Whole-genome sequencing analysis of molecular epidemiology and silent transmissions causing meticillin-resistant Staphylococcus aureus bloodstream infections in a university hospital

Background: The emergence of novel genomic-type clones, such as community-associated meticillin-resistant Staphylococcus aureus (MRSA) and livestock-associated MRSA, and their invasion into hospitals have become major concerns worldwide; however, little information is available regarding the prevalence of MRSA in Japan. Whole-genome sequencing (WGS) has been conducted to analyse various pathogens worldwide. There-fore, it is important to establish a genome database of clinical MRSA isolates available in Japan.Aim: A molecular epidemiological analysis of MRSA strains isolated from bloodstream -infected patients in a Japanese university hospital was conducted using WGS and single -nucleotide polymorphism (SNP) analysis. Additionally, through a review of patients' clin-ical characteristics, the effectiveness of SNP analysis as a tool for detecting silent noso-comial transmission that may be missed by other methods was evaluated in diverse settings and various time points of detection.Methods: Polymerase-chain-reaction-based staphylococcal cassette chromosome mec (SCCmec) typing was performed using 135 isolates obtained between 2014 and 2018, and WGS was performed using 88 isolates obtained between 2015 and 2017.Findings: SCCmec type II strains, prevalent in 2014, became rare in 2018, whereas the prevalence of SCCmec type IV strains increased from 18.75% to 83.87% of the population, and became the dominant clones. Clonal complex (CC) 5 CC8 and CC1 were detected between 2015 and 2017, with CC1 being dominant. In 88 cases, SNP analyses revealed nosocomial transmissions among 20 patients which involved highly homologous strains.Conclusions: Routine monitoring of MRSA by whole-genome analysis is effective not only for gaining knowledge regarding molecular epidemiology, but also for detecting silent nosocomial transmission. 2023 The Authors. Published by Elsevier Ltd on behalf of The Healthcare Infection Society. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Automated summary

This study conducted a molecular epidemiological analysis of MRSA strains isolated from bloodstream-infected patients in a Japanese university hospital using whole-genome sequencing (WGS) and single-nucleotide polymorphism (SNP) analysis. The results showed that the prevalence of MRSA clones changed over time, with SCCmec II strains becoming rare and SCCmec IV strains becoming dominant. In addition, SNP analysis revealed silent nosocomial transmission in the hospital, highlighting the effectiveness of whole-genome analysis in monitoring MRSA and detecting nosocomial transmission.