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High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia.

Yang XJ, Wang YB, Zhou ZW, Wang GW, Wang XH, Liu QF, Zhou SF, Wang ZH - Drug Des Devel Ther (2015)

Bottom Line: The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples.Of note, the mixed profile of causative pathogens was observed.This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.

View Article: PubMed Central - PubMed

Affiliation: Department of Intensive Care Unit, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China.

ABSTRACT
Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.

No MeSH data available.


Related in: MedlinePlus

Beta diversity analysis of 27 bronchoalveolar lavage fluid samples from patients with VAP indicated by Whittaker index.Notes: Whittaker index was used to evaluate the difference in species diversity among different samples. The higher index indicates more difference. (A) The Whittaker index of species distribution of 27 bronchoalveolar lavage fluid samples from patients with pneumonia. (B) The cluster dendrogram based on Whittaker index analyzed by Ward of hclust in R program.Abbreviation: VAP, ventilator-associated pneumonia.
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f7-dddt-9-4883: Beta diversity analysis of 27 bronchoalveolar lavage fluid samples from patients with VAP indicated by Whittaker index.Notes: Whittaker index was used to evaluate the difference in species diversity among different samples. The higher index indicates more difference. (A) The Whittaker index of species distribution of 27 bronchoalveolar lavage fluid samples from patients with pneumonia. (B) The cluster dendrogram based on Whittaker index analyzed by Ward of hclust in R program.Abbreviation: VAP, ventilator-associated pneumonia.

Mentions: Additionally, in order to evaluate the total diversity and assess the distribution and content of bacteria in these 27 bronchoalveolar lavage fluid samples from patients with VAP, the beta analysis was performed. As shown in Figure 7A and B and Figure 8A–F, there was a substantial difference in the species distribution in the 27 bronchoalveolar lavage fluid samples. The beta diversity of 27 bronchoalveolar lavage fluid samples was indicated by Whittaker index that was used to evaluate the species difference in diversity between different samples. The higher index indicates more difference. The pathogens from number 1, 2, and 12 samples showed the most different diversity from other samples (Figure 7A). According to the Ward analysis data, there were four clusters that can be further divided into ten subclusters (Figure 7B). In addition, the total diversity and distribution of bacteria in these 27 bronchoalveolar lavage fluid samples were evaluated by weighted- and unweighted-UniFrac index (Figure 8A–F), which showed a similar results to that of Whittaker index. Collectively, the results show a comparable difference in the diversity of species distribution and evolution in the 27 bronchoalveolar lavage fluid samples from patients with VAP.


High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia.

Yang XJ, Wang YB, Zhou ZW, Wang GW, Wang XH, Liu QF, Zhou SF, Wang ZH - Drug Des Devel Ther (2015)

Beta diversity analysis of 27 bronchoalveolar lavage fluid samples from patients with VAP indicated by Whittaker index.Notes: Whittaker index was used to evaluate the difference in species diversity among different samples. The higher index indicates more difference. (A) The Whittaker index of species distribution of 27 bronchoalveolar lavage fluid samples from patients with pneumonia. (B) The cluster dendrogram based on Whittaker index analyzed by Ward of hclust in R program.Abbreviation: VAP, ventilator-associated pneumonia.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4554422&req=5

f7-dddt-9-4883: Beta diversity analysis of 27 bronchoalveolar lavage fluid samples from patients with VAP indicated by Whittaker index.Notes: Whittaker index was used to evaluate the difference in species diversity among different samples. The higher index indicates more difference. (A) The Whittaker index of species distribution of 27 bronchoalveolar lavage fluid samples from patients with pneumonia. (B) The cluster dendrogram based on Whittaker index analyzed by Ward of hclust in R program.Abbreviation: VAP, ventilator-associated pneumonia.
Mentions: Additionally, in order to evaluate the total diversity and assess the distribution and content of bacteria in these 27 bronchoalveolar lavage fluid samples from patients with VAP, the beta analysis was performed. As shown in Figure 7A and B and Figure 8A–F, there was a substantial difference in the species distribution in the 27 bronchoalveolar lavage fluid samples. The beta diversity of 27 bronchoalveolar lavage fluid samples was indicated by Whittaker index that was used to evaluate the species difference in diversity between different samples. The higher index indicates more difference. The pathogens from number 1, 2, and 12 samples showed the most different diversity from other samples (Figure 7A). According to the Ward analysis data, there were four clusters that can be further divided into ten subclusters (Figure 7B). In addition, the total diversity and distribution of bacteria in these 27 bronchoalveolar lavage fluid samples were evaluated by weighted- and unweighted-UniFrac index (Figure 8A–F), which showed a similar results to that of Whittaker index. Collectively, the results show a comparable difference in the diversity of species distribution and evolution in the 27 bronchoalveolar lavage fluid samples from patients with VAP.

Bottom Line: The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples.Of note, the mixed profile of causative pathogens was observed.This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.

View Article: PubMed Central - PubMed

Affiliation: Department of Intensive Care Unit, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, People's Republic of China.

ABSTRACT
Ventilator-associated pneumonia (VAP) is a life-threatening disease that is associated with high rates of morbidity and likely mortality, placing a heavy burden on an individual and society. Currently available diagnostic and therapeutic approaches for VAP treatment are limited, and the prognosis of VAP is poor. The present study aimed to reveal and discriminate the identification of the full spectrum of the pathogens in patients with VAP using high-throughput sequencing approach and analyze the species richness and complexity via alpha and beta diversity analysis. The bronchoalveolar lavage fluid samples were collected from 27 patients with VAP in intensive care unit. The polymerase chain reaction products of the hypervariable regions of 16S rDNA gene in these 27 samples of VAP were sequenced using the 454 GS FLX system. A total of 103,856 pyrosequencing reads and 638 operational taxonomic units were obtained from these 27 samples. There were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. There were 90 different genera, of which 12 genera occurred in over ten different samples. The top five dominant genera were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium, and the most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in these 27 samples. Of note, the mixed profile of causative pathogens was observed. Taken together, the results show that the high-throughput sequencing approach facilitates the characterization of the pathogens in bronchoalveolar lavage fluid samples and the determination of the profile for bacteria in the bronchoalveolar lavage fluid samples of the patients with VAP. This study can provide useful information of pathogens in VAP and assist clinicians to make rational and effective therapeutic decisions.

No MeSH data available.


Related in: MedlinePlus