Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023–2024
- 1Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
- 2Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- 3Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
Abstract
Objectives:: Diphtheria remains endemic in Pakistan, with cases increasing following the COVID-19 pandemic despite ongoing vaccination programs. This study analyzes the genomic diversity, virulence, and antimicrobial resistance patterns of pharyngeal diphtheria strains collected during the Karachi outbreak.
Methods:: Corynebacterium diphtheriae isolates from a tertiary care hospital laboratory in Karachi (August 2023-October 2024) were included. Antimicrobial susceptibility testing and whole-genome sequencing of phenotypically confirmed isolates were performed. Phylogenetic and bioinformatics analyses were performed using diphtOscan and AMRFinderPlus tools.
Results:: A total of 47 pharyngeal C. diphtheriae isolates were included. The median age of patients was 7 years, and the male-to-female ratio was 1.6:1. The tox gene was present in 89.4% of isolates, while only 29% (n = 13/45) demonstrated toxin production. Genomic analysis identified 10 sequence types; ST384 and ST698 were most prevalent. Phenotypically, 34% (n = 16) were resistant to both erythromycin and penicillin, and 49% (n = 23) were multidrug-resistant. The most prevalent resistance genes were sul1 (100%), erm(X) (76.6%), and pbp2m (51.1%).
Conclusion:: Circulation of diverse C. diphtheriae strains with alarming antimicrobial resistance underscores the need for genomic surveillance to evaluate transmission trends. We further highlight the limitations of the Elek test in detecting toxin production and the need for improved diagnostics in low- and middle-income countries.
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BibTeX
@article{khan2026molecular,
title = {{Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023–2024}},
author = {Sobia Muhammad Asad Khan and Seema Irfan and Javaria Ashraf and Hassan Ghayas and Najia Ghanchi and Joveria Farooqi and Kauser Jabeen and Noureen Saeed and Muhammad Naeem and Sadaf Zaka and Egon A. Ozer and Rumina Hasan},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
year = {2026},
month = aug,
doi = {10.1016/j.ijid.2026.109058},
url = {https://doi.org/10.1016/j.ijid.2026.109058},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023–2024
AU - Sobia Muhammad Asad Khan
AU - Seema Irfan
AU - Javaria Ashraf
AU - Hassan Ghayas
AU - Najia Ghanchi
AU - Joveria Farooqi
AU - Kauser Jabeen
AU - Noureen Saeed
AU - Muhammad Naeem
AU - Sadaf Zaka
AU - Egon A. Ozer
AU - Rumina Hasan
PY - 2026
DA - 2026/08/20
JO - International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases
DO - 10.1016/j.ijid.2026.109058
UR - https://doi.org/10.1016/j.ijid.2026.109058
AB - Objectives:: Diphtheria remains endemic in Pakistan, with cases increasing following the COVID-19 pandemic despite ongoing vaccination programs. This study analyzes the genomic diversity, virulence, and antimicrobial resistance patterns of pharyngeal diphtheria strains collected during the Karachi outbreak. Methods:: Corynebacterium diphtheriae isolates from a tertiary care hospital laboratory in Karachi (August 2023-October 2024) were included. Antimicrobial susceptibility testing and whole-genome sequencing of phenotypically confirmed isolates were performed. Phylogenetic and bioinformatics analyses were performed using diphtOscan and AMRFinderPlus tools. Results:: A total of 47 pharyngeal C. diphtheriae isolates were included. The median age of patients was 7 years, and the male-to-female ratio was 1.6:1. The tox gene was present in 89.4% of isolates, while only 29% (n = 13/45) demonstrated toxin production. Genomic analysis identified 10 sequence types; ST384 and ST698 were most prevalent. Phenotypically, 34% (n = 16) were resistant to both erythromycin and penicillin, and 49% (n = 23) were multidrug-resistant. The most prevalent resistance genes were sul1 (100%), erm(X) (76.6%), and pbp2m (51.1%). Conclusion:: Circulation of diverse C. diphtheriae strains with alarming antimicrobial resistance underscores the need for genomic surveillance to evaluate transmission trends. We further highlight the limitations of the Elek test in detecting toxin production and the need for improved diagnostics in low- and middle-income countries.
SN - 1201-9712
SN - 1878-3511
ER -