DIPHTOSCAN : A new tool for the genomic surveillance of diphtheria
A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence
Recommendation: posted 07 August 2023, validated 08 August 2023
García-Contreras, R. (2023) DIPHTOSCAN : A new tool for the genomic surveillance of diphtheria. Peer Community In Infections, 100080. 10.24072/pci.infections.100080
One of the greatest achievements of health sciences is the eradication of infectious diseases such as smallpox that in the past imposed a severe burden on humankind, through global vaccination campaigns. Moreover, progress towards the eradication of others such as poliomyelitis, dracunculiasis, and yaws is being made.
In contrast, other infections that were previously contained are reemerging, due to several factors, including lack of access to vaccines due to geopolitical reasons, the rise of anti-vaccine movements, and the constant mobility of infected persons from the endemic sites.
One of such disease is diphtheria, caused by Corynebacterium diphtheriae and a few other related species such as C. ulcerans and C. pseudotuberculosis. Importantly, in France, diphtheria cases reported in 2022 increased 7-fold from the average of previously recorded cases per year in the previous 4 years and the situation in other European countries is similar.
Hence, as reported here, Hennart et al. (2023) developed DIPHTOSCAN, a free access bioinformatics tool with user-friendly interphase, aimed to easily identify, extract and interpret important genomic features such as the sublineage of the strain, the presence of the tox gene (as a string predictor for toxigenic disease) as well as genes coding other virulence factors such as fimbriae, and the presence of know resistant mechanisms towards antibiotics like penicillin and erythromycin currently used in the clinic to treat this infection.
The authors validated the performance of their tool with a large collection of genomes, including those obtained from the isolates of the 2022 outbreak in France, more than 1,200 other genomes isolated from France, Algeria, and Yemen, and more than 500 genomes from several countries from Europe, America, Africa, Asia, and Oceania that are available through the NCBI site.
DIPHTOSCAN will allow the rapid identification and surveillance of potentially dangerous strains such as those being tox-positive isolates and resistant to multiple drugs and/or first-line treatments and a better understanding of the epidemiology and evolution of this important reemerging disease.
Hennart M., Crestani C., Bridel S., Armatys N., Brémont S., Carmi-Leroy A., Landier A., Passet V., Fonteneau L., Vaux S., Toubiana J., Badell E. and Brisse S. (2023). A global Corynebacterium diphtheriae genomic framework sheds light on current diphtheria reemergence. bioRxiv, 2023.02.20.529124, ver 3 peer-reviewed and recommended by PCI Infections. https://doi.org/10.1101/2023.02.20.529124
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
MH was supported financially by the PhD grant “Codes4strains” from the European Joint Programme One Health, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 773830. This work used the computational and storage services provided by the IT department at Institut Pasteur. The National Reference Center for Corynebacteria of the Diphtheriae Complex is supported financially by the Ministry of Health (Public Health France) and Institut Pasteur.
Reviewed by Ankur Mutreja , 26 Jul 2023
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2023.02.20.529124
Version of the preprint: 2
Author's Reply, 07 Jul 2023
Decision by Rodolfo García-Contreras, posted 22 Jun 2023, validated 23 Jun 2023
Dear authors, based on 2 independent reviews and in my own opinion your preprint is interesting and has merits, nevertheless, there are some issues you must fix in order to make it suitable for being recommended.