The wastewater microbiome: A novel insight for COVID-19 surveillance

Gallardo‐Escárate, Cristian; Valenzuela-Muñoz, Valentina; Núñez‐Acuña, Gustavo; Valenzuela-Miranda, Diego; Benaventel, Bárbara P.; Sáez-Vera, Constanza; Urrutia, Homero; Novoa, Beatriz; Figueras, António; Roberts, Steven B.; Assmann, P.; Bravo, Marta Ortega

doi:10.1016/j.scitotenv.2020.142867

Cited by 28 publications

(21 citation statements)

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“…In the latter cohort, some of the patients showed bowel ischemia at surgery, suggesting a possible etiology of the enteritis seen on CT. A separate case report from Chiu et al [32] reported ischemic enteritis related to COVID-19. Taking these findings into consideration, along with the fact that there is expression of angiotensin-converting enzyme 2 receptors in the GI tract and the presence of detectable SARS-CoV-2 in wastewater [8,9,33], there is reason to believe the virus plays a direct role in the bowel abnormalities seen in our study and in others (Figs. 6, 7, and 8).…”

Section: Discussionsupporting

confidence: 57%

“…Abnormalities of the enteric tract have been reported in previously published radiologic series [ 5 , 6 ], and SARS-CoV-2 RNA has been isolated in the duodenal wall and feces of some patients [ 7 ]. Furthermore, wastewater has been identified as a means to monitor levels of COVID-19 in communities [ 8 , 9 ], implying that it may be shed from the gastrointestinal tract. This is not entirely unexpected, as SARS-CoV-2 is known to enter host cells via the angiotensin-converting enzyme 2 (ACE2) cell receptor, which is expressed in the esophagus, ileum, and colon in addition to the lung [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

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Abdominal imaging findings on computed tomography in patients acutely infected with SARS-CoV-2: what are the findings?

et al. 2021

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Objectives To investigate what findings are new on contrast-enhanced abdominopelvic CT in patients infected with SARS-CoV-2. Methods Contrast-enhanced CT of the abdomen and pelvis of patients with COVID-19 at a tertiary oncologic center acquired over a 2-month period were reviewed independently by two readers and scored for new imaging abnormalities compared with a prior scan. CT scans were included if the study was performed between − 3 and 45 days from the time of COVID-19 diagnosis. Clinical information was gathered from the medical records. Results A total of 63 patients (34 male, 29 female; mean age 60.6 years, range 24.4–85.0 years) were included in this retrospective cross-sectional study. Aside from new ground glass opacities seen at the lung bases (29/63, 46.0%), the most common findings were new thickening of the stomach, small bowel or colon or fluid-filled colon (14/63, 22.2%), new small volume ascites (7/63, 14.3%), gallbladder distention in those without prior cholecystectomy (3/43, 7.0%), and single cases each of acute pancreatitis (1/63, 1.6%) as well as new portal vein thrombosis (1/63, 1.6%). Conclusion Aside from lung base ground glass opacities, the most common new imaging abnormality on abdominopelvic CT in patients with COVID-19 finding in our cohort was abnormalities of the gastrointestinal tract, followed by small volume ascites, gallbladder distention, and isolated cases of pancreatitis and portal vein thrombosis. These findings overlap with those previously reported that did not have a prior scan for comparison, and provide supportive evidence that some of these findings may be related to SARS-CoV-2 infection.

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Section: Discussionsupporting

confidence: 57%

Section: Introductionmentioning

confidence: 99%

Abdominal imaging findings on computed tomography in patients acutely infected with SARS-CoV-2: what are the findings?

et al. 2021

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“…Stool and inside floor samples each had distinct sets of taxa driving the RF model compared to nares and forehead samples, which were more similar to one another. Many of the highly ranked ASVs in the stool samples are from the class Clostridiales , a polyphyletic group of obligate anaerobes that were also identified as predictive of SARS-CoV-2 status in a wastewater study [ 36 ].…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

et al. 2021

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Background SARS-CoV-2 is an RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Viruses exist in complex microbial environments, and recent studies have revealed both synergistic and antagonistic effects of specific bacterial taxa on viral prevalence and infectivity. We set out to test whether specific bacterial communities predict SARS-CoV-2 occurrence in a hospital setting. Methods We collected 972 samples from hospitalized patients with COVID-19, their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and used these bacterial profiles to classify SARS-CoV-2 RNA detection with a random forest model. Results Sixteen percent of surfaces from COVID-19 patient rooms had detectable SARS-CoV-2 RNA, although infectivity was not assessed. The highest prevalence was in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples more closely resembled the patient microbiome compared to floor samples, SARS-CoV-2 RNA was detected less often in bed rail samples (11%). SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity in both human and surface samples and higher biomass in floor samples. 16S microbial community profiles enabled high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool, and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia strongly predicted SARS-CoV-2 presence across sample types, with greater prevalence in positive surface and human samples, even when compared to samples from patients in other intensive care units prior to the COVID-19 pandemic. Conclusions These results contextualize the vast diversity of microbial niches where SARS-CoV-2 RNA is detected and identify specific bacterial taxa that associate with the viral RNA prevalence both in the host and hospital environment.

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“…Enriching the beneficial microbes in the microbiome of the host and controlling the proportion of opportunistic pathogens ( Kendall and Sperandio, 2021 ) will eventually help to prevent an inflammatory milieu, which could ease the onset of ARDS and other pathogenesis events in COVID-19 ( Kendall and Sperandio, 2021 ). Lifestyle changes would be a subtle area that can help in the favorable growth of beneficial microbes and may include less exposure to pollution, abstaining from unnecessary use of antibiotics ( Kendall and Sperandio, 2021 ), eating a diet rich in fiber, fermented foods, and prebiotics ( Bousquet et al., 2021 ; Kendall and Sperandio, 2021 ) which favor the enrichment of healthy microbiota ( Gasmi et al., 2021 ), and strict implementation of handwashing and brushing as it has been found that patients with GI symptoms suffer from worse COVID-19 outcome ( Han et al., 2021 ; Gallardo-Escárate et al., 2021 ). These would help in alleviating the risk factors of inflammation and help in securing a healthy immune system, which is a prerequisite for avoiding the trauma associated with COVID-19.…”

Section: Discussionmentioning

confidence: 99%

Role of the Microbiome in the Pathogenesis of COVID-19

2022

Front. Cell. Infect. Microbiol.

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The ongoing pandemic coronavirus disease COVID-19 is caused by the highly contagious single-stranded RNA virus, SARS-coronavirus 2 (SARS-CoV-2), which has a high rate of evolution like other RNA viruses. The first genome sequences of SARS-CoV-2 were available in early 2020. Subsequent whole-genome sequencing revealed that the virus had accumulated several mutations in genes associated with viral replication and pathogenesis. These variants showed enhanced transmissibility and infectivity. Soon after the first outbreak due to the wild-type strain in December 2019, a genetic variant D614G emerged in late January to early February 2020 and became the dominant genotype worldwide. Thereafter, several variants emerged, which were found to harbor mutations in essential viral genes encoding proteins that could act as drug and vaccine targets. Numerous vaccines have been successfully developed to assuage the burden of COVID-19. These have different rates of efficacy, including, although rarely, a number of vaccinated individuals exhibiting side effects like thrombosis. However, the recent emergence of the Britain strain with 70% more transmissibility and South African variants with higher resistance to vaccines at a time when several countries have approved these for mass immunization has raised tremendous concern regarding the long-lasting impact of currently available prophylaxis. Apart from studies addressing the pathophysiology, pathogenesis, and therapeutic targets of SARS-CoV-2, analysis of the gut, oral, nasopharyngeal, and lung microbiome dysbiosis has also been undertaken to find a link between the microbiome and the pathogenesis of COVID-19. Therefore, in the current scenario of skepticism regarding vaccine efficacy and challenges over the direct effects of currently available drugs looming large, investigation of alternative therapeutic avenues based on the microbiome can be a rewarding finding. This review presents the currently available understanding of microbiome dysbiosis and its association with cause and consequence of COVID-19. Taking cues from other inflammatory diseases, we propose a hypothesis of how the microbiome may be influencing homeostasis, pro-inflammatory condition, and the onset of inflammation. This accentuates the importance of a healthy microbiome as a protective element to prevent the onset of COVID-19. Finally, the review attempts to identify areas where the application of microbiome research can help in reducing the burden of the disease.

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The wastewater microbiome: A novel insight for COVID-19 surveillance

Cited by 28 publications

References 38 publications

Abdominal imaging findings on computed tomography in patients acutely infected with SARS-CoV-2: what are the findings?

Abdominal imaging findings on computed tomography in patients acutely infected with SARS-CoV-2: what are the findings?

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

Role of the Microbiome in the Pathogenesis of COVID-19

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