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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections.

ABSTRACT: Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eighty-seven percent of the samples were nasopharyngeal samples, and 23% of the samples were oral, nasal and oral pharyngeal swabs. We conducted bioinformatics analyses to examine differences in microbial populations of these samples, as a proxy for the nasal and oral microbiome, from SARS-CoV-2 positive and negative specimens. We found 91% concordance with the LLMDA relative to a diagnostic RT-qPCR assay for detection of SARS-CoV-2. Sixteen percent of all the samples (32/203) revealed the presence of an opportunistic bacterial or frank viral pathogen with the potential to cause co-infections. The two most detected bacteria, Streptococcus pyogenes and Streptococcus pneumoniae, were present in both SARS-CoV-2 positive and negative samples. Human metapneumovirus was the most prevalent viral pathogen in the SARS-CoV-2 negative samples. Sequence analysis of 16S rRNA was also conducted to evaluate bacterial diversity and confirm LLMDA results.

SUBMITTER: Thissen JB

PROVIDER: S-EPMC9714956 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections.

Thissen James B JB Morrison Michael D MD Mulakken Nisha N Nelson William C WC Daum Chris C Messenger Sharon S Wadford Debra A DA Jaing Crystal C

PloS one 20221201 12

Co-infections or secondary infections with SARS-CoV-2 have the potential to affect disease severity and morbidity. Additionally, the potential influence of the nasal microbiome on COVID-19 illness is not well understood. In this study, we analyzed 203 residual samples, originally submitted for SARS-CoV-2 testing, for the presence of viral, bacterial, and fungal pathogens and non-pathogens using a comprehensive microarray technology, the Lawrence Livermore Microbial Detection Array (LLMDA). Eight ...[more]

PMID: 36455065

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Project description:BackgroundThe mortality risk of co-infections/secondary infections (CoI/ScI) is under-reported in patients with non-critical COVID-19, leading to the under-management of CoI/ScI and publication bias in the medical literature. We aimed to investigate the association between CoI/ScI and mortality in patients hospitalised with mild-to-severe COVID-19.MethodsWe conducted a retrospective cohort study at a COVID-19 treatment hospital in Vietnam and collected all eligible medical records, with CoI/ScI status as the exposure (non-CoI/ScI and CoI/ScI, with the latter including nature of pathogen [bacterial, fungal, or bacterial + fungal] and multidrug-resistance pathogen [no MDRp or ≥ 1 MDRp]). The outcome was all-cause mortality, defined as in-hospital death by all causes or being discharged under critical illness. We used time-dependent analysis to report rates of mortality with 95% confidence intervals (95% CI, Poisson regression) and hazard ratios (HR) with 95% CI (Cox proportional hazards regression with Holm's method for multiplicity control).ResultsWe followed 1466 patients (median age 61, 56.4% being female) for a median of 9 days. We recorded 387 (26.4%) deaths (95/144 [66.0%] in the CoI/ScI group and 292/1322 [22.1%] in the non-CoI/ScI group). Adjusted mortality rates (per 100 person-days) of the CoI/ScI (6.4, 95% CI 5.3 to 7.8), including bacterial (8.0, 95% CI 7.2 to 8.9), no MDRp (5.9, 95% CI 4.8 to 7.4), and ≥ 1 MDRp (9.0, 95% CI 8.2 to 10.0) groups were higher than that of the non-CoI/ScI group (2.0, 95% CI 1.8 to 2.2). These corresponded to higher risks of mortality in the overall CoI/ScI (HR 3.27, 95% CI 2.58 to 4.13, adjusted p < 0.001), bacterial CoI/ScI (HR 3.79, 95% CI 2.97 to 4.83, adjusted p < 0.001), no MDRp CoI/ScI (HR 3.13, 95% CI 2.42 to 4.05, adjusted p < 0.001), and ≥ 1 MDRp CoI/ScI group (HR 3.89, 95% CI 2.44 to 6.21, adjusted p < 0.001). We could not attain reliable estimates for fungal and bacterial + fungal CoI/ScI.ConclusionCompared with the non-CoI/ScI group, patients with CoI/ScI had a significantly higher risk of all-cause mortality, regardless of resistance status. More evidence is needed to confirm the mortality risks in patients with fungal or bacterial + fungal CoI/ScI.

Project description:IntroductionIn 2019, a new virus from the coronavirus family called SARS-CoV-2, infected populations throughout the world. Coronavirus disease 2019 (COVID-19), an illness induced by this virus, attacks vital organs in the body, such as the respiratory system and the gastrointestinal tract. Recent studies have confirmed changes in the gut microbiome caused by the COVID-19 disease. We examined the alteration of the gut microbiome in COVID-19 patients compared to healthy individuals.Materials and methodsin this study, the 16s metagenomics dataset, publicly available in the Sequence Read Archive (SRA) database, was used for analysis (accession number PRJNA636824). The analysis processes were performed using the CLC Microbial Genomics Module 20.1.1 (Qiagen). At first, the sequence reads of samples were trimmed and classified into operational taxonomic units (OTUs) with 97% similarity and then assigned to the Greengenes reference database (v138). Differential abundance analysis was used to determine statistically significant differences in OTUs between COVID-19 and healthy groups. Next, biodiversity analyses including the alpha diversity (intragroup diversity) and beta diversity (intergroup diversity) using defined indexes were estimated. Then, the co-occurrence network at the species level was constructed using the Pearson correlation coefficient calculation between pairs of OTUs in R software and visualized using Cytoscape software. Ultimately, the hub OTUs at the species level were identified using the cytoHubba plugin of Cytoscape based on Maximal Clique Centrality (MCC) algorithm.ResultsThe results of the metagenomic analysis revealed that the intestinal microbiome in healthy individuals has a higher biodiversity compared to COVID-19 patients. Indeed, healthy people also have a higher percentage of beneficial bacteria such as bifidobacteria adolescentis compared to COVID-19 patients; in contrast, COVID-19 patients have higher levels of opportunistic and pathogenic bacteria such as Streptococcus anginosus than healthy people. Also, by constructing a co-occurrence network at the species level, Bifidobacterium longum in the healthy group and Veillonella parvulain the COVID-19 group were found as hub species.ConclusionThe results of this study shed light on the relationship between the gut microbiome and COVID-19. These results could be helpful for understanding the pathogenesis, clinical features, and treatment of COVID-9.

Project description:BackgroundInfection with SARS-CoV-2 may perturb normal microbiota, leading to secondary infections that can complicate the viral disease. The aim of this study was to probe the alteration of nasopharyngeal (NP) microbiota in the context of SARS-CoV-2 infection and obesity and to identify other respiratory pathogens among COVID-19 cases that may affect patients' health.MethodsA total of 107 NP swabs, including 22 from control subjects and 85 from COVID-19 patients, were processed for 6S amplicon sequencing. The respiratory pathogens causing secondary infections were identified by RT-PCR assay, using a kit that contained specific primers and probes combinations to amplify 33 known respiratory pathogens.ResultsNo significant (p > 0.05) difference was observed in the alpha and beta diversity analysis, but specific taxa differed significantly between the control and COVID-19 patient groups. Genera of Sphingomonas, Kurthia, Microbacterium, Methylobacterium, Brevibacillus, Bacillus, Acinetobacter, Lactococcus, and Haemophilus was significantly abundant (p < 0.05) in COVID-19 patients compared with a healthy control group. Staphylococcus was found in relatively high abundance (35.7 %) in the COVID-19 patient groups, mainly those treated with antibiotics. A relatively high percentage of Streptococcus was detected in COVID-19 patient groups with obesity or other comorbidities. Respiratory pathogens, including Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Salmonella species, along with Pneumocystis jirovecii fungal species were detected by RT-PCR mainly in the COVID-19 patients. Klebsiella pneumoniae was commonly found in most of the samples from the control and COVID-19 patients. Four COVID-19 patients had viral coinfections with human adenovirus, human rhinovirus, enterovirus, and human parainfluenza virus 1.ConclusionsOverall, no substantial difference was observed in the predominant NP bacterial community, but specific taxa were significantly changed between the healthy control and COVID-19 patients. Comparatively, an increased number of respiratory pathogens were identified in COVID-19 patients, and NP colonization by K. pneumoniae was probably occurring in the local population.

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Evaluation of co-circulating pathogens and microbiome from COVID-19 infections.

Publications

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections.

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