Whole-genome sequencing reveals nosocomial Clostridioides difficile transmission and a previously unsuspected epidemic scenario

Abstract

To trace the routes and frequencies of transmission of Clostridioides difficile in a tertiary-care hospital in Madrid (Spain), we sequenced the genomes from all C . difficile isolates collected over 36 months (2014–2016) that were indistinguishable from any other isolate by PCR ribotyping. From a total of 589 C . difficile infection cases, we cultivated and PCR-ribotyped 367 C . difficile isolates (62%), of which 265 were genome-sequenced. Based on close relatedness of successively collected isolates (≤2 SNPs difference in their genomes), whole-genome sequencing revealed a total of 17 independent, putative transmission clusters, caused by various C . difficile strains and each containing 2 to 18 cases, none of which had been detected previously by standard epidemiological surveillance. Proportions of linked isolates varied widely among PCR ribotypes, from 3% (1/36) for ribotype 014/020 to 60% (12/20) for ribotype 027, suggesting differential aptitudes for nosocomial spread. Remarkably, only a minority (17%) of transmission recipients had direct ward contact to their presumed donors and specific C . difficile genome types frequently went undetectable for several months before re-emerging later, suggesting reservoirs for the pathogen outside of symptomatic patients. Taken together, our analysis based on genome sequencing suggested considerable within-hospital epidemic spread of C . difficile , even though epidemiological data initially had been inconspicuous.

A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics

“…These included 176 isolates from four patients with recurring CDI ( C. difficile infection), 63 isolates from four transmission chains in multiple hospitals [14, 19, 26], and a comprehensive sample of 1158 isolates collected over several years in four hospitals in Oxfordshire, UK [13]. A strong linear relationship (R 2 , 0.71–0.93) was found in all three analyses between the pairwise differences in cgMLST alleles and non-recombinant SNPs (Fig.…”

“…Indeed, some of the outbreaks investigated here did consist of more than one HC2 cluster (). For example, nine isolates from a recently reported ribotype 018 (RT018) outbreak in Germany [26] encompassed four related HC2 clusters, and outbreaks with RT027 and RT106 in a hospital in Spain [14] were each affiliated with two or three HC2 clusters ().…”

“…Neighbour-joining trees based on cgMLST showing the phylogenetic relationships among C. difficile isolates from previously published CDI outbreaks as indicated [14, 19, 26]. Nodes are coloured by HC2.…”

“…difficile isolates of the same HC2 cluster (). For patients such as P1 and P2 where the shared ward contacts were separated in time (), transmission may have occurred indirectly through asymptomatically colonized patients or from a common reservoir, such as environmental spore contamination [14, 31, 32]. We also detected 15 HC2 clusters that included isolates from two or more hospitals in the region.…”

“…Previously, genotyping was commonly performed by PCR ribotyping or DNA macrorestriction. More recent publications have documented that genome-wide single-nucleotide polymorphisms (SNPs) from whole-genome sequences provide improved discrimination, and such analyses have enabled dramatic progress in our understanding of the emergence and spread of epidemic strains [9–12] and the epidemiology of local transmission [13, 14]. Eyre and colleagues have argued that transmission of C.…”