Regional outbreak of methicillin-resistant Staphylococcus aureus ST2725-t1784 in rural Japan

To the Editor—Novel strains of methicillin-resistant Staphylococcus aureus (MRSA) continue to be discovered,¹ and understanding the trends of these strains in each region is important because MRSA genotype affects clinical outcomes.² Despite the introduction of various interventions, the prevalence of MRSA infection in Japanese hospitals remains relatively high.³ Although MRSA USA300, which causes severe infectious disease with high mortality, is not common in Japan,⁴ other SCCmec type IV MRSA strains have become widespread.⁵

Akiha Ward has 3 hospitals serving a population of ~80,000. The local incidence of MRSA bacteremia was ~10 per 100,000 person years in 2017–2018, which is considered high.⁶ Therefore, to clarify the main route of MRSA transmission, we surveyed clinical isolates of MRSA from Akiha Ward using whole-genomic sequencing (WGS).

We collected clinical isolates of MRSA from 2 hospitals, namely, Kaetsu Hospital and Niitsu Medical Center Hospital, from April to September 2018. All clinics and a psychiatric hospital were excluded because they performed a relatively low number of bacterial tests. Despite these exclusions, our data covered most bacterial tests performed in Akiha Ward and thus can be considered to reflect the local epidemiology of MRSA infection. WGS analyses were performed at the Department of Microbiology, Niigata University of Pharmacy and Applied Life Sciences (NUPALS). The protocol was approved by the institutional review boards of NUPALS (no. H30-05), Kaetsu Hospital (approval # 2018-2), and Niitsu Medical Center Hospital (no. 2018-2). All clinically characterized MRSA isolates, including redundant ones, were further confirmed using MRSAII selective agar (Eiken-Chemical, Japan) and WGS. Additional isolates from the same patient with the same multilocus sequence typing profile were considered to be redundant samples and were therefore excluded, leaving 120 individual strains from 102 patients for further analysis.

Total DNA samples were prepared from each isolate by DNeasy Ultraclean Microbial kit (Qiagen, Germany), and WGS was performed using NexteraXT and Miseq Reagent kit v2 (500 cycles) or v3 (600 cycles) (Illumina, USA). All read sequences were deposited in the DDBJ/EMBL/GenBank database (accession nos. DRA010434–DRA010440). Multilocus sequence typing (MLST) analysis was performed using nullarbor v.2.0.20180819 (https://github.com/tseemann/nullarbor) with SPAdes v.3.12.0 as the assembler.⁷ A k-mer–based tool, stringMLST, was also used for MLST analysis when the above software failed to define the sequence type.⁸ SCCmec and spa typing were performed by SCCmecFinder v.1.2 and spaTyper (http://spatyper.fortinbras.us/), respectively.⁹ In addition, the presence of the cytotoxin Panthon–Valentine Leucocidin (accession no. AB006796.1) was determined by searching for assembled sequences with BLASTN (US National Library of Medicine).

Among the 102 patients, median age was 87 years (range, 1–100) and 68% were men. MRSA isolates were obtained from sputum (n = 91, 76%), urine (n = 12, 10%), skin and soft tissue (n = 9, 8%), blood (n = 4, 3%), and stool (n = 4, 3%). Table 1 shows the SCCmec and spa types determined by WGS analyses of all MRSA isolates. The most common type of MRSA was SCCmec type-IVa, which was detected in 92 (77%) isolates, followed by type II, type IV, and type IVg, which were detected in 20 (17%), 7 (6%), and 1 (1%) isolate(s), respectively. All isolates were negative for Panthon–Valentine Leucocidin. Surprisingly, 82 isolates (68%) were identified as SCCmec type-IVa MRSA ST2725-t1784. In addition, MRSA ST2725-t1784 was detected not only in inpatients but also in 37% of outpatients, including a 1-year-old child with low medical exposure.

Table 1. SCCmec and spa Types Determined by Whole-Genome Analysis in All MRSA Isolates

Note. MRSA, methicillin-resistant Staphylococcus aureus; CC, clonal complex; ST, sequence type.

MRSA ST2725-t1784 was observed at a high detection ratio in this study; thus, it may be easily transmissible at healthcare facilities and in the community. Moreover, 3 of 4 blood cultures tested positive for MRSA ST2725-t1784, indicating that it might be the predominate MRSA strain causing infectious disease in the area. MRSA ST2725-t1784 accounted for 44% of all MRSA strains in neonatal intensive care units in Shizuoka, which is >400 km from Niigata.¹⁰ Therefore, an epidemic of MRSA ST2725-t1784 is of concern in Japan.