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Scientific Reports Jan 2023Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic...
Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos, Mexico. Ninety oropharyngeal swabs and 97 fecal samples were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In both niches, more than 95% of the total sequence reads were represented by viruses that replicate either in humans or in plants. Regarding human viruses, three families were most abundant and frequent in the oropharynx: Herpesviridae, Picornaviridae, and Reoviridae; in fecal samples, four virus families predominated: Caliciviridae, Picornaviridae, Reoviridae, and Anelloviridae. Both niches showed a high abundance of plant viruses of the family Virgaviridae. Differences in the frequency and abundance of sequence reads and diversity of virus species were observed in both niches and throughout the year of study, with some viruses already present in the first months of life. Our results suggest that the children's virome is dynamic and likely shaped by the environment, feeding, and age. Moreover, composition analysis suggests that the virome composition is mostly individual. Whether this constant exposition to different viruses has a long-term impact on children's health or development remains to be studied.
Topics: Child; Humans; Infant; Eukaryota; Virome; Picornaviridae; Feces; Herpesviridae; Oropharynx; Metagenomics
PubMed: 36650178
DOI: 10.1038/s41598-022-26707-9 -
Journal of Clinical Sleep Medicine :... Dec 2019To explore and analyze diversity and abundance of oropharyngeal microbiota in patients with obstructive sleep apnea (OSA).
STUDY OBJECTIVES
To explore and analyze diversity and abundance of oropharyngeal microbiota in patients with obstructive sleep apnea (OSA).
METHODS
This was a cross-sectional study. Middle-aged men, suspected to have OSA, referred to full-night polysomnography, and willing to provide oropharyngeal swab samples, were consecutively enrolled. OSA severity was assessed by apnea-hypopnea index (AHI) as non-OSA (AHI < 5 events/h) and OSA (AHI ≥ 15 events/h). Bacterial DNA of oropharyngeal samples was extracted and quality test performed. Oropharyngeal microbiota was analyzed using 16S ribosomal DNA (rDNA) sequencing, and bioinformatic analysis carried out after sequencing.
RESULTS
Samples from 51 men (25 in the non-OSA group and 26 in the OSA group) were sent for examination. Of these, 40 samples were found to have sufficient concentration of DNA and were analyzed for bioinformatics. In alpha diversity analysis, the OSA group exhibited significantly lower sobs (198.33 ± 21.71 versus 216.57 ± 26.21, P = .022), chao (221.30 ± 26.62 versus 243.86 ± 26.20, P = .014), ace (222.17 ± 27.15 versus 242.42 ± 25.81, P = .028) and shannon index (3.14 ± 0.23 versus 3.31 ± 0.26, P = .035), suggesting a reduction in microbial species diversity. We further divided participants into non-OSA, moderate OSA, and severe OSA groups and observed a significant decrease in the bacterial biodiversity of OSA groups compared with the non-OSA group, with the most significant decrease occurring in the moderate OSA group. Principal coordinate analysis showed two extremely different oropharyngeal microbial communities in non-OSA and OSA groups. More interestingly, proportion of Neisseria was slightly higher in the severe OSA group (20.64%), followed by the moderate OSA and non-OSA groups (12.57% and 9.69%, respectively). Glaciecola was not detected in the OSA groups compared to the non-OSA group (0 versus 0.772 ± 0.4754, P < .001).
CONCLUSIONS
Middle-aged men with OSA showed less oropharyngeal species diversity and altered abundance, on which further confirmation is warranted.
Topics: Adult; Aged; Cross-Sectional Studies; Humans; Male; Microbiota; Middle Aged; Oropharynx; Polysomnography; Severity of Illness Index; Sleep Apnea, Obstructive
PubMed: 31855163
DOI: 10.5664/jcsm.8084 -
Archives of Pathology & Laboratory... Nov 2015The incidence of oropharyngeal squamous cell carcinoma has increased during the past decade and is related primarily to the human papillomavirus. This change in... (Review)
Review
CONTEXT
The incidence of oropharyngeal squamous cell carcinoma has increased during the past decade and is related primarily to the human papillomavirus. This change in etiology, from tobacco and alcohol to human papillomavirus, has resulted in improved survival for the disease. In the United States, open resection had largely been replaced by concurrent chemotherapy and/or radiotherapy by the early 2000s. The advent of transoral surgery has led to an increase in surgery as the primary treatment for both early- and advanced-stage oropharyngeal squamous cell carcinoma because it has potential advantages over open surgery and nonsurgical modalities.
OBJECTIVE
To provide an overview of transoral robotic surgery for oropharyngeal squamous cell carcinoma and contrast it with other surgical and nonsurgical modalities.
DATA SOURCES
Articles from 2000 to 2014 were accessioned on PubMed and reviewed for utility by the primary authors.
CONCLUSIONS
Transoral surgery has become more commonly used as a minimally invasive approach to treat oropharyngeal tumors. Other strategies, including radiation, chemotherapy with radiation, and open surgery, are still important treatment approaches. The treatment options for an individual patient rely on multiple factors, including the tumor location and size, features of the tumor, and patient comorbidities. The continued study of these techniques is important to match the patient with the most appropriate treatment.
Topics: Carcinoma, Squamous Cell; Humans; Oropharyngeal Neoplasms; Oropharynx; Quality of Life; Robotic Surgical Procedures; Treatment Outcome
PubMed: 26288397
DOI: 10.5858/arpa.2014-0573-RA -
Critical Care (London, England) 2011Mechanically ventilated critically ill patients frequently develop ventilator-associated pneumonia (VAP), a life-threatening complication. Proposed preventive measures... (Review)
Review
INTRODUCTION
Mechanically ventilated critically ill patients frequently develop ventilator-associated pneumonia (VAP), a life-threatening complication. Proposed preventive measures against VAP include, but are not restricted to, selective decontamination of the digestive tract (SDD), selective oropharyngeal decontamination (SOD) and the use of probiotics. Probiotics are live bacteria that could have beneficial effects on the host by altering gastrointestinal flora. Similar to SDD and SOD, a prescription of probiotics aims at the prevention of secondary colonization of the upper and/or lower digestive tract.
METHODS
We performed a literature review to describe the differences and similarities between SDD/SOD and probiotic preventive strategies, focusing on (a) efficacy, (b) risks, and (c) the routing of these strategies.
RESULTS
Reductions in the incidence of VAP have been achieved with SDD and SOD. Two large randomized controlled trials even showed reduced mortality with these preventive strategies. Randomized controlled trials of probiotic strategies also showed a reduction of the incidence of VAP, but trials were too small to draw firm conclusions. Preventive strategies with antibiotics and probiotics may be limited due to the risk of emerging resistance to the locally applied antibiotics and the risk of probiotic-related infections, respectively. The majority of trials of SDD and SOD did not exhaustively address the issue of emerging resistance. Likewise, trials of probiotic strategies did not adequately address the risk of colonization with probiotics and probiotic-related infection. In studies of SDD and SOD the preventive strategy aimed at decontamination of the oral cavity, throat, stomach and intestines, and the oral cavity and throat, respectively. In the vast majority of studies of probiotic therapy the preventive strategy aimed at decontamination of the stomach and intestines.
CONCLUSIONS
Prophylactic use of antibiotics in critically ill patients is effective in reducing the incidence of VAP. Probiotic strategies deserve consideration in future well-powered trials. Future studies are needed to determine if preventive antibiotic and probiotic strategies are safe with regard to development of antibiotic resistance and probiotic infections. It should be determined whether the efficacy of probiotics improves when these agents are provided to the mouth and the intestines simultaneously.
Topics: Anti-Bacterial Agents; Critical Care; Decontamination; Disinfection; Gastrointestinal Tract; Humans; Oropharynx; Pneumonia, Ventilator-Associated; Probiotics
PubMed: 21232110
DOI: 10.1186/cc9963 -
Advanced Science (Weinheim,... Oct 2021Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019... (Clinical Trial)
Clinical Trial
Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019 (COVID-19) patients is not studied. Herein, oropharyngeal swabs are collected from confirmed cases (CCs) with COVID-19 (73 subjects), suspected cases (SCs) (36), confirmed cases who recovered (21), suspected cases who recovered (36), and healthy controls (Hs) (140) and then completed MiSeq sequencing. Oropharyngeal microbial α-diversity is markedly reduced in CCs versus Hs. Opportunistic pathogens are increased, while butyrate-producing genera are decreased in CCs versus Hs. The classifier based on eight optimal microbial markers is constructed through a random forest model and reached great diagnostic efficacy in both discovery and validation cohorts. Notably, the classifier successfully diagnosed SCs with positive IgG antibody as CCs and is demonstrated from the perspective of the microbiome. Importantly, several genera with significant differences gradually increase and decrease along with recovery from COVID-19. Forty-four oropharyngeal operational taxonomy units (OTUs) are closely correlated with 11 clinical indicators of SARS-CoV-2 infection and Hs based on Spearman correlation analysis. Together, this research is the first to characterize oropharyngeal microbiota in recovered COVID-19 cases and suspected cases, to successfully construct and validate the diagnostic model for COVID-19 and to depict the correlations between microbial OTUs and clinical indicators.
Topics: Adult; COVID-19; Female; Humans; Male; Microbiota; Middle Aged; Oropharynx; SARS-CoV-2
PubMed: 34423593
DOI: 10.1002/advs.202102785 -
Frontiers in Immunology 2020Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterized by hypogammaglobulinemia and recurrent...
Common Variable Immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA) are primary antibody deficiencies characterized by hypogammaglobulinemia and recurrent infections, which can lead to structural airway disease (AD) and interstitial lung disease (ILD). We investigated associations between serum IgA, oropharyngeal microbiota composition and severity of lung disease in these patients. In this cross-sectional multicentre study we analyzed oropharyngeal microbiota composition of 86 CVID patients, 12 XLA patients and 49 healthy controls (HC) using next-generation sequencing of the 16S rRNA gene. qPCR was used to estimate bacterial load. IgA was measured in serum. High resolution CT scans were scored for severity of AD and ILD. Oropharyngeal bacterial load was increased in CVID patients with low IgA ( = 0.013) and XLA ( = 0.029) compared to HC. IgA status was associated with distinct beta (between-sample) diversity ( = 0.039), enrichment of (, and more severe radiographic lung disease ( = 0.003), independently of recent antibiotic use. AD scores were positively associated with , and , and ILD scores with and negatively with . In clinically stable patients with CVID and XLA, radiographic lung disease was associated with IgA deficiency and expansion of distinct oropharyngeal bacterial taxa. Our findings highlight IgA as a potential driver of upper respiratory tract microbiota homeostasis.
Topics: Adolescent; Adult; Child; Cross-Sectional Studies; Female; Humans; Immunoglobulin A; Immunologic Deficiency Syndromes; Lung Diseases; Male; Oropharynx; Young Adult
PubMed: 32636843
DOI: 10.3389/fimmu.2020.01245 -
International Journal of Infectious... Sep 2009Four tularemia epidemics were reported from three different regions of Turkey between 1936 and 1953. After a long interval, a new tularemia epidemic was reported from... (Review)
Review
Four tularemia epidemics were reported from three different regions of Turkey between 1936 and 1953. After a long interval, a new tularemia epidemic was reported from the area around Bursa in the northwestern part of Turkey in 1988. Following this first epidemic in Bursa, small epidemics occurred in areas around Bursa between 1988 and 2002. Other tularemia epidemics in different regions of Turkey were reported between 1988 and 2005. Almost all of the cases involved the oropharyngeal form of the disease. However, ulceroglandular and oculoglandular forms were detected in the Bursa epidemics; all of the ulceroglandular cases had dermatitis on their hands. To date, 1300 cases have been serologically confirmed. We reviewed one of the biggest tularemia epidemics in Europe.
Topics: Age Distribution; Animals; Disease Outbreaks; Female; Francisella tularensis; Humans; Male; Oropharynx; Pharyngitis; Tularemia; Turkey; Water Microbiology
PubMed: 19119037
DOI: 10.1016/j.ijid.2008.09.020 -
The European Respiratory Journal Mar 2009The diagnostic value of various signs and symptoms (clinical markers) in predicting oropharyngeal aspiration (OPA) or swallowing dysfunction has not been established in...
The diagnostic value of various signs and symptoms (clinical markers) in predicting oropharyngeal aspiration (OPA) or swallowing dysfunction has not been established in children. The present retrospective study was undertaken to: 1) identify specific clinical markers associated with radiographic evidence of OPA, isolated laryngeal penetration (ILP) and post-swallow residue (PSR); 2) determine the sensitivity and specificity of clinical markers associated with OPA; and 3) determine the influence of age and neurological impairment on clinical markers of OPA. In total, 11 clinical markers of dysphagia were compared with the videofluoroscopic swallow study (VFSS) results (OPA, ILP and PSR) in 150 children on diets of thin fluid and purée consistencies. Chi-squared and logistic regression were used to analyse the association between clinical markers and VFSS-identified swallowing dysfunction. In children with OPA, wet voice (odds ratio (OR) 8.90, 95% confidence interval (CI) 2.87-27.62), wet breathing (OR 3.35, 95% CI 1.09-10.28) and cough (OR 3.30, 95% CI 1.17-9.27) were significantly associated with thin fluid OPA. Predictive values included: wet voice (sensitivity 0.67; specificity 0.92); wet breathing (sensitivity 0.33; specificity 0.83); and cough (sensitivity 0.67; specificity 0.53). No clinical markers were significantly associated with OPA, ILP or PSR on the purée consistency. Cough was significantly associated with PSR on thin fluids (OR 3.59, 95% CI 1.22-10.55). Differences were found for age. Wet voice, wet breathing and cough were good clinical markers for children with oropharyngeal aspiration on thin fluid but not on purée. Age and neurological status influenced the significance of these clinical markers.
Topics: Child; Child, Preschool; Deglutition; Deglutition Disorders; Female; Humans; Infant; Infant, Newborn; Male; Multivariate Analysis; Odds Ratio; Oropharynx; Respiratory Aspiration; Retrospective Studies; Sensitivity and Specificity
PubMed: 19010985
DOI: 10.1183/09031936.00090308 -
MicrobiologyOpen Jan 2021Disturbance in the oropharyngeal microbiota is common in hospitalized patients and contributes to the development of nosocomial pneumonia. Lactiplantibacillus plantarum... (Randomized Controlled Trial)
Randomized Controlled Trial
Efficacy of Lactiplantibacillus plantarum 299 and 299v against nosocomial oropharyngeal pathogens in vitro and as an oral prophylactic treatment in a randomized, controlled clinical trial.
BACKGROUND
Disturbance in the oropharyngeal microbiota is common in hospitalized patients and contributes to the development of nosocomial pneumonia. Lactiplantibacillus plantarum 299 and 299v (Lp299 and Lp299v) are probiotic bacteria with beneficial effects on the human microbiome.
AIM
To investigate how Lp299 and Lp299v affect the growth of nosocomial oropharyngeal pathogens in vitro and to evaluate the efficacy in vivo when these probiotics are administered prophylactically in hospitalized patients.
METHODS
The in vitro effect of Lp299 and Lp299v on nosocomial respiratory tract pathogens was evaluated using two methods, the co-culture and agar overlay. In the clinical study, patients were randomized to orally receive either probiotics or placebo twice daily during their hospital stay. Oropharyngeal swabs were analyzed at inclusion and every fourth day throughout hospitalization.
FINDINGS
All tested pathogens were completely inhibited by both Lp299 and Lp299v using the agar-overlay method. In the co-culture experiment, Lp299 and Lp299v significantly (p < 0.05) reduced the growth of all pathogens except for Enterococcus faecalis co-incubated with Lp299. In the clinical study, daily oral treatment with Lp299 and Lp299v did not influence the development of disturbed oropharyngeal microbiota or nosocomial infection. Proton pump inhibitors, antibiotics, and steroid treatment were identified as risk factors for developing disturbed oropharyngeal microbiota.
CONCLUSIONS
Lp299 and Lp299v inhibited pathogen growth in vitro but did not affect the oropharyngeal microbiota in vivo. The ClinicalTrials.gov Identifier for this study is NCT02303301.
Topics: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Antibiosis; Bacteria; Cross Infection; Female; Humans; Lactobacillus plantarum; Male; Microbiota; Middle Aged; Oropharynx; Placebos; Probiotics; Respiratory Tract Infections; Young Adult
PubMed: 33350604
DOI: 10.1002/mbo3.1151 -
JAMA Otolaryngology-- Head & Neck... Apr 2021During the novel coronavirus disease 2019 pandemic, telehealth has become a vital component of health care delivery. For otolaryngology evaluations, examination of the... (Comparative Study)
Comparative Study
IMPORTANCE
During the novel coronavirus disease 2019 pandemic, telehealth has become a vital component of health care delivery. For otolaryngology evaluations, examination of the ear and oropharynx is important but difficult to achieve remotely.
OBJECTIVE
To assess the feasibility of patient use of low-cost digital videoscopes and smartphones for examination of the ear and oropharynx.
DESIGN, SETTING, AND PARTICIPANTS
A prospective quality improvement study was conducted in an academic adult otolaryngology clinic including 23 patients who presented for an in-person appointment and owned a smartphone device. The study was conducted from July 1 to 15, 2020.
INTERVENTIONS
Participants were asked to capture pictures and videos of their ear canals and oropharynx with digital videoscopes and their smartphones under real-time guidance over a telehealth platform. They were then surveyed about their experience.
MAIN OUTCOMES AND MEASURES
The primary outcomes were ratings by health care clinicians and a blinded otolaryngologist reviewer of image acceptability. Secondary outcomes included participant time to image acquisition and willingness to purchase digital videoscopes for telehealth use.
RESULTS
Of the 23 participants included, 14 were women (61%); mean age was 50 years (range, 21 to 80 years). Of the images obtained using the digital otoscope ear examination, 95% were considered acceptable by the health care clinicians and 91% were considered acceptable by the blinded reviewer; 16 participants (70%) reported that the otoscope was easy to use. The mean time to acquire images for both ears was 114 seconds (95% CI, 84-145 seconds). Twenty-one participants (91%) were willing to pay for a digital otoscope for telehealth use. For the oropharyngeal examination, a greater proportion of smartphone video examinations were considered acceptable by clinicians (63% acceptability) and the blinded reviewer (55%) compared with the digital endoscope (clinicians, 40%; blinded reviewer, 14%). The mean time required for the oropharyngeal examination smartphone video capture was shorter at 35 seconds compared with both the digital endoscope (difference, -27 seconds; 95% CI, -7 to -47 seconds) and smartphone photo capture (difference, -53 seconds; 95% CI, -20 to -87 seconds).
CONCLUSIONS AND RELEVANCE
Digital otoscopes and smartphones apparently can facilitate remote head and neck physical examination in telehealth. Digital otoscopes were useful for ear examinations, and smartphone videos appeared to be the most useful for oropharyngeal examinations. Further studies are required to determine specific diagnostic capabilities in various telehealth practice settings.
Topics: Adult; Aged; Aged, 80 and over; Ear Canal; Feasibility Studies; Female; Humans; Male; Middle Aged; Office Visits; Oropharynx; Otolaryngology; Otoscopes; Patient Acceptance of Health Care; Patient Satisfaction; Pilot Projects; Prospective Studies; Remote Consultation; Smartphone; Video Recording; Young Adult
PubMed: 33475683
DOI: 10.1001/jamaoto.2020.5223