Spatiotemporal persistence of multiple, diverse clades and toxins of Corynebacterium diphtheriae

Abstract

Diphtheria is a respiratory disease caused by the bacterium Corynebacterium diphtheriae. Although the development of a toxin-based vaccine in the 1930s has allowed a high level of control over the disease, cases have increased in recent years. Here, we describe the genomic variation of 502 C. diphtheriae isolates across 16 countries and territories over 122 years. We generate a core gene phylogeny and determine the presence of antimicrobial resistance genes and variation within the tox gene of 291 tox⁺ isolates. Numerous, highly diverse clusters of C. diphtheriae are observed across the phylogeny, each containing isolates from multiple countries, regions and time of isolation. The number of antimicrobial resistance genes, as well as the breadth of antibiotic resistance, is substantially greater in the last decade than ever before. We identified and analysed 18 tox gene variants, with mutations estimated to be of medium to high structural impact.

Fig. 1. Global and Indian core gene phylogenies of Corynebacterium diphtheriae and tox gene variants by decade.

A Maximum likelihood phylogenetic tree based on the core gene single nucleotide polymorphisms from the 502 global Corynebacterium diphtheriae genome collection. The country of isolation (1), decade of isolation (2), and AMR gene presence/absence heatmap made using ARIBA (3), are all annotated. Most monophyletic groups within the tree represent only one country and decade, with the major exception of the large Belarussian/German dominated group, marked with a blue star. Both the blue and orange stars highlight groups used for BEAST analysis. B The core gene maximum likelihood phylogeny of only the 122 Indian isolates, coloured by state (1) and year of isolation (2). C The proportion of the 18 tox gene variants found across 291 tox⁺ and 211 non-toxigenic isolates per decade, with the number of isolates per decade shown.

Fig. 2. Six non-synonymous mutations plotted onto diphtheria toxin model 1XDT (https://www.rcsb.org/structure/1xdt) from the Protein Data Bank using PHYRE2.

The impact of these mutations is estimated by SuSPect, with a gradient per mutation of low (dark blue) to high (orange/red).

Fig. 3. The antimicrobial resistance (AMR) gene and tox gene variant proportions represented in the 122 Corynebacterium diphtheriae genomes from India at state level.

The number of isolates from the six states sampled are shown in circles on the map. The AMR genes are coloured by the classes of antibiotic the genes offer resistance to. AGly (blue) aminoglycosides, MLS (purple) macrolide–lincosamide–streptogramin, Phe (yellow) phenicols, Sul (green) sulfonamides, Tet (orange) tetracyclines, Tmt (light blue) trimethoprim. The map was taken from Google Maps.