Bacteria and viruses in the nasopharynx immediately prior to onset of acute lower respiratory infections in Indigenous Australian children

  • Heidi C. Smith-VaughanEmail author
  • Michael J. Binks
  • Jemima Beissbarth
  • Anne B. Chang
  • Gabrielle B. McCallum
  • Ian M. Mackay
  • Peter S. Morris
  • Robyn L. Marsh
  • Paul J. Torzillo
  • Danielle F. Wurzel
  • Keith Grimwood
  • Elizabeth Nosworthy
  • Jane E. Gaydon
  • Amanda J. Leach
  • Barbara MacHunter
  • Mark D. Chatfield
  • Theo P. Sloots
  • Allen C. Cheng
Original Article


Acute lower respiratory infection (ALRI) is a major cause of hospitalization for Indigenous children in remote regions of Australia. The associated microbiology remains unclear. Our aim was to determine whether the microbes present in the nasopharynx before an ALRI were associated with its onset. A retrospective case-control/crossover study among Indigenous children aged up to 2 years. ALRI cases identified by medical note review were eligible where nasopharyngeal swabs were available: (1) 0–21 days before ALRI onset (case); (2) 90–180 days before ALRI onset (same child controls); and (3) from time and age-matched children without ALRI (different child controls). PCR assays determined the presence and/or load of selected respiratory pathogens. Among 104 children (182 recorded ALRI episodes), 120 case-same child control and 170 case-different child control swab pairs were identified. Human adenoviruses (HAdV) were more prevalent in cases compared to same child controls (18 vs 7%; OR = 3.08, 95% CI 1.22–7.76, p = 0.017), but this association was not significant in cases versus different child controls (15 vs 10%; OR = 1.93, 95% CI 0.97–3.87 (p = 0.063). No other microbes were more prevalent in cases compared to controls. Streptococcus pneumoniae (74%), Haemophilus influenzae (75%) and Moraxella catarrhalis (88%) were commonly identified across all swabs. In a pediatric population with a high detection rate of nasopharyngeal microbes, HAdV was the only pathogen detected in the period before illness presentation that was significantly associated with ALRI onset. Detection of other potential ALRI pathogens was similar between cases and controls.


Acute lower respiratory infection Bacteria Virus Adenovirus 



We wish to thank the families who participated in these studies. We also thank the Menzies Child Health Respiratory Team members Lesley Versteegh, Clare Wilson and Cate Wilson for assisting GBM with clinical data extraction, and Menzies HealthLAB team for providing study feedback to the community.


This work was supported by the Australian National Health and Medical Research Council (NHMRC, GNT1023781). This work forms part of an NHMRC Centre for Research Excellence for Lung Health in Aboriginal and Torres Strait Islander children (GNT1079557). HSV is supported by a Fellowship under the NHMRC-funded HOT NORTH collaboration (GNT1131932). MJB, GBM and RLM are supported by NHMRC Early Career Fellowships (GNT1088733, GNT1111705, GNT1034703). AJL is supported by a NHMRC Research Fellowship (GNT1020561). ABC is funded by a NHMRC Practitioner Fellowship (1058213). ACC is supported by a Career Development Fellowship (1068732). Community feedback of the study findings was through Menzies HealthLAB supported by the Rotary Club of Darwin. The contents of the published materials are solely the responsibility of the author and do not reflect the views of NHMRC.

Compliance with ethical standards

Conflict of interest

AJL and PSM received research grant funding from Wyeth (now Pfizer) for one of the original studies from which data for this analysis were derived. AJL currently receives research grant funding from GlaxoSmithKline to support infrastructure costs of pneumococcal conjugate vaccine research in remote areas (the OUTREACH project). These both are considered to be low conflicts of interest. HSV, ABC, and KG received funding from the NHMRC (Australia) related to this study; this is not considered a conflict of interest.

Ethical approval

The Human Research Ethics Committees of the NT Department of Health and Menzies School of Health Research (2011-1668) approved this retrospective study.

Informed consent

Written informed consent was obtained in the original studies. In the original studies all procedures involving human participants were in accordance with the ethical standards of the institutional human research ethics committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

The results of this study were presented at the 10th International Symposium on Pneumococci and Pneumococcal Diseases in Glasgow, Scotland, 26–30 June, 2016.

Supplementary material

10096_2018_3314_MOESM1_ESM.docx (40 kb)
ESM 1 (DOCX 39 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Heidi C. Smith-Vaughan
    • 1
    • 2
    Email author
  • Michael J. Binks
    • 1
  • Jemima Beissbarth
    • 1
  • Anne B. Chang
    • 1
    • 3
  • Gabrielle B. McCallum
    • 1
  • Ian M. Mackay
    • 4
    • 5
  • Peter S. Morris
    • 1
    • 6
  • Robyn L. Marsh
    • 1
  • Paul J. Torzillo
    • 7
  • Danielle F. Wurzel
    • 8
  • Keith Grimwood
    • 2
    • 9
    • 10
  • Elizabeth Nosworthy
    • 1
  • Jane E. Gaydon
    • 11
  • Amanda J. Leach
    • 1
  • Barbara MacHunter
    • 1
  • Mark D. Chatfield
    • 1
    • 11
  • Theo P. Sloots
    • 12
  • Allen C. Cheng
    • 13
    • 14
  1. 1.Menzies School of Health ResearchCharles Darwin UniversityDarwinAustralia
  2. 2.School of MedicineGriffith UniversityGold CoastAustralia
  3. 3.Lady Cilento Children’s HospitalQueensland University of TechnologyBrisbaneAustralia
  4. 4.Faculty of Medicine, Child Health Research CentreThe University of QueenslandBrisbaneAustralia
  5. 5.Department of Health, Public and Environmental Health Virology LaboratoryForensic and Scientific ServicesArcherfieldAustralia
  6. 6.Royal Darwin HospitalDarwinAustralia
  7. 7.Royal Prince Alfred HospitalSydneyAustralia
  8. 8.Murdoch Childrens Research InstituteThe Royal Children’s HospitalMelbourneAustralia
  9. 9.Menzies Health Institute QueenslandGriffith UniversityGold CoastAustralia
  10. 10.Departments of Infectious Disease and PaediatricsGold Coast HealthGold CoastAustralia
  11. 11.QIMR Berghofer Medical Research InstituteBrisbaneAustralia
  12. 12.UQ Centre for Child Health ResearchThe University of QueenslandBrisbaneAustralia
  13. 13.Department of Infectious DiseasesAlfred HealthMelbourneAustralia
  14. 14.School of Public Health and Preventive MedicineMonash UniversityMelbourneAustralia

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