Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant in a neonatal intensive care unit using nanopore sequencing.

Outbreaks of methicillin-resistant (MRSA) are well described in the neonatal intensive care unit (NICU) setting. Genomics has revolutionized the investigation of such outbreaks; however, to date, this has largely been completed retrospectively and has typically relied on short-read platforms. In 2022, our laboratory established a prospective genomic surveillance system using Oxford Nanopore Technologies sequencing for rapid outbreak detection.

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

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.

Outbreak of variant hand-foot-and-mouth disease caused by coxsackievirus A6 in Auckland, New Zealand.

Hand-foot-and-mouth disease is a common, usually mild childhood illness caused by enteroviruses. Over the last five years, coxsackievirus A6 has been identified as a causative agent in outbreaks in Europe, South-East Asia and America. It has an atypical presentation compared with other enteroviruses, with more widespread rash, larger blisters and subsequent skin peeling and/or nail shedding.