Successful management of a Clostridioides difficile ribotype 027 outbreak with a lean intervention bundle

Abstract

Background: In a 2015 point-prevalence study, Clostridioides difficile 027, a hypervirulent ribotype, was absent from healthcare institutions in Switzerland. In late 2016, we detected an outbreak of C. difficile infection (CDI) with ribotype 027 occurring across several hospitals in the same hospital network. Methods: The first cases of CDI due to ribotype 027 triggered an outbreak investigation, including whole genome sequencing (WGS) to identify outbreak strains. Findings: Twenty-eight patients with CDI caused by ribotype 027 between December 2016 and December 2017 were identified, out of which 20 were caused by a single clone. Commonalities among these patients were hospitalization in the same room or on the same ward, receiving care from the same healthcare workers, and shared toilet areas. In addition to the epidemiological links suggesting possible transmission pathways between cases, WGS confirmed the clonality of this C. difficile 027 outbreak. The outbreak was contained by isolation precautions, raising awareness among healthcare workers, harmonizing diagnostic algorithms, and switching to a sporicidal agent for environmental disinfection. Of note, neither default gowning and gloving nor hand washing with water and soap were implemented. Conclusion: This C. difficile 027 outbreak was recognized belatedly due to lack of screening for this ribotype in some hospitals, and was contained by a swift response with simple infection prevention measures and adapting the laboratory approach. In order to have a better understanding of C. difficile epidemiology, diagnostic approaches should be standardized, CDI declared notifiable, and longitudinal data on prevalent ribotypes collected in countries where this is not established.

Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile

“…The genomes tend to cluster in ribotype groups. RT027 (n=44) includes isolates from a previously described outbreak ( Kuenzli et al., 2020 ) and shows a maximum diversity between isolates of 12 allelic differences. Within the RT078/126 cluster (n=49), the maximum diversity between two genomes is nine allelic differences.…”

“…An outbreak of RT027 in Switzerland showed that genomes from one center clustered within three allele differences, well within the ≤6 allele cluster limit (Kuenzli et al, 2020). A SNP tree of the outbreak associated isolates showed more than 100 SNP differences between some of the isolates, and in this case the higher resolution was useful in characterizing the outbreak (Kuenzli et al, 2020). In many cases, RT can be predicted from genome assemblies via cgMLST, but sequenced reference genomes are required for comparison.…”

“…However, cgMLST does not provide the ultimate resolution, and SNP level analysis is preferable for the accurate analysis of suspected transmissions or outbreaks. An outbreak of RT027 in Switzerland showed that genomes from one center clustered within three allele differences, well within the ≤6 allele cluster limit ( Kuenzli et al., 2020 ). A SNP tree of the outbreak associated isolates showed more than 100 SNP differences between some of the isolates, and in this case the higher resolution was useful in characterizing the outbreak ( Kuenzli et al., 2020 ).…”

“…All samples were obtained from our routine laboratory at the University Hospital Basel, and originate from across Switzerland from 2015 to 2020. Additional recently published isolates, sent for PCR ribotyping and/or WGS typing from the Institute of Infectious Diseases at the University of Bern and the Labormedizinisches Zentrum Dr. Risch were included ( Kuenzli et al., 2020 ). All are clinical isolates (n=238), environmental samples taken as swabs from patient rooms (n=39), or isolates from ring trials (n=17).…”

Performance of Core Genome Multilocus Sequence Typing Compared to Capillary-Electrophoresis PCR Ribotyping and SNP Analysis ofClostridioides difficile

“…Nevertheless, we recommend a threshold of 3 alleles to compensate for any assembly artifacts when less conservative pipelines are used and for outbreaks that last longer than 124 days (36).…”