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16S rDNA sequencing of valve tissue improves microbiological diagnosis in surgically treated patients with infective endocarditis.

https://arctichealth.org/en/permalink/ahliterature134307
Source
J Infect. 2011 Jun;62(6):472-8
Publication Type
Article
Date
Jun-2011
Author
Martin Vondracek
Ulrik Sartipy
Ewa Aufwerber
Inger Julander
Dan Lindblom
Katarina Westling
Author Affiliation
Department of Clinical Microbiology, Karolinska University Hospital and Department of Clinical Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
Source
J Infect. 2011 Jun;62(6):472-8
Date
Jun-2011
Language
English
Publication Type
Article
Keywords
Adult
Aged
Bacteria - classification - genetics - isolation & purification
Bacteriological Techniques - methods
DNA, Bacterial - chemistry - genetics
DNA, Ribosomal - chemistry - genetics
Endocarditis - diagnosis - microbiology - surgery
Female
Heart Valves - microbiology
Humans
Male
Middle Aged
RNA, Ribosomal, 16S - genetics
Sensitivity and specificity
Sequence Analysis, DNA - methods
Sweden
Abstract
The aim was to evaluate 16S rDNA sequencing in heart valves in patients with infective endocarditis undergoing surgery.
Fifty-seven patients with infective endocarditis were examined in this prospective study by analysing heart valves with 16S rDNA sequencing and culturing methods and comparing the results to blood cultures. As controls, heart valves from 61 patients without any signs of endocarditis were examined.
All together 77% of the endocarditis patients were positive for 16S rDNA, 84% had positive blood cultures and 23% had positive cultures from heart valves, whereas only 16% of the cultures from heart valves were concordant with results from blood cultures or 16S rDNA. Concordant results between 16S rDNA sequencing and blood cultures were found in 75% patients. All controls were negative for 16S rDNA. In 4 out of 9 patients with negative blood cultures, the aetiology was established by 16S rDNA alone, i.e. viridans group streptococci.
In this Swedish study, 16S rDNA sequencing of valve material was shown to be a valuable addition in blood culture-negative cases. The value of heart valve culture was low. Molecular diagnosis using 16S rDNA sequencing should be recommended in patients undergoing valve replacement for infective endocarditis.
PubMed ID
21601285 View in PubMed
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[A method of accelerated detection of tuberculosis pathogen]

https://arctichealth.org/en/permalink/ahliterature91023
Source
Mikrobiol Z. 2008 Jul-Aug;70(4):39-44
Publication Type
Article
Author
Vlasenko V V
Vlasenko I H
Berezovs'kyi I V
Kolodii S A
Tkach O A
Mazhak K D
Source
Mikrobiol Z. 2008 Jul-Aug;70(4):39-44
Language
Ukrainian
Publication Type
Article
Keywords
Bacteriological Techniques - methods
Culture Media
Humans
Mycobacterium - isolation & purification
Time Factors
Tuberculosis - microbiology
Abstract
Results of a comparative study of growth properties of elaborated nutrient medium VLACON and traditional Lovenshtein-Jensen medium are presented in the paper. It is established, that the rate of mycobacterium growth on VLACON medium is 10-20 times higher than on the traditional nutrient medium. Mycobacteria preserve their tinctorial, cultural and pathogenic properties during the cultivation on VLACON medium. Besides, the possibility of use of agglutination reaction with further coloring and microscopy of agglutinates for the accelerated differentiation of human and bull mycobacterium species from the bird species and atypical mycobacteria is shown.
PubMed ID
19044010 View in PubMed
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An integrated approach to rapid diagnosis of tuberculosis and multidrug resistance using liquid culture and molecular methods in Russia.

https://arctichealth.org/en/permalink/ahliterature148389
Source
PLoS One. 2009;4(9):e7129
Publication Type
Article
Date
2009
Author
Yanina Balabanova
Francis Drobniewski
Vladyslav Nikolayevskyy
Annika Kruuner
Nadezhda Malomanova
Tatyana Simak
Nailya Ilyina
Svetlana Zakharova
Natalya Lebedeva
Heather L Alexander
Rick O'Brien
Hojoon Sohn
Anastasia Shakhmistova
Ivan Fedorin
Author Affiliation
National Mycobacterium Reference Laboratory, Institute of Cell and Molecular Sciences, Queen Mary College, Barts and the London School of Medicine, University of London, London, United Kingdom. y.balabanova@qmul.ac.uk
Source
PLoS One. 2009;4(9):e7129
Date
2009
Language
English
Publication Type
Article
Keywords
Bacterial Typing Techniques
Bacteriological Techniques - methods
Communicable Disease Control - methods
Cost-Benefit Analysis
Humans
Isoniazid - pharmacology
Microbial Sensitivity Tests
Mycobacterium tuberculosis - genetics
Phenotype
Rifampin - pharmacology
Risk factors
Russia
Tuberculosis - diagnosis - genetics
Tuberculosis, Multidrug-Resistant - diagnosis - genetics
Abstract
To analyse the feasibility, cost and performance of rapid tuberculosis (TB) molecular and culture systems, in a high multidrug-resistant TB (MDR TB) middle-income region (Samara, Russia) and provide evidence for WHO policy change.
Performance and cost evaluation was conducted to compare the BACTEC MGIT 960 system for culture and drug susceptibility testing (DST) and molecular systems for TB diagnosis, resistance to isoniazid and rifampin, and MDR TB identification compared to conventional Lowenstein-Jensen culture assays.
698 consecutive patients (2487 sputum samples) with risk factors for drug-resistant tuberculosis were recruited. Overall M. tuberculosis complex culture positivity rates were 31.6% (787/2487) in MGIT and 27.1% (675/2487) in LJ (90.5% and 83.2% for smear-positive specimens). In total, 809 cultures of M. tuberculosis complex were isolated by any method. Median time to detection was 14 days for MGIT and 36 days for LJ (10 and 33 days for smear positive specimens) and indirect DST in MGIT took 9 days compared to 21 days on LJ. There was good concordance between DST on LJ and MGIT (96.8% for rifampin and 95.6% for isoniazid). Both molecular hybridization assay results correlated well with MGIT DST results, although molecular assays generally yielded higher rates of resistance (by approximately 3% for both isoniazid and rifampin).
With effective planning and logistics, the MGIT 960 and molecular based methodologies can be successfully introduced into a reference laboratory setting in a middle incidence country. High rates of MDR TB in the Russian Federation make the introduction of such assays particularly useful.
Notes
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PubMed ID
19774085 View in PubMed
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The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition.

https://arctichealth.org/en/permalink/ahliterature138769
Source
J Microbiol Methods. 2011 Mar;84(3):388-93
Publication Type
Article
Date
Mar-2011
Author
Lilliana I Moreno
DeEtta Mills
Jill Fetscher
Krista John-Williams
Lee Meadows-Jantz
Bruce McCord
Author Affiliation
International Forensic Research Institute, Florida International University, 11200 SW 8th St. Miami, FL 33199, USA.
Source
J Microbiol Methods. 2011 Mar;84(3):388-93
Date
Mar-2011
Language
English
Publication Type
Article
Keywords
Bacteria - classification - genetics - isolation & purification
Bacteriological Techniques - methods
Biodiversity
Cadaver
Forensic Medicine - methods
Humans
Polymerase Chain Reaction - methods
Soil Microbiology
Time Factors
Abstract
The placement of cadavers in shallow, clandestine graves may alter the microbial and geochemical composition of the underlying and adjacent soils. Using amplicon length heterogeneity-PCR (LH-PCR) the microbial community changes in these soils can be assessed. In this investigation, nine different grave sites were examined over a period of 16weeks. The results indicated that measurable changes occurred in the soil bacterial community during the decomposition process. In this study, amplicons corresponding to anaerobic bacteria, not indigenous to the soil, were shown to produce differences between grave sites and control soils. Among the bacteria linked to these amplicons are those that are most often part of the commensal flora of the intestines, mouth and skin. In addition, over the 16week sampling interval, the level of indicator organisms (i.e., nitrogen fixing bacteria) dropped as the body decomposed and after four weeks of environmental exposure they began to increase again; thus differences in the abundance of nitrogen fixing bacteria were also found to contribute to the variation between controls and grave soils. These results were verified using primers that specifically targeted the nifH gene coding for nitrogenase reductase. LH-PCR provides a fast, robust and reproducible method to measure microbial changes in soil and could be used to determine potential cadaveric contact in a given area. The results obtained with this method could ultimately provide leads to investigators in criminal or missing person scenarios and allow for further analysis using human specific DNA assays to establish the identity of the buried body.
PubMed ID
21138746 View in PubMed
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[Can we rely on the results of urine microscopy and culture when tests are performed in general practice?].

https://arctichealth.org/en/permalink/ahliterature190568
Source
Ugeskr Laeger. 2002 Apr 1;164(14):1927-30
Publication Type
Article
Date
Apr-1-2002
Author
Lars Bjerrum
Per Grinsted
Per Søgaard
Author Affiliation
Syddansk Universitet, Winsløwparken 19.3. sal, DK-5000 Odense C. l-bjerrum@health.sdu.dk
Source
Ugeskr Laeger. 2002 Apr 1;164(14):1927-30
Date
Apr-1-2002
Language
Danish
Publication Type
Article
Keywords
Bacteriological Techniques - methods - standards
Bacteriuria - diagnosis
Clinical Competence
Denmark
Family Practice - methods - standards
Humans
Predictive value of tests
Reproducibility of Results
Sensitivity and specificity
Urinary Tract Infections - microbiology - urine
Abstract
Urinary tract infections (UTI) account for 2-5% of consultations in general practice, but only about half the patients with dysuria have significant bacteriuria (> 100,000 bacteria per ml). A microbiological diagnosis can be made by examination of a urine sample, and in Danish family practice the diagnosis of UTI is often reached by a microscopic analysis or a dip-slide culture test. These methods have a high validity when performed in hospital, but we need knowledge about the validity of microbiological urine examinations when performed in general practice. The aim of this study was to validate detection of bacteriuria by urine microscopy and dip-slide culture in general practice.
Urine specimens artificially produced by adding a known quantity of bacteria (Escherichia coli, Proteus mirabilis, Enterobacter cloacae, Staphylococcus epidermidis and Enterococcus faecalis) to sterile urine were sent to 25 general practices for microscopic examination and dip-slide culture. No prior instruction in testing procedure was given. As the gold standard, the results of a standardised culture method performed by skilled laboratory technicians at the Department of Microbiology, University of Southern Denmark, were used.
Significant bacteriuria was identified by microscopy with a sensitivity of 95% and a specificity of 83%. The corresponding figures for urine culture were 95% and 96%. The morphology of bacteria was interpreted correctly in 80% of microscopic examinations, and 60% of the bacteria strains were classified correctly in terms of their motility.
The results of urine microscopy and culture performed in general practice are to be relied on.
Notes
Comment In: Ugeskr Laeger. 2002 May 27;164(22):2930-112082826
Comment In: Ugeskr Laeger. 2002 May 27;164(22):2931-2; author reply 293212082827
Comment In: Ugeskr Laeger. 2002 Jul 1;164(27):355212116687
PubMed ID
11957428 View in PubMed
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[Comparative assessment of sanitary and epidemic importance of indicator coliform indices of drinking water quality].

https://arctichealth.org/en/permalink/ahliterature290156
Source
Gig Sanit. 2016; 95(6):582-8
Publication Type
Comparative Study
Journal Article
Date
2016
Author
Yu A Rakhmanin
L V Ivanova
T Z Artemova
E K Gipp
A V Zagaynova
T N Maksimkina
A V Krasnyak
P V Zhuravlev
V V Aleshnya
O P Panasovets
Source
Gig Sanit. 2016; 95(6):582-8
Date
2016
Language
Russian
Publication Type
Comparative Study
Journal Article
Keywords
Bacteriological Techniques - methods
Drinking Water - analysis - microbiology - standards
Enterobacteriaceae - isolation & purification
Enterobacteriaceae Infections - epidemiology - etiology - prevention & control
Environmental Monitoring - methods
Humans
Russia - epidemiology
Water Microbiology - standards
Water Quality - standards
Water Supply - methods - standards
Abstract
The used methodology of the scientific substantiation of indicators is in the establishment of the conformity of laws of vital activity of indicator and pathogenic microorganisms in the real conditions of the action of the complex of factors, including disinfecting agents. In the one water sample simultaneously there were determined both the general indicator (GICB), thermotolerant (TTCB), glucose positive (GPCB) coliform bacteria, E.coli. On the base of long-term research in the various regions of the Russian Federation, as well with bearing in mind the analysis of domestic and foreign data, comparing the water quality and the incidence of intestinal infections in population it is recommended to use the index of determination of the total number glucose positive coliform bacteria (GPCB), which brings together a much broader range of bacteria of the Enterobacteriaceae family in comparison with total coliform bacteria (TCB) and thermotolerant coliform bacteria (TTCB) and warrants the absence in the test volume of water as an indicator lactose positive (E.coli, TCB, TTCB) and pathogens (salmonella) and potentially pathogenic bacteria which do not ferment lactose. Proposed index of GPCB is shown to allow to assess epidemiological risks not only more accurate, but also more efficiently without increasing the cost performance of bacteriological research.
PubMed ID
29424503 View in PubMed
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Comparison between ImmunoCard STAT!(®) and real-time PCR as screening tools for both O157:H7 and non-O157 Shiga toxin-producing Escherichia coli in Southern Alberta, Canada.

https://arctichealth.org/en/permalink/ahliterature112627
Source
Diagn Microbiol Infect Dis. 2013 Sep;77(1):8-13
Publication Type
Article
Date
Sep-2013
Author
Linda Chui
Mao-Cheng Lee
Richelle Allen
Aaron Bryks
Linsey Haines
Valerie Boras
Author Affiliation
Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada. Linda.Chui@albertahealthservices.ca
Source
Diagn Microbiol Infect Dis. 2013 Sep;77(1):8-13
Date
Sep-2013
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Aged, 80 and over
Alberta
Bacteriological Techniques - methods
Child
Child, Preschool
Escherichia coli Infections - diagnosis - microbiology
Female
Humans
Immunoassay - methods
Male
Mass Screening - methods
Middle Aged
Real-Time Polymerase Chain Reaction - methods
Sensitivity and specificity
Shiga-Toxigenic Escherichia coli - genetics - immunology - isolation & purification
Young Adult
Abstract
An increasing number of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections and outbreaks have been reported. In this study, we evaluated the performance of ImmunoCard STAT!(®) (Meridian Bioscience, Inc., Cincinnati, OH, USA) as a method to screen stool specimens for STEC (O157 and non-O157). An in-house real-time PCR method was used as the "gold standard". We also evaluated the prevalence and clinical characteristics of STEC infections in the Alberta South West Zone. From July to November 2011, 819 stool specimens submitted for routine stool culture were tested. With our in-house real-time PCR, 7 O157:H7 and 10 non-O157 STEC isolates were identified for a total of 17 STECs. In comparison, ImmunoCard STAT!(®) identified a total of 6, resulting in a sensitivity and specificity of 35% and 99%, respectively (P
PubMed ID
23810166 View in PubMed
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Comparison of heart valve culture between two Danish endocarditis centres.

https://arctichealth.org/en/permalink/ahliterature127466
Source
Scand J Infect Dis. 2012 Jun;44(6):405-13
Publication Type
Article
Date
Jun-2012
Author
Marianne Voldstedlund
Kurt Fuursted
Niels Eske Bruun
Magnus Arpi
Author Affiliation
Department of Clinical Microbiology, Aarhus University Hospital, Aarhus N, Denmark. mvold@dadlnet.dk
Source
Scand J Infect Dis. 2012 Jun;44(6):405-13
Date
Jun-2012
Language
English
Publication Type
Article
Keywords
Aged
Bacteria - classification - isolation & purification
Bacteriological Techniques - methods
Denmark
Endocarditis, Bacterial - microbiology
Female
Heart Valves - microbiology
Humans
Male
Middle Aged
Sensitivity and specificity
Specimen Handling - methods
Abstract
The degree to which the results of valve culture depend on different laboratory procedures as well as other factors is unknown. The aim of this study was to compare the results of heart valve culture at 2 different endocarditis centres in order to clarify this.
The study included 223 patients with definitive endocarditis undergoing heart valve surgery at 2 Danish endocarditis centres (96 at the East centre and 127 at the West centre). The following data related to the samples were registered: transportation, time to inoculation, culture media used and duration of incubation, species distribution, and preoperative duration of appropriate antimicrobial treatment (DAAT). 16S polymerase chain reaction (PCR) of valve tissue was used to estimate the frequency of non-cultivable bacteria.
Valve culture was positive in 12.5% of cases at the East centre and 36.2% at the West centre (p
PubMed ID
22292569 View in PubMed
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Comparison of the Abbott RealTime CT new formulation assay with two other commercial assays for detection of wild-type and new variant strains of Chlamydia trachomatis.

https://arctichealth.org/en/permalink/ahliterature146719
Source
J Clin Microbiol. 2010 Feb;48(2):440-3
Publication Type
Article
Date
Feb-2010
Author
Jens Kjølseth Møller
Lisbeth Nørum Pedersen
Kenneth Persson
Author Affiliation
Department of Clinical Microbiology, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, DK-8200 Aarhus N, Denmark. jkm@dadlnet.dk
Source
J Clin Microbiol. 2010 Feb;48(2):440-3
Date
Feb-2010
Language
English
Publication Type
Article
Keywords
Adult
Bacteriological Techniques - methods
Chlamydia Infections - diagnosis - microbiology
Chlamydia trachomatis - genetics - isolation & purification
Denmark
Female
Humans
Male
Molecular Diagnostic Techniques - methods
Polymerase Chain Reaction - methods
Reagent kits, diagnostic
Sensitivity and specificity
Sweden
Urine - microbiology
Young Adult
Abstract
In an analytical-method comparison study of clinical samples, the Abbott RealTime CT new formulation assay (m2000 real-time PCR), consisting of a duplex PCR targeting different parts of the cryptic plasmid in Chlamydia trachomatis, was compared both with version 2 of the Roche Cobas TaqMan CT assay, comprising a duplex PCR for a target in the cryptic plasmid and the omp1 gene, and with the Gen-Probe Aptima Combo 2 assay (AC2) targeting the C. trachomatis 23S rRNA molecule. First-catch urine samples from Sweden were tested in Malmö, Sweden, for C. trachomatis with the m2000 real-time PCR assay and with an in-house PCR for the new variant C. trachomatis strain with a deletion in the cryptic plasmid. Aliquots of the urine samples were sent to Aarhus, Denmark, where they were further examined with the TaqMan CT and AC2 assays. A positive prevalence of 9.1% (148/1,632 urine samples examined) was detected according to the combined reference standard. The sensitivities and specificities of the three assays were as follows: for the Abbott m2000 assay, 95.3% (141/148) and 99.9% (1,483/1,485), respectively; for the Roche TaqMan assay, 82.4% (122/148) and 100.0% (1,485/1,485); and for the Gen-Probe AC2 assay, 99.3% (147/148) and 99.9% (1,484/1,485). The plasmid mutant strain was detected in 24% (36/148) of the C. trachomatis-positive samples. There is a difference in sensitivity between the new formulations of the Abbott and the Roche assays, but both assays detected the wild-type and new variant C. trachomatis strains equally well.
Notes
Cites: Euro Surveill. 2006;11(11):E061109.217213548
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Cites: Sex Transm Infect. 2009 Jun;85(3):190-319060034
Cites: J Clin Microbiol. 2008 Dec;46(12):3892-518842934
Cites: Diagn Microbiol Infect Dis. 2009 May;64(1):13-919362255
Cites: Sex Transm Dis. 2007 May;34(5):255-617483723
PubMed ID
20007394 View in PubMed
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[Comparison of the data of computed tomography and bacteriological studies in the complicated forms of primary tuberculosis in children and adolescents].

https://arctichealth.org/en/permalink/ahliterature261254
Source
Vestn Rentgenol Radiol. 2013 Nov-Dec;(6):16-21
Publication Type
Article
Author
L P Shepeleva
G I Alekseeva
Source
Vestn Rentgenol Radiol. 2013 Nov-Dec;(6):16-21
Language
Russian
Publication Type
Article
Keywords
Adolescent
Bacteriological Techniques - methods
Child
Child, Preschool
Diagnostic Errors - prevention & control
Humans
Infant
Lymph Nodes - radiography
Mycobacterium tuberculosis - isolation & purification
Russia - epidemiology
Thorax
Tomography, X-Ray Computed - methods
Tuberculosis, Lymph Node - diagnosis - epidemiology
Tuberculosis, Pulmonary - diagnosis - epidemiology
Abstract
To establish the causes of bacterial excretion in complicated primary tuberculosis in children and adolescents, by comparing the data of computed tomography and the results of bacteriological studies.
The material of the study was data on 36 children and adolescents with complicated primary tuberculosis, including 14 and 22 children and adolescents with and without bacterial excretion, respectively. All the children and adolescents underwent computed tomography and bacteriological studies encompassing luminescence microscopy and sputum and bronchial and gastric wash cultures for Mycobacterium tuberculosis.
The bacterial excretion group showed a preponderance of a tuberculous process concurrent with the involvement of lung tissue and intrathoracic lymph nodes. Bacterial excretion was detected in the primary tuberculosis complex (50%), generalized tuberculosis process with the involvement of a few organs and systems (14.3%), and caseous pneumonia (7.1%). Bacterial excretion was accompanied by the tuberculous involvement of intrathoracic lymph nodes in 28.6%. In Group 1, sputum cultures and luminescence microscopy were carried out in all the children. At the same time, the most effective result was yielded by sputum culture that showed Mycobacterium tuberculosis in 78.6%; luminescence microscopy revealed mycobacteria in only 35.7% of cases. In 72.7% of the children and adolescents without bacterial excretion, the tuberculous process was located in the intrathoracic lymph nodes, without involving lung tissue in the pathological process. In the other 27.3%, the computed tomographic pattern of changes corresponded to that of the primary tuberculosis complex; in their presence, the tuberculous process ran with lymphogenic dissemination in 54.5% of cases and with bronchopulmonary involvement in 22.7%. In Group 2, a sputum culture was done in only 36.4% of the children and adolescents; microscopy was carried out in all.
When computed tomography reveals the disseminated forms of primary tuberculosis with the concomitant involvement of lung tissue and intrathoracic lymph nodes in the presence of lung destructive changes, with the involvement of a few organs and systems in the pathological process, it is necessary to use all bacteriological studies, including culnolecular genetic methods, in order to establish the etiology of existing changes.
PubMed ID
25702438 View in PubMed
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43 records – page 1 of 5.