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Published on: August 7, 2017
Nasopharyngeal Microbiota in South African Infants With Lower Respiratory Tract Infection: A Nested Case-Control
Shantelle Claassen-Weitz1, Yao Xia2, Luke Hannan3
1Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
Insights
This study found that certain viruses and bacteria, like Haemophilus influenzae, are linked to lower respiratory tract infections (LRTI) in South African infants. Some bacteria, such as Dolosigranulum, may offer protection against LRTI.
Area of Science:
- Microbiology
- Pediatric Infectious Diseases
- Epidemiology
Background:
- Lower respiratory tract infections (LRTI) in infants are frequently caused by combined viral and bacterial pathogens.
- Understanding the interplay between nasopharyngeal (NP) microbes and LRTI is crucial for infant health.
Purpose of the Study:
- To investigate the associations between specific viruses and bacteria in the infant nasopharynx and the occurrence of LRTI.
- To identify potential protective or detrimental microbial factors contributing to LRTI in South African infants.
Main Methods:
- A case-control study design was employed within a birth cohort of South African infants.
- Nasopharyngeal swabs were analyzed using quantitative real-time polymerase chain reaction and 16S rRNA gene amplicon sequencing.
- Statistical models were used to determine associations, identify differentially abundant taxa, and explore viral-bacterial interactions.
Main Results:
- Respiratory Syncytial Virus (RSV), human rhinovirus (HRV), parainfluenza virus, adenovirus, enterovirus, Haemophilus influenzae, Klebsiella pneumoniae, and Streptococcus pneumoniae were significantly associated with LRTI.
- LRTI was linked to a decreased abundance of Dolosigranulum, Corynebacterium, and Neisseria.
- Specific viral infections showed distinct bacterial co-occurrence patterns, with Haemophilus influenzae being a key bacterial driver acting synergistically with viruses.
Conclusions:
- The microbial associations with LRTI in this population mirror findings from high-income countries.
- Haemophilus influenzae emerges as a significant bacterial contributor to LRTI, often in conjunction with viral infections.
- Dolosigranulum and Corynebacteria may confer protection against LRTI, while Staphylococcus might reduce the risk of RSV-associated LRTI. Cytomegalovirus (CMV) infection is linked to nasopharyngeal dysbiosis.
Background:
Lower 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.
Methods:
In 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.
Results:
A 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.
Conclusions:
The 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.
