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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

The OTU numbers at different taxonomy levels.Notes: The species notation for OTU was analyzed according to notation of tags obtained from 27 bronchoalveolar lavage fluid samples from patients with VAP. The horizontal axis indicates all different taxonomy levels, and vertical axis indicates the numbers of OTU in different taxonomy levels. Different taxonomy levels of OTU proportion were 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5% for phylum, class, order, family, genus, and species, respectively.Abbreviations: OTU, operational taxonomic units; VAP, ventilator-associated pneumonia.
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f2-dddt-9-4883: The OTU numbers at different taxonomy levels.Notes: The species notation for OTU was analyzed according to notation of tags obtained from 27 bronchoalveolar lavage fluid samples from patients with VAP. The horizontal axis indicates all different taxonomy levels, and vertical axis indicates the numbers of OTU in different taxonomy levels. Different taxonomy levels of OTU proportion were 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5% for phylum, class, order, family, genus, and species, respectively.Abbreviations: OTU, operational taxonomic units; VAP, ventilator-associated pneumonia.

Mentions: We next classified the obtained pyrosequencing reads using the RDP classifier at a confidence level of 95% and assigned taxonomic classifications to the sequences for biological analysis. The tag sequences of the identified DNA in 27 bronchoalveolar lavage fluid samples from patients with VAP were analyzed using the RDP to annotate species. The data showed that most of the bacterial reads were assigned to genus level and a small number of bacterial reads were assigned to species level (Figures 1 and 2). There were 638 OTUs that were obtained from the 27 bronchoalveolar lavage fluid samples from patients with VAP using Mothur, according to the tag annotation information of species for OTU comments. The Mothur analysis results are able to comment on the classification level under each OTU number (Figure 2), the classification level of each OTU ratio was phylum, class, order, family, genus, and species at 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5%, respectively.


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)

The OTU numbers at different taxonomy levels.Notes: The species notation for OTU was analyzed according to notation of tags obtained from 27 bronchoalveolar lavage fluid samples from patients with VAP. The horizontal axis indicates all different taxonomy levels, and vertical axis indicates the numbers of OTU in different taxonomy levels. Different taxonomy levels of OTU proportion were 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5% for phylum, class, order, family, genus, and species, respectively.Abbreviations: OTU, operational taxonomic units; VAP, ventilator-associated pneumonia.
© Copyright Policy
Related In: Results  -  Collection

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

f2-dddt-9-4883: The OTU numbers at different taxonomy levels.Notes: The species notation for OTU was analyzed according to notation of tags obtained from 27 bronchoalveolar lavage fluid samples from patients with VAP. The horizontal axis indicates all different taxonomy levels, and vertical axis indicates the numbers of OTU in different taxonomy levels. Different taxonomy levels of OTU proportion were 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5% for phylum, class, order, family, genus, and species, respectively.Abbreviations: OTU, operational taxonomic units; VAP, ventilator-associated pneumonia.
Mentions: We next classified the obtained pyrosequencing reads using the RDP classifier at a confidence level of 95% and assigned taxonomic classifications to the sequences for biological analysis. The tag sequences of the identified DNA in 27 bronchoalveolar lavage fluid samples from patients with VAP were analyzed using the RDP to annotate species. The data showed that most of the bacterial reads were assigned to genus level and a small number of bacterial reads were assigned to species level (Figures 1 and 2). There were 638 OTUs that were obtained from the 27 bronchoalveolar lavage fluid samples from patients with VAP using Mothur, according to the tag annotation information of species for OTU comments. The Mothur analysis results are able to comment on the classification level under each OTU number (Figure 2), the classification level of each OTU ratio was phylum, class, order, family, genus, and species at 91.4%, 84.3%, 79.0%, 72.7%, 58.2%, and 31.5%, respectively.

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