Evidence map›Paper›PMID 40241660›Full record

ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2026

Nasopharyngeal Microbiota in South African Infants With Lower Respiratory Tract Infection: A Nested Case-Control Study of the Drakenstein Child Health Study.

Shantelle Claassen-Weitz, Yao Xia, Luke Hannan, Sugnet Gardner-Lubbe, Kilaza S Mwaikono, Stephanie Harris Mounaud, William C Nierman, Lesley Workman, Felix S Dube, Samantha Africa and 5 more

Abstract read
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In one paragraph

Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. bioRxiv : the preprint server for biology · 2026
    Article
  3. Review
  4. Review
  5. Lower respiratory tract co-infection ofFrontiers in cellular and infection microbiology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Shantelle Claassen-WeitzDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID 0000-0003-2175-3776
Yao XiaMarshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia.
Luke HannanDivision of Epidemiology and Biostatistics, School of Public Health and Family Medicine, University of Cape Town, Stellenbosch, South Africa.
Sugnet Gardner-LubbeDepartment of Statistics and Actuarial Science, Faculty of Economic and Management Sciences, Stellenbosch University, Stellenbosch, South Africa.ORCID 0000-0003-2762-9944
Kilaza S MwaikonoComputational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.ORCID 0000-0002-3598-7576
Stephanie Harris MounaudJ. Craig Venter Institute, Rockville, Maryland, USA.
William C NiermanJ. Craig Venter Institute, Rockville, Maryland, USA.ORCID 0000-0002-0425-9840
Lesley WorkmanSouth African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa.ORCID 0000-0002-3433-6106
Felix S DubeInstitute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Samantha AfricaDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID 0000-0002-7688-7344
Fadheela PatelDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID 0000-0001-5177-7416
Veronica AllenDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Lemese Ah Tow EdriesDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Heather J ZarSouth African Medical Research Council Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa.
Mark P NicolDivision of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.ORCID 0000-0002-1366-4805

Funding

The nasopharyngeal microbiome and respiratory disease in African childrenU01AI110466 · NIAID · UNIVERSITY OF CAPE TOWN · PI NICOL, MARK PATRICK, ZAR, HEATHER JOY · 2013 to 2016
$1.4M
Australian National Health and Medical Research CouncilDrakenstein Child Health StudyGates Foundation OPP1017579Gates Foundation OPP1017641Investigator Grant APP1174455L'Oréal-UNESCO For Women in ScienceNational Research Foundation of South AfricaNIAID NIH HHS U01 AI110466NIH HHS 1U01AI110466-01A1South African Medical Research Council
6 · The paper itself

Abstract

backgroundLower respiratory tract infections (LRTIs) in infants are caused by viral and bacterial infections. We investigated associations between LRTI and nasopharyngeal (NP) viruses and bacteria in South African infants.

methodsIn a birth cohort, LRTI cases were identified prospectively and age-matched with controls. NP swabs were tested using polymerase chain reaction and 16S RNA gene sequencing. We calculated adjusted conditional odds ratios (aORs) and used mixed-effects models to identify differentially abundant taxa and explore viral-bacterial interactions.

resultsA total of 888 case-control samples were tested. Respiratory syncytial virus (RSV) (aOR, 5.69 [95% confidence interval, 3.03-10.69]), human rhinovirus (HRV) (1.47 [1.03-2.09]), parainfluenza virus (3.46 [1.64-7.26]), adenovirus (1.99 [1.08-3.68]), enterovirus (2.32 [1.20-4.46]), Haemophilus influenzae (1.72 [1.25-2.37]), Klebsiella pneumoniae (2.66 [1.59-4.46]), and high-density Streptococcus pneumoniae (1.53 [1.01-2.32]) were associated with LRTI. LRTI was associated with decreased relative abundance of Dolosigranulum (q = .001), Corynebacterium (q = .091), and Neisseria (q = .004). In samples positive for RSV, Staphylococcus and Alloprevotella relative abundance was higher in controls compared to cases. In samples positive for parainfluenza virus or HRV, Haemophilus relative abundance was higher in cases. Detection of cytomegalovirus (CMV) in controls was associated with reduced Corynebacterium, Dolosigranulum, and Staphylococcus.

conclusionsThe associations between bacteria, viruses and LRTIs are similar to those from high-income countries. Haemophilus is a major bacterial driver of LRTIs, acting synergistically with viruses. Dolosigranulum and Corynebacterium may reduce LRTI risk, while Staphylococcus may reduce the risk of RSV-related LRTIs. CMV is associated with dysbiotic nasopharyngeal microbiota.

Indexed as

MicrobiotaNasopharynxRespiratory Tract InfectionsBacteriaCase-Control StudiesFemaleHumansInfantInfant, NewbornMaleProspective StudiesRNA, Ribosomal, 16SSouth AfricaVirus DiseasesVirusesRNA, Ribosomal, 16S16S rRNA geneinfantlower respiratory tract infectionmicrobiotaviral

Identifiers

PMID40241660
PMCPMC13375580

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.