Molecular Characterization of Corynebacterium diphtheriae Outbreak Isolates, South Africa, March-June 2015

Abstract

In 2015, a cluster of respiratory diphtheria cases was reported from KwaZulu-Natal Province in South Africa. By using whole-genome analysis, we characterized 21 Corynebacterium diphtheriae isolates collected from 20 patients and contacts during the outbreak (1 patient was infected with 2 variants of C. diphtheriae). In addition, we included 1 cutaneous isolate, 2 endocarditis isolates, and 2 archived clinical isolates (ca. 1980) for comparison. Two novel lineages were identified, namely, toxigenic sequence type (ST) ST-378 (n = 17) and nontoxigenic ST-395 (n = 3). One archived isolate and the cutaneous isolate were ST-395, suggesting ongoing circulation of this lineage for >30 years. The absence of preexisting molecular sequence data limits drawing conclusions pertaining to the origin of these strains; however, these findings provide baseline genotypic data for future cases and outbreaks. Neither ST has been reported in any other country; this ST appears to be endemic only in South Africa.

Keywords: CRISPR; Corynebacterium diphtheriae; MLST; South Africa; bacteria; cutaneous diphtheria; diphtheria; molecular epidemiology; outbreak; respiratory diphtheria; respiratory infections; sequence type; whole-genome sequencing.

Figure 1

Global population snapshot of Corynebacterium diphtheriae sequence types. eBURST (http://eburst.mlst.net/) was used to display the C. diphtheriae isolates (n = 616) available in the PubMLST database (http://pubmlst.org/cdiphtheriae/) at the time of analysis (accessed June 13, 2017). Isolates from South Africa (n = 25) are green. The size of each circle is proportional to the number of isolates, and related sequence types are connected by lines. Blue and yellow circles indicate founding and subfounding genotypes, respectively.

Figure 2

Phylogenetic analysis of Corynebacterium diphtheriae isolates based on sequence type, KwaZulu-Natal Province, South Africa, March–June 2015. Maximum likelihood phylogenetic tree demonstrating core-genome phylogeny among isolates from South Africa (n = 25) relative to selected genomes (publicly available from GenBank) from other countries. Scale bar indicates nucleotide substitutions per site. ST, sequence type.