Stylized DNA strand interwoven with Rio de Janeiro skyline and microscopic bacteria.

Decoding Diphtheria: How Genomic Analysis Helps Us Understand This Threat

Jordan Keane in Science & Nature August 2025 • 3 min read.

"A deep dive into a nontoxigenic strain of Corynebacterium diphtheriae and its implications for public health."

Diphtheria, caused by Corynebacterium diphtheriae, remains a significant public health concern despite widespread immunization programs. While toxigenic strains are well-known, nontoxigenic strains are increasingly recognized for their ability to cause severe invasive infections, such as endocarditis and septic arthritis. These infections are not preventable by traditional vaccines, necessitating a deeper understanding of their genomic characteristics.

Recent outbreaks have highlighted the escalating genomic diversity of C. diphtheriae, emphasizing the need to investigate the plasticity and virulence determinants of these strains. This has prompted researchers to explore the genetic makeup of nontoxigenic strains to identify potential factors contributing to their pathogenicity.

A recent study focused on the genomic sequencing, annotation, and analysis of HC07, a nontoxigenic, invasive C. diphtheriae strain isolated from a patient with endocarditis in Rio de Janeiro, Brazil. This research aims to shed light on the genetic underpinnings that enable these strains to cause severe infections.

Unveiling the Genomic Landscape of HC07

Stylized DNA strand interwoven with Rio de Janeiro skyline and microscopic bacteria.

The HC07 strain, belonging to biotype gravis, was isolated in 2013 and identified through conventional microbiological methods and the API Coryne System. The strain was confirmed to be nontoxigenic via the modified Elek test and Vero cell cytotoxicity assay. Multilocus sequence typing (MLST) revealed that HC07 corresponds to sequence type ST-171, further classifying its genetic profile.

Genomic sequencing of HC07 was performed using an Illumina HiSeq 2500 sequencer, generating a high coverage of the genome. The sequence data was assembled using the A5-miseq pipeline, followed by gene prediction and annotation through the National Center for Biotechnology Information (NCBI) Prokaryotic Genomes Automatic Annotation Pipeline. This comprehensive approach provided a detailed map of the HC07 genome, revealing key insights into its genetic composition.

Key genomic features identified include:

Total genome size: 2,491,635 bp
GC content: 53.53%
Number of genes: 2,333
rRNAs: 6 (5S, 16S, 23S) and tRNAs: 51

Phylogenetic analysis, based on concatenated MLST genes, demonstrated that HC07 clusters closely with other nontoxigenic strains, such as HC03 and HC04, isolated from endocarditis patients in Rio de Janeiro. These strains, despite being isolated at different times, share a close genetic relationship, suggesting a persistent lineage in the region. Whole-genome-based phylogeny further supported this close relationship, corroborating previous findings that biovar classification does not always align with the phylogenetic relationships of C. diphtheriae.

Implications for Public Health and Future Research

The genomic analysis of HC07 provides valuable insights into the diversity and plasticity of nontoxigenic C. diphtheriae strains. The presence of specific virulence factors, a unique prophage, and various genomic islands highlights the complex genetic adaptations that contribute to the bacterium's pathogenicity. Further research is needed to fully understand the mechanisms driving the evolution and persistence of these strains and their implications for public health. Continued genomic surveillance and analysis will be crucial in developing effective strategies to combat infections caused by nontoxigenic C. diphtheriae.

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This article is based on research published under:

DOI-LINK: 10.1590/0074-02760150250, Alternate LINK

Title: Genomic Analysis Of A Nontoxigenic, Invasive Corynebacterium Diphtheriae Strain From Brazil

Subject: Microbiology (medical)

Journal: Memórias do Instituto Oswaldo Cruz

Publisher: FapUNIFESP (SciELO)

Authors: Fernando Encinas, Michel A Marin, Juliana N Ramos, Verônica V Vieira, Ana Luiza Mattos-Guaraldi, Ana Carolina P Vicente

Published: 2015-09-01

Everything You Need To Know

What is Corynebacterium diphtheriae, and why are both toxigenic and nontoxigenic strains important to understand?

Corynebacterium diphtheriae is a bacterium that causes Diphtheria. While toxigenic strains are traditionally associated with the disease, nontoxigenic strains are increasingly recognized for causing severe invasive infections like endocarditis. Understanding both types is crucial for public health.

How was the HC07 strain confirmed to be nontoxigenic, and what further classification methods were used?

The HC07 strain was identified as nontoxigenic through the modified Elek test and Vero cell cytotoxicity assay. These tests confirmed that the strain does not produce the diphtheria toxin, which is a key virulence factor in toxigenic strains. Further classification was achieved through Multilocus sequence typing (MLST), which assigned HC07 to sequence type ST-171.

Can you elaborate on the genomic sequencing process used for the HC07 strain, including the specific tools and pipelines?

Genomic sequencing of the HC07 strain involved using the Illumina HiSeq 2500 sequencer to generate a high coverage of the genome. The sequence data was assembled using the A5-miseq pipeline, followed by gene prediction and annotation through the National Center for Biotechnology Information (NCBI) Prokaryotic Genomes Automatic Annotation Pipeline. This comprehensive approach provided a detailed genetic map.

What did the phylogenetic analysis reveal about the HC07 strain's relationship to other strains, and what implications does this have for understanding the spread of C. diphtheriae?

Phylogenetic analysis of HC07, based on concatenated MLST genes, showed that it clusters closely with other nontoxigenic strains like HC03 and HC04, which were also isolated from endocarditis patients in Rio de Janeiro. This close genetic relationship suggests a persistent lineage in that geographic region. Whole-genome-based phylogeny further supported this finding, reinforcing that biovar classification does not always correlate with the phylogenetic relationships of C. diphtheriae strains.

Why is the genomic analysis of the HC07 strain important for public health, and what future research directions are recommended based on these findings?

The genomic analysis of HC07 is vital for understanding the diversity, plasticity, and pathogenicity of nontoxigenic C. diphtheriae strains. Identifying virulence factors, unique prophages, and genomic islands helps in understanding how these strains cause severe infections. Continued genomic surveillance and analysis are essential for developing strategies to combat infections caused by these strains, especially since traditional vaccines do not protect against them.