Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023-2024.

Sobia Muhammad Asad Khan; Seema Irfan; Javaria Ashraf; Hassan Ghayas; Najia Ghanchi; Joveria Farooqi; Kauser Jabeen; Noureen Saeed; Muhammad Naeem; Sadaf Zaka; Egon A Ozer; Rumina Hasan

doi:10.1016/j.ijid.2026.109058

PubMed · 42624284

Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023-2024.

Sobia Muhammad Asad Khan·Seema Irfan·Javaria Ashraf·Hassan Ghayas·Najia Ghanchi·Joveria Farooqi·Kauser Jabeen·Noureen Saeed·Muhammad Naeem·Sadaf Zaka·Egon A Ozer·Rumina Hasan

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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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Sobia Muhammad Asad Khan, Seema Irfan, Javaria Ashraf, Hassan Ghayas, Najia Ghanchi, Joveria Farooqi, Kauser Jabeen, Noureen Saeed, Muhammad Naeem, Sadaf Zaka, Egon A Ozer, Rumina Hasan. 2026-08-20. Molecular epidemiology and antimicrobial resistance determinants of Corynebacterium diphtheriae causing infections in Karachi, Pakistan, 2023-2024.. https://doi.org/10.1016/j.ijid.2026.109058

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