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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

Bacterial community composition of 27 bronchoalveolar lavage fluid samples at genus level.Notes: It shows bacterial community composition of each sample at genus level. (A) The vertical axis represents relative bacterial abundance of corresponding phylum. The horizontal axis represents 27 bronchoalveolar lavage fluid samples. Different color components represent different genus. Taxonomic name of higher abundance is shown in these charts. Those failed to meet the lower abundance was assigned the label “Others”. “Unknown” indicates that the taxonomy level is unable to be defined according to the abundance. (B) The vertical axis represents the number of samples, and the horizontal axis represents genus of bacterial. There were 15 major genera and much mixed infection in the samples.
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f6-dddt-9-4883: Bacterial community composition of 27 bronchoalveolar lavage fluid samples at genus level.Notes: It shows bacterial community composition of each sample at genus level. (A) The vertical axis represents relative bacterial abundance of corresponding phylum. The horizontal axis represents 27 bronchoalveolar lavage fluid samples. Different color components represent different genus. Taxonomic name of higher abundance is shown in these charts. Those failed to meet the lower abundance was assigned the label “Others”. “Unknown” indicates that the taxonomy level is unable to be defined according to the abundance. (B) The vertical axis represents the number of samples, and the horizontal axis represents genus of bacterial. There were 15 major genera and much mixed infection in the samples.

Mentions: Further, the comparison of the pathogens among the 27 bronchoalveolar lavage fluid samples from patients with VAP was performed. The pathogen profile at phylum and genus level was analyzed (Figures 5 and 6). The relative abundance of each pathogen was determined in the 27 bronchoalveolar lavage fluid samples (Figures 5A and 6A). At phylum level, there were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (Figure 5B), to a lesser extent, Fusobacteria, Deinococcus-Thermus, Spirochaetes, Nitrospira, Planctomycetes, Synergistetes, and Tenericutes. Of note, Proteobacteria and Firmicutes were widely distributed in all of the samples (Figure 5A); Bacteroidetes and Actinobacteria occurred in half of the samples (Figure 5A). At genus level, these sequences represented 90 different genera (Figure 6A), and there were 12 genera occurring in over ten different samples (Figure 6B). The top five dominant genera, which contained the largest number of sequences, were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium (Figure 6A). The most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in the 27 bronchoalveolar lavage fluid samples, and Prevotella, Sphingomonas, Aquabacterium, Corynebacterium, Klebsiella, Pseudomonas, Peptostreptococcus, Porphyromonas, and Tepidimonas were distributed to a lesser extent (Figure 6B; ≥10 samples).


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)

Bacterial community composition of 27 bronchoalveolar lavage fluid samples at genus level.Notes: It shows bacterial community composition of each sample at genus level. (A) The vertical axis represents relative bacterial abundance of corresponding phylum. The horizontal axis represents 27 bronchoalveolar lavage fluid samples. Different color components represent different genus. Taxonomic name of higher abundance is shown in these charts. Those failed to meet the lower abundance was assigned the label “Others”. “Unknown” indicates that the taxonomy level is unable to be defined according to the abundance. (B) The vertical axis represents the number of samples, and the horizontal axis represents genus of bacterial. There were 15 major genera and much mixed infection in the samples.
© Copyright Policy
Related In: Results  -  Collection

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

f6-dddt-9-4883: Bacterial community composition of 27 bronchoalveolar lavage fluid samples at genus level.Notes: It shows bacterial community composition of each sample at genus level. (A) The vertical axis represents relative bacterial abundance of corresponding phylum. The horizontal axis represents 27 bronchoalveolar lavage fluid samples. Different color components represent different genus. Taxonomic name of higher abundance is shown in these charts. Those failed to meet the lower abundance was assigned the label “Others”. “Unknown” indicates that the taxonomy level is unable to be defined according to the abundance. (B) The vertical axis represents the number of samples, and the horizontal axis represents genus of bacterial. There were 15 major genera and much mixed infection in the samples.
Mentions: Further, the comparison of the pathogens among the 27 bronchoalveolar lavage fluid samples from patients with VAP was performed. The pathogen profile at phylum and genus level was analyzed (Figures 5 and 6). The relative abundance of each pathogen was determined in the 27 bronchoalveolar lavage fluid samples (Figures 5A and 6A). At phylum level, there were four dominant phyla, including Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes (Figure 5B), to a lesser extent, Fusobacteria, Deinococcus-Thermus, Spirochaetes, Nitrospira, Planctomycetes, Synergistetes, and Tenericutes. Of note, Proteobacteria and Firmicutes were widely distributed in all of the samples (Figure 5A); Bacteroidetes and Actinobacteria occurred in half of the samples (Figure 5A). At genus level, these sequences represented 90 different genera (Figure 6A), and there were 12 genera occurring in over ten different samples (Figure 6B). The top five dominant genera, which contained the largest number of sequences, were Streptococcus, Acinetobacter, Limnohabitans, Neisseria, and Corynebacterium (Figure 6A). The most widely distributed genera were Streptococcus, Limnohabitans, and Acinetobacter in the 27 bronchoalveolar lavage fluid samples, and Prevotella, Sphingomonas, Aquabacterium, Corynebacterium, Klebsiella, Pseudomonas, Peptostreptococcus, Porphyromonas, and Tepidimonas were distributed to a lesser extent (Figure 6B; ≥10 samples).

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