Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission
Background: Healthcare-associated COVID-19 infections caused by SARS-CoV-2 have increased morbidity and mortality. Hospitals and skilled nursing facilities (SNFs) have been challenged by infection control and management. Methods: This case study presents an outbreak investigation in a COVID-19-desig...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | Journal of Microbiology, Immunology and Infection |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1684118223000026 |
| _version_ | 1797812089605062656 |
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| author | Yi-Chia Huang Hsiao-Chen Tu Han-Yueh Kuo Pei-Lan Shao Yu-Nong Gong Hui-Ying Weng Hung-Yu Shu Chiung-Hui Kuo Po-Hsien Kuo Chien-Hui Chien Chen-Chi Wu Ding-Cheng (Derrick) Chan Meng-Kun Tsai Shih-Feng Tsai Chong-Jen Yu |
| author_facet | Yi-Chia Huang Hsiao-Chen Tu Han-Yueh Kuo Pei-Lan Shao Yu-Nong Gong Hui-Ying Weng Hung-Yu Shu Chiung-Hui Kuo Po-Hsien Kuo Chien-Hui Chien Chen-Chi Wu Ding-Cheng (Derrick) Chan Meng-Kun Tsai Shih-Feng Tsai Chong-Jen Yu |
| author_sort | Yi-Chia Huang |
| collection | DOAJ |
| description | Background: Healthcare-associated COVID-19 infections caused by SARS-CoV-2 have increased morbidity and mortality. Hospitals and skilled nursing facilities (SNFs) have been challenged by infection control and management. Methods: This case study presents an outbreak investigation in a COVID-19-designated hospital and a hospital-based SNF. Real-time polymerase chain reaction (PCR) and other studies were performed on samples obtained from SNF residents, hospital patients, and healthcare workers (HCWs). The results of the laboratory tests and field epidemiological data were analyzed. Genome sequencing and phylogenetic analysis of SARS-CoV-2 were performed to identify the associations between cases. The tracer gas was released and recorded by a thermal imaging camera to investigate the spatial relations within clusters. Results: During the outbreak, 29 COVID-19 infections in 3 clusters were identified through hospital-wide, risk-guided, and symptom-driven PCR tests. This included 12 HCWs, 5 patients, and 12 SNF residents who had been hospitalized for at least 14 days. Serology tests did not identify any cases among the PCR-negative individuals. The phylogenetic analysis revealed that viral strains from the 3 clusters shared a common mutation of G3994T and were phylogenetically related, which suggested that this outbreak had a common source rather than multiple introductions from the community. Linked cases exhibited vertical spatial distribution, and the sulfur hexafluoride release test confirmed a potential airborne transmission. Conclusions: This report addressed the advantage of a multi-disciplinary team in outbreak investigation. Identifying an airborne transmission within an outbreak highlighted the importance of regular maintenance of ventilation systems. |
| first_indexed | 2024-03-13T07:33:20Z |
| format | Article |
| id | doaj.art-5ad903e71bea4c0cb5be61665517a67d |
| institution | Directory Open Access Journal |
| issn | 1684-1182 |
| language | English |
| last_indexed | 2024-03-13T07:33:20Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Microbiology, Immunology and Infection |
| spelling | doaj.art-5ad903e71bea4c0cb5be61665517a67d2023-06-04T04:23:25ZengElsevierJournal of Microbiology, Immunology and Infection1684-11822023-06-01563547557Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmissionYi-Chia Huang0Hsiao-Chen Tu1Han-Yueh Kuo2Pei-Lan Shao3Yu-Nong Gong4Hui-Ying Weng5Hung-Yu Shu6Chiung-Hui Kuo7Po-Hsien Kuo8Chien-Hui Chien9Chen-Chi Wu10Ding-Cheng (Derrick) Chan11Meng-Kun Tsai12Shih-Feng Tsai13Chong-Jen Yu14National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, TaiwanInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Corresponding author. No. 2, Sec. 1, Shengyi Rd., Zhubei City, Hsinchu County, Taiwan.National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, TaiwanResearch Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan; International Master Degree Program for Molecular Medicine in Emergency Viral Infection, Collage of Medicine, Chang Gung University, Taoyuan, TaiwanNational Yang-Ming University, Taipei, Taiwan; National Yang Ming Chiao Tung University, Taipei, TaiwanChang Jung Christian University, Tainan, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, TaiwanNational Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Department of Geriatrics and Gerontology, Department of Internal Medicine, National Taiwan University Hospital, Taipei, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, TaiwanInstitute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, TaiwanNational Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan; National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan; Corresponding author. No. 2, Sec. 1, Shengyi Rd., Zhubei City, Hsinchu County, Taiwan.Background: Healthcare-associated COVID-19 infections caused by SARS-CoV-2 have increased morbidity and mortality. Hospitals and skilled nursing facilities (SNFs) have been challenged by infection control and management. Methods: This case study presents an outbreak investigation in a COVID-19-designated hospital and a hospital-based SNF. Real-time polymerase chain reaction (PCR) and other studies were performed on samples obtained from SNF residents, hospital patients, and healthcare workers (HCWs). The results of the laboratory tests and field epidemiological data were analyzed. Genome sequencing and phylogenetic analysis of SARS-CoV-2 were performed to identify the associations between cases. The tracer gas was released and recorded by a thermal imaging camera to investigate the spatial relations within clusters. Results: During the outbreak, 29 COVID-19 infections in 3 clusters were identified through hospital-wide, risk-guided, and symptom-driven PCR tests. This included 12 HCWs, 5 patients, and 12 SNF residents who had been hospitalized for at least 14 days. Serology tests did not identify any cases among the PCR-negative individuals. The phylogenetic analysis revealed that viral strains from the 3 clusters shared a common mutation of G3994T and were phylogenetically related, which suggested that this outbreak had a common source rather than multiple introductions from the community. Linked cases exhibited vertical spatial distribution, and the sulfur hexafluoride release test confirmed a potential airborne transmission. Conclusions: This report addressed the advantage of a multi-disciplinary team in outbreak investigation. Identifying an airborne transmission within an outbreak highlighted the importance of regular maintenance of ventilation systems.http://www.sciencedirect.com/science/article/pii/S1684118223000026COVID-19Infectious disease outbreaksPhylogenetic analysisSulfur hexafluorideAirborne transmission |
| spellingShingle | Yi-Chia Huang Hsiao-Chen Tu Han-Yueh Kuo Pei-Lan Shao Yu-Nong Gong Hui-Ying Weng Hung-Yu Shu Chiung-Hui Kuo Po-Hsien Kuo Chien-Hui Chien Chen-Chi Wu Ding-Cheng (Derrick) Chan Meng-Kun Tsai Shih-Feng Tsai Chong-Jen Yu Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission Journal of Microbiology, Immunology and Infection COVID-19 Infectious disease outbreaks Phylogenetic analysis Sulfur hexafluoride Airborne transmission |
| title | Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| title_full | Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| title_fullStr | Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| title_full_unstemmed | Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| title_short | Outbreak investigation in a COVID-19 designated hospital: The combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| title_sort | outbreak investigation in a covid 19 designated hospital the combination of phylogenetic analysis and field epidemiology study suggesting airborne transmission |
| topic | COVID-19 Infectious disease outbreaks Phylogenetic analysis Sulfur hexafluoride Airborne transmission |
| url | http://www.sciencedirect.com/science/article/pii/S1684118223000026 |
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