Sequencing

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11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting GENETIC CHARACTERIZATION OF STX2 PRODUCING ESCHERICHIA COLI (STEC) ISOLATED IN THE COUNTRY OF GEORGIA Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.01) Tea Tevdoradze, Gvantsa Chanturia, Ekaterine Zhgenti, Giorgi Dzavashvili, Lia Tevzadze National Center for Disease Control and Public Health, Georgia Shiga toxin‐producing Escherichia coli (STEC) infection is among the leading causes of bloody diarrheal disease complicated by hemolytic uremic syndrome (HUS) in the country of Georgia. Since 2009, many human cases of bloody diarrhea in Georgia complicated with HUS have been caused by E. coli strains positive for the Shiga toxin 2 gene (stx2). In this study we characterized three stx2 producing E. coli strains isolated from three patients with HUS (in 2012, 2014, 2015 respectively). In previous studies isolates were characterized by confirmatory STEC (stx1, stx2, eae, ehxA), O104 (stx2, terD, rfbO104, fliC H4) and enteroaggregative (pCVD, AGGR) conventional multiplex PCR assays. STEC strains were genotyped by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Draft whole‐genome sequenc‐ ing (WGS) of isolates was performed using the next‐generation sequencing (NGS) Illumina MiSeq platform. Obtained reads were further analyzed using the CLC Genomics Workbench (CLC Bio) software package. In the present study, WGS‐based SNP phylogenetic analysis was performed using the EDGE bioinformatics software; we also determined the virulence and the resistance genes profiles of three STEC strains based on the Center for Genomic Epidemiology database, Denmark (https://cge.cbs.dtu.dk). Two enteroaggregative 0104: H4 strains that belonged to sequence type ST‐678 revealed a very similar set of virulence and resistance genes. The strain isolated in 2012 contained an additional resistance gene blaCTX‐M‐14 that was not present in the 2015 strain. The third non‐O104 STEC strain ST‐677, which could not be characterized with classical serotyping methods, was identified as E. coli O174:H21. Comparative sequence analysis performed against reference strains in established E. coli databases (https://cge.cbs.dtu.dk) indicated this strain lacked known resistance genes and encoded a limited range of virulence factors. WGS‐based SNP phylogenetic analysis revealed all 0104:H4 strains studied showed close affiliation with historical STEC isolates from Georgia (2009) and German (2011) outbreak strains. The third 0174:H21 isolate, lacking virulence genes, showed more genetic similarity with a single E. coli O152:H28 strain (SE11) isolated in Japan in 2008. 35
11th Annual <strong>Sequencing</strong>, Finishing, and Analysis in the Future Meeting COMPARISON OF 12 FRANCISELLA TULARENSIS WHOLE GENOMES FROM THE COUNTRY OF GEORGIA Wednesday, 1st June 18:30 La Fonda NM Room (1st floor) Poster (PS‐1a.02) Gvantsa Chanturia 1 , Giorgi Dzavashvili 1 , Jason Farlow 2 1 National Center for Disease Control and Public Health, Georgia , 2 Farlow Scientific Consulting Company, LLC The select agent Francisella tularensis is widely spread in the eastern part of Georgia. The National Center for Disease Control and Public Health of Georgia (NCDC) performs active surveillance of this pathogen by seasonal field sampling of vectors and amplifiers at two main foci. A collection of more than one hundred strains of F. tularensis currently exists at the NCDC‐ Lugar Center for Public Health Research. The SNP and MLVA genotyping of archival strains was performed in the scope of previous studies in collaboration with Northern Arizona University (NAU) and Walter Reed Army Institute of Research (WRAIR). Whole genome SNP comparison of one F. tularensis strain from the NCDC collection and another F. tularensis reference genome revealed the Georgian strain as basal for most of the European clades. Country‐specific SNPs were discovered and used for typing and phylogenetic analysis of the rest of the strains. Twelve F. tularensis strains from the NCDC collection were selected for whole genome sequencing at WRAIR and Lugar Center using next generation sequencing platfor Bioinformatics tools available at the Lugar Center including CLC‐Bio and EDGE were used for data processing and phylogenetic analysis. The F. tularensis SCHU S4 and Live Vaccine Strain (LVS) genomes were used for reference read mapping analyses. Close relatives to the Georgian clade reference strains were added from the NCBI database for phylogenetic analysis. Phylogenetic analyses based on new SNPs and InDels among Georgian F. tularensis strains placed these isolates in separate branches that were not previously observed after PCR‐based SNP typing. Whole‐genome‐based SNP analysis allowed the discovery of new diversity patterns inside the previously‐established canonical SNP lineage (B.Br.013). 36
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Reliable solutions for focused NGS
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Sequencing

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