Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data
Antimicrobial resistance is a global health concern, and methicillin-resistant Staphylococcus aureus (MRSA) is one of the highest-priority organisms exhibiting this phenotype. Here, we performed a national surveillance integrating patient clinical data of S. aureus isolated from bloodstream infections. We performed genome sequencing, standardized antimicrobial susceptibility testing, and collected clinical metadata of 580 S. aureus isolates collected during 2019-2020. We focused on three predominant clonal complexes (CC1, CC5, and CC8) and assesses their microbiological and clinical significance, as well as their distribution across eastern and western Japan. Furthermore, we conducted a genomic comparison of the isolates of 2019-2000 with those of 1994-2000 and investigated the evolutionary trajectory of emerging clones from the three dominant clonal complexes. We revealed that the emerging MRSA ST764-SCCmecII showed the highest mortality rate within 30 days of hospitalization. This high-risk clone diverged from the New York/Japan clone (ST5-SCCmecII), which was inferred to have undergone repeated infections with phages carrying superantigen toxin genes and acquired antimicrobial resistance genes via mobile genetic elements, leading to its emergence around 1994. Overall, we provide a blueprint for a national genomic surveillance study that integrates clinical data and enables the identification and evolutionary characterization of a high-risk clone.
Authors
- Tomoyuki Mizukami (ORCID: https://orcid.org/0000-0002-2508-2810)
- Koichi Nitta
- Kasumi Ishida‐Kuroki (ORCID: https://orcid.org/0000-0002-1694-3711)
- Yukihiro Zaizen
- Kenji Yamamoto (ORCID: https://orcid.org/0000-0003-4482-5816)
- Kazuya Takahashi (ORCID: https://orcid.org/0000-0002-3097-9841)
- Yutaka Satō (ORCID: https://orcid.org/0000-0002-5245-232X)
- Koji Yahara (ORCID: https://orcid.org/0000-0003-4289-1115)
- Yumi Suzuki (ORCID: https://orcid.org/0000-0001-8444-4714)
- Shinji Tamaki (ORCID: https://orcid.org/0000-0002-7106-6854)
- Katsuyuki Tomita (ORCID: https://orcid.org/0000-0002-4050-775X)
- Kazuko Shiozawa
- Shoko Kutsuno
- Kazutoshi Hiyama
- Shoko Nishihara (ORCID: https://orcid.org/0000-0002-1668-2603)
- Isamu Kamimaki
- H Ejima
- Takahiro Fujita (ORCID: https://orcid.org/0000-0003-4994-1250)
- Takeo Endo
- Yo Sugawara (ORCID: https://orcid.org/0000-0002-9897-3905)
- Seiji Aratake
- Toshiki Kajihara (ORCID: https://orcid.org/0000-0002-7576-2654)
- Osamu Okamura
- Hiroki Ohge (ORCID: https://orcid.org/0000-0001-7267-9823)
- Masami Watanabe
- Motoyuki Sugai (ORCID: https://orcid.org/0000-0001-9252-7739)
- Katsuhiro Kuwahara
- Nobuteru Kubo (ORCID: https://orcid.org/0000-0002-0626-8142)
- Yasuhito Hamaguchi (ORCID: https://orcid.org/0000-0001-5305-7770)
- Akihiko Goto (ORCID: https://orcid.org/0000-0002-4875-9599)
- Sanae Otawa
- Hitoshi Inoue (ORCID: https://orcid.org/0000-0002-8321-4201)
- Tomoku Ichimiya
- Shizuo Kayama (ORCID: https://orcid.org/0000-0003-2420-3542)
- T Tsuchiya
- Yuta Hayashi
- Takeshi Takahashi (ORCID: https://orcid.org/0000-0002-3898-5883)
- Keiichi Kanno (ORCID: https://orcid.org/0000-0002-3759-7643)
- Sami Fujihara
- Toshio Makie
- Norikazu Kitamura (ORCID: https://orcid.org/0009-0006-3738-3545)
- Fumio Kawano
- T. Yuda
- H Mizukoshi
- Masanobu Shigeta (ORCID: https://orcid.org/0000-0002-4239-8040)
- Hiroki Kitagawa (ORCID: https://orcid.org/0000-0003-1651-0091)
- Takao Yokoe
- Michiyo Misawa
- Nobuyuki Takayama (ORCID: https://orcid.org/0000-0001-9418-9657)
- Toshio Saito
- Kentaro Wakamatsu (ORCID: https://orcid.org/0000-0003-4311-887X)
- Toshikazu Ikeda (ORCID: https://orcid.org/0000-0003-0132-4296)
- Kazuyoshi Nakamura (ORCID: https://orcid.org/0000-0002-6219-407X)
- Tatsuo Kato
- Yutaka Fujiwara
- Naoko Maeda
- Takafumi Okada
- Takashi Saito (ORCID: https://orcid.org/0000-0002-5672-8856)
- Toshitaka Muto
- Yoshinori Inoue
- Yasuhisa Iwao
- Y. Tsunashima
- Yusuke Mimura
- Shigeru Sugitani
- Mariko Ueda
- Hitomi Kawamura
- Yukari Kato
- K. Okita
- Kozue Miyazaki
- Sachiko Hara
- Toru Yamanaka
- Junzo Hisatsune
- Yumiko Owatari
- Shimoeda Hirokazu
- Kazutaka Yassuda
- Ayumi Maeoka
- Eriko Shigyo
- Chiharu Kuriwaki
Institutions
- Hiroshima University (JP)
- Hokuriku Electric Power Company (Japan) (JP)
- Nagara Medical Center (JP)
- National Institute of Infectious Diseases (JP)
- National Hospital Organization Kochi National Hospital (JP)
- Hyogo Chuo National Hospital (JP)
- Kobe Medical Center (JP)
- Kanazawa Medical Center (JP)
- Municipal Tsuruga Hospital (JP)
- Oita Medical Center (JP)
- Miwa Hospital (JP)
- National Hospital Organization Mito Medical Center (JP)
- Maizuru Municipal Hospital (JP)
- National Hospital Organization Hokkaido Medical Center (JP)
- Toneyama National Hospital (JP)
- Kurihama Medical and Addiction Center (JP)
- Omuta hospital (JP)
- National Hospital Organization Takasaki Medical Center (JP)
- National Sanyo Hospital (JP)
- Nara City Hospital (JP)
- National Institute of Technology, Yonago College (JP)
- National Sagamihara Hospital (JP)
- Nagasaki Medical Center (JP)
- Tottori University Hospital (JP)
- Fukuyama Cardiovascular Hospital (JP)
- Hiroshima University Hospital (JP)
- Higashihiroshima Medical Center (JP)
- Fukuoka Higashi Medical Center (JP)
- National Institute of Technology, Suzuka College (JP)
- Shizuoka Medical Center (JP)
- Beppu Medical Center (JP)
- National Hospital Organization (JP)
- National Hospital Organization Miyazaki Higashi Hospital (JP)
- Kasumigaura Medical Center (JP)
- Kagoshima Medical Center (JP)
- Utano Hospital (JP)
- Nagano National Hospital (JP)
- National Mie Hospital (JP)
- Okayama Medical Center (JP)
- Tokyo National Hospital (JP)
- Nishi Niigata Chuo National Hospital (JP)
- Tokushima Hospital (JP)
- Kure Medical Center (JP)
- Shikoku Medical Center for Children and Adults (JP)
- Higashi Nagoya National Hospital (JP)
- Sapporo National Hospital (JP)
- Kumamoto Medical Center (JP)
- National Hospital Organization Saitama Hospital
Publication Details
- Journal
- Nature Communications
- Published
- 2025-03-19
- DOI
- https://doi.org/10.1038/s41467-025-57575-2
- Citations
- 13
- Primary Topic
- Antimicrobial Resistance in Staphylococcus
- Type
- article
- Field-Weighted Citation Impact
- 18.15
Funders
- Japan Agency for Medical Research and Development