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

Increasing prevalence and widespread of Clostridioides difficile infection (CDI) caused by the epidemic DH/NAP11/106/ST-42 has been observed worldwide, probably fostered by its great capacity to produce spores or the higher resistance rates found in some strains. Previous studies have also attributed higher recurrence rates to RT106 as compared to others. This study describes the genetic analysis by whole genome sequencing (WGS) of primary and recurrent isolates of RT106 to determine if the higher rate of recurrence associated to RT106 is due to relapses, caused by the same strain, or reinfections, caused by different strains. The whole-genome sequences of ten primaries and fourteen recurrent RT106 isolates from ten patients were obtained to determine MLST profiles, resistance mutations and phylogenetic relatedness between the different isolates by comparative single nucleotide variants (SNV) analysis using the C. difficile DH/NAP11/106/ST-42 genome as reference (GenBank accession: GCA_002234355.1). All isolates were classified as ST42 and SNVs comparative analysis showed that those belonging to the same patient were isogenic (differed by [≤]3 SNVs), with one exception (6 SNVs); while strains belonging to different patients were not (differing by 4 to 43 SNVs) with two exceptions of isogenic isolates from different patients, suggesting putative transmission events. Phylogenetic analysis suggested the presence of similar local epidemic lineages, except for one patient whose isolates clustered with different US isolates. All the isolates, except those clustering with the US lineage, were also associated to moxifloxacin resistant since all of them were resistant by agar diffusion (MIC >32) and contained the Thr82Ile mutation in gyrA. Our results evidence that recurrent Clostridioides difficile infections caused by RT06/ST42 are mainly due to relapses, caused by primary strains, showing the great capacity of RT106/ST42 to persist and cause recurrences as compared to other ribotypes.