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Aziz F, Hisatsune J, Ono HK, Kajimura J, Yu L, Masuda K, Kitagawa H, Sato'o Y, Yahara K, Yamaoka M, Nakane A, Kawasaki H, Obata S, Fukushima-Nomura A, Ito Y, Aung MS, Amagai M, Salasia SIO, Ohge H, Kusunoki Y, Sugai M. Genomic analysis and identification of a novel superantigen, SargEY, in Staphylococcus argenteus isolated from atopic dermatitis lesions. mSphere 2024; 9:e0050524. [PMID: 38990001 PMCID: PMC11288046 DOI: 10.1128/msphere.00505-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
During surveillance of Staphylococcus aureus in lesions from patients with atopic dermatitis (AD), we isolated Staphylococcus argenteus, a species registered in 2011 as a new member of the genus Staphylococcus and previously considered a lineage of S. aureus. Genome sequence comparisons between S. argenteus isolates and representative S. aureus clinical isolates from various origins revealed that the S. argenteus genome from AD patients closely resembles that of S. aureus causing skin infections. We previously reported that 17%-22% of S. aureus isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of S. argenteus isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of S. argenteus revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among S. argenteus. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4+ and CD8+ T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. SargEY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. SargEY and SEY may play roles in exacerbating the respective toxin-producing strains in AD. IMPORTANCE Staphylococcus aureus is frequently isolated from active lesions of atopic dermatitis (AD) patients. We reported that 17%-22% of S. aureus isolated from AD patients produced a novel superantigen staphylococcal enterotoxin Y (SEY). Unlike many S. aureus superantigens that activate T cells via T-cell receptor (TCR) Vß, SEY activates T cells via TCR Vα and stimulates cytokine secretion. Staphylococcus argenteus was isolated from AD patients during the surveillance for S. aureus. Phylogenetic comparison of the genome indicated that the isolate was very similar to S. aureus causing skin infections. The isolate encoded a SEY-like protein, designated SargEY, which, like SEY, activated T cells via the TCR Vα. ST2250 is the only lineage positive for SargEY gene. ST2250 S. argenteus harboring a superantigen SargEY gene may be a novel staphylococcal clone that infects human skin and is involved in the exacerbation of AD.
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Affiliation(s)
- Fatkhanuddin Aziz
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima City, Hiroshima, Japan
- Veterinary Technology Program, Department of Bioresources Technology and Veterinary, Vocational College, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Junzo Hisatsune
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima City, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Hisaya K. Ono
- Laboratory of Zoonoses, Kitasato University School of Veterinary Medicine, Towada, Aomori, Japan
| | - Junko Kajimura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima City, Hiroshima, Japan
| | - Liansheng Yu
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Kanako Masuda
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima City, Hiroshima, Japan
| | - Hiroki Kitagawa
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima City, Hiroshima, Japan
| | - Yusuke Sato'o
- Division of Bacteriology, Department of Infection and Immunity, School of Medicine, Jichi Medical University, Shimotsuke-shi, Tochigi, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Mika Yamaoka
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima City, Hiroshima, Japan
| | - Akio Nakane
- Department of Microbiology and Immunology, Hirosaki University, Hirosaki, Aomori, Japan
| | - Hiroshi Kawasaki
- Department of Dermatology, Keio University School of Medicine, Shijuku-ku, Tokyo, Japan
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
- Laboratory for Developmental Genetics, RIKEN, Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shoko Obata
- Department of Dermatology, Keio University School of Medicine, Shijuku-ku, Tokyo, Japan
| | | | - Yoshihiro Ito
- Department of Dermatology, Keio University School of Medicine, Shijuku-ku, Tokyo, Japan
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Shijuku-ku, Tokyo, Japan
- Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Siti Isrina Oktavia Salasia
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima City, Hiroshima, Japan
| | - Yoichiro Kusunoki
- Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima City, Hiroshima, Japan
| | - Motoyuki Sugai
- Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima City, Hiroshima, Japan
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
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Inagawa T, Hisatsune J, Kutsuno S, Iwao Y, Koba Y, Kashiyama S, Ota K, Shime N, Sugai M. Genomic characterization of Staphylococcus aureus isolated from patients admitted to intensive care units of a tertiary care hospital: epidemiological risk of nasal carriage of virulent clone during admission. Microbiol Spectr 2024; 12:e0295023. [PMID: 38709078 PMCID: PMC11237438 DOI: 10.1128/spectrum.02950-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 04/05/2024] [Indexed: 05/07/2024] Open
Abstract
We conducted a molecular epidemiological study of Staphylococcus aureus using whole-genome sequence data and clinical data of isolates from nasal swabs of patients admitted to the intensive care unit (ICU) of Hiroshima University hospital. The relationship between isolate genotypes and virulence factors, particularly for isolates that caused infectious diseases during ICU admission was compared with those that did not. The nasal carriage rates of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) in patients admitted to the ICU were 7.0% and 20.1%, respectively. The carriage rate of community-acquired (CA)-MRSA was 2.3%, accounting for 32.8% of all MRSA isolates. Whole-genome sequencing analysis of the MRSA isolates indicated that most, including CA-MRSA and healthcare-associated (HA)-MRSA, belonged to clonal complex (CC) 8 [sequence type (ST) 8] and SCCmec type IV. Furthermore, results for three disease foci (pneumonia, skin and soft tissue infection, and deep abscess) and the assessment of virulence factor genes associated with disease conditions [bacteremia, acute respiratory distress syndrome (ARDS), disseminated intravascular coagulopathy (DIC), and septic shock] suggested that nasal colonization of S. aureus clones could represent a risk for patients within the ICU. Particularly, MRSA/J and MSSA/J may be more likely to cause deep abscess infection; ST764 may cause ventilation-associated pneumonia, hospital-acquired pneumonia and subsequent bacteremia, and ARDS, and tst-1-positive isolates may cause DIC onset.IMPORTANCENasal colonization of MRSA in patients admitted to the intensive care unit (ICU) may predict the development of MRSA infections. However, no bacteriological data are available to perform risk assessments for Staphylococcus aureus infection onset. In this single-center 2-year genomic surveillance study, we analyzed all S. aureus isolates from nasal swabs of patients admitted to the ICU and those from the blood or lesions of in-patients who developed infectious diseases in the ICU. Furthermore, we identified the virulent clones responsible for causing infectious diseases in the ICU. Herein, we report several virulent clones present in the nares that are predictive of invasive infections. This information may facilitate the design of preemptive strategies to identify and eradicate virulent MRSA strains, reducing nosocomial infections within the ICU.
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Affiliation(s)
- Takahiro Inagawa
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan
| | - Junzo Hisatsune
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shoko Kutsuno
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yasuhisa Iwao
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yumiko Koba
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan
- Division of Laboratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Seiya Kashiyama
- Section of Clinical Laboratory, Division of Clinical Support, Hiroshima University Hospital, Hiroshima, Japan
- Division of Laboratory Medicine, Hiroshima University Hospital, Hiroshima, Japan
| | - Kohei Ota
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan
| | - Nobuaki Shime
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Minami-ku, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
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Yang K, Yong JY, He Y, Yu L, Luo GN, Chen J, Ge YM, Yang YJ, Ding WJ, Hu YM. Melatonin restores DNFB-induced dysbiosis of skin microbiota in a mouse model of atopic dermatitis. Life Sci 2024; 342:122513. [PMID: 38387700 DOI: 10.1016/j.lfs.2024.122513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/04/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND The epidermic microbiota plays crucial roles in the pathogenesis of atopic dermatitis (AD), a common inflammatory skin disease. Melatonin (MLT) has been shown to ameliorate skin damage in AD patients, yet the underlying mechanism is unclear. METHODS Using 2,4-dinitrofluorobenzene (DNFB) to induce an AD model, MLT intervention was applied for 14 days to observe its pharmaceutical effect. Skin lesions were observed using HE staining, toluidine blue staining and electron microscopy. Dermal proinflammatory factor (IL-4 and IL-13) and intestinal barrier indices (ZO1 and Occludin) were assessed by immunohistochemistry and RT-qPCR, respectively. The dysbiotic microbiota was analyzed using 16S rRNA sequencing. RESULTS MLT significantly improved skin lesion size; inflammatory status (mast cells, IgE, IL-4, and IL-13); and the imbalance of the epidermal microbiota in AD mice. Notably, Staphylococcus aureus is the key bacterium associated with dysbiosis of the epidermal microbiota and may be involved in the fine modulation of mast cells, IL-4, IL-13 and IgE. Correlation analysis between AD and the gut revealed that intestinal dysbiosis occurred earlier than that of the pathological structure in the gut. CONCLUSION Melatonin reverses DNFB-induced skin damage and epidermal dysbiosis, especially in S. aureus.
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Affiliation(s)
- Kun Yang
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Jiang-Yan Yong
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China; Hospital of Chengdu University of Traditional Chinese Medicine, No.39 Shi-er-qiao Road, Chengdu, 610072, SichuanProvince, China
| | - Yan He
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Lu Yu
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Gui-Ning Luo
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Jilan Chen
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Yi-Man Ge
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China; Hospital of Chengdu University of Traditional Chinese Medicine, No.39 Shi-er-qiao Road, Chengdu, 610072, SichuanProvince, China
| | - You-Jun Yang
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China
| | - Wei-Jun Ding
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China.
| | - Yi-Mei Hu
- Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Chengdu, Sichuan 611137, China; Hospital of Chengdu University of Traditional Chinese Medicine, No.39 Shi-er-qiao Road, Chengdu, 610072, SichuanProvince, China.
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Ohta T, Hananoe A, Fukushima-Nomura A, Ashizaki K, Sekita A, Seita J, Kawakami E, Sakurada K, Amagai M, Koseki H, Kawasaki H. Best practices for multimodal clinical data management and integration: An atopic dermatitis research case. Allergol Int 2024; 73:255-263. [PMID: 38102028 DOI: 10.1016/j.alit.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND In clinical research on multifactorial diseases such as atopic dermatitis, data-driven medical research has become more widely used as means to clarify diverse pathological conditions and to realize precision medicine. However, modern clinical data, characterized as large-scale, multimodal, and multi-center, causes difficulties in data integration and management, which limits productivity in clinical data science. METHODS We designed a generic data management flow to collect, cleanse, and integrate data to handle different types of data generated at multiple institutions by 10 types of clinical studies. We developed MeDIA (Medical Data Integration Assistant), a software to browse the data in an integrated manner and extract subsets for analysis. RESULTS MeDIA integrates and visualizes data and information on research participants obtained from multiple studies. It then provides a sophisticated interface that supports data management and helps data scientists retrieve the data sets they need. Furthermore, the system promotes the use of unified terms such as identifiers or sampling dates to reduce the cost of pre-processing by data analysts. We also propose best practices in clinical data management flow, which we learned from the development and implementation of MeDIA. CONCLUSIONS The MeDIA system solves the problem of multimodal clinical data integration, from complex text data such as medical records to big data such as omics data from a large number of patients. The system and the proposed best practices can be applied not only to allergic diseases but also to other diseases to promote data-driven medical research.
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Affiliation(s)
- Tazro Ohta
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan; Institute for Advanced Academic Research, Chiba University, Chiba, Japan; Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ayaka Hananoe
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan; Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan
| | | | - Koichi Ashizaki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan
| | - Aiko Sekita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Jun Seita
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan; Medical Data Deep Learning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan; Medical Data Sharing Unit, Infrastructure Research and Development Division, RIKEN Information R&D and Strategy Headquarters, RIKEN, Saitama, Japan
| | - Eiryo Kawakami
- Medical Data Mathematical Reasoning Team, Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan; Institute for Advanced Academic Research, Chiba University, Chiba, Japan; Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kazuhiro Sakurada
- Advanced Data Science Project, RIKEN Information R&D and Strategy Headquarters, RIKEN, Kanagawa, Japan; Department of Extended Intelligence for Medicine, The Ishii-Ishibashi Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Amagai
- Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan
| | - Hiroshi Kawasaki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan; Department of Dermatology, Keio University School of Medicine, Tokyo, Japan; Laboratory for Skin Homeostasis, RIKEN Center for Integrative Medical Sciences, RIKEN, Kanagawa, Japan.
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