Certain Fecal Fungal Microbiome Patterns Found in COVID-19 Patients

Tao Zuo, PhD

Certain patterns and diversity from fecal samples might be useful in identifying those infected by the coronavirus disease 2019 (COVID-19).

A team, led by Tao Zuo, Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, examined the changes in the fecal fungal microbiomes (mycobiome) of patients with a SARS-CoV-2 infection during hospitalization and following recovery.

SARS-CoV-2 infects intestinal cells and could impact the intestinal microbiota.

The investigators performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 COVID-19 patients in Hong Kong between February 5 and May 12, collecting fecal samples 2-3 times per week from the time of hospitalization until discharge.

The team then compared fecal mycobiome compositions of patients with COVID-19 with those from 9 individuals with community-acquired pneumonia and 30 healthy control participants. They also assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples.

The investigators discovered infected patients had significant alterations in their fecal mycobiomes compared to the control group. This was characterized by the enrichment of Candia albicans, as well as a highly heterogeneous mycobiome configuration at the time of hospitalization.

While fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from the control group during times of hospitalization, 8 out of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition through the last collected sample.

The diversity of the fecal mycobiome of the last sample collected was 2.5-fold higher in COVID-19 patients than it was in the control group (P <0.05) and had increased proportions of opportunity fungal pathogens—Candida albicans, Candida auris, and Aspergillus flavus—at all timepoints when compared to the control group.

A pair of respiratory-associated fungal pathogens—Aspergillus flavus and Aspergillus niger—were found in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and the resolution of respiratory symptoms.

“In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls,” the authors wrote. “Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2.”

The investigators said further studies are needed to determine whether alterations in intestinal fungi contribute to or result from a SARS-CoV-2 infection and what the effects of the changes in disease progression are.

While many clinicians were looking at fever and cough in patients, gastrointestinal issues and stool samples were identified fairly early in the pandemic as early signs of a COVID-19 infection.

Former studies on SARS, which is related to COVID-19 and can present with similar symptoms, showed that the viral respiratory illness was verified in patients after detection in biopsy specimens and stool. This was true even after the patients had been discharged from the hospital.

The study, “Alterations in Fecal Fungal Microbiome of Patients With COVID-19 During Time of Hospitalization until Discharge,” was published online in Gastroenterology.