Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study

Russell, C. D. et al. (2021) Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe, 2(8), e354-e365. (doi: 10.1016/S2666-5247(21)00090-2) (PMID:34100002) (PMCID:PMC8172149)

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Background: Microbiological characterisation of co-infections and secondary infections in patients with COVID-19 is lacking, and antimicrobial use is high. We aimed to describe microbiologically confirmed co-infections and secondary infections, and antimicrobial use, in patients admitted to hospital with COVID-19. Methods: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol UK (CCP-UK) study is an ongoing, prospective cohort study recruiting inpatients from 260 hospitals in England, Scotland, and Wales, conducted by the ISARIC Coronavirus Clinical Characterisation Consortium. Patients with a confirmed or clinician-defined high likelihood of SARS-CoV-2 infection were eligible for inclusion in the ISARIC WHO CCP-UK study. For this specific study, we excluded patients with a recorded negative SARS-CoV-2 test result and those without a recorded outcome at 28 days after admission. Demographic, clinical, laboratory, therapeutic, and outcome data were collected using a prespecified case report form. Organisms considered clinically insignificant were excluded. Findings: We analysed data from 48 902 patients admitted to hospital between Feb 6 and June 8, 2020. The median patient age was 74 years (IQR 59–84) and 20 786 (42·6%) of 48 765 patients were female. Microbiological investigations were recorded for 8649 (17·7%) of 48 902 patients, with clinically significant COVID-19-related respiratory or bloodstream culture results recorded for 1107 patients. 762 (70·6%) of 1080 infections were secondary, occurring more than 2 days after hospital admission. Staphylococcus aureus and Haemophilus influenzae were the most common pathogens causing respiratory co-infections (diagnosed ≤2 days after admission), with Enterobacteriaceae and S aureus most common in secondary respiratory infections. Bloodstream infections were most frequently caused by Escherichia coli and S aureus. Among patients with available data, 13 390 (37·0%) of 36 145 had received antimicrobials in the community for this illness episode before hospital admission and 39 258 (85·2%) of 46 061 patients with inpatient antimicrobial data received one or more antimicrobials at some point during their admission (highest for patients in critical care). We identified frequent use of broad-spectrum agents and use of carbapenems rather than carbapenem-sparing alternatives. Interpretation: In patients admitted to hospital with COVID-19, microbiologically confirmed bacterial infections are rare, and more likely to be secondary infections. Gram-negative organisms and S aureus are the predominant pathogens. The frequency and nature of antimicrobial use are concerning, but tractable targets for stewardship interventions exist. Funding: National Institute for Health Research (NIHR), UK Medical Research Council, Wellcome Trust, UK Department for International Development, Bill & Melinda Gates Foundation, EU Platform for European Preparedness Against (Re-)emerging Epidemics, NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool, and NIHR HPRU in Respiratory Infections at Imperial College London.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Robertson, Professor David and Palmarini, Professor Massimo and Seaton, Dr Andrew and Da Silva Filipe, Dr Ana and Ho, Dr Antonia and Scott, Dr Janet and Thomson, Professor Emma
Authors: Russell, C. D., Fairfield, C. J., Drake, T. M., Turtle, L., Seaton, R. A., Wootton, D. G., Sigfrid, L., Harrison, E. M., Docherty, A. B., de Silva, T. I., Egan, C., Pius, R., Hardwick, H. E., Merson, L., Girvan, M., Dunning, J., Nguyen-Van-Tam, J. S., Openshaw, P. J. M., Baillie, J. K., Semple, M. G., Ho, A., Baillie, J. K., Semple, M. G., Openshaw, P. J., Carson, G., Alex, B., Bach, B., Barclay, W. S., Bogaert, D., Chand, M., Cooke, G. S., Docherty, A. B., Dunning, J., da Silva Filipe, A., Fletcher, T., Green, C. A., Harrison, E. M., Hiscox, J. A., Ho, A. Y., Horby, P. W., Ijaz, S., Khoo, S., Klenerman, P., Law, A., Lim, W. S., Mentzer, A. J., Merson, L., Meynert, A. M., Noursadeghi, M., Moore, S. C., Palmarini, M., Paxton, W. A., Pollakis, G., Price, N., Rambaut, A., Robertson, D. L., Russell, C. D., Sancho-Shimizu, V., Scott, J. T., de Silva, T., Sigfrid, L., Solomon, T., Sriskandan, S., Stuart, D., Summers, C., Tedder, R. S., Thomson, E. C., Thompson, A. R., Thwaites, R. S., Turtle, L. C., Gupta, R. K., Palmieri, C., Zambon, M., Hardwick, H., Donohue, C., Lyons, R., Griffiths, F., Oosthuyzen, W., Norman, L., Pius, R., Drake, T. M., Fairfield, C. J., Knight, S. R., Mclean, K. A., Murphy, D., Shaw, C. A., Dalton, J., Girvan, M., Saviciute, E., Roberts, S., Harrison, J., Marsh, L., Connor, M., Halpin, S., Jackson, C., Gamble, C., Leeming, G., Law, A., Wham, M., Clohisey, S., Hendry, R., Scott-Brown, J., Greenhalf, W., Shaw, V., McDonald, S. E., Keating, S., Ahmed, K. A., Armstrong, J. A., Ashworth, M., Asiimwe, I. G., Bakshi, S., Barlow, S. L., Booth, L., Brennan, B., Bullock, K., Catterall, B. W., Clark, J. J., Clarke, E. A., Cole, S., Cooper, L., Cox, H., Davis, C., Dincarslan, O., Dunn, C., Dyer, P., Elliott, A., Evans, A., Finch, L., Fisher, L. W., Foster, T., Garcia-Dorival, I., Greenhalf, W., Gunning, P., Hartley, C., Jensen, R. L., Jones, C. B., Jones, T. R., Khandaker, S., King, K., Kiy, R. T., Koukorava, C., Lake, A., Lant, S., Latawiec, D., Lavelle-Langham, L., Lefteri, D., Lett, L., Livoti, L. A., Mancini, M., McDonald, S., McEvoy, L., McLauchlan, J., Metelmann, S., Miah, N. S., Middleton, J., Mitchell, J., Moore, S. C., Murphy, E. G., Penrice-Randal, R., Pilgrim, J., Prince, T., Reynolds, W., Ridley, P. M., Sales, D., Shaw, V. E., Shears, R. K., Small, B., Subramaniam, K. S., Szemiel, A., Taggart, A., Tanianis-Hughes, J., Thomas, J., Trochu, E., van Tonder, L., Wilcock, E., Zhang, J. E., Flaherty, L., Maziere, N., Cass, E., Doce Carracedo, A., Carlucci, N., Holmes, A., Massey, H., Murphy, L., Wrobel, N., McCafferty, S., Morrice, K., MacLean, A., Adeniji, K., Agranoff, D., Agwuh, K., Ail, D., Aldera, E. L., Alegria, A., Angus, B., Ashish, A., Atkinson, D., Bari, S., Barlow, G., Barnass, S., Barrett, N., Bassford, C., Basude, S., Baxter, D., Beadsworth, M., Bernatoniene, J., Berridge, J., Best, N., Bothma, P., Chadwick, D., Brittain-Long, R., Bulteel, N., Burden, T., Burtenshaw, A., Caruth, V., Chadwick, D., Chambler, D., Chee, N., Child, J., Chukkambotla, S., Clark, T., Collini, P., Cosgrove, C., Cupitt, J., Cutino-Moguel, M.-T., Dark, P., Dawson, C., Dervisevic, S., Donnison, P., Douthwaite, S., DuRand, I., Dushianthan, A., Dyer, T., Evans, C., Eziefula, C., Fegan, C., Finn, A., Fullerton, D., Garg, S., Garg, S., Garg, A., Gkrania-Klotsas, E., Godden, J., Goldsmith, A., Graham, C., Hardy, E., Hartshorn, S., Harvey, D., Havalda, P., Hawcutt, D. B., Hobrok, M., Hodgson, L., Hormis, A., Jacobs, M., Jain, S., Jennings, P., Kaliappan, A., Kasipandian, V., Kegg, S., Kelsey, M., Kendall, J., Kerrison, C., Kerslake, I., Koch, O., Koduri, G., Koshy, G., Laha, S., Laird, S., Larkin, S., Leiner, T., Lillie, P., Limb, J., Linnett, V., Little, J., Lyttle, M., MacMahon, M., MacNaughton, E., Mankregod, R., Masson, H., Matovu, E., McCullough, K., McEwen, R., Meda, M., Mills, G., Minton, J., Mirfenderesky, M., Mohandas, K., Mok, Q., Moon, J., Moore, E., Morgan, P., Morris, C., Mortimore, K., Moses, S., Mpenge, M., Mulla, R., Murphy, M., Nagel, M., Nagarajan, T., Nelson, M., O'Shea, M. K., Otahal, I., Ostermann, M., Pais, M., Panchatsharam, S., Papakonstantino, D., Paraiso, H., Patel, B., Pattison, N., Pepperell, J., Peters, M., Phull, M., Pintus, S., Singh Pooni, J., Post, F., Price, D., Prout, R., Rae, N., Reschreiter, H., Reynolds, T., Richardson, N., Roberts, M., Roberts, D., Rose, A., Rousseau, G., Ryan, B., Saluja, T., Shah, A., Shanmuga, P., Sharma, A., Shawcross, A., Sizer, J., Shankar-Hari, M., Smith, R., Snelson, C., Spittle, N., Staines, N., Stambach, T., Stewart, R., Subudhi, P., Szakmany, T., Tatham, K., Thomas, J., Thompson, C., Thompson, R., Tridente, A., Tupper-Carey, D., Twagira, M., Ustianowski, A., Vallotton, N., Vincent-Smith, L., Visuvanathan, S., Vuylsteke, A., Waddy, S., Wake, R., Walden, A., Welters, I., Whitehouse, T., Whittaker, P., Whittington, A., Papineni, P., Wijesinghe, M., Williams, M., Wilson, L., Sarah, S., Winchester, S., Wiselka, M., Wolverson, A., Wootton, D. G., Workman, A., Yates, B., and Young, P.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Medicine, Dentistry & Nursing
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
Journal Name:Lancet Microbe
Publisher:Lancet Publishing Group
ISSN (Online):2666-5247
Published Online:02 June 2021
Copyright Holders:Copyright © 2021 The Authors
First Published:First published in Lancet Microbe 2(8): e354-e365
Publisher Policy:Reproduced under a Creative Commons License
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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
310665ISARIC - Coronavirus Clinical Characterisation ConsortiumAntonia HoMedical Research Council (MRC)MC_PC_19059 - 9815274III - Centre for Virus Research