Pathogens in the upper respiratory tract of Congolese children with radiologically confirmed pneumonia

Abstract Background Acute pneumonia remains a leading cause of death among children below 5 years of age in the Democratic Republic of the Congo (DR Congo), despite introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in 2013. Pathogens in the nasopharynx of hospitalised children with pneumonia have not been studied previously in DR Congo. Here we compare clinical characteristics, risk factors and nasopharyngeal occurrence of bacteria and viruses between children with severe and non-severe pneumonia Methods Between June 2015 and June 2017, 116 children aged from 2 to 59 months hospitalised due to radiologically confirmed pneumonia at Panzi referral university hospital, Bukavu, eastern DR Congo were included in the study and sampled from nasopharynx. A multiplex real-time PCR assay for detection of 15 different viruses and 5 bacterial species was performed and another multiplex PCR assay was used for pneumococcal serotype/serogroup determination. Results During the study period 85 (73%) of the children with radiologically confirmed pneumonia met the WHO classification criteria of severe pneumonia and 31 (27%) had non-severe pneumonia. The fatality rate was 9.5%. Almost all (87%) children were treated with antibiotics before they were hospitalised, in most cases with amoxicillin (58%) or trimethoprim-sulfamethoxazole (20%). Children with severe pneumonia were more commonly treated with trimethoprim-sulfamethoxazole before hospitalisation than children with non-severe pneumonia (OR 4.75; 95%CI 1.04–21.65, p = 0.043), as were children who died at the hospital as compared to children who recovered (OR 3.98; 95%CI 1.1–14.4, p = 0.035). Any viral or bacterial nucleic acids present at high levels in nasopharynx were significantly associated with severe pneumonia as compared with non-severe cases (52% versus 29%, p = 0.032). High levels of pneumococci or respiratory syncytial virus (RSV) were associated with fatal outcome. One or more serotypes/serogroups could be identified in 61 patients, and out of all identified pneumococcal serotypes 31/83 (37%) were non-PCV13 serotypes. Conclusions The occurrence of any bacteria or any viruses at high levels, irrespective of species, was associated with severe pneumonia. High levels of RSV or pneumococci were associated with higher risk of fatality. Pre-hospitalisation treatments with broad spectrum antibiotics were common but were associated with a more severe outcome.