Whole-genome sequencing reveals a unique outbreak of methicillin-resistant Staphylococcus aureus clone USA400/J in Japan

TL;DR

Whole-genome sequencing identified a unique outbreak of a specific MRSA strain, USA400/J, in a Japanese hospital, showing it evolved independently in Japan.

Contribution

The study reveals that the USA400/J MRSA clone in Japan forms a distinct genetic cluster, indicating independent evolution.

Findings

MRSA strains isolated included ST1-IV, ST8-IV, ST764-II, and ST89-V, with ST1-IV and ST764-II showing high clone homology.

Genome-based phylogenetic analysis showed that Japanese CC1-IV strains form a unique cluster distinct from overseas ST1-IV strains.

The findings suggest the need for targeted surveillance and infection control for USA400/J in Japan.

Abstract

Panton-Valentine leukocidin (PVL)-negative, sequence type 1-staphylococcal cassette chromosome mec (SCCmec) type IV (ST1-IV) methicillin-resistant Staphylococcus aureus (MRSA) is prevalent in Japanese hospitals. The PVL-negative ST1-IV MRSA strain is known as USA400/J in Japan. In this study, we analysed an MRSA outbreak at a Japanese university hospital using conventional methods, SCCmec typing, pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS).

We analysed 12 MRSA strains isolated from the neonatal intensive care unit of Aichi Medical University Hospital. SCCmec typing and gene detection were performed using polymerase chain reaction. Molecular epidemiological analyses were performed using multi-locus sequence typing and PFGE. Genome-based phylogenetic analyses were performed for some strains.

The isolated MRSA strains were classified as ST1-IV (N = 4), ST8-IV (N = 1), ST764-II (N = 6) and ST89-V (N = 1). PFGE analysis showed that the ST1-IV and ST764-II strains exhibited high homology within their clones. Phylogenetic analysis based on the genomes of the USA400/J strains isolated in this study and ST1-IV isolates from overseas showed that clonal complex 1-SCCmec type IV (CC1-IV) strains isolated in Japan formed a unique cluster that was distinct from the ST1-IV strains from overseas. This suggests that CC1-IV evolved and spread independently in Japan.

These findings highlight the need for increased surveillance and infection control measures that specifically target USA400/J.

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