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Published Papers 【 display / non-display 】

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• Virus-Specific Impact of Respiratory Viruses on Adult Emergency Department Outcomes

  Nabeya D, Kinjo T, Nishiyama N, Kami W, Arakaki W, Okamoto T, Kuniyoshi K, Nishiyama M, Nakamura H, Haranaga S, Fujita J, Yamamoto K, Shiiki S, Kishaba T.

  Journal of Medical Virology   98 ( 7 ) e71039   2026.06 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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• Cloverleaf-like Nuclei and Cytoplasmic Tails in Hypersensitivity Pneumonitis.

  Arakaki W, Kinjo T, Ikemiyagi N, Yamamoto K

  Internal medicine (Tokyo, Japan) ( 一般社団法人 日本内科学会 )  65 ( 1 ) 193 - 193   2026.01

  Type of publication: Research paper (scientific journal)

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• Bacterial pneumonia co-infection in adult inpatients with coronavirus disease 2019 during the Omicron variants epidemic in Okinawa, Japan: risk factors and clinical outcomes.

  Kami W, Ideguchi S, Miyagi K, Tasato D, Higa F, Nakamura H, Kinjo T, Nakamatsu M, Haranaga S, Tokushige A, Fujita J, Yamamoto K

  Respiratory investigation ( Respiratory Investigation )  63 ( 6 ) 1087 - 1092   2025.11 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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  BACKGROUND: The clinical characteristics and risk factors for bacterial pneumonia co-infection in patients with coronavirus disease 2019 (COVID-19) since the epidemic of Omicron variants remain unclear. METHODS: This retrospective study included adult inpatients with COVID-19 at four tertiary hospitals in Okinawa, Japan, between May and July 2023. Bacterial pneumonia co-infection was diagnosed on the basis of new infiltrates on chest radiography, the presence of neutrophils on sputum Gram stain with a positive culture, and the requirement for antimicrobial therapy. We evaluated patient characteristics, detected microbes, assessed patient outcomes, and analyzed the risk factors for bacterial pneumonia co-infection. RESULTS: Among 458 patients initially considered, 358 were eligible (median age 77 years; 55 % male, and 19 % unvaccinated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Bacterial pneumonia was identified in 60 patients (17 %). The most common pathogens were Klebsiella pneumoniae, Staphylococcus aureus, and Haemophilus influenzae, with oral flora detected in 40 % of cases. Mortality was significantly higher in patients with bacterial pneumonia than in those without. Multivariate analysis identified age, male sex, cerebrovascular disease, delayed antiviral therapy, and lower oxygen saturation to fraction of inspired oxygen ratio as independent risk factors for bacterial pneumonia co-infection. CONCLUSIONS: Co-infection with bacterial pneumonia significantly affected the outcomes of patients with COVID-19 during the XBB Omicron variant epidemic. Early antiviral therapy and targeted prevention strategies, particularly for patients with cerebrovascular disease, can help reduce the risk of bacterial pneumonia-associated complications.

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• Evaluation of mlstverse system for accurate subspecies identification and drug resistance prediction in Mycobacterium abscessus species.

  Arakaki W, Kinjo T, Kami W, Hashioka H, Nabeya D, Nagano H, Yoshida S, Tsuyuguchi K, Matsumoto Y, Nakamura S, Fujita J, Yamamoto K

  Microbiology spectrum ( Microbiology Spectrum )  13 ( 9 ) e0064325   2025.09 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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  UNLABELLED: Accurate subspecies identification and drug susceptibility testing (DST) are essential for appropriate clinical management, particularly in patients infected with Mycobacterium abscessus species (MABS). We developed a novel software, mlstverse, which uses multi-locus sequence typing to identify non-tuberculous mycobacteria (NTM) species, demonstrating rapid and accurate diagnostic performance. However, these studies included only a limited number of MABS samples. In this study, we focused on MABS and evaluated the diagnostic accuracy of the system for subspecies identification and drug resistance prediction for clarithromycin (CAM) and amikacin (AMK). A total of 56 clinical isolates, previously identified as MABS by conventional methods, were analyzed. The mlstverse identified two isolates as M. intracellulare and 54 isolates as MABS, with 28 identified as M. abscessus subsp. abscessus (MAB) and 26 as M. abscessus subsp. massiliense (MMA). All results obtained through mlstverse were fully consistent with the species/subspecies exhibiting the highest average nucleotide identity (ANI) values. In contrast to the identification by ANI values, the mlstverse system clearly distinguished between MABS subspecies, with the mean differences between the highest and second-highest MLST scores of 0.16 for MAB and 0.33 for MMA, respectively. The system predicted drug susceptibility to CAM and AMK with high concordance to phenotypic DST (CAM: 98.1%, AMK: 100%). These results suggest that mlstverse provides a reliable method for accurate subspecies identification and drug resistance prediction in MABS, supporting the potential of integrating portable next-generation sequencing technologies with real-time software analysis for improved diagnostic accuracy and treatment strategies in patients with NTM infections. IMPORTANCE: Accurate subspecies identification and drug susceptibility testing (DST) are essential for appropriate clinical management of Mycobacterium abscessus species (MABS) infections. We previously developed mlstverse, a novel software utilizing multi-locus sequence typing to identify non-tuberculous mycobacteria (NTM species, demonstrating rapid and accurate diagnostic performance. However, these studies included only a limited number of MABS samples. In this study, we focused on MABS and evaluated the diagnostic accuracy of the system for subspecies identification and drug resistance prediction for clarithromycin (CAM) and amikacin (AMK). We showed that mlstverse can clearly distinguish MAB subspecies compared to ANI values and predicted drug susceptibility to CAM and AMK with high concordance to phenotypic DST. The mlstverse system provides a reliable method for accurate subspecies identification and drug resistance prediction in MABS, supporting the potential of integrating portable next-generation sequencing technologies with real-time software analysis for improved diagnostic accuracy and treatment strategies in patients with NTM infections.

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• A retrospective observational study of the nosocomial outbreak caused by human rhinovirus A34.

  Fujita M, Kinjo T, Kami W, Arakaki W, Nabeya D, Kohama M, Tohyama J, Oki H, Motooka D, Nakamura S, Yamamoto K, Fujita J

  Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy ( Journal of Infection and Chemotherapy )  31 ( 9 ) 102778 - 102778   2025.09 [ Peer Review Accepted ]

  Type of publication: Research paper (scientific journal)

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  BACKGROUND: Past reports of nosocomial outbreak due to human rhinovirus (HRV) in adults are limited. We report a case of nosocomial outbreak of HRV-A34 in a long-term care facility with a literature review. METHODS: Multiplex real-time polymerase chain reaction assay (Allplex™ RV Essential Assay) was used for the detection of HRV. After whole genome sequencing (WGS), genomic data of HRV-A strains obtained from the GenBank database were used for phylogenetic comparison with outbreak strains. RESULTS: A nosocomial outbreak of HRV occurred between August 22 and September 4, 2021. During the outbreak, 17 patients had respiratory symptoms and 14 patients were positive for HRV. Additionally, HRV was detected in nine asymptomatic patients. The attack rate reached 58 %. HRV was identified five days after the onset of index case and the outbreak was terminated in 13 days. There were no significant differences on their median age (37 vs 44 years old, p = 0.1221) and sex (male gender 61 % vs 39 %, p = 1.000) between symptomatic and asymptomatic HRV patients. No patients developed pneumonia and died. WGS showed that outbreak strains were genetically identical and belonged to the HRV-A34. Literature review showed past outbreaks were caused by either HRV-A or HRV-C, and the mortality rate was reported to be 22 % at highest. The present report is the first case of nosocomial outbreak of HRV-A34. CONCLUSION: Although nosocomial HRV infection is difficult to suppress, even with strengthened infection control measures, prompt identification of HRV is important. HRV should not be underestimated, especially in long-term care facilities.

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Books 【 display / non-display 】

Books 【 display / non-display 】

• Influenza -Advances in Diagnosis and Management-

  Kinjo T, Fujita J ( Part: Multiple Authorship ,  Differential diagnosis between influenza and other respiratory viral infections: what are the differential diagnoses? )

  Springer Singapore  2021

• Influenza -Advances in Diagnosis and Management-

  Kinjo T, Fujita J ( Part: Multiple Authorship ,  Differential diagnosis between influenza and other respiratory viral infections: what are the differential diagnoses? )

  Springer Singapore  2021

Other Papers 【 display / non-display 】

Other Papers 【 display / non-display 】

• ベリムマブが有効であった全身性エリテマトーデスによる間質性肺炎の一例

  金城 武士, 石田 明夫, 藤田 次郎

  日本臨床免疫学会総会プログラム・抄録集 ( 日本臨床免疫学会 )  47回   130 - 130   2019.10

   

• クリゾチニブ内服6年で完全奏効を維持しているALK融合遺伝子陽性肺腺がんの1例

  古堅 誠, 柴原 大典, 笠島 志穂, 瀬戸口 倫香, 山入端 一貴, 兼久 梢, 山城 朋子, 橋岡 寛恵, 新垣 若子, 鍋谷 大二郎, 仲村 秀太, 金城 武士, 宮城 一也, 原永 修作, 藤田 次郎

  肺癌 ( (NPO)日本肺癌学会 )  59 ( 3 ) 306 - 306   2019.06

   

• 器質化肺炎にて発症し7年後に全身性強皮症の診断に至った1例

  宮城 一也, 當銘 玲央, 池宮城 七重, 新垣 若子, 金城 武士, 原永 修作, 藤田 次郎

  気管支学 ( (NPO)日本呼吸器内視鏡学会 )  41 ( Suppl. ) S359 - S359   2019.06

   

• 免疫抑制剤使用中に出現,消退を繰り返したスリガラス様陰影の診断に際し種々のアプローチを要した一例

  仲間 海人, 宮城 一也, 柴原 大典, 山入端 一貴, 橋岡 寛恵, 仲村 秀太, 金城 武士, 原永 修作, 健山 正男, 藤田 次郎

  沖縄医学会雑誌 ( 沖縄県医師会医学会 )  58 ( 1 ) 81 - 81   2019.06

   

• AIDS患者のMAC症(M.avium感染症)に経気道感染はあり得るのか?

  日比谷 健司, 健山 正男, 稲嶺 盛史, 田里 大輔, 仲村 秀太, 宮城 一也, 古堅 誠, 金城 武士, 屋良 さとみ, 原永 修作, 比嘉 太, 藤田 次郎

  結核 ( (一社)日本結核病学会 )  94 ( 3 ) 337 - 337   2019.03

   

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Grant-in-Aid for Scientific Research 【 display / non-display 】

Grant-in-Aid for Scientific Research 【 display / non-display 】

• Genomic Epidemiological Study of Mycobacteria circulating in Indonesia

  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))

  Project Year: 2020.10  -  2023.03 

  Direct: 14,300,000 (YEN)  Overheads: 18,590,000 (YEN)  Total: 4,290,000 (YEN)