Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID‐19 patients

Abstract

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related‐ microbiome imbalance caused by SARS‐CoV‐2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID‐19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha‐diversity but significant enrichment of opportunistic microorganisms in patients with COVID‐19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID‐19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID‐19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy‐noting microbiome diversity and function alteration were observed. Finally, we noticed that the co‐occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS‐CoV‐2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS‐CoV‐2 and the antibiotics treatment should be critically considered.