Oropharyngeal Microbiota Research Articles

Respiratory tract bacteria distribution and transmission patterns among individuals in close contact.

Respiratory disease outbreaks frequently occur in settings where individuals are in close contact, for example, schools and factories. However, the transmission patterns of oropharyngeal microbiota among healthy individuals living in clusters are unclear. Therefore, we aimed to investigate the respiratory tract bacteria distribution and transmission patterns among individuals in close contact. A total of 36 freshmen from Peking University Medical School participated in the study. We collected pharyngeal swabs on the first day of enrollment, 15, 30, and 60 days after cohabitation. DNA was extracted from the swabs and subjected to high-throughput sequencing to profile the microbial composition. Statistical analyses were performed to assess diversity and significance. Neisseriaceae, Prevotellaceae, and Streptococcaceae were the most abundant bacterial families detected. Over time, changes were observed in the bacterial communities, with a tendency for increased similarity between dormitory room members. By day 60 of cohabitation, the bacterial communities appeared to be more similar compared to the baseline (prior to cohabitation). The transmission patterns included spreading with colonization, spreading without colonization, and non-spreading. Bacteria belonging to the core genera are most likely to spread and colonize easily. The risk of healthy cohabitants acquiring respiratory pathogens through close contact may be overestimated in epidemiological studies. Therefore, monitoring the spread of core genera that are easily transmitted and colonized is crucial for effective prevention of respiratory pathogen transmission.

Comparative analysis of the postadmission and antemortem oropharyngeal and rectal swab microbiota of ICU patients

Shotgun metabarcoding was conducted to examine the microbiota in a total of 48 samples from 12 critically ill patients, analyzing samples from both the oropharynx and rectum. We aimed to compare their postadmission microbiota, characterized as moderately dysbiotic, with the severely dysbiotic antemortem microbiota associated with patients’ deaths. We found that, compared with postadmission samples, patient antemortem swab samples presented moderate but not significantly decreased diversity indices. The antemortem oropharyngeal samples presented an increase in biofilm-forming bacteria, including Streptococcus oralis, methicillin-resistant Staphylococcus aureus (MRSA), and Enterococcus faecalis. Although the septic shock rate was 67%, no significant differences were detected in the potential pathogen ratios when the microbiota was analyzed. A notable strain-sharing rate between the oropharynx and intestine was noted. By comparing postadmission and antemortem samples, microbial biomarkers of severe dysbiosis were pinpointed through the analysis of differentially abundant and uniquely emerging species in both oropharyngeal and rectal swabs. Demonstrating strong interconnectivity along the oral-intestinal axis, these biomarkers could serve as indicators of the progression of dysbiosis. Furthermore, the microbial networks of the oropharyngeal microbiota in deceased patients presented the lowest modularity, suggesting a vulnerable community structure. Our data also highlight the critical importance of introducing treatments aimed at enhancing the resilience of the oral cavity microbiome, thereby contributing to better patient outcomes.

Features of the oropharyngeal microbiota of healthy children and those with acute respiratory infections. A prospective single-center randomized study

Background. The oropharyngeal microbiota is involved in the development of colonization resistance, affecting viral adhesion and metabolism. Any deviations in the stability of the environmental microbial niches of the oropharynx alter the local immune response and can trigger severe chronic somatic disorders. Aim. To compare the composition of the microbiota of children during an episode of respiratory infection and healthy volunteers examined in different periods of convalescence. The obtained data can be used to predict the course of the disease, analyze the risk of complications, and assess the frequency of the diseases in the future. Materials and methods. From 20.01.2022 to 23.12.2022, an open-label prospective single-center randomized comparative study was conducted, which included 120 children aged 5-10 who presented with symptoms of acute respiratory infection. The control group consisted of 15 asymptomatic children examined at different periods of convalescence. The study compared changes in the oral microbiota composition of patients and healthy children. The evaluation was performed using complete 16S rRNA gene sequencing on the Oxford Nanopore platform. Taxonometric analysis at the species and genera level was performed using the Knomics-Biota platform. The R programming language was used for statistical processing. In addition, the parameters of α- and β-diversity of the microbiota were assessed. The Chao1 and Shannon indices were calculated to assess α-diversity (diversity within one community). The Chao1 index is based on the number of species found in the sample and also rare species that are found only 1 or 2 times, thus preventing underestimation of diversity. The Shannon index includes both the number of species and their uniformity in the community. A change in the index indicates the dominance of one or more species. The following indicators were used to assess the β-diversity describing the differences between two microbiota samples at the species and genera level: Bray–Curtis dissimilarity (characterizing the ratios of common and different microorganisms between the samples) and the Aitchison distance (reflecting the differences in the proportions of microorganisms). In addition, the balance between the two groups of microorganisms was evaluated using the NearesBalance method, which characterizes the differences between the microbiota of the main and control groups. Results. The results of our study show that during respiratory infection, the state of the oropharyngeal microbiota is characterized by an increase in α-diversity, which is associated with an increase in the proportion of species of Streptococcus salivarius, Streptococcus pneumoniae, Streptococcus pseudopneumoniae, Streptococcus pyogenes, Streptococcus thermophilus and A12 versus the proportion of Streptococcus mitis, Streptococcus oralis, Streptococcus gwangjuense, Streptococcus sanguinis, Streptococcus gordonii and FDAARGOS_192. In the control group, the oropharyngeal microbiota was divided into two clusters. The dominance of streptococci was observed in the first group (control), while the second group had a more uniform representation. Analysis of the changes in microbial communities in the main and control groups can show the stages of oral microbiota recovery after an acute respiratory infection episode. Conclusion. More research is needed in the field of the oropharyngeal microbiome on a larger sample of healthy children, to standardize the communities of the oropharyngeal microbiota, to study the interaction within communities and with the body as a whole. Analysis of the impact of the microbiota on the frequency and course of respiratory infections and the rate of complications opens up new prospects in treating, rehabilitating, and preventing diseases. These research areas can contribute to improving children's health and quality of life and introducing new approaches into clinical practice.

Assessed correlation between biological diversity of oropharyngeal microbiota and atopic dermatitis severity and exacerbations

Atopic dermatitis (AtD) is a multifactorial inflammatory skin disease characterized by itching, chronic recurrent course and age-related features of lesions. AtD pathogenesis has not been fully elucidated yet. An important factor for AtD emergence and progression is the imbalance in symbiotic microbiota. The research publications provide a few studies about a role for oropharyngeal microorganisms in AtD immunopathogenesis. The aim of the study is to analyze biological diversity of oropharyngeal microbial communities in varying AtD severity. 97 male patients, aged from 16 to 19 years, with different AtD severity were included in the study. Culture study of oropharyngeal discharge was also performed. Biological material was seeded on the expanded list of growth media and incubated for 5 days at the 37°С. To assess the biological diversity of the oropharyngeal microbiota, the coefficient of constancy (C) was used, in order to classify individual microorganisms as permanent, additional or transient. Statistical data processing was performed using the Stat Tech software (version 4.0.0, Stattech LLC, Russia). While examining biological diversity of the oropharyngeal microbiota in AtD patients, 58 microbial species were isolated and identified. After statistical analysis the significant differences in frequency of isolation, depending on different AtD severity were observed for microbes such asStreptococcus vestibularisandRothia dentocariosa. WhenR. dentocariosais isolated from the oropharynx, the chances of AtD exacerbation emergence decreased by 6 times, whereas in case ofS. vestibularis, on the contrary, it increased by 5 times. Therefore, identification of transitions of individual microbes from transient to additional and permanent microbiota and vice versa, depending on the AtD stage and severity, allows to analyze an influence of specific microorganisms in AtD pathological processes and to establish definite new microbiological predictors of AtD exacerbation and remission.

Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19

The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.

A pilot study on the characterization and correlation of oropharyngeal and intestinal microbiota in children with type 1 diabetes mellitus

BackgroundType 1 Diabetes Mellitus (T1DM) is one of the most common endocrine disorders of childhood and adolescence, showing a rapidly increasing prevalence worldwide. A study indicated that the composition of the oropharyngeal and gut microbiota changed in T1DM. However, no studies have yet associated the changes between the microbiomes of the oropharyngeal and intestinal sites, nor between the flora and clinical indicators. In this study, we examined the composition and characteristics of oropharyngeal and intestinal flora in patients with T1DM in compared to healthy children. We identified correlations between oropharyngeal and intestinal flora and evaluated their association with clinical laboratory tests in patients with T1DM.MethodsThe oropharyngeal and fecal samples from 13 T1DM and 20 healthy children were analyzed by high-throughput sequencing of the V3–V4 region of 16S rRNA. The associations between microbes and microorganisms in oropharyngeal and fecal ecological niches, as well as the correlation between these and clinical indicators were further analyzed.ResultsIt was revealed that T1DM children had distinct microbiological characteristics, and the dominant oropharyngeal microbiota genus included Streptococcus, Prevotella, Leptotrichia, and Neisseria; that of intestinal microbiota included Blautia, Fusicatenibacter, Bacteroides, and Eubacterium_hallii_group. Furthermore, oropharyngeal Staphylococcus was significantly positively correlated with intestinal norank_f__Ruminococcaceae and Ruminococcus_torques_group in TIDM children. Moreover, in these children, differential genes in oropharyngeal and intestinal samples were enriched in metabolic pathways such as amino acid generation, fatty acid metabolism, and nucleotide sugar biosynthesis. Additionally, correlation analysis between the oropharyngeal/intestinal microbiome with laboratory tests showed significant correlations between several bacterial taxa in the oropharynx and intestines and glycated hemoglobin and C-peptide.ConclusionUnique microbial characteristics were found in the oropharynx and intestine in children with T1DM compared to healthy children. Positive correlations were found between changes in the relative abundance of oropharyngeal and gut microbiota in children with T1DM. Associations between the oropharyngeal/intestinal microbiota and laboratory investigations in children with T1DM suggest that the composition of the oropharyngeal and intestinal flora in children with T1DM may have some impact on glycemic control.

Cranial osteomyelitis associated with Pasteurella canis in broiler chickens

Species of the Pasteurella genus are part of the oropharyngeal microbiota of many animal species. In poultry, Pasteurella multocida causes fowl cholera, the chronic manifestation of which can include neurological symptoms. Pasteurella canis causes osteomyelitis and other infections in humans. To the best of our knowledge, this is the first report of cranial osteomyelitis associated with Pasteurella canis in broiler chickens in Chile.

Comparative analysis of oropharyngeal microbiota in healthcare workers post-COVID-19.

To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored. Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated. The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications. During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.

Evaluation of the dynamics of oral pathogenic microbiota in COVID-19 patients by genomic sequencing after application of foam with antimicrobial action

Relevance. The COVID-19 pandemic caused by the SARS-CoV-2 virus has demonstrated the critical importance of understanding the mechanisms of transmission and finding effective methods of prevention. Particular attention has been paid to the role of oral hygiene, as the oral cavity serves as a major route of transmission. Studies show that the composition of the oral microbiota can influence the course and outcome of COVID-19 disease. Therefore, there is a need to study the effects of oral antiseptics on the microbiome, which may offer new opportunities for the prevention and treatment of this disease.Objective. The aim of this study is to evaluate the effectiveness of the oral cleansing foam «Parodontol PROF» in reducing the pathogenic microflora of the oral cavity in patients with COVID-19 and to assess its effect on the risk of secondary infections.Materials and methods. The study was conducted on the basis of the Clinical Medical Centre «Kuskovo» of Russian University of Medicine. It included 450 patients with a confirmed diagnosis of COVID-19. The participants were divided into two groups: the test group used oral cleansing foam, while the control group used no additional oral hygiene. Comparative analyses of the taxonomic composition of the oropharyngeal microbiota and dental plaque before and after the use of the cleansing foam were performed.Results. The study showed that patients who regularly used the cleansing foam «Parodontol PROF» had a significant decrease in the representation of pathogens, including Mycoplasma, and an increase in the number of beneficial commensals such as Lactococcus and Lactobacillus. These changes indicate the potential efficacy of this product to improve oral hygiene and reduce the risk of secondary infections.Conclusion. The study supports the hypothesis that improving oral hygiene with specialised antiseptic agents, such as a cleansing foam, may help to reduce pathogenic microflora in the oral cavity in patients with COVID-19. This, in turn, may reduce the risk of pathogen migration into the lower respiratory tract and the development of secondary infections. The findings emphasise the importance of further research in this area and the development of comprehensive approaches to oral hygiene management in the context of infectious diseases.

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

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.

Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study

ObjectiveTo explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA.MethodsBefore adeno-tonsillectomy, we collected throat swab samples from different parts of the oropharynx and nasopharynx of 30 OSA patients and 10 non-OSA patients and collected throat swab samples from the oropharynx of the above patients one month after the adeno-tonsillectomy. The 16 S rRNA V3–V4 region was sequenced to identify the microbial communities. The correlation analysis was conducted based on clinical characteristics.ResultsThere was a significant difference of alpha diversity in different parts of the upper airway of pediatric OSA, but this difference was not found in children with non-OSA. Beta diversity was significantly different between non-OSA and pediatric OSA. At the genus level, the composition of flora in different parts is different between non-OSA and pediatric OSA. The correlation analysis revealed that the relative abundance of Neisseria was significantly correlated with obstructive apnea hypopnea index. Furthermore, the functional prediction revealed that pathways related to cell proliferation and material metabolism were significantly different between non-OSA and pediatric OSA. Besides, the adeno-tonsillectomy has minimal impact on oral microbiota composition in short term.ConclusionThe changes in upper airway microbiome are highly associated with pediatric OSA. The relative abundance of some bacteria was significantly different between OSA and non-OSA. These bacteria have the potential to become new diagnostic and early warning biomarkers.

The effect of local use of etiotropic drugs on the oropharyngeal microbiota in children with acute respiratory infection

Introduction. The microbiota of the oral cavity and oropharynx, actively interacts with the epithelium of the mucous membrane and the immune system, creates antagonistic conditions for the growth and reproduction of pathogens. Microbiocenosis-preserving therapy can provide conditions for maintaining colonization resistance and reduce the likelihood of adhesion of respiratory viruses.Aim. To evaluate the effect of local use of various antimicrobial drugs on the microbiota of the oropharyngeal mucosa in children with acute respiratory infection.Materials and methods. 120 children (5–10 years old) with acute respiratory infection were divided into three groups, in which they were used as part of complex therapy: in group 1st – hexetidine-containing aerosol, in group 2nd – a children’s spray containing gramicidin S and cetylpyridinium chloride, in the 3rd – 0.01% solution of benzyldimethyl-myristoylamino-propylammonium. On the 1st and 12th days of observation, participants had a throat swab taken to study the state of the oropharyngeal microbiota using 16S rRNA sequencing. The results obtained were compared with those of healthy peers.Results. According to sequencing data, the microbiota of participants in all groups before treatment differed from the microbiota of healthy peers in terms of alpha and beta diversity, as well as in the results obtained by the nearest balance method. Local use of antiseptic drugs influenced the microbiota at the level of species and genera of microorganisms. After treatment in the 2nd group, in contrast to the 1st and 3rd, statistically significant changes in the balances at the level of microorganism species were revealed towards the indicators of healthy peers.Conclusions. A combined drug containing cetylpyritinium chloride and the bacteriocin-like antimicrobial peptide gramicidin S demonstrated no negative effect on commensal microbiota and contributed to the stabilization of the regional microbiota.

An Update Review to Cast Light on the Possible Role of Altered Oropharyngeal Microbiota in Differentiating True Psychosis from Malingered Psychosis in a Forensic Psychiatric Setting

Over the past few years, malingered psychosis has had a progressive occurrence since a great deal of attention has been directed to the closures of long-stay psychiatric institutions and care in the community. Therefore, malingered psychosis needs to be identified to conduct precise forensic assessments and prevent miscarriages of justice and misuse of restricted healthcare resources. Although, over the past decades, researchers have introduced a number of workable psychometric strategies and tools for diagnosing true psychosis, it is still sometimes challenging to differentiate between true and malingered psychosis. Hence, identifying reliable and innovative diagnostic alternatives seems crucial. Accordingly, a summary of gathered evidence is provided by the present review for enhancing future evaluation of oropharyngeal microbiome composition as a practical indicator for diagnosing true psychosis in a forensic psychiatric setting. As per the systematic search terms (namely, “diagnostic marker,” “oropharyngeal microbiome,” “forensic psychiatric setting,” “psychosis,” and “oropharyngeal microbiota”), relevant English publications were searched from January 1, 1980, to September 15, 2023, in Scopus, the Web of Science, Embase, Cochrane Library, PubMed, and Google Scholar databases. Finally, eight articles were included in the present review. Also, we adopted the narrative technique so that the material synthesis leads to a cohesive and compelling story. The results revealed that the periodontal disease and saliva microbiome were possibly associated with true psychosis. Thus, since oropharyngeal microbial compositions are highly different among healthy controls and patients with true psychosis, future research can take advantage of saliva to differentiate between fake and true fake psychosis throughout the initial stages of forensic psychiatric assessment. As a substrate of interest, saliva could also be used for characterizing the various stages of psychosis under a forensic psychiatric setting.

The possible role of altered oropharyngeal microbiota in differentiating true psychosis from malingered psychosis in a forensic psychiatric setting

Over the past few years, malingered psychosis has had a progressive occurrence since a great deal of attention has been directed to the closures of long-stay psychiatric institutions and care in the community. Therefore, malingered psychosis needs to be identified to conduct precise forensic assessments and prevent miscarriages of justice and misuse of restricted healthcare resources. Although, over the past decades, some practical psychometric and strategic tools have been introduced to diagnose true psychosis, it is still sometimes challenging to differentiate between true and malingered psychosis. Hence, identifying reliable and innovative diagnostic alternatives seems crucial. In this respect, some preliminary results revealed the saliva microbiome and periodontal disease were potentially associated with true psychosis. Therefore, since oropharyngeal microbial compositions are highly different among healthy controls and patients with true psychosis, we hypothesized that future research can take advantage of oropharyngeal microbiota composition to differentiate between true and fake psychosis during the early stages of forensic psychiatric evaluation. As a substrate of interest, oropharyngeal secretion samples could also be used for characterizing the various stages of psychosis in a forensic psychiatric setting.

The impact of dysbiosis in oropharyngeal and gut microbiota on systemic inflammatory response and short-term prognosis in acute ischemic stroke with preceding infection.

Stroke is a devastating disease and ranks as the second leading cause of death and disability globally. Several studies have shown that preceding infection (PI) of upper respiratory tract are strongly associated with acute ischemic stroke (AIS). However, the clinical implications and underlying pathological mechanisms remain unclear. In this study, 16S rRNA gene sequencing was employed to compare the structural characteristics of oropharyngeal and gut microbiota in AIS patients with or without PI and normal controls (NCs; 30 cases each), and systemic inflammatory markers were detected to explore the relationship between upper respiratory tract infections (URTIs) and subsequent stroke severity and functional outcome and the potential mechanism. We found that patients with AIS-PI exhibited elevated serum WBC, NE, CRP, and Hcy levels, as well as a higher 90-day mRS score. Oropharyngeal and gut microbiota analysis showed that AIS and AIS-PI patients exhibited increased microbial richness in sequence. Principal coordinate analysis of the microbiota demonstrated significant differences in microbiota composition among the three groups. In AIS-PI patients, Megamonas, Megasphaera, Ruminococcaceae UCG 004, Rothia, and Streptococcus were significantly enriched in the gut. Opportunistic pathogens, including Thermus, uncultured Veillonella sp., and Oribacterium sinu, were found to be significantly enriched in the oropharynx. The dysregulated microbiota were positively correlated with systemic inflammatory markers, stroke severity, and poor prognosis. In contrast, short-chain fatty acid-producing bacteria Eisenbergiella, bacterium NLAE, Fusicatenibacter, Ruminococcaceae, and Faecalibacterium were enriched in NCs. Their abundances were negatively correlated with systemic inflammatory markers, stroke severity and poor prognosis. Our findings suggest that PIs of the upper respiratory tract may contribute to poor short-term functional outcome in AIS patients by causing disturbance of the oropharyngeal and gut microbiota and promoting elevated systemic inflammation levels.

The compromised microbial topography between nasopharyngeal and oropharyngeal microbiota associate with pediatric pneumonia

The compromised microbial topography between nasopharyngeal and oropharyngeal microbiota associate with pediatric pneumonia

The gut microbiota composition is linked to subsequent occurrence of ventilator-associated pneumonia in critically ill patients.

Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critically ill-ventilated patients. Oropharyngeal and lung microbiota have been demonstrated to be associated with VAP occurrence, but the involvement of gut microbiota has not been investigated so far. Therefore, the aim of this study is to compare the composition of the gut microbiota between patients who subsequently develop VAP and those who do not. A rectal swab was performed at admission of every consecutive patient into the intensive care unit (ICU) from October 2019 to March 2020. After DNA extraction, V3-V4 and internal transcribed spacer 2 regions deep-sequencing was performed on MiSeq sequencer (Illumina) and data were analyzed using Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline. Among 255 patients screened, 42 (16%) patients with invasive mechanical ventilation for more than 48 h were included, 18 (43%) with definite VAP and 24 without (57%). Patients who later developed VAP had similar gut bacteriobiota and mycobiota α-diversities compared to those who did not develop VAP. However, gut mycobiota was dissimilar (β-diversity) between these two groups. The presence of Megasphaera massiliensis was associated with the absence of VAP occurrence, whereas the presence of the fungal genus Alternaria sp. was associated with the occurrence of VAP. The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop VAP and those who do not. This study encourages large multicenter cohort studies investigating the role of gut-lung axis and oropharyngeal colonization in the development of VAP in ICU patients. Trial registration number: NCT04131569, date of registration: 18 October 2019. IMPORTANCE The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop ventilator-associated pneumonia (VAP) and those who do not. Investigating gut microbiota composition could help to tailor probiotics to provide protection against VAP.

Pharynx infectious and inflammatory diseases local etiotropic therapy efficacy comprehensive assessment in preschool and primary school-age children

Background. The oropharyngeal microbiota is important in maintaining resistance, eliminating viruses and regulating local protective reactions in response to inflammation in acute respiratory infections.
 Aim. To evaluate of the effect of topical etiotropic therapy on clinical manifestations, elimination of viruses and on oropharyngeal microbiota in the treatment of acute infectious inflammation of the throat that occurred as part of acute respiratory infections in children aged 510 years.
 Materials and methods. 120 outpatient patients randomized into 3 equal groups were treated for 7 days: in Group 1 0.2% hexethidine-containing aerosol, in Group 2 0.03 mg combined spray gramicidin S and 0.1 mg cetylpyridinium chloride, in Group 3 0.01% topical solution containing benzyldimethyl-myristoylamino-propylammonium. Changes in the severity of clinical manifestations were compared (integral indicator modified Tonsillopharyngitis Severity Score TSSm for children, the severity of the "sore throat" symptom on the WongBaker scale, the severity of local signs of inflammation according to pharyngoscopy data) in groups at Visit 2 (day 51) and Visit 3 (day 121) compared with the Visit 1. The elimination of acute respiratory infection pathogens was evaluated: polymerase chain reaction (PCR) of oropharyngeal smears obtained on days 1, 3 and 5 (1) PCR-1, PCR-2, PCR-3 respectively, with the detection of 12 respiratory viruses, including SARS-CoV-2. The state of the microbiota was assessed by sequencing the full-size 16S gene in samples obtained before and after treatment 1st and 12th (1) days, and compared with 19 indicators in healthy.
 Results. By Visit 3, the decrease in TSSm indicators was: 4.01.07 in Group 1; 5.01.48 in Group 2 and 4.01.02 in Group 3. The intergroup differences between Group 2 and 1, Group 2 and 3 were statistically significant (p0.05). The severity of sore throat by Visit 3 decreased in groups 1, 2 and 3 respectively by 2.00.90, 2.50.61 and 2.10.60, intergroup differences between groups 2 and 1, 2 and 3 had statistical significance at p0.05. The time to achieve complete relief of the disease according to the TSSm indicator was (day, MSE): 16.61.47 in Group 1; 11.91.13 in Group 2 and 12.41.38 in Group 3, intergroup differences (groups 1 and 2) are significant, p0.05. The time of complete relief from sore throat for groups 13 was 12.60.96, 8.00.87 and 9.41.01 respectively, intergroup differences (groups 1 and 2) were significant, p0.05. By Visit 2, the proportion of patients with a negative PCR result increased in Group 1 by 25%, in Group 2 by 43% and in Group 3 by 38%, which corresponded to the elimination of 81, 92 and 74% of viruses detected in groups according to PCR-1 and PCR-2. The microbiota of participants in all groups before treatment differed from the microbiota of healthy in terms of alpha and beta diversity, as well as in terms of indicators obtained by the NearesBalance method. After completion of treatment, changes in the microbiota in terms of beta diversity were observed in all groups compared to the initial state. In contrast to groups 1 and 3, in Group 2 there were statistically significant changes in species-level balances between groups of microbes that distinguish between sick and healthy, towards indicators of healthy.
 Conclusion. Topical etiotropic medications provide rapid relief of complaints and local signs of inflammation in the treatment of patients aged 510 years with sore throat in acute respiratory infections and contribute to the rapid elimination of pathogens of acute respiratory infections. A combined preparation containing an antiseptic and a bacteriocin-like antimicrobial peptide gramicidin S provides a more pronounced therapeutic effect at an earlier time and the elimination of 90% of all respiratory viruses, including SARS-CoV-2, by the fifth day of therapy, and also has the most sparing effect on the oropharyngeal microbiota compared to antiseptic monopreparations, which may explain its more pronounced anti-inflammatory effect.

The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children

BackgroundThe microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children.ResultsDifferential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children’s upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis.ConclusionsOur study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults.1wFNzyNDfM8ZUGXDxQYKLxVideo

Gut microbiota trajectory in β-thalassemia major children who underwent allogeneic hematopoietic stem cell transplantation.

The gut microbiota of patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) changes, leading to complications such as acute graft-versus-host disease (GVHD). This study aimed to evaluate the human microbiota composition before and after HSCT in β-thalassemia major (β-TM) children. Twenty-two β-TM children who received allo-HSCT between December 2018 and March 2020 were enrolled. They were followed up for more than 100 days after HSCT, and their gut microbiota information and disease data were recorded at five-time points. The dominant bacteria were Bacteroidetes and Firmicutes at the phylum level and Lachnospiraceae at the family level before and after HSCT. In the differential analysis, Ruminococcaceae constantly decreased after HSCT. Besides, Rothia mucilaginosa was the most abundant 2 months after HSCT compared to before it. Additionally, GVHD patients presented decreased levels of Bacteroidetes compared to those without GVHD. Moreover, Blautia levels significantly decreased in critically ill GVHD patients. The gut microbiota of the 22 β-TM children showed a clear trend of destruction and reconstruction within 100 days after HSCT. The extra-oral infections and inflammations of Rothia mucilaginosa, a Gram-positive bacterium of the normal oropharyngeal tract microbiota, might play an important role in the recovery process of HSCT. Finally, decreased Bacteroidetes levels were associated with GVHD onset.