Study provides comprehensive analysis of bacterial and fungal changes in COVID-19

The 2019 coronavirus disease (COVID-19) pandemic was caused by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date, COVID-19 has claimed the lives of approximately 7 million people worldwide.

Due to its high mortality rate, scientists have extensively studied various aspects of SARS-CoV-2, including the body’s response to the virus and the potential for co-infection and secondary infections. Optimal clinical approaches to reduce mortality and protect more people from COVID-19 are also being researched.

study: Analysis of the lung microbiome of hospitalized COVID-19 patients. Image credit: Crystal Light / Shutterstock.com

Background

The primary site of infection for SARS-CoV-2 is the human respiratory tract. The clinical outcome of chronic respiratory disease is greatly influenced by the interaction between the human respiratory microbiota and the host’s immune system.

Several studies have shown that respiratory microbiota alterations after viral respiratory infections potentially alter host innate immune responses, thereby facilitating co-infection and secondary infections. The respiratory microbiome also influences pathogen colonization and proliferation.

SARS-CoV-2 infection promotes microbial intestinal dysbiosis by altering the nasal, oropharyngeal, and lung microenvironments. This microbial gut microbiota dysbiosis facilitates co-infection or secondary infection, leading to increased morbidity and mortality in SARS-CoV-2-infected patients. To design better pharmaceutical approaches and diagnostics, it is important to understand the link between the respiratory microbiota and the pathogenesis of COVID-19.

There is still a paucity of research related to the lung microbiome due to limitations in sampling techniques and difficulties in assessing the lower airway. Several small studies have evaluated the bacterial composition in the lungs of COVID-19 patients, but have not discussed the presence of other microorganisms, such as fungi, that may similarly affect the lungs. Therefore, there remains a need to investigate the prevalence of both bacteria and fungi in the lungs of patients with COVID-19.

About research

Recent Pathogen In this study, we used nanopore sequencing to identify fungal and bacterial microbiota in the lungs of patients with COVID-19 and non-COVID-19.

Bronchoalveolar lavage fluid (BALF) and sputum samples were collected from 38 hospitalized patients with COVID-19 and 26 patients with non-COVID-19 pneumonia. All patients were treated from February 1, 2020 to August 15, 2020 at Zhongnan Hospital, Wuhan University, China.

Subsequently, microbial DNA was extracted from the samples and subjected to nanopore-targeted sequencing according to standardized procedures.

research result

Both study groups consisted of participants identical with respect to mean age and gender proportions. More than 75% of his patients present in both groups had comorbidities such as diabetes, coronary artery disease, hypertension, chronic infections and chronic lung disease.

Patients hospitalized with SARS-CoV-2 infection required more oxygenation, invasive ventilation, and non-invasive ventilation compared with non-COVID-19 patients. Both study groups received antibiotic treatment. However, antiviral and antifungal treatments were more commonly prescribed to patients with COVID-19. A total of 12 COVID-19 patients and 6 non-COVID-19 patients died during hospitalization.

Consistent with previous studies, the laboratory results of this study showed significantly decreased lymphocyte counts and hemoglobin levels, and increased serum amyloid A (SAA) levels and neutrophil-to-leukocyte ratios in patients with COVID-19.

Significant reductions in microbial diversity and severe dysbiosis were observed in COVID-19 patients. Of note, both bacterial and fungal distributions in COVID-19 patients were significantly different from those in non-COVID-19 patients.

In patients with COVID-19, higher numbers of opportunistic pathogens that disrupt the lung ecosystem were identified. These pathogens can facilitate superinfection and secondary infection and influence disease severity.

Metagenomic sequencing showed that compared with non-COVID-19 patients, Acinetobacter baumannii It was present in significantly higher amounts in most COVID-19 patients. Previous studies have shown that patients infected with this pathogen are more susceptible to severe novel coronavirus disease (COVID-19).

Further studies are needed to understand the underlying mechanisms of A.Synetobacter Overgrows in the lungs of COVID-19. This finding could potentially be used to develop effective therapies that target this bacterium–virus interaction and improve clinical outcomes.

Rich Candida seeds, especially Candida glabrata, candida parapsilosis, and Candida albicanswas also observed in the lungs of COVID-19 patients. Moreover, many bacterial taxa found in the lungs of COVID-19 patients showed strong correlations with inflammatory indices.

Conclusion

SARS-CoV-2 infection can cause severe to fatal symptoms in certain populations, including the elderly, those with underlying medical conditions, and those with weakened immune systems.

In this study, we observed significant differences in the lung microbiome between novel coronavirus disease (COVID-19) and non-coronavirus (COVID-19) controls. More specifically, COVID-19 patients had a particularly high abundance of opportunistic pathogens. Acinetobacter baumannii and Candida Species Notably, specific pathogens present in the lungs of COVID-19 patients affected changes in specific inflammatory indices.