engleski

Genotyping and clonal spread of Clostridioides difficile

Clostridioides difficile (CD) is the leading cause of hospital-associated diarrhea, with a high potential for recurrence (relaps or reinfection) and possess a considerable burden on the healthcare system. Genotyping is essential for hospital outbreak investigations and surveillance of emerging strains and transmission. There are several routine typing technique, including PCR ribotyping, pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem repeat analysis (MLVA) and multilocus sequence typing (MLST). However, none of the listed methods meets all the criteria regarding standardization, reproducibility, discriminatory power, cost and turnaround time (TAT). MLST provide easy-to- obtain, rapid and highly reproducible data, but doesn't provide sufficient discriminatory power to track the transmission. A commonly used typing technique for C. difficile is PCR ribotyping, which can be performed on cultured C. difficile isolates or directly on total fecal DNA. At the begining of the 21st century, hypervirulent RT027 emerged from North America to other regions and today constitutes up to 19% of all clinicaly significant C. difficile strains. RT distribution differs significantly between different countries (RT001, RT014 and RT027 are prevalent strains in North America, Europe and Australia, while RT017 is frequently detected in East Asia). Nowdays, whole-genome sequencing (WGS) is increasingly used as a fingerprinting method. WGW allows precise tracking of transmission and differentiation relapes from CD reinfections, but cost and lack of standardization still limit its broad utilization. Two-step algorithm, with MLST as a first step in routine typing of CD followed by WGS for MLST concordant strains is a less technically demanding and cost-saving, compared with WGS alone. This approach would be most beneficial for routine surveillance in hospital settings where the number of isolates is not significantly high. ESCMID study group proposed similar two-step algorithm for outbreak investigation, with capillary electrophoresis PCR ribotyping as a firt step, followed by WGS or MLVA.

C. difficile

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