Genomic analysis of endemic clones of toxigenic and non-toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s

Abstract

BackgroundDiphtheria remains a major public health concern with multiple recent outbreaks around the world. Moreover, invasive non-toxigenic strains have emerged globally causing severe infections. A diphtheria epidemic in the former Soviet Union in the 1990s resulted in ~5000 deaths. In this study, we analysed the genome sequences of a collection of 93 C. diphtheriae strains collected during and after this outbreak (1996 – 2014) in a former Soviet State, Belarus to understand the evolutionary dynamics and virulence capacities of these strains.Results C. diphtheriae strains from Belarus belong to ten sequence types (STs). Two major clones, non-toxigenic ST5 and toxigenic ST8, encompassed 76% of the isolates that are associated with sore throat and diphtheria in patients, respectively. Core genomic diversity is limited within outbreak-associated ST8 with relatively higher mutation rates (8.9 × 10−7 substitutions per strain per year) than ST5 (5.6 × 10−7 substitutions per strain per year) where most of the diversity was introduced by recombination. A variation in the virulence gene repertoire including the presence of tox gene is likely responsible for pathogenic differences between different strains. However, strains with similar virulence potential can cause disease in some individuals and remain asymptomatic in others. Eight synonymous single nucleotide polymorphisms were observed between the tox genes of the vaccine strain PW8 and other toxigenic strains of ST8, ST25, ST28, ST41 and non-toxigenic tox gene-bearing (NTTB) ST40 strains. A single nucleotide deletion at position 52 in the tox gene resulted in the frameshift in ST40 isolates, converting them into NTTB strains.ConclusionsNon-toxigenic C. diphtheriae ST5 and toxigenic ST8 strains have been endemic in Belarus both during and after the epidemic in 1990s. A high vaccine coverage has effectively controlled diphtheria in Belarus; however, non-toxigenic strains continue to circulate in the population. Recombination is an important evolutionary force in shaping the genomic diversity in C. diphtheriae. However, the relative role of recombination and mutations in diversification varies between different clones.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4276-3) contains supplementary material, which is available to authorized users.

Genomic analyses reveal two distinct lineages of Corynebacterium ulcerans strains

“…These data do not show any clear variations in the virulence gene repertoire among the strains isolated from patients with disease and asymptomatic carriers. Our previous study showed that the same C. diphtheriae strains can cause diphtheria in some individuals and remain asymptomatic in others [17] .…”

“…Several genes encoding virulence associated proteins such as phospholipase D (Pld), neuraminidase H (NanH), corynebacterial protease (CP40), venom serine protease (Vsp1 and Vsp2), ribosomal-binding protein (Rbp, similar to Shiga-like toxin) and adhesive surface pili are present in different C. ulcerans strains [3] , [9] , [16] . Variations in virulence may depend on the differences in the virulence gene repertoire among individual strains [17] , [18] .…”

Distinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.

“…Despite the relatively large differences in ANI between groups, 16S rRNA gene conservation between all C. diphtheriae strains was above 99% identity, suggesting that the new clade should be classified as part of the C. diphtheriae species (data not shown). Interestingly, CCUG 5865 was recently used by Grosse-Kock et al ( 2017 ) as an outgroup for their core genome phylogeny because it belonged to lineage-2. The multilocus sequence types of CHUV 2995 and CMCNS703 also cluster with lineage-2 (Figure S1 and Data Sheet 3 ).…”

Carriage of a Single Strain of Nontoxigenic Corynebacterium diphtheriae bv. Belfanti ( Corynebacterium belfantii ) in Four Patients with Cystic Fibrosis

“…The MLST genotype of the isolates, ST208, was not reported previously in the C. diphtheriae MLST database and was also never observed previously from another patient in the French national surveillance of C. diphtheriae, suggesting that it is not common. Whole-genome sequencing defines the genetic relatedness among C. diphtheriae isolates with high precision (24)(25)(26). This approach demonstrated that the five isolates belong to the same strain and provided strong support for the hypothesis of cross-transmission among patients and/or contamination from a common source.…”