Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

Kumar, Dinesh; Pandit, Ramesh; Sharma, Satyawati; Raval, Janvi; Patel, Zarna; Joshi, Madhvi; Joshi, Chaitanya

doi:10.1016/j.micpath.2022.105829

Cited by 15 publications

(13 citation statements)

References 60 publications

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“…This study also agreed with [40], who isolated Rhizobium radiobacter from samples of AMF01 Mask respirators by 94%, and isolated Staphylococcus hominis, Staphylococcus epidermidis, and Sphingomonas paucimobilis from other types of medical masks in varying proportions, and stated that some of these bacteria have Symptoms similar to the respiratory illness caused by COVID-19 can make it difficult to diagnose and treat the virus. The presence of Ochrobactrum anthropic in Erbil patients was in agreement with [41] who observed the presence of Ochrobactrum anthropic in low numbers of total pathogenic bacteria such as O. anthropic, O. tritici and B. cepacia from the mouth and nose of patients recovered from COVID-19. Contrary to its numbers in infected and healthy subjects, the results also agreed with the presence of the genus Pseudomonas and did not agree with the presence of the genera Veillonella, Porphyromonas, Gemella and Bulleidia compared with our study.…”

Section: Governoratessupporting

confidence: 89%

“…Although Pseudomonas is an opportunistic pathogen of the respiratory tract, especially of the sinuses [42]. However, its protective role through its ability to produce mucin in the respiratory tract acts as a barrier against viral infection, and may prevent SARS-CoV-2 infection if present in high numbers [41]. The presence of Kocuria kristinae in the results of healthy subjects from Baghdad and Anbar for this study is consistent with what was mentioned by [43] that it is a normal flora of the skin and oral mucosa, but it has the ability to cause infections in people with immunodeficiency.…”

Section: Governoratesmentioning

confidence: 99%

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The Role of Dietary Proteins During Infection with Covid-19 and the Effect of Infection on the Balance of Oral Microbiota in Different Regions of Iraq

Khashan,

Thalij,

Yaseen

2023

IOP Conf. Ser.: Earth Environ. Sci.

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This study was conducted in the laboratories of the Department of Life Sciences - College of Sciences - Tikrit University and laboratories of the Department of Food Sciences - College of Agriculture - University of Anbar and public health laboratories - Anbar for the period from December 2021 to February 2022 AD. The study included 150 people from three Iraqi governorates (Baghdad, Anbar, and Erbil). (30 infected people and 20 healthy people from each governorate, with ages ranging from 18-80 years, randomly, men and women. The results of the blood biochemical parameters values when infected with the SARS-COV2 virus showed a significant decrease at the probability level (p<0.05) in the concentration of albumin in the group of patients who were in quarantine and using artificial respiration, compared with the group of patients outside the quarantine and the healthy group from the mentioned governorates. The concentrations are 26.3, 30.4, and 34.7 (g/l). It also caused a significant decrease in the total protein and albumin concentration in all patients compared to the healthy subjects. In contrast, globulin concentration decreased slightly to be close to its value in the healthy group. Cultural, phenotypic, biochemical, and confirmatory tests through the Vitec2 compact diagnostic system showed that oral bacterial isolates purified from patients in the three provinces were Gram-positive Staphylococcus and Enterococcus versus four Gram-negative genera: Sphingomonas, Rhizobium, Aeromonas, and Ochrobactrum, compared with isolates purified from healthy subjects, which belongs to four genera of Gram-positive Staphylococcus, Enterococcus, Kocuria, and Leuconostoc, and one genus of Gram-negative Pseudomonas.

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Section: Governoratessupporting

confidence: 89%

Section: Governoratesmentioning

confidence: 99%

The Role of Dietary Proteins During Infection with Covid-19 and the Effect of Infection on the Balance of Oral Microbiota in Different Regions of Iraq

Khashan,

Thalij,

Yaseen

2023

IOP Conf. Ser.: Earth Environ. Sci.

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“…Hernández-Terán et al found differences in the abundance of specific phyla and genera between healthy control and mild symptomatic COVID-19 patients, but they observed no differences in alpha and beta diversity [28] . A study from India reported a substantial shift in the composition of the nasal microbiome in SARS-CoV-2-infected individuals in the PCoA and NMDS plots, but they did not observe any significant difference in the alpha diversity based on Shannon, Simpson, Cho1, and Abundance-based Coverage Estimator indexes [34] . In contrast, some studies showed an increase in COVID-19-associated respiratory tract microbiota diversity [32] .…”

Section: Discussionmentioning

confidence: 90%

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

Yasir

Al-Sharif

Alsubhi

et al. 2023

Journal of Infection and Public Health

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“…We have compared our observation with other URT microbiome studies (number of studies = 7) ( 11 , 12 , 17 , 19 , 20 , 58 , 59 ) on COVID-19 patients and healthy controls who have only performed 16S rRNA gene sequencing (Supplementary information; Table S4). We have seen that in those studies Acinetobacter , Pseudomonas, and Staphylococcus are mostly found in the URT of COVID-19 patients (5/7; 70% of the studies) (Supplementary information; Table S4).…”

Section: Discussionmentioning

confidence: 99%

Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups

Nath,

Sarkar,

Maddheshiya

et al. 2023

Microbiol Spectr

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The pandemic caused by the SARS-CoV-2 virus is the reason for many deaths globally. It is hypothesized that the upper respiratory tract (URT) microbiome shares similarities with lung microbiota and can modulate host immune responses to the virus. During the pandemic, several SARS-CoV-2 variants have emerged with different clinical outcomes and immune dysfunction, yet their association with changes in the URT microbiome has not been identified, which may provide an assessment of lung health in the presence of those variants with differential disease outcomes. In this study, we sequenced V3–V4 region of the 16S rRNA gene from the URT microbiome of healthy controls (HC), Delta- and Omicron-infected patients from Eastern India, which showed higher inter-individual diversity (β) and lower intra-individual diversity (α) in COVID-19 patients compared to healthy controls. Healthy control microbiome showed enrichment of commensals like Streptococcus symci , Prevotella melaninogenica , Neisseria perflava , Veillonella tobetsuensis, Veillonella nakazawae, Haemophilus parainfluenzae, Fusobacterium pseudoperiodonticum , and Bifidobacterium longum compared to COVID-19 samples. Ct value of patients significantly positively correlated with Streptococcus symci and Streptococcus toyakuensis indicating a possible inverse relation with viral load. We also observed few bacterial taxa like Staphylococcus caprae, Pseudomonas aeruginosa , Vibrio tritonious , and Rothia mucilaginosa are discriminating Omicron from Delta which is, in turn, enriched mostly with Enterobacter mori , Acinetobacter baumannii, and Klebsiella pneumoniae . Further investigation showed nine control-associated bacteria had higher to lower trends among three groups viz., Control > Omicron > Delta. These bacteria also contributed to the successful prediction of disease groups with high accuracy (90% ± 0.5%) by random forest analysis. IMPORTANCE The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies. The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. However, although it has been known that different SARS-CoV-2 variants manifest distinct transmissibility and mortality rates in human populations, their effect on the composition and diversity of the URT microbiome has not been studied to date. Unlike the older variant (Delta), the newer variant (Omicron) have become more transmissible with lesser mortality and the symptoms have also changed significantly. Hence, in the present study, we have investigated the change in the URT microbiome associated with Delta and Omicron variants and identified variant-specific signatures that will be useful in the assessment of lung health and can be utilized for nasal probiotic therapy in the future.

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Nasopharyngeal microbiome of COVID-19 patients revealed a distinct bacterial profile in deceased and recovered individuals

Cited by 15 publications

References 60 publications

The Role of Dietary Proteins During Infection with Covid-19 and the Effect of Infection on the Balance of Oral Microbiota in Different Regions of Iraq

The Role of Dietary Proteins During Infection with Covid-19 and the Effect of Infection on the Balance of Oral Microbiota in Different Regions of Iraq

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

Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups

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