Analysis of the nasopharyngeal microbiome and respiratory pathogens in COVID-19 patients from Saudi Arabia

Yasir, Muhammad; Al-Sharif, Hessa A.; Alsubhi, Tagreed L.; Sindi, Anees; Bokhary, Diyaa H; El-Daly, Mai M.; Alosaimi, Bandar; Hamed, Maaweya E.; Karim, Asad Mustafa; Hassan, Ahmed M.; AlShawdari, Mustafa M.; Alawi, Maha; El‐Kafrawy, Sherif A.; Azhar, Esam I.

doi:10.1016/j.jiph.2023.03.001

Cited by 6 publications

(3 citation statements)

References 50 publications

(86 reference statements)

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“…Several studies have shown that in 2020, during the first months of the COVID-19 pandemic, the incidence of S. pneumoniae invasive diseases (IPDs), including bacteremic pneumonia, was significantly reduced, particularly in children < 5 years of age [ 81 , 82 , 83 , 84 , 85 , 86 , 87 ]. This finding was generally attributed to the impact of NPIs, although it was not definitively clarified whether the greater role was played by the reduction of interpersonal transmission of the pathogen or by the suppression of the activity of several seasonal respiratory viruses.…”

Section: Sars-cov-2 Circulation and Incidence Of Bacterial Infectionsmentioning

confidence: 99%

Epidemiology of Respiratory Infections during the COVID-19 Pandemic

Principi

Autore

Ramundo

et al. 2023

Viruses

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To face the COVID-19 outbreak, a wide range of non-pharmaceutical interventions (NPIs) aimed at limiting the spread of the virus in communities, such as mask-wearing, hand hygiene, social distancing, travel restrictions, and school closures, were introduced in most countries. Thereafter, a significant reduction of new asymptomatic and symptomatic COVID-19 cases occurred, although there were differences between countries according to the type and duration of the NPIs. In addition, the COVID-19 pandemic has been accompanied by significant variations in the global incidence of diseases due to the most common non-SARS-CoV-2 respiratory viruses and some bacteria. In this narrative review, the epidemiology of the most common non-SARS-CoV-2 respiratory infections during the COVID-19 pandemic is detailed. Moreover, factors that could have had a role in modifying the traditional circulation of respiratory pathogens are discussed. A literature analysis shows that NPIs were the most important cause of the general reduction in the incidence of influenza and respiratory syncytial virus infection in the first year of the pandemic, although the different sensitivity of each virus to NPIs, the type and duration of measures used, as well as the interference among viruses may have played a role in modulating viral circulation. Reasons for the increase in the incidences of Streptococcus pneumoniae and group A Streptococcus infections seem strictly linked to immunity debt and the role played by NPIs in reducing viral infections and limiting bacterial superimposed infections. These results highlight the importance of NPIs during pandemics, the need to monitor the circulation of infectious agents that cause diseases similar to those caused by pandemic agents, and the need to make efforts to improve coverage with available vaccines.

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Section: Sars-cov-2 Circulation and Incidence Of Bacterial Infectionsmentioning

confidence: 99%

Epidemiology of Respiratory Infections during the COVID-19 Pandemic

Principi

Autore

Ramundo

et al. 2023

Viruses

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“…Kumar et al [28] also showed that the abundance of Corynebacterium and Staphylococcus was increased in patients with COVID-19 who died compared to patients who recovered. However, Yasir et al [29] and Mostafa et al [30] found a decrease in the relative abundance of Corynebacterium with an increasing severity of COVID-19 infection. A study by Szabo et al [31] revealed that Corynebacterium spp., especially C. accolens, showed significantly higher abundance in the nasopharynx of uninfected individuals versus patients with COVID-19, with the downregulation of angiotensin-converting enzyme 2 (ACE-2) and transmembrane serine protease 2 (TMPRSS2) and inhibition of S1-ACE-2 binding being proposed as the main mechanisms of reduced susceptibility to infection in patients who harbor Corynebacterium spp.…”

Section: Discussionmentioning

confidence: 97%

Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study

Siasios,

Giosi,

Ouranos

et al. 2024

JPM

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Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.

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“…Meanwhile, as one of the viruses infecting our respiratory tract, SARS-CoV-2 infects and contacts the nasopharyngeal cells first. It is not surprising that the salivary and nasopharyngeal microbiota was altered during SARS-CoV-2 infection, 47 , 48 such as depletion of oral Bifidobacterium , Lactobacillus , and Solobacterium , and nasopharyngeal Paracoccus , and enrichment of nasopharyngeal Proteus , Cupravidus , and Lactobacillus in severe COVID-19 patients. 47 Similar phenomena were also found in the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients who were characterized with Pseudomonas alcaligenes , Clostridium hiranonis , Acinetobacter schindleri , Sphingobacterium spp., Acinetobacter spp.…”

Section: Gi Microbiome and Metabolites In Long Covidmentioning

confidence: 99%