Throat swabs in children with respiratory tract infection: Associations with clinical presentation and potential targets for point-of-care testing

Hannah V. Thornton*, Alastair D. Hay, Niamh M. Redmond, Sophie L. Turnbull, Hannah Christensen, Tim J. Peters, John P. Leeming, Andrew Lovering, Barry Vipond, Peter Muir, Peter S. Blair

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Citations (Scopus)


Background and objectives. Diagnostic uncertainty over respiratory tract infections (RTIs) in primary care contributes to over-prescribing of antibiotics and drives antibiotic resistance. If symptoms and signs predict respiratory tract microbiology, they could help clinicians target antibiotics to bacterial infection. This study aimed to determine relationships between symptoms and signs in children presenting to primary care and microbes from throat swabs. Methods. Cross-sectional study of children ≥3 months to < 16 years presenting with acute cough and RTI, with subset follow-up. Associations and area under receiver operating curve (AUROC) statistics sought between clinical presentation and baseline microbe detection. Microbe prevalence compared between baseline (symptomatic) and follow-up (asymptomatic) visits. Results. At baseline, ≥1 bacteria was detected in 1257/2113 (59.5%) children and ≥1 virus in 894/2127 (42%) children. Clinical presentation was not associated with detection of ≥1 bacteria [AUROC 0.54 (95% CI 0.52-0.56)] or ≥1 virus [0.64 (95% CI 0.61-0.66)]. Individually, only respiratory syncytial virus (RSV) was associated with clinical presentation [AUROC 0.80 (0.77-0.84)]. Prevalence fell between baseline and follow-up; more so in viruses (68% versus 26%, P < 0.001) than bacteria (56% versus 40%, P = 0.01); greatest reductions seen in RSV, influenza B and Haemophilus influenzae. Conclusion. Findings demonstrate that clinical presentation cannot distinguish the presence of bacteria or viruses in the upper respiratory tract. However, individual and overall microbe prevalence was greater when children were unwell than when well, providing some evidence that upper respiratory tract microbes may be the cause or consequence of the illness. If causal, selective microbial point-of-care testing could be beneficial.

Original languageEnglish
Pages (from-to)407-415
Number of pages9
JournalFamily Practice
Issue number4
Publication statusPublished - 1 Aug 2017

Bibliographical note

Funding Information:
The National Institute for Health Research funds the Programme Grant for Applied Research TARGET Programme grant at the University of Bristol and NHS Bristol Clinical Commissioning Group. The TARGET Programme is funded by the National Institute for Health Research’s Programme Grant for Applied Research Programme. This paper presents independent research funded by the National Institute for Health Research (NIHR) under its Programme Grant for Applied Research (Grant Reference Number RP-PG-0608-10018). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health. Hannah Christensen is a member of the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Evaluation of Interventions at University of Bristol in partnership with Public Health England (PHE). The views expressed in this publication are those of the authors and not necessarily those of the NHS, the NIHR, the Department of Health or Public Health England. Niamh Redmond’s time is supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care West (CLAHRC West) at University Hospitals Bristol NHS Foundation Trust. Alastair Hay is funded by NIHR Research Professorship (NIHR-RP-02-12-012). Index of Multiple Deprivation data: ©Crown Copyright 2006. Source: National Statistics / Ordnance Survey. The authors are extremely grateful to the children, parents/ carers and families who have participated in the study, all GP practices including recruiting clinicians, administrative and research contacts and all other staff whose participation made this study possible. We thank all our colleagues from the TARGET Programme, the TARGET Programme Management Group and the TARGET Programme Steering Committee (Sandra Eldridge, Nick Francis, Joe Kai, Victoria Senior, Anna Thursby-Pelham and Mireille Williams) for their time, expertise and support. We are grateful to the following individuals who have helped with the study; James Austin, Denis Baird, Tony Beard, Stephen Beckett, Issy Bray, Peter Brindle, Kate Brooks, Sue Broomfield, Joanna Cordell, Judy Cordell, Tania Crabb, Hazel Crabb-Wyke, Mike Crawford, Julie Cunningham, Christina Currie, Rachel Davies, Elizabeth Derodra, Elena Domenech, Stevo Durbaba, Felicity Elder, Lucy Feather, Caroline Footer, Emily Gale, Anna Gilbertson, Victoria Hardy, Rose Hawkins, Abigail Hay, Lisa Hird, Sandra Hollinghurst, Julie Hooper, Catherine Jameson, Jonathan Hubb, Grania Jenkins, Amy Jepps, Mari-Rose Kennedy, Michael Lawton, Mel Lewcock, Lyn Liddiard, Sandra Mulligan, Sharen O’Keefe, Lucy O’Reilly, Marilyn Peters, Aled Picton, Ilaria Pinna, Fiona Redmond, Isabel Richards, Kim Roden, Sharon Salt, Douglas Shedden, Ella Simmonds, Sue Smith, Carol Stanton, Kate Taylor, Elizabeth Thomas, Nicki Thorne, Sara Tonge, Abby Waterhouse, Eleanor Woodward. The TARGET study team acknowledges the support of the National Institute for Health Research, through the Comprehensive Clinical Research Network.

Funding Information:
Funding: this paper summarizes independent research funded by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0608-10018). Ethical approval: the TARGET cohort study and the follow-up study were approved by the South West Central Bristol Research Ethics Committee, UK (reference numbers 10/H0102/54 and 12/SW/0075 respectively) and research governance approvals obtained across all areas prior to the start of recruitment. Conflict of interest: during the past 5 years, PM has received funding and expenses from companies with an interest in diagnostic microbiology in RTI, including Nanosphere Inc and Hologic. HC reports receiving an honorarium from Sanofi Pasteur in 2015 and 2016,and consultancy fees from IMS Health and AstraZeneca all paid to her employer. All other authors declare no conflict of interest.

Publisher Copyright:
© The Author 2017. Published by Oxford University Press. All rights reserved.


  • Bronchitis
  • Common cold
  • Diagnostic tests
  • Laboratory
  • Pediatrics
  • Primary care
  • Ultrasound
  • Upper respiratory infections


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