Leveraging Pathogen Genomics for Enhanced Diphtheria Outbreak Response: The Kano Experience with KNCDC

Abstract

The recent diphtheria outbreak in Kano, which accounted for over 85% of Nigeria’s burden, brought to light the transformative role of pathogen genomics in epidemic preparedness and response. The Kano State Nigeria Centre for Disease Control (KNCDC)—Nigeria’s only subnational CDC—led a coordinated and genomically informed response that significantly enhanced outbreak control efforts.

Through the deployment of Next-Generation Sequencing (NGS) and Real-Time Polymerase Chain Reaction (RT-PCR), KNCDC rapidly identified the circulating Corynebacterium diphtheriae strain. Genomic analysis confirmed the presence of toxigenic strains harboring the tox gene responsible for diphtheria toxin production, which is the primary virulence factor in clinical disease. This enabled targeted case management, antimicrobial stewardship, and focused public health interventions.

Genomic surveillance offered real-time insights into transmission chains, single nucleotide polymorphism (SNP) variations, and possible introductions from outside the state. This level of resolution improved understanding of outbreak dynamics and guided evidence-based decision-making that led to the control of the outbreak in Kano.

A key component of this success was the collaboration between KNCDC and the Genomics Laboratory of the Kano Independent Research Centre Trust (KIRCT). This partnership ensured rapid sequencing turnaround, high-quality bioinformatics analysis, and capacity building for local scientists as well as shortened time of response. In collaboration with global partners, we also informed strategic deployment of the pentavalent vaccine, using genomic data to support immunization planning.

The Kano outbreak response underscores the value of embedding genomics and microbiological studies into public health. Despite infrastructure challenges, our approach improved surveillance, outbreak tracking, and response coordination. KNCDC is committed to scaling genomics capabilities and strengthening partnerships to support early detection and control of infectious diseases in northern Nigeria.