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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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A2ML1 and otitis media: novel variants, differential expression, and relevant pathways.

https://arctichealth.org/en/permalink/ahliterature310601
Source
Hum Mutat. 2019 08; 40(8):1156-1171
Publication Type
Journal Article
Multicenter Study
Research Support, N.I.H., Extramural
Date
08-2019
Author
Eric D Larson
Jose Pedrito M Magno
Matthew J Steritz
Erasmo Gonzalo D V Llanes
Jonathan Cardwell
Melquiadesa Pedro
Tori Bootpetch Roberts
Elisabet Einarsdottir
Rose Anne Q Rosanes
Christopher Greenlee
Rachel Ann P Santos
Ayesha Yousaf
Sven-Olrik Streubel
Aileen Trinidad R Santos
Amanda G Ruiz
Sheryl Mae Lagrana-Villagracia
Dylan Ray
Talitha Karisse L Yarza
Melissa A Scholes
Catherine B Anderson
Anushree Acharya
Samuel P Gubbels
Michael J Bamshad
Stephen P Cass
Nanette R Lee
Rehan S Shaikh
Deborah A Nickerson
Karen L Mohlke
Jeremy D Prager
Teresa Luisa G Cruz
Patricia J Yoon
Generoso T Abes
David A Schwartz
Abner L Chan
Todd M Wine
Eva Maria Cutiongco-de la Paz
Norman Friedman
Katerina Kechris
Juha Kere
Suzanne M Leal
Ivana V Yang
Janak A Patel
Ma Leah C Tantoco
Saima Riazuddin
Kenny H Chan
Petri S Mattila
Maria Rina T Reyes-Quintos
Zubair M Ahmed
Herman A Jenkins
Tasnee Chonmaitree
Lena Hafrén
Charlotte M Chiong
Regie Lyn P Santos-Cortez
Author Affiliation
Department of Otolaryngology, University of Colorado School of Medicine, Aurora, Colorado.
Source
Hum Mutat. 2019 08; 40(8):1156-1171
Date
08-2019
Language
English
Publication Type
Journal Article
Multicenter Study
Research Support, N.I.H., Extramural
Keywords
Adolescent
Adult
Child
Child, Preschool
Down-Regulation
Female
Finland
Gene Expression Profiling - methods
Gene Expression Regulation
Genetic Predisposition to Disease
Humans
Infant
Male
Middle Aged
Mutation
Otitis Media - genetics
Pakistan
Pedigree
Philippines
Sequence Analysis, DNA - methods
Sequence Analysis, RNA
Signal Transduction
United States
Young Adult
alpha-Macroglobulins - genetics
Abstract
A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061?+?1?G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.
PubMed ID
31009165 View in PubMed
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Analysis of Swedish Bordetella pertussis isolates with three typing methods: characterization of an epidemic lineage.

https://arctichealth.org/en/permalink/ahliterature149892
Source
J Microbiol Methods. 2009 Sep;78(3):297-301
Publication Type
Article
Date
Sep-2009
Author
A. Advani
H G J Van der Heide
H O Hallander
F R Mooi
Author Affiliation
Department of bacteriology, Swedish Institute for Infectious Disease Control (SMI), S-171 82 Solna, Sweden. reza.advani@smi.se
Source
J Microbiol Methods. 2009 Sep;78(3):297-301
Date
Sep-2009
Language
English
Publication Type
Article
Keywords
Alleles
Bacterial Typing Techniques - methods
Bordetella pertussis - classification - genetics - isolation & purification
Cluster analysis
DNA Fingerprinting - methods
DNA, Bacterial - chemistry - genetics
Electrophoresis, Gel, Pulsed-Field - methods
Humans
Minisatellite Repeats
Molecular Epidemiology - methods
Molecular Sequence Data
Polymerase Chain Reaction - methods
Sensitivity and specificity
Sequence Analysis, DNA - methods
Sweden - epidemiology
Whooping Cough - epidemiology - microbiology
Abstract
Three Bordetella pertussis typing methods, pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and multi-locus variable number tandem repeat analysis (MLVA) were compared using a collection of Swedish strains. Of the three typing methods used, PFGE was found to be the most discriminatory. MLVA and MLST were less discriminatory, but may be valuable for strain discrimination when culture is not possible as they are based on PCR. The combination of MLVA/MLST was found to be equally discriminatory as PFGE and should therefore also be considered. The relationship between predominant lineages in Sweden and The Netherlands, characterized by the PFGE type BpSR11 and the allele for the pertussis toxin promoter ptxP3, respectively, was investigated. Linkage was found between the PFGE type BpSR11 and ptxP3 in that all BpSR11 strains carried ptxP3. On the other hand ptxP3 was found in several other PFGE-types. The presence of the ptxP3 allele in different genetic backgrounds may indicate horizontal gene transfer within B. pertussis or homoplasy. Alternatively, this observation may be due to convergence of PFGE types.
PubMed ID
19577594 View in PubMed
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Application of state-of-art sequencing technologies to indigenous food fermentations.

https://arctichealth.org/en/permalink/ahliterature120880
Source
Curr Opin Biotechnol. 2013 Apr;24(2):178-86
Publication Type
Article
Date
Apr-2013
Author
Sacha A F T van Hijum
Elaine E Vaughan
Rudi F Vogel
Author Affiliation
NIZO Food Research, Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 20, 6710 BA Ede, The Netherlands. svhijum@cmbi.ru.nl
Source
Curr Opin Biotechnol. 2013 Apr;24(2):178-86
Date
Apr-2013
Language
English
Publication Type
Article
Keywords
Beverages - microbiology
Diet
Ecosystem
Fermentation - genetics
Food Microbiology - methods
Humans
Metagenome - genetics
Sequence Analysis, DNA - methods
Abstract
Fermented foods and beverages are an integral part of the human diet globally. Understanding the microbial interactions within these fermenting ecosystems is required to deliver safe products with desirable consumer properties, and moreover, maintenance of these traditions. Effective tools are required for documentation of cultures in traditional and artisanal fermented products, for sensory quality and safety improvements, in some cases for starter culture design for commercialization and potentially for supporting sustainable food systems. Here we trace the developments of sequence-based molecular technologies for investigating the diversity and functionality of microbiota in traditional or indigenous fermented foods and beverages. The opportunities of phylobiomics, metagenomics and metatranscriptomics to enrich our knowledge of fermenting microbial ecosystems are presented.
PubMed ID
22960050 View in PubMed
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Assessment of the extirpated Maritimes walrus using morphological and ancient DNA analysis.

https://arctichealth.org/en/permalink/ahliterature260057
Source
PLoS One. 2014;9(6):e99569
Publication Type
Article
Date
2014
Author
Brenna A McLeod
Timothy R Frasier
Zoe Lucas
Source
PLoS One. 2014;9(6):e99569
Date
2014
Language
English
Publication Type
Article
Keywords
Animals
Canada
DNA - genetics
DNA, Mitochondrial - genetics
Discriminant Analysis
Extinction, Biological
Female
Geography
Haplotypes
Male
Mandible - anatomy & histology
Molecular Sequence Data
Oceans and Seas
Phylogeny
Sequence Analysis, DNA - methods
Skull - anatomy & histology
Walruses - anatomy & histology - genetics
Abstract
Species biogeography is a result of complex events and factors associated with climate change, ecological interactions, anthropogenic impacts, physical geography, and evolution. To understand the contemporary biogeography of a species, it is necessary to understand its history. Specimens from areas of localized extinction are important, as extirpation of species from these areas may represent the loss of unique adaptations and a distinctive evolutionary trajectory. The walrus (Odobenus rosmarus) has a discontinuous circumpolar distribution in the arctic and subarctic that once included the southeastern Canadian Maritimes region. However, exploitation of the Maritimes population during the 16th-18th centuries led to extirpation, and the species has not inhabited areas south of 55°N for ~250 years. We examined genetic and morphological characteristics of specimens from the Maritimes, Atlantic (O. r. rosmarus) and Pacific (O. r. divergens) populations to test the hypothesis that the first group was distinctive. Analysis of Atlantic and Maritimes specimens indicated that most skull and mandibular measurements were significantly different between the Maritimes and Atlantic groups and discriminant analysis of principal components confirmed them as distinctive groups, with complete isolation of skull features. The Maritimes walrus appear to have been larger animals, with larger and more robust tusks, skulls and mandibles. The mtDNA control region haplotypes identified in Maritimes specimens were unique to the region and a greater average number of nucleotide differences were found between the regions (Atlantic and Maritimes) than within either group. Levels of diversity (h and p) were lower in the Maritimes, consistent with other studies of species at range margins. Our data suggest that the Maritimes walrus was a morphologically and genetically distinctive group that was on a different evolutionary path from other walrus found in the north Atlantic.
Notes
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PubMed ID
24924490 View in PubMed
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Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA.

https://arctichealth.org/en/permalink/ahliterature130568
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Publication Type
Article
Date
Apr-2012
Author
Sanne Boessenkool
Laura S Epp
James Haile
Eva Bellemain
Mary Edwards
Eric Coissac
Eske Willerslev
Christian Brochmann
Author Affiliation
National Centre for Biosystematics, Natural History Museum, University of Oslo, Oslo, Norway. sanneboessenkool@gmail.com
Source
Mol Ecol. 2012 Apr;21(8):1806-15
Date
Apr-2012
Language
English
Publication Type
Article
Keywords
Animals
DNA - analysis - isolation & purification
DNA Contamination
DNA Primers - genetics
Fossils
Geologic Sediments - chemistry
Humans
Ice
Perissodactyla - classification - genetics
Polymerase Chain Reaction - methods
Sequence Analysis, DNA - methods
Siberia
Abstract
Analyses of degraded DNA are typically hampered by contamination, especially when employing universal primers such as commonly used in environmental DNA studies. In addition to false-positive results, the amplification of contaminant DNA may cause false-negative results because of competition, or bias, during the PCR. In this study, we test the utility of human-specific blocking primers in mammal diversity analyses of ancient permafrost samples from Siberia. Using quantitative PCR (qPCR) on human and mammoth DNA, we first optimized the design and concentration of blocking primer in the PCR. Subsequently, 454 pyrosequencing of ancient permafrost samples amplified with and without the addition of blocking primer revealed that DNA sequences from a diversity of mammalian representatives of the Beringian megafauna were retrieved only when the blocking primer was added to the PCR. Notably, we observe the first retrieval of woolly rhinoceros (Coelodonta antiquitatis) DNA from ancient permafrost cores. In contrast, reactions without blocking primer resulted in complete dominance by human DNA sequences. These results demonstrate that in ancient environmental analyses, the PCR can be biased towards the amplification of contaminant sequences to such an extent that retrieval of the endogenous DNA is severely restricted. The application of blocking primers is a promising tool to avoid this bias and can greatly enhance the quantity and the diversity of the endogenous DNA sequences that are amplified.
PubMed ID
21988749 View in PubMed
Less detail
Source
Clin Genet. 2012 Nov;82(5):405-7
Publication Type
Article
Date
Nov-2012
Author
J. Richer
T N Nelson
J. Evans
L. Armstrong
J. Lauzon
B. McGillivray
Author Affiliation
Medical Genetics, CHEO, Ottawa, Ontario, Canada.
Source
Clin Genet. 2012 Nov;82(5):405-7
Date
Nov-2012
Language
English
Publication Type
Article
Keywords
Canada
Genetic Testing - standards
Humans
Patents as Topic
Sequence Analysis, DNA - methods
Sequence Analysis, RNA - methods
PubMed ID
23051176 View in PubMed
Less detail

Clonality of epidemic methicillin-resistant Staphylococcus aureus strains in Finland as defined by several molecular methods.

https://arctichealth.org/en/permalink/ahliterature158778
Source
Eur J Clin Microbiol Infect Dis. 2008 Jul;27(7):545-55
Publication Type
Article
Date
Jul-2008
Author
A. Vainio
M. Kardén-Lilja
S. Ibrahem
A M Kerttula
S. Salmenlinna
A. Virolainen
J. Vuopio-Varkila
Author Affiliation
Department of Bacterial and Inflammatory Diseases, National Public Health Institute, Mannerheimintie 166, 00300, Helsinki, Finland. anni.vainio@ktl.fi
Source
Eur J Clin Microbiol Infect Dis. 2008 Jul;27(7):545-55
Date
Jul-2008
Language
English
Publication Type
Article
Keywords
Bacterial Typing Techniques
Chromosomes, Bacterial
Cluster analysis
DNA Fingerprinting
DNA, Bacterial - genetics
Electrophoresis, Gel, Pulsed-Field
Finland - epidemiology
Genotype
Humans
Incidence
Methicillin Resistance
Sequence Analysis, DNA - methods
Staphylococcal Infections - epidemiology - microbiology
Staphylococcal Protein A - genetics
Staphylococcus aureus - classification - drug effects - isolation & purification
Statistics as Topic
Abstract
In Finland, the incidence of methicillin-resistant Staphylococcus aureus (MRSA) strains has increased ten fold within the last decade. In order to follow the changing epidemiology of MRSA, accurate typing of S. aureus strains is important. The purpose of this study was to reanalyse 44 previously recognised Finnish epidemic MRSA strains (EMRSA) by several molecular typing methods and to revise their nomenclature. The 44 EMRSA strains were grouped into 26 pulsed-field gel electrophoresis (PFGE) clusters, 20 multi locus sequence typing (MLST) sequence types (ST) belonging to 12 clonal complexes (CC) of which CC8 was the most prevalent, and 27 spa types belonging to four clonal complexes. The staphylococcal cassette chromosome mec (SCCmec) type IV was predominant, and 48% of the strains were nonmultiresistant to antibiotics. The discriminatory power of PFGE clusters, MLST, and spa typing was high. The overall concordance values of typing methods differed when assessed by two different methods. Adjusted Rand coefficient provided fairly low correlations for all comparisons. However, spa type was able to efficiently predict types and clonal complexes of most of the other methods with high probability (> or =80%).
PubMed ID
18274796 View in PubMed
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Comparing whole-genome sequencing with Sanger sequencing for spa typing of methicillin-resistant Staphylococcus aureus.

https://arctichealth.org/en/permalink/ahliterature267071
Source
J Clin Microbiol. 2014 Dec;52(12):4305-8
Publication Type
Article
Date
Dec-2014
Author
Mette Damkjær Bartels
Andreas Petersen
Peder Worning
Jesper Boye Nielsen
Hanna Larner-Svensson
Helle Krogh Johansen
Leif Percival Andersen
Jens Otto Jarløv
Kit Boye
Anders Rhod Larsen
Henrik Westh
Source
J Clin Microbiol. 2014 Dec;52(12):4305-8
Date
Dec-2014
Language
English
Publication Type
Article
Keywords
Denmark - epidemiology
Humans
Methicillin-Resistant Staphylococcus aureus - classification - genetics
Molecular Epidemiology - methods
Molecular Typing - methods
Sequence Analysis, DNA - methods
Staphylococcal Infections - epidemiology - microbiology
Staphylococcal Protein A - genetics
Abstract
spa typing of methicillin-resistant Staphylococcus aureus (MRSA) has traditionally been done by PCR amplification and Sanger sequencing of the spa repeat region. At Hvidovre Hospital, Denmark, whole-genome sequencing (WGS) of all MRSA isolates has been performed routinely since January 2013, and an in-house analysis pipeline determines the spa types. Due to national surveillance, all MRSA isolates are sent to Statens Serum Institut, where the spa type is determined by PCR and Sanger sequencing. The purpose of this study was to evaluate the reliability of the spa types obtained by 150-bp paired-end Illumina WGS. MRSA isolates from new MRSA patients in 2013 (n = 699) in the capital region of Denmark were included. We found a 97% agreement between spa types obtained by the two methods. All isolates achieved a spa type by both methods. Nineteen isolates differed in spa types by the two methods, in most cases due to the lack of 24-bp repeats in the whole-genome-sequenced isolates. These related but incorrect spa types should have no consequence in outbreak investigations, since all epidemiologically linked isolates, regardless of spa type, will be included in the single nucleotide polymorphism (SNP) analysis. This will reveal the close relatedness of the spa types. In conclusion, our data show that WGS is a reliable method to determine the spa type of MRSA.
Notes
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PubMed ID
25297335 View in PubMed
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Comparison of seven techniques for typing international epidemic strains of Clostridium difficile: restriction endonuclease analysis, pulsed-field gel electrophoresis, PCR-ribotyping, multilocus sequence typing, multilocus variable-number tandem-repeat analysis, amplified fragment length polymorphism, and surface layer protein A gene sequence typing.

https://arctichealth.org/en/permalink/ahliterature160131
Source
J Clin Microbiol. 2008 Feb;46(2):431-7
Publication Type
Article
Date
Feb-2008
Author
George Killgore
Angela Thompson
Stuart Johnson
Jon Brazier
Ed Kuijper
Jacques Pepin
Eric H Frost
Paul Savelkoul
Brad Nicholson
Renate J van den Berg
Haru Kato
Susan P Sambol
Walter Zukowski
Christopher Woods
Brandi Limbago
Dale N Gerding
L Clifford McDonald
Author Affiliation
Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
Source
J Clin Microbiol. 2008 Feb;46(2):431-7
Date
Feb-2008
Language
English
Publication Type
Article
Keywords
Amplified Fragment Length Polymorphism Analysis - methods
Bacterial Proteins - genetics
Bacterial Toxins - genetics
Bacterial Typing Techniques - methods
Canada
Clostridium difficile - classification
DNA, Bacterial - genetics
Disease Outbreaks
Electrophoresis, Gel, Pulsed-Field - methods
Enterocolitis, Pseudomembranous - epidemiology - microbiology
Genotype
Great Britain
Humans
Minisatellite Repeats
Molecular Epidemiology - methods
Netherlands
Reproducibility of Results
Restriction Mapping - methods
Ribotyping - methods
Sensitivity and specificity
Sequence Analysis, DNA - methods
United States
Abstract
Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.
Notes
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PubMed ID
18039796 View in PubMed
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69 records – page 1 of 7.