Early identification of a ward-based outbreak of using prospective multilocus sequence type-based Oxford Nanopore genomic surveillance.
Max Bloomfield, Samantha Hutton, Megan Burton, Claire Tarring, Charles Velasco, Carolyn Clissold, Michelle Balm, Matthew Kelly, Donia Macartney-Coxson, Rhys White
Author Information
Max Bloomfield: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand. ORCID
Samantha Hutton: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand.
Megan Burton: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand.
Claire Tarring: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand.
Charles Velasco: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand.
Carolyn Clissold: Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand.
Michelle Balm: Awanui Labs Wellington, Department of Microbiology and Molecular Pathology, Wellington, New Zealand.
Matthew Kelly: Te Whatu Ora/Health New Zealand, Infection Prevention and Control, Capital, Coast and Hutt Valley, Wellington, New Zealand.
Donia Macartney-Coxson: Institute of Environmental Science and Research, Health Group, Porirua, New Zealand. ORCID
Rhys White: Institute of Environmental Science and Research, Health Group, Porirua, New Zealand. ORCID
OBJECTIVE: To describe an outbreak of sequence type (ST)2 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 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 using ONT sequencing permitted the identification of an outbreak of ST2 CDI that would have otherwise gone undetected.
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