Post-acute COVID-19 associated with evidence of bystander T-cell activation and a recurring antibiotic-resistant bacterial pneumonia

The COVID-19 pandemic has brought with it the largest ever cohort of patients requiring mechanical ventilation. Here we describe such a patient who developed a recurring ventilator-associated pneumonia caused by a strain of Pseudomonas aeruginosa that acquired increasing levels of antimicrobial resistance (AMR) in response to treatment. Metagenomic analysis recovered whole genomes of the bacterium directly from samples, revealing the AMR genotype. While immunological analysis of longitudinally-collected blood samples revealed escalating levels of T-cell activation targeting both bacteria and virus, with evidence of bystander-activation, a feature which may have contributed to the continuing inflammation and prolonged requirement for ventilation.