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Early identification of a ward-based outbreak of Clostridioides difficile using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance

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journal contribution
posted on 2024-09-09, 23:59 authored by Max Bloomfield, Samantha Hutton, Megan Burton, Claire Tarring, Charles Velasco, Carolyn Clissold, Michelle Balm, Matthew Kelly, Donia Macartney-Coxson, Rhys White

Objective: To describe an outbreak of sequence type (ST)2 Clostridioides difficile infection (CDI) detected by a recently implemented multilocus sequence type (MLST)-based prospective genomic surveillance system using Oxford Nanopore Technologies (ONT) sequencing.

Setting: Hemato-oncology ward of a public tertiary referral centre.

Methods: From February 2022, we began prospectively sequencing all C. difficile isolated from inpatients at our institution on the ONT MinION device, with the output being an MLST. Bed-movement data are used to construct real-time ST-specific incidence charts based on ward exposures over the preceding three months.

Results: Between February and October 2022, 76 of 118 (64.4%) CDI cases were successfully sequenced. There was wide ST variation across cases and the hospital, with only four different STs being seen in >4 patients. A clear predominance of ST2 CDI cases emerged among patients with exposure to our hemato-oncology ward between May and October 2022, which totalled ten patients. There was no detectable rise in overall CDI incidence for the ward or hospital due to the outbreak. Following a change in cleaning product to an accelerated hydrogen peroxide wipe and several other interventions, no further outbreak-associated ST2 cases were detected. A retrospective phylogenetic analysis using original sequence data showed clustering of the suspected outbreak cases, with the exception of two cases that were retrospectively excluded from the outbreak.

Conclusions: Prospective genomic surveillance of C. difficile using ONT sequencing permitted the identification of an outbreak of ST2 CDI that would have otherwise gone undetected.

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Submitter

Salila Bryant