The microbiome of the nasopharynx

Analysis on the pharyngeal microbiota in patients with laryngopharyngeal reflux disease

OBJECTIVE(S)

In this study, the laryngopharynx microbiome alterations were characterized after proton pump inhibitor treatment in patients with Laryngopharyngeal Reflux Disease (LPRD) and healthy people. The potential outcome-predictive biomarker was explored.

METHODS

Patients with LPRD and healthy controls were enrolled. The composition of their laryngopharynx microbiota was analyzed both by traditional plate count of the main bacterial groups and PCR amplification followed by denaturing gradient gel electrophoresis. Shannon-Wiener index and evenness index based on Dice index were used to assess the bacterial diversity. Droplet digital PCR was used to determine the total bacterial RNA and relative abundance of Klebsiella oxytoca. Receiver operating characteristic curve was plotted to explore the potential of Klebsiella oxytoca as an outcome-predictive biomarker.

RESULTS

A total of 29 LPRD cases and 28 healthy subjects were enrolled. The composition of the laryngopharynx microbiota was almost similar, except Klebsiella oxytoca. The cluster analysis showed that the similarity between healthy and treatment-effective groups, as well as pretreatment and treatment-invalid groups, was close. Statistical analysis showed that there were differences in the diversity index and richness among the healthy, treatment-effective, pretreatment and treatment-invalid groups. The abundance of Klebsiella oxytoca in the treatment-effective LPRD group was lower than that of the treatment-invalid LPRD group. The abundance of Klebsiella oxytoca can distinguish treatment-effective and -invalid groups (AUC=0.859) with a sensitivity of 77.78% and specificity of 90.91%.

CONCLUSION

There were differences in the diversity of cecal contents microbial community between treatment-invalid and treatment-effective LPRD groups. Klebsiella oxytoca has potential to distinguish treatment outcomes.

LEVEL OF EVIDENCE

How common is the problem? Level 1. Is this diagnostic or monitoring test accurate? (Diagnosis) Level 4. What will happen if we do not add a therapy? (Prognosis) Level 5. Does this intervention help? (Treatment Benefits) Level 4. What are the COMMON harms? (Treatment Harms) Level 4. What are the RARE harms? (Treatment Harms) Level 4. Is this (early detection) test worthwhile?(Screening) Level 4.

Use of RT-PCR in conjunction with a respiratory pathogen assay to concurrently determine the prevalence of bacteria and SARS-CoV-2 from the nasopharynx of outpatients

Introduction

COVID-19 has emerged as a highly contagious and debilitating disease caused by the SARS-CoV-2 virus and has claimed the lives of over 7.7 million people worldwide. Bacterial co-infections are one of many co-morbidities that have been suggested to impact the outcome of COVID-19 in patients. The goals of this study are to elucidate the presence of bacteria in the nasopharynx of SARS-CoV-2 positive and negative patients and to describe demographic categories that may be associated with the detection of these organisms during one of the initial waves of the COVID-19 pandemic.

Methods

To this end, we investigated SARS-CoV-2 and bacterial co-detection from outpatient RT-PCR testing in Texas.

Results

The results indicate that Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae, Moraxella catarrhalis, and Haemophilus influenzae were the most frequently detected bacteria in both SARS-CoV-2 positive and SARS-CoV-2 negative patients and that these bacteria were present in these two patient populations at similar proportions. We also detected Staphylococcus aureus in a significantly larger proportion of males relative to females and people under 65 years of age relative to those 65 and over. Finally, we observed that SARS-CoV-2 was more commonly detected in Hispanics compared to non-Hispanics; however, low disclosure rates make volunteer bias a concern when interpreting the effects of demographic variables.

Discussion

This study describes the bacteria present in the nasopharynx of SARS-CoV-2 positive and negative patients, highlights associations between patient demographics and SARS-CoV-2 as well as bacterial co-detection. In addition, this study highlights RT-PCR based molecular testing as a tool to detect bacteria simultaneously when SARS-CoV-2 tests are performed.

Postmortem Nasopharyngeal Microbiome Analysis of Zambian Infants With and Without Respiratory Syncytial Virus Disease: A Nested Case Control Study

BACKGROUND

Respiratory syncytial virus (RSV) is the most common cause of bronchiolitis and lower respiratory tract infections in children in their first year of life, disproportionately affecting infants in developing countries. Previous studies have found that the nasopharyngeal (NP) microbiome of infants with RSV infection has specific characteristics that correlate with disease severity, including lower biodiversity, perturbations of the microbiota and differences in relative abundance. These studies have focused on infants seen in clinical or hospital settings, predominantly in developed countries.

METHODS

We conducted a nested case control study within a random sample of 50 deceased RSV+ infants with age at death ranging from 4 days to 6 months and 50 matched deceased RSV- infants who were all previously enrolled in the Zambia Pertussis and RSV Infant Mortality Estimation (ZPRIME) study. All infants died within the community or within 48 hours of facility admittance. As part of the ZPRIME study procedures, all decedents underwent one-time, postmortem NP sampling. The current analysis explored the differences between the NP microbiome profiles of RSV+ and RSV- decedents using the 16S ribosomal DNA sequencing.

RESULTS

We found that Moraxella was more abundant in the NP microbiome of RSV+ decedents than in the RSV- decedents. Additionally, Gemella and Staphylococcus were less abundant in RSV+ decedents than in the RSV- decedents.

CONCLUSIONS

These results support previously reported findings of the association between the NP microbiome and RSV and suggest that changes in the abundance of these microbes are likely specific to RSV and may correlate with mortality associated with the disease.

Analysis of Intestinal and Nasopharyngeal Microbiota of Children with Meningococcemia in Pediatric Intensive Care Unit: INMACS-PICU Study

Microbiota composition might play a role in the pathophysiology and course of sepsis, and understanding its dynamics is of clinical interest. Invasive meningococcal disease (IMD) is an important cause of community-acquired serious infection, and there is no information regarding microbiota composition in children with meningococcemia. In this study, we aimed to evaluate the intestinal and nasopharyngeal microbiota composition of children with IMD. Materials and Methods: In this prospective, multi-center study, 10 children with meningococcemia and 10 age-matched healthy controls were included. Nasopharyngeal and fecal samples were obtained at admission to the intensive care unit and on the tenth day of their hospital stay. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Results: Regarding the alpha diversity on the day of admission and on the tenth day at the PICU, the Shannon index was significantly lower in the IMD group compared to the control group (p = 0.002 at admission and p = 0.001, on the tenth day of PICU). A statistical difference in the stool samples was found between the IMD group at Day 0 vs. the controls in the results of the Bray-Curtis and Jaccard analyses (p = 0.005 and p = 0.001, respectively). There were differences in the intestinal microbiota composition between the children with IMD at admission and Day 10 and the healthy controls. Regarding the nasopharyngeal microbiota analysis, in the children with IMD at admission, at the genus level, Neisseria was significantly more abundant compared to the healthy children (p < 0.001). In the children with IMD at Day 10, genera Moraxella and Neisseria were decreased compared to the healthy children. In the children with IMD on Day 0, for paired samples, Moraxella, Neisseria, and Haemophilus were significantly more abundant compared to the children with IMD at Day 10. In the children with IMD at Day 10, the Moraxella and Neisseria genera were decreased, and 20 different genera were more abundant compared to Day 0. Conclusions: We first found alterations in the intestinal and nasopharyngeal microbiota composition in the children with IMD. The infection itself or the other care interventions also caused changes to the microbiota composition during the follow-up period. Understanding the interaction of microbiota with pathogens, e.g., N. meningitidis, could give us the opportunity to understand the disease's dynamics.

Analysis of microbial communities of ocular prostheses and anophthalmic sockets using 16S rRNA gene sequencing

Ocular prostheses are liable to host microbial adhesion, which can favor conjunctival inflammation. Knowing the microbiota of the ocular prosthesis and anophthalmic socket is important for predicting infection-related pathogens. This study evaluated the microbiota of the prostheses and anophthalmic sockets of six individuals by 16S rRNA sequencing. The microbial abundance and diversity were analyzed using the Operational Taxonomic Units at the genus level. Forty-seven phyla, capturing 1,258 named genera, were recorded in the sample set. In both sites, the most frequent genera were Fusobacterium, Staphylococcus, Prevotella, and Streptococcus. The microbial abundance was higher for the anophthalmic socket than for the prosthesis. Alpha diversity showed no significant differences in bacterial richness or diversity between sites. Although the microbial abundance in the anophthalmic socket was higher, both sites had similar microbiota with high diversity and low dominance among the genera.

Air pollution from livestock farms and the oropharyngeal microbiome of COPD patients and controls

Air pollution from livestock farms is known to affect respiratory health of patients with chronic obstructive pulmonary disease (COPD). The mechanisms behind this relationship, however, remain poorly understood. We hypothesise that air pollutants could influence respiratory health through modulation of the airway microbiome. Therefore, we studied associations between air pollution exposure and the oropharyngeal microbiota (OPM) composition of COPD patients and controls in a livestock-dense area. Oropharyngeal swabs were collected from 99 community-based (mostly mild) COPD cases and 184 controls (baseline), and after 6 and 12 weeks. Participants were non-smokers or former smokers. Annual average livestock-related outdoor air pollution at the home address was predicted using dispersion modelling. OPM composition was analysed using 16S rRNA-based sequencing in all baseline samples and 6-week and 12-week repeated samples of 20 randomly selected subjects (n = 323 samples). A random selection of negative control swabs, taken every sampling day, were also included in the downstream analysis. Both farm-emitted endotoxin and PM₁₀ levels were associated with increased OPM richness in COPD patients (p < 0.05) but not in controls. COPD case-control status was not associated with community structure, while correcting for known confounders (multivariate PERMANOVA p > 0.05). However, members of the genus Streptococcus were more abundant in COPD patients (Benjamini-Hochberg adjusted p < 0.01). Moderate correlation was found between ordinations of 20 subjects analysed at 0, 6, and 12 weeks (Procrustes r = 0.52 to 0.66; p < 0.05; Principal coordinate analysis of Bray-Curtis dissimilarity), indicating that the OPM is relatively stable over a 12 week period and that a single sample sufficiently represents the OPM. Air pollution from livestock farms is associated with OPM richness of COPD patients, suggesting that the OPM of COPD patients is susceptible to alterations induced by exposure to air pollutants.

Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection: A Systematic Review

Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs (p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.