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Updated: Jul 30, 2026
Biosensor for Detection of Antibiotic Resistant Staphylococcus Bacteria
Published on: May 8, 2013
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus
Rhys T White1, Sarah Bakker1, Megan Burton2
1Institute of Environmental Science and Research, Health Group, Porirua 5022, New Zealand.
Abstract:
Outbreaks of methicillin-resistant Staphylococcus aureus (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. Herein, using this system, we describe the detection and control of an outbreak of sequence-type (ST)97 MRSA in our NICU. The outbreak was identified 13 days after the first MRSA-positive culture and at a point where there were only two known cases. Ward screening rapidly defined the extent of the outbreak, with six other infants found to be colonized. There was minimal transmission once the outbreak had been detected and appropriate infection control measures had been instituted; only two further ST97 cases were detected, along with three unrelated non-ST97 MRSA cases. To contextualize the outbreak, core-genome single-nucleotide variants were identified for phylogenetic analysis after de novo assembly of nanopore data. Comparisons with global (n=45) and national surveillance (n=35) ST97 genomes revealed the stepwise evolution of methicillin resistance within this ST97 subset. A distinct cluster comprising nine of the ten ST97-IVa genomes from the NICU was identified, with strains from 2020 to 2022 national surveillance serving as outgroups to this cluster. One ST97-IVa genome presumed to be part of the outbreak formed an outgroup and was retrospectively excluded. A second phylogeny was created using Illumina sequencing, which considerably reduced the branch lengths of the NICU isolates on the phylogenetic tree. However, the overall tree topology and conclusions were unchanged, with the exception of the NICU outbreak cluster, where differences in branch lengths were observed. This analysis demonstrated the ability of a nanopore-only prospective genomic surveillance system to rapidly identify and contextualize an outbreak of MRSA in a NICU.
Insights
A new prospective genomic surveillance system using Nanopore sequencing rapidly detected and controlled a methicillin-resistant Staphylococcus aureus (MRSA) outbreak in a neonatal intensive care unit (NICU). This system enabled timely intervention and phylogenetic analysis of the MRSA strains.
Area of Science:
- Microbiology
- Genomics
- Infectious Disease Epidemiology
Background:
- Outbreaks of methicillin-resistant Staphylococcus aureus (MRSA) are a significant concern in neonatal intensive care units (NICUs).
- Traditional outbreak investigations often rely on retrospective analysis and short-read sequencing platforms.
- There is a need for rapid, prospective genomic surveillance systems for timely MRSA outbreak detection and control.
Purpose of the Study:
- To establish and evaluate a prospective genomic surveillance system using Oxford Nanopore Technologies for rapid MRSA outbreak detection in a NICU.
- To characterize the ST97 MRSA outbreak using real-time nanopore sequencing and phylogenetic analysis.
- To assess the effectiveness of infection control measures implemented after genomic detection of the outbreak.
Main Methods:
- Implementation of a prospective genomic surveillance system utilizing Oxford Nanopore Technologies sequencing.
- Rapid identification of MRSA outbreak cases through routine surveillance and ward screening.
- Whole-genome sequencing (WGS) of MRSA isolates for phylogenetic analysis using nanopore and Illumina platforms.
- Comparative genomic analysis with global and national ST97 MRSA surveillance data.
Main Results:
- The prospective genomic surveillance system detected an ST97 MRSA outbreak 13 days after the first positive culture, when only two cases were known.
- Ward screening identified six additional colonized infants, and minimal transmission occurred after implementing infection control measures.
- Phylogenetic analysis revealed a distinct cluster of NICU ST97-IVa isolates and elucidated the evolution of methicillin resistance.
- Nanopore sequencing provided rapid and comparable phylogenetic insights to Illumina sequencing for outbreak investigation.
Conclusions:
- A nanopore-only prospective genomic surveillance system is effective for rapid identification and contextualization of MRSA outbreaks in NICUs.
- Real-time genomic data facilitates prompt implementation of infection control measures, minimizing transmission.
- Prospective genomic surveillance enhances our ability to understand pathogen evolution and transmission dynamics during outbreaks.
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