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Yang CY, Chen RJ, Chou WL, Lee YJ, Lo YS. An Integrated Influenza Surveillance Framework Based on National Influenza-Like Illness Incidence and Multiple Hospital Electronic Medical Records for Early Prediction of Influenza Epidemics: Design and Evaluation. J Med Internet Res 2019; 21:e12341. [PMID: 30707099 PMCID: PMC6376337 DOI: 10.2196/12341] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 12/18/2018] [Accepted: 01/20/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Influenza is a leading cause of death worldwide and contributes to heavy economic losses to individuals and communities. Therefore, the early prediction of and interventions against influenza epidemics are crucial to reduce mortality and morbidity because of this disease. Similar to other countries, the Taiwan Centers for Disease Control and Prevention (TWCDC) has implemented influenza surveillance and reporting systems, which primarily rely on influenza-like illness (ILI) data reported by health care providers, for the early prediction of influenza epidemics. However, these surveillance and reporting systems show at least a 2-week delay in prediction, indicating the need for improvement. OBJECTIVE We aimed to integrate the TWCDC ILI data with electronic medical records (EMRs) of multiple hospitals in Taiwan. Our ultimate goal was to develop a national influenza trend prediction and reporting tool more accurate and efficient than the current influenza surveillance and reporting systems. METHODS First, the influenza expertise team at Taipei Medical University Health Care System (TMUHcS) identified surveillance variables relevant to the prediction of influenza epidemics. Second, we developed a framework for integrating the EMRs of multiple hospitals with the ILI data from the TWCDC website to proactively provide results of influenza epidemic monitoring to hospital infection control practitioners. Third, using the TWCDC ILI data as the gold standard for influenza reporting, we calculated Pearson correlation coefficients to measure the strength of the linear relationship between TMUHcS EMRs and regional and national TWCDC ILI data for 2 weekly time series datasets. Finally, we used the Moving Epidemic Method analyses to evaluate each surveillance variable for its predictive power for influenza epidemics. RESULTS Using this framework, we collected the EMRs and TWCDC ILI data of the past 3 influenza seasons (October 2014 to September 2017). On the basis of the EMRs of multiple hospitals, 3 surveillance variables, TMUHcS-ILI, TMUHcS-rapid influenza laboratory tests with positive results (RITP), and TMUHcS-influenza medication use (IMU), which reflected patients with ILI, those with positive results from rapid influenza diagnostic tests, and those treated with antiviral drugs, respectively, showed strong correlations with the TWCDC regional and national ILI data (r=.86-.98). The 2 surveillance variables-TMUHcS-RITP and TMUHcS-IMU-showed predictive power for influenza epidemics 3 to 4 weeks before the increase noted in the TWCDC ILI reports. CONCLUSIONS Our framework periodically integrated and compared surveillance data from multiple hospitals and the TWCDC website to maintain a certain prediction quality and proactively provide monitored results. Our results can be extended to other infectious diseases, mitigating the time and effort required for data collection and analysis. Furthermore, this approach may be developed as a cost-effective electronic surveillance tool for the early and accurate prediction of epidemics of influenza and other infectious diseases in densely populated regions and nations.
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Affiliation(s)
- Cheng-Yi Yang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Ray-Jade Chen
- Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Taipei Medical University Hospital, Taipei, Taiwan
| | - Wan-Lin Chou
- Taipei Medical University Hospital, Taipei, Taiwan
| | - Yuarn-Jang Lee
- Division of Infectious Disease, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Yu-Sheng Lo
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
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Swaan C, van den Broek A, Kretzschmar M, Richardus JH. Timeliness of notification systems for infectious diseases: A systematic literature review. PLoS One 2018; 13:e0198845. [PMID: 29902216 PMCID: PMC6002046 DOI: 10.1371/journal.pone.0198845] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/25/2018] [Indexed: 11/18/2022] Open
Abstract
Introduction Timely notification of infectious diseases is crucial for prompt response by public health services. Adequate notification systems facilitate timely notification. A systematic literature review was performed to assess outcomes of studies on notification timeliness and to determine which aspects of notification systems are associated with timely notification. Methodology Articles reviewing timeliness of notifications published between 2000 and 2017 were searched in Pubmed and Scopus. Using a standardized notification chain, timeliness of reporting system for each article was defined as either sufficient (≥ 80% notifications in time), partly sufficient (≥ 50–80%), or insufficient (< 50%) according to the article’s predefined timeframe, a standardized timeframe for all articles, and a disease specific timeframe. Electronic notification systems were compared with conventional methods (postal mail, fax, telephone, email) and mobile phone reporting. Results 48 articles were identified. In almost one third of the studies with a predefined timeframe (39), timeliness of notification systems was either sufficient or insufficient (11/39, 28% and 12/39, 31% resp.). Applying the standardized timeframe (45 studies) revealed similar outcomes (13/45, 29%, sufficient notification timeframe, vs 15/45, 33%, insufficient). The disease specific timeframe was not met by any study. Systems involving reporting by laboratories most often complied sufficiently with predefined or standardized timeframes. Outcomes were not related to electronic, conventional notification systems or mobile phone reporting. Electronic systems were faster in comparative studies (10/13); this hardly resulted in sufficient timeliness, neither according to predefined nor to standardized timeframes. Conclusion A minority of notification systems meets either predefined, standardized or disease specific timeframes. Systems including laboratory reporting are associated with timely notification. Electronic systems reduce reporting delay, but implementation needs considerable effort to comply with notification timeframes. During outbreak threats, patient, doctors and laboratory testing delays need to be reduced to achieve timely detection and notification. Public health authorities should incorporate procedures for this in their preparedness plans.
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Affiliation(s)
- Corien Swaan
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- * E-mail:
| | - Anouk van den Broek
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Mirjam Kretzschmar
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
- University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Khan Y, Fazli G, Henry B, de Villa E, Tsamis C, Grant M, Schwartz B. The evidence base of primary research in public health emergency preparedness: a scoping review and stakeholder consultation. BMC Public Health 2015; 15:432. [PMID: 25925775 PMCID: PMC4415223 DOI: 10.1186/s12889-015-1750-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Effective public health emergency preparedness and response systems are important in mitigating the impact of all-hazards emergencies on population health. The evidence base for public health emergency preparedness (PHEP) is weak, however, and previous reviews have noted a substantial proportion of anecdotal event reports. To investigate the body of research excluding the anecdotal reports and better understand primary and analytical research for PHEP, a scoping review was conducted with two objectives: first, to develop a thematic map focused on primary research; and second, to use this map to inform and guide an understanding of knowledge gaps relevant to research and practice in PHEP. METHODS A scoping review was conducted based on established methodology. Multiple databases of indexed and grey literature were searched based on concepts of public health, emergency, emergency management/preparedness and evaluation/evidence. Inclusion and exclusion criteria were applied iteratively. Primary research studies that were evidence-based or evaluative in nature were included in the final group of selected studies. Thematic analysis was conducted for this group. Stakeholder consultation was undertaken for the purpose of validating themes and identifying knowledge gaps. To accomplish this, a purposive sample of researchers and practicing professionals in PHEP or closely related fields was asked to complete an online survey and participate in an in-person meeting. Final themes and knowledge gaps were synthesized after stakeholder consultation. RESULTS Database searching yielded 3015 citations and article selection resulted in a final group of 58 articles. A list of ten themes from this group of articles was disseminated to stakeholders with the survey questions. Survey findings resulted in four cross-cutting themes and twelve stand-alone themes. Several key knowledge gaps were identified in the following themes: attitudes and beliefs; collaboration and system integration; communication; quality improvement and performance standards; and resilience. Resilience emerged as both a gap and a cross-cutting theme. Additional cross-cutting themes included equity, gender considerations, and high risk or at-risk populations. CONCLUSIONS In this scoping review of the literature enhanced by stakeholder consultation, key themes and knowledge gaps in the PHEP evidence base were identified which can be used to inform future practice-oriented research in PHEP.
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Affiliation(s)
- Yasmin Khan
- Public Health Ontario, 480 University Avenue, Suite 300, Toronto, ON, M5G 1V2, Canada.
- Division of Emergency Medicine, Department of Medicine, University of Toronto, 2075 Bayview Ave, C753, Toronto, ON, M4N 3M5, Canada.
| | - Ghazal Fazli
- Public Health Ontario, 480 University Avenue, Suite 300, Toronto, ON, M5G 1V2, Canada.
- School of Public Health and Health Systems, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
| | - Bonnie Henry
- British Columbia Centre for Disease Control, 655 W 12th Ave, Vancouver, BC, V5Z 4R4, Canada.
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, 2206 East Mall, Vancouver, BC, V6T 1Z3, Canada.
| | - Eileen de Villa
- Peel Public Health, 7120 Hurontario Street, P.O Box 667 - RPO Streetsville, Mississauga, ON, L5M 2C2, Canada.
- Dalla Lana School of Public Health, University of Toronto, 155 College St, Toronto, ON, M5T 3M7, Canada.
| | - Charoula Tsamis
- Public Health Ontario, 480 University Avenue, Suite 300, Toronto, ON, M5G 1V2, Canada.
| | - Moira Grant
- Public Health Ontario, 480 University Avenue, Suite 300, Toronto, ON, M5G 1V2, Canada.
| | - Brian Schwartz
- Public Health Ontario, 480 University Avenue, Suite 300, Toronto, ON, M5G 1V2, Canada.
- Dalla Lana School of Public Health, University of Toronto, 155 College St, Toronto, ON, M5T 3M7, Canada.
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Zhang Y, Li L, Dong X, Kong M, Gao L, Dong X, Xu W. Influenza surveillance and incidence in a rural area in China during the 2009/2010 influenza pandemic. PLoS One 2014; 9:e115347. [PMID: 25542003 PMCID: PMC4277345 DOI: 10.1371/journal.pone.0115347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 11/22/2014] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Most influenza surveillance is based on data from urban sentinel hospitals; little is known about influenza activity in rural communities. We conducted influenza surveillance in a rural region of China with the aim of detecting influenza activity in the 2009/2010 influenza season. METHODS The study was conducted from October 2009 to March 2010. Real-time polymerase chain reaction was used to confirm influenza cases. Over-the-counter (OTC) drug sales were daily collected in drugstores and hospitals/clinics. Space-time scan statistics were used to identify clusters of ILI in community. The incidence rate of ILI/influenza was estimated on the basis of the number of ILI/influenza cases detected by the hospitals/clinics. RESULTS A total of 434 ILI cases (3.88% of all consultations) were reported; 64.71% of these cases were influenza A (H1N1) pdm09. The estimated incidence rate of ILI and influenza were 5.19/100 and 0.40/100, respectively. The numbers of ILI cases and OTC drug purchases in the previous 7 days were strongly correlated (Spearman rank correlation coefficient [r] = 0.620, P = 0.001). Four ILI outbreaks were detected by space-time permutation analysis. CONCLUSIONS This rural community surveillance detected influenza A (H1N1) pdm09 activity and outbreaks in the 2009/2010 influenza season and enabled estimation of the incidence rate of influenza. It also provides a scientific data for public health measures.
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Affiliation(s)
- Ying Zhang
- Department of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Lin Li
- Department of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Xiaochun Dong
- Department of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Mei Kong
- Institute of Pathogenic Microbiology, Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Lu Gao
- Department of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, China
| | - Xiaojing Dong
- Hangu Centers for Disease Control and Prevention, Binhai New Area, Tianjin, China
| | - Wenti Xu
- Department of Infectious Disease, Tianjin Centers for Disease Control and Prevention, Tianjin, China
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Chandler DP, Griesemer SB, Cooney CG, Holmberg R, Thakore N, Mokhiber B, Belgrader P, Knickerbocker C, Schied J, St. George K. Rapid, simple influenza RNA extraction from nasopharyngeal samples. J Virol Methods 2012; 183:8-13. [PMID: 22425698 PMCID: PMC3348996 DOI: 10.1016/j.jviromet.2012.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 02/24/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
Abstract
This report describes the development and pre-clinical testing of a new, random-access RNA sample preparation system (TruTip) for nasopharyngeal samples. The system is based on a monolithic, porous nucleic acid binding matrix embedded within an aerosol-resistant pipette tip and can be operated with single or multi-channel pipettors. Equivalent extraction efficiencies were obtained between automated QIAcube and manual TruTip methods at 10(6) gene copies influenza A per mL nasopharyngeal aspirate. Influenza A and B amended into nasopharyngeal swabs (in viral transport medium) were detected by real-time RT-PCR at approximately 745 and 370 gene copies per extraction, respectively. RNA extraction efficiency in nasopharyngeal swabs was also comparable to that obtained on an automated QIAcube instrument over a range of input concentrations; the correlation between threshold cycles (or nucleic acid recovery) for TruTip and QIAcube-purified RNA was R(2)>0.99. Preclinical testing of TruTip on blinded nasopharyngeal swab samples resulted in 98% detection accuracy relative to a clinically validated easyMAG extraction method. The physical properties of the TruTip binding matrix and ability to customize its shape and dimensions likewise make it amenable to automation and/or fluidic integration.
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Affiliation(s)
| | - Sara B. Griesemer
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany NY 12208 and
| | | | - Rebecca Holmberg
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick MD 21701
| | - Nitu Thakore
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick MD 21701
| | - Becca Mokhiber
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick MD 21701
| | - Phillip Belgrader
- Akonni Biosystems, Inc., 400 Sagner Avenue, Suite 300, Frederick MD 21701
| | | | - Jeanmarie Schied
- Little Company of Mary Hospital, Pediatric Hospitalist Program, University of Chicago, 2800 West 95 Street, Evergreen Park, IL 60805
| | - Kirsten St. George
- Laboratory of Viral Diseases, Wadsworth Center, New York State Dept of Health, 120 New Scotland Avenue, Albany NY 12208 and
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