Whole genome sequencing evidences higher rates of relapse in Clostridioides difficile infection caused by PCR ribotype 106

During the last years, an increasing prevalence and widespread of Clostridioides difficile infection (CDI) caused by PCR-ribotype 106 (also identified as restriction endonuclease analysis [REA] group DH) has been observed in Europe and North America. Previous works have documented the higher recurrence rate that this ribotype shows compared to other ribotypes possibly due to its higher ability to produce spores. The present study describes the genetic analysis by whole genome sequencing (WGS) of primary and recurrent isolates of PCR-ribotype 106 from patients with recurrent CDI with the objective to determine if the higher rate of recurrence associated to this ribotype is actually due to relapses (caused by the same strain) or reinfections (caused by different strain). WGS in Illumina Miseq® equipment was performed for ten primaries and fourteen recurrent isolates of PCR-ribotype 106 from ten different patients to determine MLST profile and analyze relatedness between the different isolates by comparative single nucleotide variants (SNV) analysis with reference to the C. difficile DH/NAP11/106/ST-42 genome (GenBank accession: GCA_002234355.1). Paired-ended reads were aligned to the C. difficile DH/NAP11/106/ST-42 reference genome (GenBank accession: GCA_002234355.1). All the isolates were classified as ST42 by the MLST analysis. SNVs comparative showed that strains belonging to the same patient differed by ≤3 SNVs, with one exception (6 SNVs) while strains belonging to different patients differed by 4-43 SNVs, with two exceptions were the isolates between different patients showed ≤2 SNVs of difference, suggesting a possible transmission between them. Recurrent Clostridioides difficile infections caused by PCR-ribotype 106 are mainly due to relapses caused by the primary strain, suggesting that PCR-ribotype 106 has capacity to persist and cause greater number of recurrences than other ribotypes.