Hypervariable-Locus Melting Typing: a Novel Approach for More Effective High-Resolution Melting-Based Typing,...

Area of Science:

• Microbiology and Infectious Diseases
• Molecular Epidemiology
• Biotechnology

Background:

• Effective pathogen typing is critical for detecting and controlling high-risk bacterial clones in healthcare settings.
• Current methods like PFGE, MLST, and WGS are often too slow or expensive for real-time surveillance.
• High-resolution melting (HRM) offers a potentially faster and cheaper alternative, but developing discriminatory protocols is challenging.

Purpose of the Study:

• To introduce Hypervariable-Locus Melting Typing (HLMT), a novel HRM-based approach for enhanced pathogen discrimination.
• To evaluate the efficacy of HLMT for typing Klebsiella pneumoniae, a significant nosocomial pathogen.
• To compare HLMT performance against established typing methods including WGS, MLST, PFGE, and wzi gene analysis.

Main Methods:

• Developed and applied a novel HLMT protocol targeting the hypervariable wzi gene in Klebsiella pneumoniae.
• Typed 134 K. pneumoniae strains collected from hospital surveillance programs using HLMT.
• Compared HLMT results (HLMT-assignment and HLMT-clustering) with wzi, MLST, WGS, and PFGE typing data.

Main Results:

• HLMT effectively distinguished most high-risk K. pneumoniae clones, showing sensitivity comparable to PFGE and MLST+wzi.
• Epidemiological surveillance curves generated by HLMT were consistent with those from MLST+wzi, PFGE, and WGS.
• HLMT-assignment results showed 95% consistency with wzi typing, achieving a Jaccard index of 0.9.

Conclusions:

• HLMT is a rapid, scalable, and cost-effective pathogen typing method suitable for real-time microbiological surveillance in hospitals.
• The method's affordability makes it applicable for infection control programs, particularly in low- and middle-income countries.
• HLMT facilitates early detection of outbreaks, thereby enhancing the effectiveness of hospital infection control strategies.