Patients in hospital with confirmed bacterial airway infection are significantly more likely to have a respiratory virus co-infection

Abstract

Introduction. Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed. Gap Statement. The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies. Aim. The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture. Methodology. A total of 83 lower airway samples – 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates – were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined. Results. Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ²: P=0.04; P=0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50–0.82); diagnostic accuracy 83.13% (73.32–90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ² (χ²: 2.4 P=0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection. Conclusion. Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.