Healthcare-Associated Infections - Community Interface Activity (HAIC) Laboratory Testing: Transitioning from PCR-ribotyping to whole genome sequencing-based analysis for the molecular characterization of Clostridioides difficile isolates

CDC's Emerging Infections Program (EIP) Healthcare-Associated Infections - Community Interface Activity (HAIC) engages a network of state health departments and their academic medical center partners to help answer critical questions about healthcare-associated infection (HAI) threats, including Clostridioides difficile - a leading cause of healthcare-associated infection in the United States. The EIP HAIC C. difficile infection (CDI) surveillance program was launched in 2009 in 7 EIP sites. Since 2011, EIP HAIC CDI surveillance has operated in selected counties in 10 EIP sites across the United States. Data from the EIP HAIC network are used to measure the burden of infections in the population, characterize pathogen strains associated with disease, and monitor trends in disease over time. Explore the frequency and incidence of CDI in ten EIP sites.

As the molecular epidemiology of C. difficile continues to evolve¹, monitoring temporal strain dynamics remains important. For many years, use of capillary-based polymerase-chain-reaction ribotyping (PCR-ribotyping)² has been the preferred method for C. difficile strain typing; however, this method poses challenges for inter-laboratory comparisons. In contrast, sequence-based typing approaches allow laboratories to generate data that can be analyzed and compared using a standardized database. However, a crosswalk between PCR-ribotyping and sequence-based typing is necessary to provide backwards compatibility for assessing trends in historical ribotype (RT) data.

The CDC has performed an evaluation of the concordance between PCR-ribotyping and whole genome sequencing (WGS)-based typing methods using a convenience sample of C. difficile isolates that were submitted to CDC through the EIP. C. difficile isolates representing common RTs observed from previous EIP surveillance years were characterized by PCR-ribotyping and WGS analysis, including multi-locus sequence typing (MLST) based on the alleles of 7 housekeeping genes (Clostridioides difficile | PubMLST). The MLSTs (STs) and their associated RTs for the top five STs collected during 2018-2020 are provided in Table 1. While two STs (ST8 and ST34) corresponded to a single RT, the remaining STs contained multiple or overlapping RTs. Therefore, MLST data alone does not provide a one-to-one translation between ST and RTs, making comparisons to historical trends challenging. This crosswalk represents a tool to assist with the transition to WGS-based isolate typing, but higher resolution genomic analyses are necessary to further discriminate between overlapping RTs. This crosswalk will be updated as new STs are added.

*Isolates with ribotype profiles that did not match strains in the CDC's reference collection were assigned an internal identifier starting with the letter A (e.g. A27, A30, and A75).