and GC content are 3.4 Mb and 43.4%, respectively. The 16S rRNA sequences of strain 5179-1A and P. okhotskensis MD17T are 100% identical.

scholarly journals Dissimilatory Arsenate Reduction with Sulfide as Electron Donor: Experiments with Mono Lake Water and Isolation of Strain MLMS-1, a Chemoautotrophic Arsenate Respirer

2004 ◽  
Vol 70 (5) ◽  
pp. 2741-2747 ◽  
Author(s):  
Shelley E. Hoeft ◽  
Thomas R. Kulp ◽  
John F. Stolz ◽  
James T. Hollibaugh ◽  
Ronald S. Oremland
Keyword(s):  
Electron Donor ◽  
Lake Water ◽  
Electron Donors ◽  
Mono Lake ◽  
Arsenate Reduction ◽  
Curved Rod ◽  
Gene Probing ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Anoxic bottom water from Mono Lake, California, can biologically reduce added arsenate without any addition of electron donors. Of the possible in situ inorganic electron donors present, only sulfide was sufficiently abundant to drive this reaction. We tested the ability of sulfide to serve as an electron donor for arsenate reduction in experiments with lake water. Reduction of arsenate to arsenite occurred simultaneously with the removal of sulfide. No loss of sulfide occurred in controls without arsenate or in sterilized samples containing both arsenate and sulfide. The rate of arsenate reduction in lake water was dependent on the amount of available arsenate. We enriched for a bacterium that could achieve growth with sulfide and arsenate in a defined, mineral medium and purified it by serial dilution. The isolate, strain MLMS-1, is a gram-negative, motile curved rod that grows by oxidizing sulfide to sulfate while reducing arsenate to arsenite. Chemoautotrophy was confirmed by the incorporation of H14CO3 − into dark-incubated cells, but preliminary gene probing tests with primers for ribulose-1,5-biphosphate carboxylase/oxygenase did not yield PCR-amplified products. Alignment of 16S rRNA sequences indicated that strain MLMS-1 was in the δ-Proteobacteria, located near sulfate reducers like Desulfobulbus sp. (88 to 90% similarity) but more closely related (97%) to unidentified sequences amplified previously from Mono Lake. However, strain MLMS-1 does not grow with sulfate as its electron acceptor.

scholarly journals Filamentous Bacterium Eikelboom Type 0092 in Activated Sludge Plants in Australia Is a Member of the Phylum Chloroflexi

2009 ◽  
Vol 75 (8) ◽  
pp. 2446-2452 ◽  
Author(s):  
Lachlan Speirs ◽  
Tadashi Nittami ◽  
Simon McIlroy ◽  
Sarah Schroeder ◽  
Robert J. Seviour
Keyword(s):  
In Situ Hybridization ◽  
Activated Sludge ◽  
Molecular Data ◽  
Phosphate Removal ◽  
Filamentous Bacterium ◽  
Eastern Australia ◽  
Intracellular Aggregates ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Molecular data show that the filamentous bacterium Eikelboom type 0092, frequently seen in Australian activated sludge plants, is a member of the phylum Chloroflexi. Fluorescence in situ hybridization (FISH) probes designed against cloned 16S rRNA sequences from a full-scale enhanced biological phosphate removal-activated sludge plant community, where this was a dominant filament morphotype, suggest that it can exist as two variants, differing in their trichome diameter. When applied to samples from several treatment plants in eastern Australia, each FISH probe targeted only the type 0092 filament morphotype against which it was designed. The patterns of FISH signals generated with both were consistent with the ribosomes not being evenly distributed but arranged as intracellular aggregates. The FISH survey data showed that these two variants appeared together in most but not all of the plants examined. None stained positively for intracellular presence of either poly-β-hydroxyalkanoates or polyphosphate.

scholarly journals Detection of Escherichia coli O157 by Peptide Nucleic Acid FluorescenceIn SituHybridization (PNA-FISH) and Comparison to a Standard Culture Method

2013 ◽  
Vol 79 (20) ◽  
pp. 6293-6300 ◽  
Author(s):  
C. Almeida ◽  
J. M. Sousa ◽  
R. Rocha ◽  
L. Cerqueira ◽  
S. Fanning ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Food Samples ◽  
High Morbidity ◽  
Content Type ◽  
E Coli ◽  
Fish Method ◽  
The World ◽  
Pna Fish

ABSTRACTDespite the emergence of non-O157 Shiga toxin-producingEscherichia coli(STEC) infections,E. coliserotype O157 is still the most commonly identified STEC in the world. It causes high morbidity and mortality and has been responsible for a number of outbreaks in many parts of the world. Various methods have been developed to detect this particular serotype, but standard bacteriological methods remain the gold standard. Here, we propose a new peptide nucleic acid fluorescencein situhybridization (PNA-FISH) method for the rapid detection ofE. coliO157. Testing on 54 representative strains showed that the PNA probe is highly sensitive and specific toE. coliO157. The method then was optimized for detection in food samples. Ground beef and unpasteurized milk samples were artificially contaminated withE. coliO157 concentrations ranging from 1 × 10−2to 1 × 102CFU per 25 g or ml of food. Samples were then preenriched and analyzed by both the traditional bacteriological method (ISO 16654:2001) and PNA-FISH. The PNA-FISH method performed well in both types of food matrices with a detection limit of 1 CFU/25 g or ml of food samples. Tests on 60 food samples have shown a specificity value of 100% (95% confidence interval [CI], 82.83 to 100), a sensitivity of 97.22% (95% CI, 83.79 to 99.85%), and an accuracy of 98.33% (CI 95%, 83.41 to 99.91%). Results indicate that PNA-FISH performed as well as the traditional culture methods and can reduce the diagnosis time to 1 day.

Response surface methodology to optimize peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in Saccharomyces cerevisiae

LWT ◽  
2017 ◽  
Vol 80 ◽  
pp. 27-31 ◽  
Author(s):  
Rita S. Santos ◽  
Carolina C. Lima ◽  
Daniel Carvalho ◽  
Francisco Meireles ◽  
Nuno Guimarães ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Response Surface Methodology ◽  
In Situ Hybridization ◽  
Nucleic Acid ◽  
Fluorescence In Situ Hybridization ◽  
Response Surface ◽  
Peptide Nucleic Acid ◽  
Pna Fish
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