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J Bacteriol. 2012 September; 194(17): 4738.
PMCID: PMC3415510

Draft Genome Sequence of Corynebacterium diphtheriae Biovar Intermedius NCTC 5011


We report an annotated draft genome of the human pathogen Corynebacterium diphtheriae bv. intermedius NCTC 5011. This strain is the first C. diphtheriae bv. intermedius strain to be sequenced, and our results provide a useful comparison to the other primary disease-causing biovars, C. diphtheriae bv. gravis and C. diphtheriae bv. mitis. The sequence has been deposited at DDBJ/EMBL/GenBank with the accession number AJVH01000000.


Prior to the introduction of mass vaccination in the United Kingdom, Corynebacterium diphtheriae, which is the etiological agent of diphtheria, was a major cause of human disease, with more than 50,000 cases per year (6). The main mechanism of virulence is through the bacteriophage-carried diphtheria toxin (1). Currently, there are four recognized biovars, C. diphtheriae bv. gravis, C. diphtheriae bv. mitis, C. diphtheriae bv. intermedius, and C. diphtheriae bv. belfanti, based on biochemical and morphogenic properties (3, 5). The molecular basis for these differences is not well defined and requires further investigation. To address this, we have sequenced the whole genome of C. diphtheriae bv. intermedius NCTC 5011, a strain deposited in the culture collection prior to the introduction of mass vaccination in the United Kingdom and therefore not subject to the evolutionary selective pressure of vaccination.

Sequencing of the C. diphtheriae bv. intermedius strain NCTC 5011 whole genome was performed using whole-genome shotgun sequencing on a Roche GS-Junior 454 apparatus at the University of Strathclyde. The reads were assembled using the GS de novo Assembler (Roche), which led to a final assembly of 34 contigs of >300 bp. The total size of the assembly was 2.38 Mbp, with a mean contig size of 70 kbp (average of 31-fold coverage) and a G+C content of 53.6%. Contigs were reordered onto the C. diphtheriae bv. gravis NCTC 13129 reference genome (1) by using the Mauve program (4) and were annotated using the Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) at NCBI and xbase (2).

The whole genome of C. diphtheriae bv. intermedius NCTC 5011 is estimated to have a total of 2,318 coding sequences (CDS). The genome differs from C. diphtheriae bv. gravis by 108 kb. Analysis using mGenomesubstractor (8) indicated that 2,050 CDS were present in both strains, with 104 CDS being present in C. diphtheriae bv. intermedius NCTC 5011 that were not present in C. diphtheriae bv. gravis NCTC 13129. The majority of C. diphtheriae bv. intermedius-specific sequences were transposons and restriction-modification systems (type I and type III); additionally, the presence of short repeat regions is suggestive of cas/CRISPR systems, indicating that genomic plasticity and barriers to lateral gene transfer may be responsible for the majority of differences observed between C. diphtheriae biovars.

The genome sequence of C. diphtheriae bv. intermedius advances our understanding of the genome and population structure of C. diphtheriae and adds to data relating to other recent C. diphtheriae sequencing efforts (7, 9).

Nucleotide sequence accession numbers.

The results of this C. diphtheriae bv. intermedius (NCTC 5011) annotated genome project have been deposited at DDBJ/EMBL/GenBank under accession number AJVH00000000. The version described in this paper is the first version, AJVH01000000.


The P.A.H. laboratory is supported by Medical Research Scotland (grant 422 FRG) and the University of Strathclyde. A.B. is supported by the Deutsche Forschungsgemeinschaft (SFB796, B5).


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