A New SNP-Based Genotyping Method for C. psittaci: Application to Field Samples for Quick Identification

Area of Science:

• Veterinary Microbiology
• Infectious Diseases
• Molecular Diagnostics

Background:

• Chlamydia (C.) psittaci causes avian chlamydiosis and human psittacosis.
• Accurate and rapid genotyping is crucial for understanding transmission and controlling outbreaks.
• Existing methods like whole-genome sequencing and MLST are time-consuming and resource-intensive.

Purpose of the Study:

• To develop a novel, rapid genotyping assay for C. psittaci.
• To identify and characterize major C. psittaci lineages based on whole-genome data.
• To validate the new assay's performance against established genotyping techniques.

Main Methods:

• Whole-genome sequencing of 55 C. psittaci strains to identify single-nucleotide polymorphisms (SNPs).
• Development of a combined PCR/high-resolution melting (HRM) assay targeting eight phylogenetically informative SNPs.
• Validation using 11 reference strains and 118 field isolates, comparing results with ompA/MLST genotyping.

Main Results:

• Eight major, often host-related, C. psittaci lineages were identified.
• The PCR-HRM assay demonstrated high concordance with previous genotyping methods.
• Application to clinical samples identified genotypes linked to common sources (ducks, pigeons) and a novel Mat116-like genotype.

Conclusions:

• The developed PCR-HRM assay provides a rapid, cost-effective alternative for C. psittaci genotyping.
• This method facilitates quick identification of infection sources in both animal and human cases.
• The assay supports efficient epidemiological surveillance and outbreak investigation of C. psittaci.