Lecture's guest Feb_10_2012_Sequence_Based_typing_of_Legionella_spp

Allow comparison over a long period of time

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Unformatted text preview: ison between different laboratories (ex: travel associated outbreak). • Allow comparison over a long period of time (retrospective analysis). • Sharable: For Legionella a regularly implemented web database is available University of Toronto, February 10, 2012 Toronto, SBT Typing Principle • Sequencing of 7 genes: asd, flaA, mip, momps, pilE, proA and neuA. = • Predetermined order of loci. • Each allele is assigned a specific number ST25 = 4,7,11,3,11,12,1. • For a new allele, 0 is assigned and a new allele will be added to a database. University of Toronto, February 10, 2012 Toronto, SBT typing protocol Lp1 DNA extractor Purified DNA PCR Electrophoresis Web database 4, 3 , 1, 1 , 7, 12, 7, 6 Sequence type DNA sequencer Quality assesment DNA sequence University of Toronto, February 10, 2012 Toronto, SBT Quality Report Quality Report for the Consensus sequence and the trimmed sequence http://www.hpa-bioinformatics.org.uk/legionella/legionella_sbt/php/sbt_homepage.php Sequence data are aligned and trimmed using EWGLI Sequence Legionella SBT Quality Assessment system (Phred). Legionella University of Toronto, February 10, 2012 Toronto, Data mining using EWGLI web-database Data Queries based on: - Sequence type - Allele combination - Serogroup - Location (Countries) http://www.hpa-bioinformatics.org.uk/legionella/legionella_sbt/php/sbt_homepage.php bioinformatics.org.uk/legionella/legionella_sbt/php/sbt_homepage Retrieve data from previously reported isolates matching the Sequence Type of the query University of Toronto, February 10, 2012 Toronto, Data mining using EWGLI Web-database Data Result page of the queries provides: Sequence type (ST), serogroup, Result serogroup Isolation date, source, town, country and investigation context. University of Toronto, February 10, 2012 University Toronto, Epidemiological investigations using Sequence Based Typing using Problematic: - In 2007, 67 specimens from Public Health Unit 32 Problematic: In (Southern Ontario). Diagnosis: Diagnosis: Question: Question: - Five cases of Legionellosis over 2 months. Outbreak or isolated cases? Outbreak Ontario Public Health laboratories received 3 isolates. SBT ST109 ST109 SBT ST222 ST222 ST232 ST232 Sequence based typing...
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