In young children, a diagnosis of a lower respiratory tract infection (LRTI) was associated with the detection of Haemophilus influenzae or Klebsiella spp in the upper respiratory tract (URT), according to results of a study published in Clinical Microbiology and Infection.

Researchers performed a systematic review and meta-analysis of studies published between 1923 and 2020 that investigated URT bacteria among children younger than 5 years of age with and without acute LRTI.

Among a total of 50 studies conducted in 29 countries were included in the analysis, 40 were singlecenter and 10 were multicenter studies. Most participants were residents of low-income (23%) or lower-middle-income (39%) countries. Nasopharyngeal specimens were tested in 41 studies and 44 had a cross-sectional design.

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Compared with participants without acute LRTI, those with an LRTI were found to have an increased prevalence of H influenzae (pooled odds ratio [OR], 1.60; 95% CI, 1.23-2.07) and Klebsiella spp (pooled OR, 2.04; 95% CI, 1.17-3.55) on analysis of nasopharyngeal specimens. The researchers noted an association between most studies (62%) which used culture or polymerase chain reaction (PCR) testing and an increased prevalence of Streptococcus pneumoniae among participants with an LRTI, but the association was not significant on analysis of the pooled OR(pooled OR, 1.16; 95% CI, 0.86-1.57). On subgroup analysis of 8 studies in which the prevalence of antibiotic treatment prior to sampling was increased among participants with vs those without an LRTI,  the researchers found no significant difference in the prevalence of S pneumonia detected among between the 2 groups(pooled OR, 1.41; 95% CI, 1.04-1.90). In 1 study in which a pathogen-specific PCR density threshold (>6.9 log10 copies/mL) was applied, S pneumonia was found to be associated with an increased risk for LRTI.

Although genus-level sequencing supported the associations that were found between the presence of H influenzae and S pneumoniae spp in the URT and an increased risk for LRTI, no conclusive evidence was found in regard to the role of Moraxella catarrhalis or Staphylococcus aureus detected in the URT and the risk for LRTI.

The study limitations included the targeted detection of few bacterial species by many studies, potential amplification bias, and the limited ability to discriminate at the species level for studies using 16S rRNA sequencing or short-read 16S rRNA sequencing. Included studies also had limited ability to address pathogenic mechanisms.

The researchers concluded that “longitudinal studies assessing URT microbial communities, together with environmental and host factors are needed to better understand pathogenesis of childhood LRTI.”


Claassen-Weitz S, Lim KY, Mullally C, Zar HJ, Nicol MP. The association between bacteria colonizing the upper respiratory tract and lower respiratory tract infection in young children: a systematic review and meta-analysis. Clin Microbiol Infect. 2021;(9):1262-1270. doi: 10.1016/j.cmi.2021.05.034