COVID-19 Profile is a longitudinal clinical study and bio resource established in 2020 in the setting of an Australian, low-transmission population, to investigate immunity and immune dysregulation elicited by SARS-CoV-2, through time and after infection, vaccination and reinfection.
The cohort comprised of 178 adultsnenrolled in a community setting, who had either recovered from a SARS-CoV-2 infection. or were SARS-CoV-2-naive at recruitment (household contacts). We selected 68 participants, focusing on those with the largest number of longitudinal samples, for microbial metatranscriptomic profiling by enrichment sequencing of 376 nasopharyngeal swabs, to detect a wide range of bacterial and viral respiratory pathogens. We were able to detect several common bacterial commensal and pathogens, including Haemophillus influenza, Streptococcus pneumoniae, Nocardia asteroids, Neisseria meningitidis, Staphylococcus aureus and Listeria monocytogenes in approximately 70% of swab samples.
In our study, neither coronavirus infection, reinfection nor vaccination appears to be associated with long-term changes in colonisation by major bacterial species associated with the human nasopharynx. However, there is a clear evidence that SARS-CoV-2 infection disrupts bacterial colonisation, likely through the destruction of the nasopharyngeal epithelium,s (as previously reported). We propose that bacterial re-colonisation and reestablishment of the nasopharyngeal biofilm may provide an opportunity to reset individual's resident flora, potentially influencing the dynamics of microbial communities and overall respiratory health.
The sampling of 47 COVID-exposed and 18 COVID-naive individuals over 700 days presents a substantial longitudinal , multi-pathogen surveillance study. This dataset offers valuable insights and provides a robust platform to challenge prevailing assumptions about the dynamics of bacterial carriage in the context of infection.