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Kim M, Park SJ, Park YJ, Choi J, Song J, Kim HJ, Chang J, Park S, Kim J, Lee H, Oh SN, Jeong S, Kim KH, Son JS, Park SM. Antibiotic Exposure and Risk of Parkinson Disease in South Korea: A Nationally Representative Retrospective Cohort Study. Neurol Clin Pract 2025; 15:e200400. [PMID: 39569393 PMCID: PMC11575412 DOI: 10.1212/cpj.0000000000200400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 09/03/2024] [Indexed: 11/22/2024]
Abstract
Background and Objectives Recent studies have suggested that antibiotics could be a contributing factor to Parkinson disease (PD), but validation in other population cohorts, such as Asians, is needed. This study examined the association between exposure to antibiotics and PD risk in the Korean population. Methods Using the National Health Insurance Service (NHIS) database, this population-level cohort research study from Korea included 298,379 people aged 40 years and older who underwent a national health examination in 2004-2005. Cumulative antibiotic exposure days were investigated over 4 years (2002-2005), and new cases of PD were followed for 14 years (2006-2019). Various covariates, such as infectious diseases, were considered in the analysis. Multivariable Cox proportional hazards regression was used to calculate adjusted hazard ratios (aHRs) and CIs for the PD risk from antibiotic exposure. Results PD risk was statistically significantly higher in those exposed to antibiotics for ≥121 days than in those not exposed to antibiotics (aHR, 1.29; 95% CI 1.07-1.55). In addition, compared with those exposed to antibiotics for 1-14 days, those exposed to antibiotics for ≥121 days had a higher risk of PD (aHR, 1.37; 95% CI 1.17-1.61). The results of sensitivity analyses that applied washout periods or extended antibiotic exposure periods were consistent with those of the main analyses. Discussion Extended usage of antibiotics was linked to a higher incidence of PD, even after controlling for several risk variables. Further research is needed to warrant the causation and mechanisms of antibiotic exposure and PD.
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Affiliation(s)
- Minkyung Kim
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Sun Jae Park
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Young Jun Park
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Jiwon Choi
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Jihun Song
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Hye Jun Kim
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Jooyoung Chang
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Sangwoo Park
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Jaewon Kim
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Hyeokjong Lee
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Si Nae Oh
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Seogsong Jeong
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Kyae Hyung Kim
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Joung Sik Son
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
| | - Sang Min Park
- Department of Biomedical Sciences (MK, SJP, JS, HJK, Jooyoung Chang, SP, JK, HL, SMP), Seoul National University Hospital, Seoul National University College of Medicine; College of Nursing (MK), Korea University, Seoul; Medical Research Center (YJP), Genomic Medicine Institute, Seoul National University; Department of Public Health (Jiwon Choi), Graduate School of Public Health, Seoul National University; Department of Family Medicine (SNO), National Health Insurance Service Ilsan Hospital, Goyang; Department of Medicine (SNO), Yonsei University Graduate School, Seoul; Department of Medical Informatics (SJ), Korea University College of Medicine, Seoul; Department of Family Medicine (KHK, SMP), Seoul National University Hospital, Seoul National University College of Medicine; Comprehensive Care Clinic (KHK), Public Healthcare Center, Seoul National University Hospital; and Department of Internal Medicine (JSS), Hanyang University Hospital, Seoul, South Korea
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Mechtersheimer D, Ding W, Xu X, Kim S, Sue C, Cao Y, Yang J. IMPACT: interpretable microbial phenotype analysis via microbial characteristic traits. Bioinformatics 2024; 41:btae702. [PMID: 39658259 PMCID: PMC11687948 DOI: 10.1093/bioinformatics/btae702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 08/23/2024] [Accepted: 12/09/2024] [Indexed: 12/12/2024] Open
Abstract
MOTIVATION The human gut microbiome, consisting of trillions of bacteria, significantly impacts health and disease. High-throughput profiling through the advancement of modern technology provides the potential to enhance our understanding of the link between the microbiome and complex disease outcomes. However, there remains an open challenge where current microbiome models lack interpretability of microbial features, limiting a deeper understanding of the role of the gut microbiome in disease. To address this, we present a framework that combines a feature engineering step to transform tabular abundance data to image format using functional microbial annotation databases, with a residual spatial attention transformer block architecture for phenotype classification. RESULTS Our model, IMPACT, delivers improved predictive accuracy performance across multiclass classification compared to similar methods. More importantly, our approach provides interpretable feature importance through image classification saliency methods. This enables the extraction of taxa markers (features) associated with a disease outcome and also their associated functional microbial traits and metabolites. AVAILABILITY AND IMPLEMENTATION IMPACT is available at https://github.com/SydneyBioX/IMPACT. We providedirect installation of IMPACT via pip.
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Affiliation(s)
- Daniel Mechtersheimer
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Wenze Ding
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Xiangnan Xu
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Sanghyun Kim
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Carolyn Sue
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Yue Cao
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited (D24H), New Territories, Hong Kong SAR, China
| | - Jean Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW 2006, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Laboratory of Data Discovery for Health Limited (D24H), New Territories, Hong Kong SAR, China
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