Culture Collections

NCTC 3000 diversity of bacterial strains

 

NCTC 3000 is an exciting, large scale whole genome sequencing project undertaken in collaboration by Culture Collections (part of Public Health England), the Wellcome Trust Sanger Institute (WTSI) and Pacific Biosciences (Pac Bio). The project involves sequencing the genomes of bacteria which are of global public health importance from the National Collection of Type Cultures (NCTC).

At the end of December 2015, 1070 strains from 27 families had been sequenced. 54% (578) of the strains sequenced were form the Enterobacteriaceae family. Within the last 10 months bacteria from many more families have been included, more closely reflecting the great diversity of bacteria held within the NCTC collection.

Diversity of bacterial strains - December 2015  

27 families sequenced including those listed in the chart below.

 NCTC Diversity Chart 1

 

As of October 2016, nucleic acid of 1901 bacterial strains has been extracted and sent to WTSI for sequencing, including 523 Type strains. The strains come from 613 species representing 66 different bacterial families with 38.6% (719) strains sequenced from Enterobacteriaceae.

In order to widen the diversity of strains there were several challenges to overcome. Firstly, the methods used for inactivating sporulating bacteria were improved for both Bacillus and Clostridium and there are now 15 and 45 strains sequenced of each genus respectively.

Another challenge was the growth of mycoplasmas. Mycoplasma cells are small fastidious, slow-growing bacteria and difficult to detect with a conventional microscope,  yet many of Mycoplasma strains are of clinical importance. 24 species of mycoplasma have now been sequenced.

Diversity of bacterial strains - October 2016

66 families including those listed in the chart below. For the full list of bacterial families click here

NCTC Diversity Chart 2 

The aim now is to provide raw and annotated Pac Bio sequence data for all 900 Type strains as well as the well-defined control strains supplied by NCTC which includes UK SMI controls, EUCAST internal and extend QC controls and the WHO Neisseria gonorrhoea panel of resistant strains. In addition, emerging strains of public health concern and strains of historical significance will be added as the sequences become available. Our next major challenge is the sequencing of a selection of Hazard Group 3 strains as part of a wider project to deliver DNA products for some of the most hazardous bacteria in NCTC.

Keep up to date with our progress with the project on Twitter @NCTC_3000 

 

Related Links

NCTC 300 project

 

November 2016

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