Bacterial and Fungal Gut Dysbiosis and Clostridium difficile in COVID-19

Abstract

Background: Gastrointestinal symptoms are common in Coronavirus Disease 2019 (COVID-19), related to infection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) of intestinal cells through the angiotensin converting enzyme 2 (ACE2) receptor in the brush border. Also, patients are treated with multiple antibiotics. Therefore, an increase in gut dysbiosis and in the prevalence of Clostridium difficile infection (CDI) is expected in patients with COVID-19. Methods: A PubMed search was conducted using the terms “gut microbiota,” “gut mycobiota,” “dysbiosis” AND “COVID-19”; “Clostridium difficile,” “Clostridioides difficile” AND “COVID-19”; “probiotics,” “bacteriotherapy AND COVID-19.” Only case series, observational and experimental studies were included. Results: A total of 384 papers were retrieved and 21 fulfilled selection criteria. Later, a new paper was identified, thus 22 papers were reviewed. Main findings: (1) gut bacterial dysbiosis has been found in fecal samples of COVID-19 patients, with enrichment of opportunistic organisms and decrease of beneficial commensals such as Faecalibacterium prausnitizii. Dysbiosis is related to inflammatory markers and illness severity. (2) There is evidence for abnormal gut barrier and bacterial translocation with a negative impact in the lungs. (3) Fungal dysbiosis correlating with pulmonary mycobiota, has also been found. (4) There is controversy in the CDI rates among COVID-19 patients versus controls and pandemic versus prepandemic era. (5) There is no available evidence yet to support bacteriotherapy in COVID-19. (6) Fecal microbiota transplantation (FMT) has been proposed for COVID-19, although there is no evidence to support it. Also, FMT can be safely used during the pandemic for CDI if strict screening protocols for donors and fecal product are implemented. Conclusions: In COVID-19 there is bacterial and fungal dysbiosis that correlates with systemic and pulmonary inflammation, and illness severity. Further investigations are warranted to determine the efficacy of bacteriotherapy and FMT for modulating gut dysbiosis in COVID-19.

Gastrointestinal symptoms and the severity of COVID‐19: Disorders of gut–brain interaction are an outcome

“… 41 The infection of the gut epithelial cells triggers an increase in permeability, a low‐grade inflammation with calprotectin secretion, 42 and dysbiosis. 43 Mediators of the low‐grade inflammation can stimulate the enteric nerves with projections to the central nervous system, factors that together with the stress of having COVID‐19, anxiety, and depression, can generate symptoms of post‐COVID‐19 DGBI. 16 In fact, these mechanisms have been described and postulated for other post‐infection‐DGBI, such as PI‐IBS.…”

“…As for the underlying mechanism for the post‐COVID‐19 DGBI, it is possibly related to the high expression of the angiotensin‐converting enzyme‐2 (ACE2) in the gut epithelial cells, a receptor that is required for the SARS‐CoV‐2 virus to infect human cells 41 42 and dysbiosis 43 16 .…”

Long-Term Impact of the COVID-19 Pandemic on In-Hospital Antibiotic Consumption and Antibiotic Resistance: A Time Series Analysis (2015–2021)

“…According to a recent systematic review and meta-analysis of data collected between February 2020 and February 2021, CDI incidence rates ranged from 1.4 to 4.4 CDI cases per 10,000 patient-days [ 48 ]. The heterogeneity of these findings could also be explained by the difficulty in correctly diagnosing CDIs in the COVID-19 era [ 51 , 52 ]. The real impact of COVID-19 on the CDI burden is still unknown and requires further studies.…”

Role of Microbiota in Viral Infections and Pathological Progression

“…A microbiota analysis tends to be an observational study, but it is also important to elucidate the mechanisms of virus–host–microbiota interactions at the molecular level. The analysis of the role of fungi in disease progression is also important and should be reported more frequently [ 219 ]. Elucidating the role of symbiotic bacterial species, their coexistence with humans, and their interactions at the molecular and genetic levels will help advance our knowledge of infectious diseases.…”