SNP typing
High throughput bacterial SNP typing identifies distinct clusters of SalmonellaTyphi causing typhoid in Nepalese children
... This work was funded by The Wellcome Trust. We thank Mark Achtman for access to GyrA SNP typing in his laboratory. S. Typhi isolates analyzed in this study were collected during the course of a larger study ...
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A Simplified Van Erth Single Nucleotide Polymorphism (SNP) Typing Method of Bacillus Anthracis Applicable by Traditional Thermocycler Machines
... SNP typing is now a well-established genotyping system in Bacillus anthracis studies. In the original standard method of Van Erth, SNPs at 13 loci of the B. anthracis genome were analyzed. In order to ...
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Whole genome SNP typing to investigate methicillin-resistant Staphylococcus aureus carriage in a health-care provider as the source of multiple surgical site infections
... In this study, a hospital infection control team identi- fied a cluster of MRSA SSIs from a single surgical team. Antibiotic susceptibility profiles suggested that the cases were related. The surgical team in question ...
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Peopling of the North Circumpolar Region--insights from Y chromosome STR and SNP typing of Greenlanders.
... The human population in Greenland is characterized by migration events of Paleo- and Neo-Eskimos, as well as admixture with Europeans. In this study, the Y-chromosomal varia- tion in male Greenlanders was investigated in ...
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Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak
... In cgMLST a set of loci, 3002 for the Salmonella scheme described here, is used for gene-by-gene comparisons of assembled bacterial iso- lates. These schemes summarise the diversity present within the nu- cleotide ...
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Challenges to Analysis of Ancestral Inference Using Mitochondrial DNA Hypervariable Region 1 SNP Typing
... Non-African groups as a subset of continental African genetic diversity unequivocally supports bottlenecks and founder effects that came about due to migrant Africans w[r] ...
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Genome Wide Single Nucleotide Polymorphism Typing Method for Identification of Bacillus anthracis Species and Strains among B cereus Group Species
... for SNP alleles, 17 other available genomic sequences of ...for SNP identification using in silico analysis (Table 1; ...whole SNP alleles (Fig. 2). SNP variation showed the corresponding ...
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The clinical and molecular epidemiology of Staphylococcus aureus infections in Fiji
... Of the remaining 303 MSSA isolates, 105 underwent SNP-typing. There was a wide distribution of CCs among the MSSA isolates (Figure 1) with the most common be- ing CC5, 7, 14, 75 and 121. As the CC75 lineage ...
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A Differential typing of Campylobacter
... that SNP typing is the method of choice. SNP typing is relatively easy to implement and is directly related to MLST, hence it is easy to compare results with other researchers from around the ...
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Rapid and robust phylotyping of spa t003, a dominant MRSA clone in Luxembourg and other European countries
... genome SNP typing (WGST) to compare to the SNP assays, spa typing, MLVA and ...molecular typing of MRSA [20,21], as well as for other bacteria [22,23] and fungal pathogens ...other ...
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Comparing Pulsed Field Gel Electrophoresis with Multilocus Sequence Typing, spa Typing, Staphylococcal Cassette Chromosome mec (SCCmec) Typing, and PCR for Panton Valentine Leukocidin, arcA, and opp3 in Methicillin Resistant Staphylococcus aureus Isolates at a U S Medical Center
... Methicillin-resistant Staphylococcus aureus (MRSA) has become a common cause of skin infections and invasive infections in community dwellers in the United States since the late 1990s. Isolates characterized as USA300 by ...
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Phylogenetically typing bacterial strains from partial SNP genotypes observed from direct sequencing of clinical specimen metagenomic data
... Arizona SNP Pipeline (NASP), is publically available ...reference SNP identification is to use only the non-redundant core genome sequences to avoid missing data and misuse of paralogous ...
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Immunoblots, antimicrobial resistance, and bacteriophage typing of oxacillin resistant Staphylococcus aureus
... Immunoblotting correlated weli with phage typing, offered an alternative method for typing isolates that could not be typed by phage typing, and was superior to susceptibility testing an[r] ...
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Comparison of restriction endonuclease analysis and phenotypic typing methods for differentiation of Yersinia enterocolitica isolates
... The discriminatory power of the method was compared with H-antigen typing, biotyping, phage typing, antimicrobial susceptibility typing, and restriction enzyme analysis of the virulence [r] ...
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Bacteriophage typing of Shigella sonnei
... Of all the typing methods, bacteriophage typing appears to be the most sensitive; therefore, the purpose of this study was to evaluate phage-typing schemas that others have used and to s[r] ...
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Racial differences in the association of CD14 polymorphisms with serum total IgE levels and allergen skin test reactivity
... C-159T SNP with total serum immunoglobulin E (IgE) levels and ...C-159T SNP in subjects of African ...C-159T SNP and other CD14 SNPs (C1188G, C1341T) were associated with total serum IgE levels and ...
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Performance of Phenotypic and Genotypic Methods To Determine the Clinical Relevance of Serial Blood Isolates ofStaphylococcus epidermidis in Patients with Septicemia
... a typing method must be easy to perform and results must be ...antibiogram typing, PFGE, and AFLP were highly discriminatory and correlated with the epidemiological features, demonstrating the usefulness of ...
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A Novel Test for Detecting SNP–SNP Interactions in Case-Only Trio Studies
... ABSTRACT Epistasis plays a significant role in the genetic architecture of many complex phenotypes in model organisms. To date, there have been very few interactions replicated in human studies due in part to the ...
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Criteria for selecting microhaplotypes: mixture detection and deconvolution
... regenerated although it is clear that certain combina- tions among the more common haplotypes are not seen at the frequencies that might occur if recombination were very frequent. Even a high recombination rate of 1% ...
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SNIT: SNP identification for strain typing
... report SNP loci that can be mapped to the reference ...strain typing, it should be noted that the pipe- line is not intended to provide a comprehensive list of all SNPs among the input ...
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