NCTC3000 A Type Culture Reference Genome Project
Author(s): ,
Sarah Alexander
Affiliations:
Public Health England
,
Mohammed Abbas Fazal
Affiliations:
Public Health England
,
Nicholas Grayson
Affiliations:
WTSI
,
Edward Burnett
Affiliations:
Public Health England
,
Ana Deheer-Graham
Affiliations:
Public Health England
,
Julian Parkhill
Affiliations:
WTSI
Julie E. Russell
Affiliations:
Public Health England
PHE ePoster Library. Alexander S. 03/20/18; 205882; 12495
Dr. Sarah Alexander
Dr. Sarah Alexander
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Abstract
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Abstract Background: The National Collection of Type Cultures (NCTC) is the world's longest established bacterial strain collection specifically founded for providing strains to third parties. NCTC, contains over 5200 type and reference strains of medical and veterinary importance. NCTC3000 is a collaborative Whole Genome Sequencing (WGS) project between Public Health England, the Wellcome Trust Sanger Institute and PacBio. This community resource project aims to generate 3000 high quality reference genomes from strains within the collection and make the data publically available to scientists globally via a website which will combine strain metadata and WGS data. Methods: High Molecular weight (HMW) DNA was isolated from 3200 strains using either the Qiagen midi or Epicentre Masterpure extraction kits. DNA quality (>60kb) and quantity (>3 µg) was assessed using the Agilent 2200 TapeStation and Qubit® dsDNA BR Assay Kit respectively. WGS was performed using the PacBio SMRT® Sequencing technology followed by genome assembly and automated annotation with Prokka.Results: HMW DNA was successfully extracted from over 3000 NCTC strains, representing over 800 different bacterial species. To date 90% of the type strains within NCTC have been included in the project. Todate genomes from 1255 strains have been assembled, annotated and are now publically available (http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/). Of the strains with assembled genomes 56.5% have been closed into a single contig and 23.1% have evidence of one or more plasmids in the WGS dataset. A comparative analysis of the Agilent TapeStation electropherogram peaks with the WGS data however, reveals that small plasmids (<10kb) maybe missing from the final WGS data in approximately 10.9% (86/783) of strains analysed. Conclusions: The WGS data generated by the NCTC3000 project represents an important public health resource which can be used to advance the scientific knowledge of these important pathogens. Going forward investigating missing plasmid data will be a priority area.
Abstract Background: The National Collection of Type Cultures (NCTC) is the world's longest established bacterial strain collection specifically founded for providing strains to third parties. NCTC, contains over 5200 type and reference strains of medical and veterinary importance. NCTC3000 is a collaborative Whole Genome Sequencing (WGS) project between Public Health England, the Wellcome Trust Sanger Institute and PacBio. This community resource project aims to generate 3000 high quality reference genomes from strains within the collection and make the data publically available to scientists globally via a website which will combine strain metadata and WGS data. Methods: High Molecular weight (HMW) DNA was isolated from 3200 strains using either the Qiagen midi or Epicentre Masterpure extraction kits. DNA quality (>60kb) and quantity (>3 µg) was assessed using the Agilent 2200 TapeStation and Qubit® dsDNA BR Assay Kit respectively. WGS was performed using the PacBio SMRT® Sequencing technology followed by genome assembly and automated annotation with Prokka.Results: HMW DNA was successfully extracted from over 3000 NCTC strains, representing over 800 different bacterial species. To date 90% of the type strains within NCTC have been included in the project. Todate genomes from 1255 strains have been assembled, annotated and are now publically available (http://www.sanger.ac.uk/resources/downloads/bacteria/nctc/). Of the strains with assembled genomes 56.5% have been closed into a single contig and 23.1% have evidence of one or more plasmids in the WGS dataset. A comparative analysis of the Agilent TapeStation electropherogram peaks with the WGS data however, reveals that small plasmids (<10kb) maybe missing from the final WGS data in approximately 10.9% (86/783) of strains analysed. Conclusions: The WGS data generated by the NCTC3000 project represents an important public health resource which can be used to advance the scientific knowledge of these important pathogens. Going forward investigating missing plasmid data will be a priority area.
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