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Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data

Shanya Sivakumaran, Mohammad Al Sallakh Orcid Logo, Ronan Lyons Orcid Logo, Jennifer K. Quint Orcid Logo, Gwyneth Davies Orcid Logo

Journal of Infection, Volume: 86, Issue: 3, Pages: 233 - 238

Swansea University Authors: Shanya Sivakumaran, Mohammad Al Sallakh Orcid Logo, Ronan Lyons Orcid Logo, Gwyneth Davies Orcid Logo

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DOI (Published version): 10.1016/j.jinf.2023.01.012

Abstract

Objectives: To characterise microbiology testing and results associated with emergency admissions for acute exacerbation of COPD (AECOPD), and determine the accuracy of ICD-10 codes in retrospectively identifying laboratory-confirmed respiratory pathogens in this setting.Methods: Using person-level...

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Published in: Journal of Infection
ISSN: 0163-4453
Published: Elsevier BV 2023
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URI: https://cronfa.swan.ac.uk/Record/cronfa62439
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We further used these data to assess the accuracy of pathogen-specific ICD-10 codes.Results: We analysed data from 15,950 people who had 25,715 emergency admissions for COPD over the two-year period. 99.5% of admissions could be linked to a laboratory test within 7 days of admission date. Sputum was collected in 5,013 (19.5%) of admissions, and respiratory virus testing in 1,219 (4.7%). Where respiratory virus testing was undertaken, 46.7% returned any positive result. Influenza was the virus most frequently detected, in 21.5% of admissions where testing was conducted. ICD-10 codes exhibited low sensitivity in detecting laboratory-confirmed respiratory pathogens.Conclusions: In people admitted to hospital with AECOPD, increased testing for respiratory viruses could enable more effective antibiotic stewardship and isolation of cases. Linkage with microbiology data achieves more accurate and reliable case definitions.</abstract><type>Journal Article</type><journal>Journal of Infection</journal><volume>86</volume><journalNumber>3</journalNumber><paginationStart>233</paginationStart><paginationEnd>238</paginationEnd><publisher>Elsevier BV</publisher><placeOfPublication/><isbnPrint/><isbnElectronic/><issnPrint>0163-4453</issnPrint><issnElectronic/><keywords>Respiratory Tract Infections, Pulmonary Disease, Chronic Obstructive, Electronic Health Records.</keywords><publishedDay>1</publishedDay><publishedMonth>3</publishedMonth><publishedYear>2023</publishedYear><publishedDate>2023-03-01</publishedDate><doi>10.1016/j.jinf.2023.01.012</doi><url>http://dx.doi.org/10.1016/j.jinf.2023.01.012</url><notes/><college>COLLEGE NANME</college><department>Medical School</department><CollegeCode>COLLEGE CODE</CollegeCode><DepartmentCode>MEDS</DepartmentCode><institution>Swansea University</institution><apcterm>SU Library paid the OA fee (TA Institutional Deal)</apcterm><funders>This study was funded by Swansea University Medical School with the support of BREATHE &#x2013; The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK.</funders><projectreference/><lastEdited>2023-04-21T12:48:14.0550881</lastEdited><Created>2023-01-25T10:20:54.4602151</Created><path><level id="1">Faculty of Medicine, Health and Life Sciences</level><level id="2">Swansea University Medical School - Health Data Science</level></path><authors><author><firstname>Shanya</firstname><surname>Sivakumaran</surname><order>1</order></author><author><firstname>Mohammad</firstname><surname>Al Sallakh</surname><orcid>0000-0002-8333-7279</orcid><order>2</order></author><author><firstname>Ronan</firstname><surname>Lyons</surname><orcid>0000-0001-5225-000X</orcid><order>3</order></author><author><firstname>Jennifer K.</firstname><surname>Quint</surname><orcid>0000-0003-0149-4869</orcid><order>4</order></author><author><firstname>Gwyneth</firstname><surname>Davies</surname><orcid>0000-0003-1218-1008</orcid><order>5</order></author></authors><documents><document><filename>62439__27091__60fdb427bb9b40568b3d6f11a93e0caf.pdf</filename><originalFilename>62439.VOR.pdf</originalFilename><uploaded>2023-04-18T11:33:35.9162801</uploaded><type>Output</type><contentLength>483002</contentLength><contentType>application/pdf</contentType><version>Version of Record</version><cronfaStatus>true</cronfaStatus><documentNotes>Distributed under the terms of a Creative Commons Attribution 4.0 License.</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language><licence>https://creativecommons.org/licenses/by/4.0/</licence></document></documents><OutputDurs/></rfc1807>
spelling 2023-04-21T12:48:14.0550881 v2 62439 2023-01-25 Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data 2799501bc10dea3008518d41ca0339a2 Shanya Sivakumaran Shanya Sivakumaran true false 6efc53139ba1416418a6c6e584a25f2d 0000-0002-8333-7279 Mohammad Al Sallakh Mohammad Al Sallakh true false 83efcf2a9dfcf8b55586999d3d152ac6 0000-0001-5225-000X Ronan Lyons Ronan Lyons true false 92d69cf8519a334ced3f55142c811d95 0000-0003-1218-1008 Gwyneth Davies Gwyneth Davies true false 2023-01-25 MEDS Objectives: To characterise microbiology testing and results associated with emergency admissions for acute exacerbation of COPD (AECOPD), and determine the accuracy of ICD-10 codes in retrospectively identifying laboratory-confirmed respiratory pathogens in this setting.Methods: Using person-level data from the Secure Anonymised Information Linkage Databank in Wales, we extracted emergency admissions for COPD from 1/12/2016 to 30/11/2018 and undertook linkage of admissions data to microbiology data to identify laboratory-confirmed infection. We further used these data to assess the accuracy of pathogen-specific ICD-10 codes.Results: We analysed data from 15,950 people who had 25,715 emergency admissions for COPD over the two-year period. 99.5% of admissions could be linked to a laboratory test within 7 days of admission date. Sputum was collected in 5,013 (19.5%) of admissions, and respiratory virus testing in 1,219 (4.7%). Where respiratory virus testing was undertaken, 46.7% returned any positive result. Influenza was the virus most frequently detected, in 21.5% of admissions where testing was conducted. ICD-10 codes exhibited low sensitivity in detecting laboratory-confirmed respiratory pathogens.Conclusions: In people admitted to hospital with AECOPD, increased testing for respiratory viruses could enable more effective antibiotic stewardship and isolation of cases. Linkage with microbiology data achieves more accurate and reliable case definitions. Journal Article Journal of Infection 86 3 233 238 Elsevier BV 0163-4453 Respiratory Tract Infections, Pulmonary Disease, Chronic Obstructive, Electronic Health Records. 1 3 2023 2023-03-01 10.1016/j.jinf.2023.01.012 http://dx.doi.org/10.1016/j.jinf.2023.01.012 COLLEGE NANME Medical School COLLEGE CODE MEDS Swansea University SU Library paid the OA fee (TA Institutional Deal) This study was funded by Swansea University Medical School with the support of BREATHE – The Health Data Research Hub for Respiratory Health [MC_PC_19004], which is funded through the UK Research and Innovation Industrial Strategy Challenge Fund and delivered through Health Data Research UK. 2023-04-21T12:48:14.0550881 2023-01-25T10:20:54.4602151 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Health Data Science Shanya Sivakumaran 1 Mohammad Al Sallakh 0000-0002-8333-7279 2 Ronan Lyons 0000-0001-5225-000X 3 Jennifer K. Quint 0000-0003-0149-4869 4 Gwyneth Davies 0000-0003-1218-1008 5 62439__27091__60fdb427bb9b40568b3d6f11a93e0caf.pdf 62439.VOR.pdf 2023-04-18T11:33:35.9162801 Output 483002 application/pdf Version of Record true Distributed under the terms of a Creative Commons Attribution 4.0 License. true eng https://creativecommons.org/licenses/by/4.0/
title Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
spellingShingle Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
Shanya Sivakumaran
Mohammad Al Sallakh
Ronan Lyons
Gwyneth Davies
title_short Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
title_full Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
title_fullStr Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
title_full_unstemmed Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
title_sort Estimating the contribution of respiratory pathogens to acute exacerbations of COPD using routine data
author_id_str_mv 2799501bc10dea3008518d41ca0339a2
6efc53139ba1416418a6c6e584a25f2d
83efcf2a9dfcf8b55586999d3d152ac6
92d69cf8519a334ced3f55142c811d95
author_id_fullname_str_mv 2799501bc10dea3008518d41ca0339a2_***_Shanya Sivakumaran
6efc53139ba1416418a6c6e584a25f2d_***_Mohammad Al Sallakh
83efcf2a9dfcf8b55586999d3d152ac6_***_Ronan Lyons
92d69cf8519a334ced3f55142c811d95_***_Gwyneth Davies
author Shanya Sivakumaran
Mohammad Al Sallakh
Ronan Lyons
Gwyneth Davies
author2 Shanya Sivakumaran
Mohammad Al Sallakh
Ronan Lyons
Jennifer K. Quint
Gwyneth Davies
format Journal article
container_title Journal of Infection
container_volume 86
container_issue 3
container_start_page 233
publishDate 2023
institution Swansea University
issn 0163-4453
doi_str_mv 10.1016/j.jinf.2023.01.012
publisher Elsevier BV
college_str Faculty of Medicine, Health and Life Sciences
hierarchytype
hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Health Data Science{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Health Data Science
url http://dx.doi.org/10.1016/j.jinf.2023.01.012
document_store_str 1
active_str 0
description Objectives: To characterise microbiology testing and results associated with emergency admissions for acute exacerbation of COPD (AECOPD), and determine the accuracy of ICD-10 codes in retrospectively identifying laboratory-confirmed respiratory pathogens in this setting.Methods: Using person-level data from the Secure Anonymised Information Linkage Databank in Wales, we extracted emergency admissions for COPD from 1/12/2016 to 30/11/2018 and undertook linkage of admissions data to microbiology data to identify laboratory-confirmed infection. We further used these data to assess the accuracy of pathogen-specific ICD-10 codes.Results: We analysed data from 15,950 people who had 25,715 emergency admissions for COPD over the two-year period. 99.5% of admissions could be linked to a laboratory test within 7 days of admission date. Sputum was collected in 5,013 (19.5%) of admissions, and respiratory virus testing in 1,219 (4.7%). Where respiratory virus testing was undertaken, 46.7% returned any positive result. Influenza was the virus most frequently detected, in 21.5% of admissions where testing was conducted. ICD-10 codes exhibited low sensitivity in detecting laboratory-confirmed respiratory pathogens.Conclusions: In people admitted to hospital with AECOPD, increased testing for respiratory viruses could enable more effective antibiotic stewardship and isolation of cases. Linkage with microbiology data achieves more accurate and reliable case definitions.
published_date 2023-03-01T20:31:52Z
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