The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid

Akata, Kentaro; Yatera, Kazuhiro; Yamasaki, Kei; Kawanami, Toshinori; Naito, Keisuke; Noguchi, Shingo; Fukuda, Kazumasa; Ishimoto, Hiroshi; Taniguchi, Hatsumi; Mukae, Hiroshi

doi:10.1186/s12890-016-0235-z

Cited by 68 publications

(63 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Of the 53 taxa that we found shifted between sampling groups, the most dramatic change was in a Streptococcus taxon, which was much more abundant in aspirating children ( Figure S19). An increase in this taxon has previously been reported in adult humans with pneumonia by Akata et al (2016). We also found an increase in Haemophilus (Jacobs & Harris, 1979), Moraxella (Claesson & Leinonen, 1994), Neisseria (Johnson, Drew, & Roberts, 1981), and…”

Section: Inferences On Empirical Datasupporting

confidence: 86%

Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data

Harrison

Calder

Shastry

et al. 2020

Molecular Ecology Resources

View full text Add to dashboard Cite

Molecular ecology regularly requires the analysis of count data that reflect the relative abundance of features of a composition (e.g., taxa in a community, gene transcripts in a tissue). The sampling process that generates these data can be modelled using the multinomial distribution. Replicate multinomial samples inform the relative abundances of features in an underlying Dirichlet distribution. These distributions together form a hierarchical model for relative abundances among replicates and sampling groups. This type of Dirichlet‐multinomial modelling (DMM) has been described previously, but its benefits and limitations are largely untested. With simulated data, we quantified the ability of DMM to detect differences in proportions between treatment and control groups, and compared the efficacy of three computational methods to implement DMM—Hamiltonian Monte Carlo (HMC), variational inference (VI), and Gibbs Markov chain Monte Carlo. We report that DMM was better able to detect shifts in relative abundances than analogous analytical tools, while identifying an acceptably low number of false positives. Among methods for implementing DMM, HMC provided the most accurate estimates of relative abundances, and VI was the most computationally efficient. The sensitivity of DMM was exemplified through analysis of previously published data describing lung microbiomes. We report that DMM identified several potentially pathogenic, bacterial taxa as more abundant in the lungs of children who aspirated foreign material during swallowing; these differences went undetected with different statistical approaches. Our results suggest that DMM has strong potential as a statistical method to guide inference in molecular ecology.

show abstract

Section: Inferences On Empirical Datasupporting

confidence: 86%

Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data

Harrison

Calder

Shastry

et al. 2020

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…The results of this study imply that the laryngopharynx of the elderly with fewer teeth, poorer dental hygiene, and more dental caries experience is constantly exposed to bacterial populations containing a higher relative abundance of group I commensals. Although Prevotella , Veillonella , and Streptococcus are not typical respiratory pathogens, they were identified as etiologic agents of pulmonary infections such as aspiration pneumonia ( 22 ) and lung abscesses ( 23 ). Our prospective cohort study demonstrated that a higher relative abundance of group I commensals on the tongue was implicated in an increased mortality risk from pneumonia in frail elderly adults in nursing homes ( 15 ).…”

Section: Discussionmentioning

confidence: 99%

Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults

Asakawa

Takeshita

Furuta

et al. 2018

mSphere

View full text Add to dashboard Cite

Aspiration of oral contents can lead to pneumonia, which is a major cause of death among elderly adults susceptible to swallowing impairments. Tongue microbiota are a dominant source of oral microbial populations that are ingested with saliva. This large-scale population-based study revealed variations in the tongue microbiota among community-dwelling elderly adults. The total bacterial density was independent of the conditions of teeth surrounding the tongue, whereas the microbiota composition, especially the relative abundances of predominant commensals, showed an association with tooth conditions. Our results demonstrate that the elderly with fewer teeth, poorer dental hygiene, and more dental caries experience constantly ingest more dysbiotic microbiota, which could be harmful for their respiratory health.

show abstract

“…Our previous reports investigating pneumonia showed that there was a higher ratio of patients with mixed infections of healthcare‐associated pneumonia (HCAP) and hospital‐acquired pneumonia (HAP) compared to patients with community‐acquired pneumonia (CAP). In addition, streptococci were highly detected in elderly pneumonia patients and pneumonia patients with poor general health conditions . In patients with bacterial pleuritis, culture‐based mixed infection was reported in 9.8%–24.0% of patients, with insufficient data detailing the combination of bacterial species.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, streptococci were highly detected in elderly pneumonia patients and pneumonia patients with poor general health conditions. [14][15][16]26 In patients with bacterial pleuritis, culture-based mixed infection was reported in 9.8%-24.0% 25,27,28 of patients, with insufficient data detailing the combination of bacterial species. In this study, 10 patients were categorized in the 'mixed bacterial-dominant' group and 9 of 10 (90%) patients in the 'mixed bacterial dominant' group were also sorted into the obligate anaerobic group.…”

Section: Discussionmentioning

confidence: 99%

Clinical characteristics of patients with bacterial pleuritis in the presence of Streptococcus anginosus group and obligate anaerobes detected by clone library analysis

Hata

Kawanami

Noguchi

et al. 2019

Clinical Respiratory J

Self Cite

View full text Add to dashboard Cite

Introduction Bacterial pleuritis is one of the most important pleural and respiratory infectious diseases, in addition, there have been no reports describing the clinical characteristics of patients with bacterial pleuritis according to molecular methods. An accurate understanding of the clinical characteristics and etiology of bacterial pleuritis is an issue that must be addressed. Objectives The aim of this study was to clarify the clinical characteristics of the bacterial species in bacterial pleuritis. Methods Pleural effusion samples were obtained from 29 patients with bacterial pleuritis. The microbiota of pleural effusion samples was analyzed by clone library analysis using the 16S ribosomal RNA gene. Results The phylotypes of Fusobacterium spp. (24.1%) were most frequently the predominant phylotypes, followed by those of Streptococcus anginosus group (SAG) (20.7%) and S. aureus (17.2%). The predominant phylotypes of obligate anaerobes, including the Fusobacterium spp., were detected in 11 of 29 patients (37.9%). Patients in the SAG group were significantly older and presented lower serum albumin levels than those in the obligate anaerobe and other bacterial groups. Patients from the obligate anaerobe group took longer to present symptoms, and therefore the diagnosis of pleuritis was also delayed, in comparison to patients in the other bacterial groups. Conclusions Our results demonstrated that there were characteristic differences between patients in SAG, obligate anaerobe and other bacterial groups. Physicians may need to consider treatment strategy options based on the clinical characteristics of patients with bacterial pleuritis.

show abstract

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid

Cited by 68 publications

References 30 publications

Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data

Dirichlet‐multinomial modelling outperforms alternatives for analysis of microbiome and other ecological count data

Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults

Clinical characteristics of patients with bacterial pleuritis in the presence of Streptococcus anginosus group and obligate anaerobes detected by clone library analysis

Contact Info

Product

Resources

About