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Longitudinal phylogenomic tracking of methicillin-resistant Staphylococcus aureus clones persisting over years in a
Tatsuya Miyata1, Yasuhiro Gotoh2, Yoshitomo Motomura3
1Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan; Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
Introduction:
Infection control measures against methicillin-resistant Staphylococcus aureus (MRSA) are challenging in advanced neonatal intensive care units (NICUs) providing care for high-risk newborns. To design and implement better infection control strategies, it is necessary to identify endemic MRSA clones that are recurrently detected and understand how they survive and transmit in the NICU.
Methods:
We performed whole-genome sequencing (WGS) for all MRSA strains isolated in the level II-IV NICU in Kyushu University Hospital, Fukuoka, Japan, from March 2015 to December 2021. Strains within pairwise 250 allelic distances in core genome multi-locus sequence typing (cgMLST) were clustered as cgMLST250 clusters, which were further divided into subclusters within pairwise 30 single nucleotide polymorphism (SNP) distances in the core genome-based phylogenetic analysis (SNP30 clusters). SNP30 clusters were defined as persistently present when they were identified in ≥5 patients over 12 months.
Results:
A total of 235 strains from 226 patients were analysed. Three major clonal complexes (CC1, CC5, and CC8) accounted for 91.2% of the strains. Multi-step phylogenomic analyses identified eight putative persistent clones defined by SNP30 clustering, five of which contained 10-32 isolates. These five clones were isolated for 15-40 months, often without overlap of inpatient periods, and in several cases, with isolation intervals of over one year.
Conclusions:
Unidentified long-term and/or multiple reservoirs and multiple/repeated MRSA re-introduction into the NICU may contribute to prolonged detection of transmissible MRSA clones in the NICU. Intensive control of these reservoirs and re-introduction may be mandatory, particularly in advanced NICUs.
Insights
Persistent methicillin-resistant Staphylococcus aureus (MRSA) clones challenge infection control in neonatal intensive care units (NICUs). Identifying and controlling reservoirs and reintroduction are crucial for advanced NICU patient safety.
Area of Science:
- Infectious Disease Epidemiology
- Genomic Epidemiology
- Neonatal Healthcare-Associated Infections
Background:
- Methicillin-resistant Staphylococcus aureus (MRSA) poses significant infection control challenges in advanced neonatal intensive care units (NICUs).
- Understanding the persistence and transmission dynamics of endemic MRSA clones is vital for developing effective control strategies in high-risk newborn populations.
Purpose of the Study:
- To identify and characterize persistent methicillin-resistant Staphylococcus aureus (MRSA) clones within a neonatal intensive care unit (NICU).
- To understand the long-term survival and transmission patterns of MRSA in an advanced NICU setting.
Main Methods:
- Whole-genome sequencing (WGS) was performed on all MRSA strains isolated from March 2015 to December 2021 in a level II-IV NICU.
- Core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP) phylogenetic analyses were used to cluster MRSA strains.
- Persistent clones were defined as those identified in ≥5 patients over 12 months.
Main Results:
- A total of 235 MRSA strains from 226 patients were analyzed, with three major clonal complexes (CC1, CC5, CC8) dominating (91.2%).
- Phylogenomic analysis identified eight putative persistent clones, five of which were isolated for 15-40 months.
- These persistent clones were often detected without overlapping inpatient periods, indicating long-term reservoirs or repeated introductions.
Conclusions:
- Prolonged detection of transmissible MRSA clones in NICUs may be attributed to unidentified long-term reservoirs and repeated introductions.
- Intensive control measures targeting these reservoirs and reintroduction pathways are essential for advanced NICUs.
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