Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data

Junzo Hisatsune (), Shoko Kutsuno, Yasuhisa Iwao, Kasumi Ishida-Kuroki, Koji Yahara, Norikazu Kitamura, Toshiki Kajihara, Shizuo Kayama, Yo Sugawara, Hiroki Kitagawa, Hiroki Ohge, Tomoyuki Mizukami, Takeshi Takahashi, Fumio Kawano and Motoyuki Sugai ()
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Junzo Hisatsune: National Institute of Infectious Diseases
Shoko Kutsuno: National Institute of Infectious Diseases
Yasuhisa Iwao: National Institute of Infectious Diseases
Kasumi Ishida-Kuroki: National Institute of Infectious Diseases
Koji Yahara: National Institute of Infectious Diseases
Norikazu Kitamura: National Institute of Infectious Diseases
Toshiki Kajihara: National Institute of Infectious Diseases
Shizuo Kayama: National Institute of Infectious Diseases
Yo Sugawara: National Institute of Infectious Diseases
Hiroki Kitagawa: Hiroshima University
Hiroki Ohge: Hiroshima University
Tomoyuki Mizukami: National Hospital Organization Kumamoto Medical Center
Takeshi Takahashi: National Hospital Organization Kumamoto Medical Center
Fumio Kawano: National Hospital Organization Kumamoto Medical Center
Motoyuki Sugai: National Institute of Infectious Diseases

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-57575-2

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