Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae

Area of Science:

• Microbiology
• Genomics
• Population Genetics

Background:

• Haemophilus influenzae is a common bacterium in the human nose and a significant cause of invasive diseases.
• The genetic diversity of H. influenzae requires advanced methods for population structure analysis.

Purpose of the Study:

• To develop and validate a high-resolution core genome multilocus sequence typing (cgMLST) scheme for H. influenzae.
• To enhance genomic analysis and population structure determination of this important pathogen.

Main Methods:

• Utilized pangenome analysis tools to identify core genes in H. influenzae.
• Developed and validated a cgMLST scheme using complete and draft genomes (N=2297).
• Performed phylogenetic analyses using allelic profiles and core genome sequences.

Main Results:

• A robust cgMLST scheme comprising 1037 core genes was established.
• Over 70% of core genes are involved in essential metabolic or genetic processes.
• The cgMLST allelic profile accurately represents phylogenetic relatedness (R² = 0.945).

Conclusions:

• The developed cgMLST scheme provides a high-resolution tool for analyzing H. influenzae population structure.
• This scheme improves the genomic-based epidemiological surveillance and understanding of H. influenzae.