Abstract:Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community… Show more
“…Across studies, the nasopharyngeal microbiome was dominated by Staphylococcus and Corynebacterium , or by oral commensals similar to those found in the oropharynx, such as Streptococcus, Prevotella, and Veillonella . A major confounding factor for many nasopharyngeal studies was the storage of samples in viral transport media, as many studies looked at the microbiome using swabs that were initially collected for viral testing or sequencing [ 55 – 58 ]. Fig.…”
Section: The Nasopharyngeal Microbiome In Covid-19mentioning
confidence: 99%
“…The most common association found across studies was a decrease in relative abundance of the phylum Bacteroidota [ 41 , 56 , 61 ], though this association was still not significant in most studies. Similarly, two studies found alpha diversity was lower in COVID-19 patients [ 51 , 61 ], while eight studies found no significant difference [ 50 , 52 , 55 , 56 , 58 – 60 , 62 , 63 ], suggesting that the effect on alpha diversity is possibly negative and likely small.…”
Section: The Nasopharyngeal Microbiome In Covid-19mentioning
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown—did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions.
“…Across studies, the nasopharyngeal microbiome was dominated by Staphylococcus and Corynebacterium , or by oral commensals similar to those found in the oropharynx, such as Streptococcus, Prevotella, and Veillonella . A major confounding factor for many nasopharyngeal studies was the storage of samples in viral transport media, as many studies looked at the microbiome using swabs that were initially collected for viral testing or sequencing [ 55 – 58 ]. Fig.…”
Section: The Nasopharyngeal Microbiome In Covid-19mentioning
confidence: 99%
“…The most common association found across studies was a decrease in relative abundance of the phylum Bacteroidota [ 41 , 56 , 61 ], though this association was still not significant in most studies. Similarly, two studies found alpha diversity was lower in COVID-19 patients [ 51 , 61 ], while eight studies found no significant difference [ 50 , 52 , 55 , 56 , 58 – 60 , 62 , 63 ], suggesting that the effect on alpha diversity is possibly negative and likely small.…”
Section: The Nasopharyngeal Microbiome In Covid-19mentioning
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown—did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions.
“…Factors such as appliance wearing, tooth brushing habits and the restorative state of the dentition are recognised as modifying the oral microbiome, which, in turn, may alter oral function [25]. While less studied than the oral microbiome, the nasal microbiome may similarly have an impact of the process of olfaction [26], and its composition has been implicated in differentiating COVID-19 patients pre-and postrecovery [27].…”
Background and Objectives: Loss of smell is one of the strongest predictors of coronavirus disease 2019 (COVID-19) and can persist long after other symptoms have resolved. “Long” cases (>28 days) of smell dysfunction present future challenges to medical and dental professionals, as there is a lack of evidence on the causes and any exacerbating or relieving factors. This study aimed to explore the persistence of COVID-19-induced smell loss and association with physical, lifestyle and oral health factors. Materials and Methods: This study was a cross-sectional survey of 235 participants. Recovery of smell was explored, comparing rapid recovery (≤28 days) with prolonged recovery (>28 days). Associative factors included age, sex, illness severity, diet, BMI, vitamin D supplementation, antidepressants, alcohol use, smoking, brushing frequency, flossing, missing teeth, appliances and number of dental restorations. Results: Smell loss showed 87% resolution within 30 days. Prolonged smell loss was significantly associated with older age (mean ± 95%, CI = 31.53 ± 1.36 years for rapid recovery vs. mean ± 95%, CI = 36.0 ± 3 years for prolonged recovery, p = 0.003) and increased self-reported illness severity (mean ± 95%, CI = 4.39 ± 0.27 for rapid recovery vs. 5.01 ± 0.54 for prolonged recovery, p = 0.016). Fisher’s exact test revealed flossing was associated with rapid recovery, with flossers comprising 75% of the rapid-recovery group, compared to 56% in the prolonged-recovery group (odds ratio ± 95%, CI = 2.26 (1.23–4.15), p = 0.01). All other factors were not significantly associated (p > 0.05). Conclusions: Increased age and illness severity were associated with prolonged smell recovery. Use of floss was the only modifiable factor associated with rapid recovery of smell loss. As 87% of cases resolve within 30 days, future studies may benefit from targeted recruitment of individuals experiencing prolonged sense loss. This would increase statistical confidence when declaring no association with the other factors assessed, avoiding type II errors.
“…11,12 Recent studies have revealed overall compositional changes in the NP microbiota and an increase in the number of opportunistic pathogens such as Rothia and Veillonella in COVID-19 patients with shortness of breath. 11,13,14 Secondary infections in patients with COVID-19 are associated with the abundance of opportunistic pathogens such as Moraxella, Corynebacterium, Haemophilus, Stenotrophomonas, Acinetobacter, Fusobacterium periodonticum, Mycobacterium spp., Mycoplasma pneumonia and Pseudomonas aeruginosa. [15][16][17][18][19] The treatment modalities of SARS-CoV2 infection are not yet established and patients are administered immunosuppressants to regulate the cytokine storm, thereby creating an environment conducive for the growth of opportunistic pathogens and co-infections in COVID-19 patients.…”
Section: Introductionmentioning
confidence: 99%
“…11,12 Recent studies have revealed overall compositional changes in the NP microbiota and an increase in the number of opportunistic pathogens such as Rothia and Veillonella in COVID-19 patients with shortness of breath. 11,13,14 Secondary infections in patients with COVID-19 are associated with the abundance of opportunistic pathogens such as Moraxella , Corynebacterium , Haemophilus , Stenotrophomonas , Acinetobacter , Fusobacterium periodonticum , Mycobacterium spp., Mycoplasma pneumonia and Pseudomonas aeruginosa. 15–19…”
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