A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence

Abstract

Background: Diphtheria, caused by Corynebacterium diphtheriae, reemerges in Europe since 2022. Genomic sequencing can inform on transmission routes and genotypes of concern, but currently, no standard approach exists to detect clinically important genomic features and to interpret emergence in the global C. diphtheriae population framework. Methods: We developed the bioinformatics pipeline diphtOscan (available at https://gitlab.pasteur.fr/BEBP/diphtoscan) to extract from genomes of Corynebacteria of the diphtheriae species complex, medically relevant features including tox gene presence and disruption. We analyzed 101 human C. diphtheriae isolates collected in 2022 in metropolitan and overseas France (France-2022). To define the population background of this emergence, we sequenced 379 additional isolates (mainly from France, 2018-2021) and collated 870 publicly-available genomes. Results: The France-2022 isolates comprised 45 tox-positive (44 toxigenic) isolates, mostly imported, belonging to 10 sublineages (<500 distinct core genes). The global dataset comprised 245 sublineages and 33.9% tox-positive genomes, with diphtOscan predicting non-toxigenicity in 16.0% of these. 12% of the global isolates, and 43.6% of France-2022 ones, were multidrug resistant. Convergence of toxigenicity with penicillin and erythromycin resistance was observed in 2 isolates from France-2022. Phylogenetic lineages Gravis and Mitis contrasted strikingly in their pathogenicityassociated genes. Conclusions: This work provides a bioinformatics tool and global population framework to analyze C. diphtheriae genomes, revealing important heterogeneities in virulence and resistance features. Emerging genotypes combining toxigenicity and first-line antimicrobial resistance represent novel threats. Genomic epidemiology studies of C. diphtheriae should be intensified globally to improve understanding of reemergence and spatial spread.

Phenotypic and genomic analysis of a large-scaleCorynebacterium diphtheriaeoutbreak among migrant populations in Europe

“…Our study extends earlier local observations 11,12,27 , and has enabled a thorough analysis of the event at continental scale. The simultaneous expansion of multiple GCs across several reporting countries is consistent with genomic investigations of a previous outbreak 20 .…”

“…The Centers for Disease Control (CDC), the WHO, and guidelines of many European countries recommend either erythromycin or penicillin as first line treatment (https://www.cdc.gov/diphtheria/clinicians.html). Previous studies reported resistance to erythromycin 25,26 , including a recent association with penicillin reduced susceptibility in C. diphtheriae isolates from North and Western Africa 27 .…”

Multidrug-resistant Corynebacterium diphtheriae in people with travel history from West Africa to France, March to September 2023

“…Despite this, the risk of dissemination within high-vaccination countries seems limited. In France in 2023, no secondary cases were reported, as also observed for cases imported from other areas in 2022 [9].…”

“…Gene pbp2m typically confers low-level resistance to penicillin and amoxicillin [8]. In our previous global genomic survey, we reported pbp2m in less than 5% of non-duplicate C. diphtheriae isolates [9]. Here, six of 10 isolates were carrying pbp2m, a remarkable observation given that these isolates belong to ten distinct genomedefined types.…”

“…Three isolates were linked in a single household and had the same genome sequence, only the index case was included in further analysis. The 10 deduplicated isolates were characterised using biovar determination, antimicrobial susceptibility testing (AST) and genomic sequencing (Nextera genomic library and Illumina NextSeq-500 chemistry) as described [8,9]. Methods for AST and interpretation of the results followed the European Committee on Antimicrobial Susceptibility Testing (EUCAST) 2023 recommendations [10] and for some of them Antibiogram Committee of the French Society of Microbiology recommendations [11,12] (Table 2).…”