The role of viruses and bacteria in childhood acute lower respiratory infections in Africa

Acute lower respiratory infections (ALRI) are the leading cause of childhood mortality worldwide and account for an estimated 1.3 million deaths each year in children less than five years of age. The burden of ALRI is greatest in the developing world and an estimated 43% of ALRI-associated deaths occur in sub-Saharan Africa. It is widely accepted that interactions between respiratory viruses and bacteria as well as the host immune response play a critical role in the pathogenesis of ALRI. Epidemiological studies on childhood ALRI in Africa conducted during the 1980s led to management programs coordinated by the World Health Organization which resulted in a substantial reduction in ALRI-associated childhood mortality. However, the HIV epidemic that has since engulfed many African countries has reversed much of this progress. Hence, the current epidemiology and aetiology of childhood ALRI in Africa is not well understood and requires further investigation.

Recent advances in molecular methods such as PCR for the detection of respiratory viruses led to the identification of several new viruses and viral species such as a third HRV species, HRV-C, first reported in 2006. Studies of HRV species in children with ALRI or asthma, predominantly from developed countries, report HRV-C to be the most prevalent HRV species and often associated with more severe illness. Only three studies have investigated HRV species in children with respiratory illness in Africa with conflicting findings on the most prevalent species. Similarly, the recent advent of sequencing technologies such as 16S rRNA gene sequencing, has led to the discovery of far more diverse respiratory microbial communities in the upper and lower respiratory tract than previously thought. However, there is no data on the respiratory microbiome in children from Africa. Finally, it is widely accepted that altered host immune responses such as cytokine responses play a key role in the pathogenesis of ALRI. However, reports of cytokine levels in children with ALRI and HIV in Africa are non-existent.

This PhD project investigated respiratory viruses and bacteria as well as host immune responses in childhood ALRI in South Africa, Mozambique and Morocco. More specifically, this thesis described the prevalence of respiratory viruses, respiratory microbiome profiles and cytokine responses in children with and without ALRI and addressed the hypotheses that 1) HRV, and in particular HRV-C, is the most common respiratory virus in childhood ALRI in Africa, 2) respiratory viruses and HIV cause a disordered respiratory microbiome and 3) cytokine profiles are unique between children with and without ALRI, with and without HIV and with and without specific respiratory viral infections.

Regarding respiratory viral infections, HRV was the most commonly identified virus in children with ALRI in South Africa (49%), Mozambique (33%) and Morocco (53%). HRV-A and HRV-C were identified almost equally in children with ALRI in South Africa (26.7% and 21.0% respectively) and Mozambique (17.0% and 12.6% respectively). Among HRV-positive children with ALRI from Morocco, HRV-C was the most commonly identified HRV species (identified in 56.7% of HRV-positive children) and was significantly associated with wheezing while HRV-A (identified in 38.2% of HRV-positive children) was significantly associated with pneumonia. Analysis of the respiratory microbiome using 16S rRNA sequencing methods revealed that among children both with and without ALRI from South Africa and Mozambique, Streptococcus was the most common bacterial genus identified, comprising approximately half of all 16S rRNA sequence reads. We also identified significant differences in several operational taxonomic units between ALRI cases and non-ALRI controls, HIV-infected and HIV-uninfected children and between children with and without respiratory viruses. Finally, we found significant associations between several of 30 investigated cytokines and ALRI, HIV infection and respiratory virus identification in children both with and without ALRI and with and without HIV from South Africa. Mean cytokine concentrations for four cytokines were higher in ALRI cases than in non-respiratory controls. Mean cytokine concentrations for seven cytokines were significantly lower in HIV-infected cases than in HIV-uninfected cases while only two (IP-10 and MIG) were significantly higher in HIV-infected cases than in HIV-uninfected cases. Principal component analysis identified distinct cytokine patterns and inflammatory signatures associated with disease and specific respiratory viral infections.

In conclusion, the findings from this thesis illustrate the contribution of respiratory viruses, bacteria and the host immune response to the pathogenesis of ALRI in African children. Many of the findings in this thesis are unique to this geographic location, or for the first time included a HIV-infected subject group. These findings provide valuable epidemiological and aetiological data on childhood ALRI in Africa and contribute original research towards understanding the causes and mechanisms leading to ALRI.