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1997-1998 influenza season: Canadian laboratory diagnoses and strain characterization.

https://arctichealth.org/en/permalink/ahliterature203270
Source
Can Commun Dis Rep. 1999 Jan 15;25(2):9-12
Publication Type
Article
Date
Jan-15-1999
Author
Y. Li
Author Affiliation
Respiratory Viruses Section, Bureau of Microbiology, LCDC, Federal Laboratories, Winnipeg, MB.
Source
Can Commun Dis Rep. 1999 Jan 15;25(2):9-12
Date
Jan-15-1999
Language
English
French
Publication Type
Article
Keywords
Bacterial Typing Techniques
Canada - epidemiology
Clinical Laboratory Techniques
Disease Outbreaks - statistics & numerical data
Humans
Incidence
Influenza, Human - diagnosis - epidemiology - virology
Orthomyxoviridae - classification - isolation & purification
Population Surveillance
Seasons
PubMed ID
9926488 View in PubMed
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Abyssivirga alkaniphila gen. nov., sp. nov., an alkane-degrading, anaerobic bacterium from a deep-sea hydrothermal vent system, and emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.

https://arctichealth.org/en/permalink/ahliterature275915
Source
Int J Syst Evol Microbiol. 2016 Apr;66(4):1724-34
Publication Type
Article
Date
Apr-2016
Author
Anders Schouw
Tove Leiknes Eide
Runar Stokke
Rolf Birger Pedersen
Ida Helene Steen
Gunhild Bødtker
Source
Int J Syst Evol Microbiol. 2016 Apr;66(4):1724-34
Date
Apr-2016
Language
English
Publication Type
Article
Keywords
Alkanes - metabolism
Arctic Regions
Bacterial Typing Techniques
Base Composition
Biodegradation, Environmental
Clostridiales - classification - genetics - isolation & purification
DNA, Bacterial - genetics
Fatty Acids - chemistry
Glycolipids - chemistry
Hydrothermal Vents - microbiology
Molecular Sequence Data
Peptidoglycan - chemistry
Phospholipids - chemistry
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Abstract
A strictly anaerobic, mesophilic, syntrophic, alkane-degrading strain, L81T, was isolated from a biofilm sampled from a black smoker chimney at the Loki's Castle vent field. Cells were straight, rod-shaped, Gram-positive-staining and motile. Growth was observed at pH?6.2-9.5, 14-42?°C and 0.5-6?% (w/w) NaCl, with optima at pH?7.0-8.2, 37?°C and 3% (w/w) NaCl. Proteinaceous substrates, sugars, organic acids and hydrocarbons were utilized for growth. Thiosulfate was used as an external electron acceptor during growth on crude oil. Strain L81T was capable of syntrophic hydrocarbon degradation when co-cultured with a methanogenic archaeon, designated strain LG6, isolated from the same enrichment. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain L81T is affiliated with the family Lachnospiraceae, and is most closely related to the type strains of Natranaerovirga pectinivora (92?% sequence similarity) and Natranaerovirga hydrolytica (90%). The major cellular fatty acids of strain L81T were C15?:?0, anteiso-C15?:?0 and C16?:?0, and the profile was distinct from those of the species of the genus Natranaerovirga. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids, four unidentified glycolipids and two unidentified phosphoglycolipids. The G+C content of genomic DNA was determined to be 31.7?mol%. Based on our phenotypic, phylogenetic and chemotaxonomic results, strain L81T is considered to represent a novel species of a new genus of the family Lachnospiraceae, for which we propose the name Abyssivirga alkaniphila gen. nov., sp. nov. The type strain of Abyssivirga alkaniphila is L81T (=DSM 29592T=JCM 30920T). We also provide emended descriptions of Natranaerovirga pectinivora and Natranaerovirga hydrolytica.
PubMed ID
26822139 View in PubMed
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Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.

https://arctichealth.org/en/permalink/ahliterature292492
Source
Antonie Van Leeuwenhoek. 2017 Dec; 110(12):1705-1717
Publication Type
Journal Article
Date
Dec-2017
Author
Imen Nouioui
Christian Rückert
Joost Willemse
Gilles P van Wezel
Hans-Peter Klenk
Tobias Busche
Jörn Kalinowski
Harald Bredholt
Sergey B Zotchev
Author Affiliation
School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
Source
Antonie Van Leeuwenhoek. 2017 Dec; 110(12):1705-1717
Date
Dec-2017
Language
English
Publication Type
Journal Article
Keywords
Actinobacteria - chemistry - classification - genetics - isolation & purification
Animals
Bacterial Typing Techniques
Computational Biology - methods
Genes, Bacterial
Genome, Bacterial
Genomics - methods
High-Throughput Nucleotide Sequencing
Metabolomics - methods
Molecular Sequence Annotation
Multigene Family
Phenotype
Phylogeny
Porifera - microbiology
Secondary Metabolism - genetics
Abstract
Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates.
Notes
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PubMed ID
28770445 View in PubMed
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[ACTUAL PROBLEMS OF EPIDEMIOLOGIC CONTROL, LABORATORY DIAGNOSTICS AND PROPHYLAXIS OF CHOLERA IN RUSSIAN FEDERATION].

https://arctichealth.org/en/permalink/ahliterature271672
Source
Zh Mikrobiol Epidemiol Immunobiol. 2016 Jan-Feb;(1):89-101
Publication Type
Article
Author
G G Onischenko
A Yu Popova
V V Kutyrev
N I Smirnova
S A Scherbakova
E A Moskvitina
S V Titova
Source
Zh Mikrobiol Epidemiol Immunobiol. 2016 Jan-Feb;(1):89-101
Language
Russian
Publication Type
Article
Keywords
Bacterial Typing Techniques
Cholera - diagnosis - epidemiology - prevention & control - transmission
Disease Outbreaks
Epidemiological Monitoring
Genotype
Humans
Oligonucleotide Array Sequence Analysis
Phylogeny
Retrospective Studies
Russia - epidemiology
Serogroup
Vibrio cholerae - classification - genetics - isolation & purification - pathogenicity
Water Microbiology
Abstract
Main problems of system of epidemiologic control for cholera active in Russian Federation, as well as laboratory diagnostics and vaccine prophylaxis of this especially dangerous infection, that had emerged in the contemporary period of the ongoing 7th pandemic of cholera, are discussed. Features of the genome of natural strains of Vibrio cholerae of El Tor biovar, that possess a poten- tial epidemic threat, as well as problems, that have emerged during isolation of these strains from samples of water of surface water bodies during their monitoring, are also examined. The main direction of enhancement of the system of epidemiologic control for cholera consist in develop- ment of a new algorithm of differentiation of administrative territories of Russian Federation by types of epidemic manifestations, as well as optimization of monitoring of environment objects. Integration of modern highly informative technologies into practice, as well as development of new generation diagnostic preparations based on DNA-chips and immunechips is necessary to increase effectiveness of the conducted operative and retrospective diagnostics in the contemporary period. Creation of national cholera vaccine, ensuring simultaneous protection from cholera causative agents of both O1 and O139 serogroups, is also required.
PubMed ID
27029123 View in PubMed
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Adapting spa typing for national laboratory-based surveillance of methicillin-resistant Staphylococcus aureus.

https://arctichealth.org/en/permalink/ahliterature137554
Source
Eur J Clin Microbiol Infect Dis. 2011 Jun;30(6):789-97
Publication Type
Article
Date
Jun-2011
Author
A. Vainio
S. Koskela
A. Virolainen
J. Vuopio
S. Salmenlinna
Author Affiliation
Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare (THL), PO Box 30, 00271 Helsinki, Finland. anni.vainio@thl.fi
Source
Eur J Clin Microbiol Infect Dis. 2011 Jun;30(6):789-97
Date
Jun-2011
Language
English
Publication Type
Article
Keywords
Bacteremia - microbiology
Bacterial Typing Techniques - economics - methods
Cluster analysis
Electrophoresis, Gel, Pulsed-Field
Finland
Genotype
Humans
Methicillin-Resistant Staphylococcus aureus - classification - genetics - isolation & purification
Molecular Epidemiology - methods
Molecular Typing - economics - methods
Staphylococcal Infections - microbiology
Time Factors
Abstract
Laboratory-based surveillance of methicillin-resistant Staphylococcus aureus (MRSA) monitors the baseline occurrence of different genotypes and identifies strains and transmission chains responsible for outbreaks. The consequences of substituting pulsed-field gel electrophoresis (PFGE) with spa typing as a first-line typing method were analyzed by typing 589 strains isolated between 1997 and 2006, with a focus on both short- and long-term correspondence between the PFGE and spa typing results. The study, covering these ten years, included all Finnish MRSA blood isolates and representatives of the two most prevalent MRSA strains (PFGE types FIN-4 and FIN-16) in Finland. In addition, all sporadic isolates from 2006 were included. spa typing was more expensive but approximately four times faster to perform than PFGE. Nearly 90% of FIN-4 and FIN-16 isolates showed consistent spa types, t172 and t067, respectively. spa typing predicted the PFGE result of the blood isolates by a Wallace coefficient of 0.9009, recognized internationally successful strains (t041, t067) to be common also in Finland, and identified a separate cluster of isolates, also related in time and place among the FIN-4 strains. Additional typing by another method was needed to provide adequate discrimination or to characterize isolates with a newly recognized spa type in Finland.
PubMed ID
21271269 View in PubMed
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Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera).

https://arctichealth.org/en/permalink/ahliterature291960
Source
Int J Syst Evol Microbiol. 2018 May; 68(5):1762-1770
Publication Type
Journal Article
Date
May-2018
Author
Jane Ludvigsen
Davide Porcellato
Gro V Amdam
Knut Rudi
Author Affiliation
1?Faculty of Chemistry, Biotechnology, and Food Science, Norwegian University of Life Sciences (NMBU), Chr. M. Fahlsensvei 1, 1433 Ås, Norway.
Source
Int J Syst Evol Microbiol. 2018 May; 68(5):1762-1770
Date
May-2018
Language
English
Publication Type
Journal Article
Keywords
Animals
Bacterial Typing Techniques
Base Composition
Bees - microbiology
DNA, Bacterial - genetics
Fatty Acids - chemistry
Gammaproteobacteria - classification - genetics - isolation & purification
Gastrointestinal Tract - microbiology
Norway
Phylogeny
RNA, Ribosomal, 16S - genetics
Sequence Analysis, DNA
Symbiosis
Ubiquinone - chemistry
Abstract
The gut microbiota of honeybees (Apis) and bumblebees (Bombus) include the symbiotic bacterial genus Gilliamella. This genus shows a high degree of functional and genomic diversity and separates into distinct lineages. Gilliamella apicola wkB1T, which was isolated from Apis, was the first species to be described. Recently four new species, isolated from Bombus, were identified. In this paper, we compare several genomes/strains from previous studies spanning this diversity, which gives insight into the phylogenetic relationship among different Gilliamella species. We show that one lineage, isolated only from Apis, is different from other gilliamellas described, based on average nucleotide identity calculation (about 80?%) and phenotypic characterizations. We propose the new species name for this lineage: Gilliamella apis sp. nov. We present the characterization of the type strain NO3T (=DSM 105629T=LMG 30293T), a strain isolated from the Western honeybee Apis mellifera, which clusters within this lineage. Cells of strain NO3T grow best in a microaerophilic atmosphere with enhanced CO2 levels at 36?°C and pH 7.0-7.5. Cells also grow well in anaerobic conditions, but not in aerobic conditions. Cells are approximately 1?µm in length and rod-shaped, and the genomic G+C content is 34.7?mol%. Differential characteristics between strain NO3T and the different type strains of Gilliamella were revealed based on API kit tests and genomic content comparisons. The main respiratory quinone of strain NO3T was ubiquinone-8, and the predominant fatty acids were C18?:?1?7c/C18?:?1?6c, C16?:?0, consistent with the genus Gilliamella.
PubMed ID
29624166 View in PubMed
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Adhesin and superantigen genes and the capacity of Staphylococcus aureus to colonize the infantile gut.

https://arctichealth.org/en/permalink/ahliterature132145
Source
J Infect Dis. 2011 Sep 1;204(5):714-21
Publication Type
Article
Date
Sep-1-2011
Author
Forough L Nowrouzian
Olivier Dauwalder
Helene Meugnier
Michele Bes
Jerome Etienne
François Vandenesch
Erika Lindberg
Bill Hesselmar
Robert Saalman
Inga-Lisa Strannegård
Nils Aberg
Ingegerd Adlerberth
Agnes E Wold
Gerard Lina
Author Affiliation
Institution for Biomedicine, Department of Infectious Disease, University of Gothenburg, Sweden. forough.nowrouzian@microbio.gu.se
Source
J Infect Dis. 2011 Sep 1;204(5):714-21
Date
Sep-1-2011
Language
English
Publication Type
Article
Keywords
Adhesins, Bacterial - genetics
Alleles
Bacterial Load
Bacterial Proteins - genetics
Bacterial Typing Techniques
Enterotoxins - genetics
Feces - microbiology
Humans
Infant
Infant, Newborn
Longitudinal Studies
Polymerase Chain Reaction
Staphylococcal Infections - genetics
Staphylococcus aureus - genetics - pathogenicity
Superantigens - genetics
Sweden
Trans-Activators - genetics
Virulence Factors - genetics
Abstract
Staphylococcus aureus is a pathogen and a skin commensal that is today also common in the infant gut flora. We examine the role of S. aureus virulence factors for gut colonization. S. aureus isolated from quantitative stool cultures of 49 Swedish infants followed from birth to 12 months of age were assessed for 30 virulence-associated genes, spa type, and agr allele by serial polymerase chain reaction (PCR) assays. Strains carrying genes encoding collagen-binding protein, and the superantigens S. aureus enterotoxin O/M (SEO/SEM) had higher stool counts than strains lacking these genes, whereas genes for S. aureus enterotoxin A (SEA) were associated with low counts. A cluster of strains belonging to agr allele I and the spa clonal cluster 630 (spa-CC 630) that carried genes encoding SEO/SEM, SEC, collagen-binding protein, and elastin-binding protein were all long-time colonizers. Thus, certain S. aureus virulence factors might promote gut colonization.
PubMed ID
21844297 View in PubMed
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Aetiological diagnosis of infective endocarditis by direct amplification of rRNA genes from surgically removed valve tissue. An 11-year experience in a Finnish teaching hospital.

https://arctichealth.org/en/permalink/ahliterature168994
Source
Ann Med. 2006;38(4):263-73
Publication Type
Article
Date
2006
Author
Pirkko Kotilainen
Maija Heiro
Jari Jalava
Veikko Rantakokko
Jukka Nikoskelainen
Simo Nikkari
Kaisu Rantakokko-Jalava
Author Affiliation
Department of Medicine, Turku University Hospital, Finland. pirkko.kotilainen@utu.fi
Source
Ann Med. 2006;38(4):263-73
Date
2006
Language
English
Publication Type
Article
Keywords
Bacterial Typing Techniques
Bartonella - classification - genetics
DNA, Bacterial - analysis
DNA, Ribosomal - analysis
Endocarditis, Bacterial - diagnosis - microbiology
Female
Finland
Heart Valves - microbiology
Hospitals, Teaching
Humans
Male
Polymerase Chain Reaction
Predictive value of tests
Prospective Studies
Sequence Analysis, DNA
Staphylococcus - classification - genetics
Streptococcus - classification - genetics
Abstract
The aetiology of infective endocarditis (IE) can be determined directly from surgically removed valve tissue using broad-range bacterial rDNA polymerase chain reaction (PCR) followed by sequencing. We sought to assess the value of this methodology in a routine clinical setting.
Broad-range PCR with primers targeting conserved bacterial rDNA sequences was applied to directly analyse valve samples from 56 patients operated on for diagnosed or suspected IE. Identification of the aetiological agent was performed by partial DNA sequencing of the 16S and 23S rDNA genes.
The final diagnosis was definite IE in 36 patients and possible IE in 2 patients, while the diagnosis of IE was rejected in 18 patients. PCR analysis from removed valve tissue was positive in 25 patients with IE. Molecular identification was consistent with the blood culture finding in 20 of these patients. The PCR approach was the only method to yield the aetiological diagnosis in additional 4 patients (2 Staphylococcus species, 1 Streptococcus bovis, 1 Bartonella quintana), all of whom had received antimicrobials before blood cultures were taken. The mean duration of preoperative antimicrobial treatment for the patients with PCR-positive valves was 19.6 (range 1-58) days.
Bacterial DNA may persist during treatment in infected valves for long periods. The PCR method is especially useful when the causative agent of IE is fastidious or when the specimen is taken during antimicrobial treatment.
PubMed ID
16754257 View in PubMed
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Algibacter amylolyticus sp. nov., isolated from intertidal sediment.

https://arctichealth.org/en/permalink/ahliterature266892
Source
Int J Syst Evol Microbiol. 2015 May;65(Pt 5):1556-60
Publication Type
Article
Date
May-2015
Author
De-Chao Zhang
Jiang Wu
Kathrin Neuner
Jianting Yao
Rosa Margesin
Source
Int J Syst Evol Microbiol. 2015 May;65(Pt 5):1556-60
Date
May-2015
Language
English
Publication Type
Article
Keywords
Bacterial Typing Techniques
Base Composition
DNA, Bacterial - genetics
Fatty Acids - chemistry
Flavobacteriaceae - classification - genetics - isolation & purification
Geologic Sediments - microbiology
Islands
Molecular Sequence Data
Nucleic Acid Hybridization
Phosphatidylethanolamines - chemistry
Phylogeny
Pigmentation
RNA, Ribosomal, 16S - genetics
Russia
Seawater - microbiology
Sequence Analysis, DNA
Vitamin K 2 - analogs & derivatives - chemistry
Abstract
A Gram-reaction-negative, rod-shaped, yellow-pigmented, motile by gliding bacterial strain, designated RU-4-M-4(T), was isolated from intertidal sediment of Sakhalin Island in Russia. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RU-4-M-4(T) was related to the genus Algibacter and had highest 16S rRNA gene sequence similarity with Algibacter pectinivorans KACC 14153(T) (97.2%). The major cellular fatty acids were iso-C15 : 0 3-OH, C15: 0 and iso-C15 : 1 G. The predominant menaquinone was MK-6. The polar lipid profile contained phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content of strain RU-4-M-4(T) was 36.4 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain RU-4-M-4(T) is a representative of a novel species of the genus Algibacter , for which we propose the name Algibacter amylolyticus sp. nov. (type strain RU-4-M-4(T)?=LMG 28383(T)?=DSM 29199(T)).
PubMed ID
25713044 View in PubMed
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Alkaliphilus namsaraevii sp. nov., an alkaliphilic iron- and sulfur-reducing bacterium isolated from a steppe soda lake.

https://arctichealth.org/en/permalink/ahliterature285198
Source
Int J Syst Evol Microbiol. 2017 Jun;67(6):1990-1995
Publication Type
Article
Date
Jun-2017
Author
Anastasiya Zakharyuk
Lyudmila Kozyreva
Elena Ariskina
Olga Troshina
Dmitry Kopitsyn
Viktoria Shcherbakova
Source
Int J Syst Evol Microbiol. 2017 Jun;67(6):1990-1995
Date
Jun-2017
Language
English
Publication Type
Article
Keywords
Alkalies
Bacterial Typing Techniques
Base Composition
Clostridiales - classification - genetics - isolation & purification
DNA, Bacterial - genetics
Fatty Acids - chemistry
Ferric Compounds - metabolism
Lakes - microbiology
Phylogeny
RNA, Ribosomal, 16S - genetics
Russia
Sequence Analysis, DNA
Sulfur
Sulfur-Reducing Bacteria - classification - genetics - isolation & purification
Abstract
A novel alkaliphilic spore-forming bacterium was isolated from the benthic sediments of the highly mineralized steppe Lake Khilganta (Transbaikal Region, Russia). Cells of the strain, designated ?-07-2T, were straight to slightly curved rods, Gram-stain-positive and motile. Strain ?-07-2T grew in the pH range from 7.0 to 10.7 (optimum pH 9.6-10.3). Growth was observed at 25-47?°C (optimum 30?°C) and at an NaCl concentration from 5 to 150?g l-1 with an optimum at 40?g l-1. Strain ?-07-2T was a chemo-organoheterotroph able to reduce amorphous ferric hydroxide, Fe(III) citrate and elemental sulfur in the presence of yeast extract as the electron donor. It used tryptone, peptone and trypticase with Fe(III) citrate as the electron acceptor. The predominant fatty acids in cell walls were C16:1?8, iso-C15:0, C14?:?0 3-OH and C16?:?0. The DNA G+C content was 32.6?mol%. 16S rRNA gene sequence analysis revealed that strain ?-07-2T was related most closely to members of the genus Alkaliphilus within the family Clostridiaceae. The closest relative was Alkaliphilus peptidifermentans Z-7036T (96.4?% similarity). On the basis of the genotypic, chemotaxonomic and phenotypic data, strain ?-07-2T represents a novel species in the genus Alkaliphilus, for which the name Alkaliphilus namsaraevii sp. nov. is proposed. The type strain is ?-07-2T (=VKM ?-2746?=DSM 26418?).
PubMed ID
28632119 View in PubMed
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462 records – page 1 of 47.