Acute SARS-CoV-2 infection is associated with an expansion of bacteria pathogens in the nose including Pseudomonas Aeruginosa.
Nicholas S RhoadesAmanda PinskiAlisha N MonsibaisAllen JankeelBrianna M DorattIsaac R CincoIzabela IbraimIlhem MessaoudiPublished in: bioRxiv : the preprint server for biology (2021)
Much of the research conducted on SARS-CoV-2 and COVID-19 has focused on the systemic host response, especially that generated by severely ill patients. Very few studies have investigated the impact of acute SARS-CoV-2 within the nasopharynx, the site of initial infection and viral replication. In this study we profiled changes in the nasal microbial communities as well as in host transcriptional profile during acute SARS-CoV-2 infection using 16S amplicon sequencing and RNA sequencing. These analyses were coupled to viral genome sequencing. Our microbiome analysis revealed that the nasal microbiome of COVID patients was unique and was marked by an expansion of bacterial pathogens. Some of these microbes (i.e. Acinetobacter ) were shared with COVID negative health care providers from the same medical center but absent in COVID negative outpatients seeking care at the same institutions suggesting acquisition of nosocomial respiratory pathogens. Specifically, we report a distinct increase in the prevalence and abundance of the pathogen Pseudomonas aeruginosa in COVID patients that correlated with viral RNA load. These data suggest that the inflammatory environment caused by SARS-CoV-2 infection and potentially exposure to the hospital environment leads to an expansion of bacterial pathogens in the nasal cavity that could contribute to increased incidence of secondary bacterial infections. Additionally, we observed a robust host transcriptional response in the nasal epithelia of COVID patients, indicative of an antiviral innate immune repones and neuronal damage. Finally, analysis of viral genomes did not reveal an association between viral loads and viral sequences.
Keyphrases
- sars cov
- respiratory syndrome coronavirus
- pseudomonas aeruginosa
- single cell
- healthcare
- liver failure
- gram negative
- respiratory failure
- cystic fibrosis
- drug induced
- antimicrobial resistance
- gene expression
- end stage renal disease
- acinetobacter baumannii
- risk factors
- oxidative stress
- chronic rhinosinusitis
- multidrug resistant
- genome wide
- emergency department
- transcription factor
- ejection fraction
- coronavirus disease
- dna methylation
- palliative care
- staphylococcus aureus
- pain management
- deep learning
- peritoneal dialysis
- electronic health record
- candida albicans
- brain injury
- mass spectrometry
- subarachnoid hemorrhage
- blood brain barrier
- respiratory tract
- data analysis
- single molecule