Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study

Edgar Badell (1, 2) , Abdulilah Alharazi (3) , Alexis Criscuolo (4) , Khaled Abdullah Ali Almoayed (5) , Noémie Lefrancq (6) , Valérie Bouchez (1) , Julien Guglielmini (4) , Melanie Hennart (1, 7) , Annick Carmi-Leroy (1, 2) , Nora Zidane (1) , Marine Pascal-Perrigault (1) , Manon Lebreton (1) , Helena Martini (8) , Henrik Salje (6, 9) , Julie Toubiana (1, 2, 10) , Fekri Dureab (11) , Ghulam Dhabaan (12, 13) , Sylvain Brisse (1, 2) , Ncphl Diphtheria Outbreak Working Group

1 Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens
2 CNR - Centre national de Référence des Corynebactéries du Complexe Diphtheriae - National Reference Center Corynebacteria of the diphtheriae complex
3 National Centre of the Public Health Laboratories [Sana'a, Yemen]
4 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
5 Ministry of Public Health and Population [Sana'a, Yemen]
6 Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases
7 Collège Doctoral
8 VUB - Vrije Universiteit Brussel
9 CAM - University of Cambridge [UK]
10 CHU Necker - Enfants Malades [AP-HP]
11 Akkon University of Human Sciences - Akkon Hochschule für Humanwissenschaften [Berlin, Allemagne]
12 Universität Heidelberg [Heidelberg] = Heidelberg University
13 University of Toronto

An outbreak of diphtheria, declared in Yemen in October, 2017, is ongoing. We did a cross-sectional study to investigate the epidemiological, clinical, and microbiological features of the outbreak. Probable cases of diphtheria that were defined clinically and recorded through a weekly electronic diseases early warning system (from 2017, week 22, to 2020, week 17) were used to identify trends of the outbreak (we divided the epidemic into three time periods: May 29, 2017, to June 10, 2018; June 11, 2018, to June 3, 2019; and June 4, 2019, to April 26, 2020). We used the line list of diphtheria reports for governorate-level descriptions. Vaccination coverage was estimated using the 2017 and 2018 annual reports by the national Expanded Programme on Immunization. To confirm cases biologically, Corynebacterium diphtheriae was isolated and identified from throat swabs using standard microbiological culture and identification procedures. We assessed differences in the temporal and geographical distributions of cases, including between different age groups. For in-depth microbiological analysis, tox gene and species-specific rpoB real-time PCR, Illumina genomic sequencing, antimicrobial susceptibility analysis (disk diffusion, E-test), and the Elek diphtheria toxin production test were done on confirmed cases. We used genomic data for phylogenetic analyses and to estimate the nucleotide substitution rate.

Domains: Life Sciences [q-bio]

Edgar Badell, Abdulilah Alharazi, Alexis Criscuolo, Khaled Abdullah Ali Almoayed, Noémie Lefrancq, et al.. Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study. The Lancet Microbe, 2021, ⟨10.1016/s2666-5247(21)00094-x⟩. ⟨pasteur-03239537⟩