Genomics of bacterial coinfections from COVID-19 patients: insights into disease severity and antimicrobial resistance

Patients with SARS-CoV-2 often present with bacterial/fungal coinfections which can then impact the severity of the disease and mortality. But the impact of coinfections is currently unclear. Additionally, the effect of different policies and procedures regarding antibiotic use to treat COVID-19 infections around the world on the evolution of antibiotic resistance has also not been investigated. By improving our understanding of bacterial coinfections in COVID-19 patients and its impact on disease progression, more informed and improved approaches may be made for better treatment and infection control.
Using samples from COVID-19 patients with bacterial infections from various healthcare centres in Europe and India, whole genome sequencing carried out by Nanopore and Illumina technologies on 125 bacterial isolates so far in the pilot study has revealed a wide range of different bacterial species with Staphylococcus aureus and Klebsiella spp. occurring especially frequently. Multidrug resistant bacterial clones originating from community- and hospital- acquired have also been indicated in preliminary analysis. Furthermore, sequencing of multiple isolates from individual patients has suggested multiple clones causing infections with sequential isolates varying in antibiotic sensitivity. This suggests the emergence of antibiotic resistance during treatment.
This project will use population genomics and phylogenetics to analyse bacterial strain isolated from COVID-19 patients to help further our understanding of disease severity and antimicrobial resistance. It will aim to investigate the genetic diversity of bacteria causing coinfections in COVID-19 patients and the impact that bacterial coinfections and specific genetic subtypes have on the severity of infections and disease outcome in COVID-19 patients. Moreover, the influence of antibiotic resistance for treatment of COVID-19 and the evolution of antimicrobial resistance in bacteria coinfecting COVID-19 patients will be studied to help optimise infection control and reduce antimicrobial overuse to limit antimicrobial resistance evolution. How community-acquired and hospital-acquired bacterial infections may differ and contribute in COVID-19 patients will also be explored.
A comparative genomic approach will allow the genetic diversity of the coinfecting bacteria in COVID-19 to be studied as well as their origins to be understood. In addition, it will help our understanding of the evolution of antimicrobial resistance among bacteria. This knowledge will hopefully improve future treatment procedures while also restricting the rise of antimicrobial resistance.