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Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.

Lu X, Zhang XX, Wang Z, Huang K, Wang Y, Liang W, Tan Y, Liu B, Tang J - PLoS ONE (2015)

Bottom Line: However, presence of the residual A. butzleri in the final effluent still deserves more concerns.The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment.Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.

ABSTRACT
This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.

No MeSH data available.


Related in: MedlinePlus

Occurrence and abundance of potential pathogens at genus and species levels revealed by 454 pyrosequencing of 16S rRNA gene amplicons.(A) Relative abundance of potential pathogens at genus level. The effective pyrosequencing reads were classified using MEGAN. Rare genera refer to the taxa with maximum abundance <1% in any sample, including Bacillus, Campylobacter, Helicobacter, Klebsiella, Leptospira, Neisseria and Serratia. (B) Sequence number of potential pathogens at species level under the same sequencing depth (6200 reads). (C) Relative abundance of potential pathogens at species level. All the effective sequences identified as potentially pathogenic species were aligned using the local BLASTN tool. The relative abundance was obtained by normalizing the sequence number of each pathogenic taxon to the total number of all pathogenic taxa in one sample.
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pone.0125549.g001: Occurrence and abundance of potential pathogens at genus and species levels revealed by 454 pyrosequencing of 16S rRNA gene amplicons.(A) Relative abundance of potential pathogens at genus level. The effective pyrosequencing reads were classified using MEGAN. Rare genera refer to the taxa with maximum abundance <1% in any sample, including Bacillus, Campylobacter, Helicobacter, Klebsiella, Leptospira, Neisseria and Serratia. (B) Sequence number of potential pathogens at species level under the same sequencing depth (6200 reads). (C) Relative abundance of potential pathogens at species level. All the effective sequences identified as potentially pathogenic species were aligned using the local BLASTN tool. The relative abundance was obtained by normalizing the sequence number of each pathogenic taxon to the total number of all pathogenic taxa in one sample.

Mentions: Pyrosequencing of 16S rRNA gene amplicons revealed that the bacterial community shifted greatly along the treatment processes (S2 Fig). At genus level, the relative number of the sequences assigned to known pathogens was 3,428 (55.33%) for SI, 3,883 (62.63%) for PE, 102 (1.65%) for AS, 76 (1.23%) for SE, 83 (1.34%) for FFE and 56 (0.90%) for FRE (S5 Table), and a total of 20 genera containing potentially pathogenic species were detected in the six samples (Fig 1A). Among the genera identified, Acrobacter had the highest abundance in each of SI, PE, AS, SE and FFE, accounting for 43.42%-97.37% of all pathogenic sequences, and the genus also occupied 14.29% in FRE (Fig 1A). At species level, pyrosequencing showed that 1,422 (6 species, 22.95%), 1,302 (7 species, 21.00%), 23 (7 species, 0.37%), 23 (4 species, 0.37%), 21 (7 species, 0.34%) and 6 (4 species, 0.10%) sequences were closely related (with similarity over 97%) to known pathogens in SI, PE, AS, SE, FFE and FRE, respectively (Fig 1B), demonstrating that the sewage treatment processes can effectively reduce the relative abundance of the pathogens. In absolute terms, over 99% of the potential pathogens in SI (2.68×104 sequences per milliliter) were eliminated by the treatment processes (S6 Table). Among the species identified, Arcobacter butzleri had the highest abundance in the STP, and the relative abundance ranged from 33.33% to 94.87% of total pathogenic bacteria in the six samples (Fig 1C). Additionally, Aeromonas hydrophila was also found prevalent in SE and FRE (Fig 1C).


Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.

Lu X, Zhang XX, Wang Z, Huang K, Wang Y, Liang W, Tan Y, Liu B, Tang J - PLoS ONE (2015)

Occurrence and abundance of potential pathogens at genus and species levels revealed by 454 pyrosequencing of 16S rRNA gene amplicons.(A) Relative abundance of potential pathogens at genus level. The effective pyrosequencing reads were classified using MEGAN. Rare genera refer to the taxa with maximum abundance <1% in any sample, including Bacillus, Campylobacter, Helicobacter, Klebsiella, Leptospira, Neisseria and Serratia. (B) Sequence number of potential pathogens at species level under the same sequencing depth (6200 reads). (C) Relative abundance of potential pathogens at species level. All the effective sequences identified as potentially pathogenic species were aligned using the local BLASTN tool. The relative abundance was obtained by normalizing the sequence number of each pathogenic taxon to the total number of all pathogenic taxa in one sample.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4418606&req=5

pone.0125549.g001: Occurrence and abundance of potential pathogens at genus and species levels revealed by 454 pyrosequencing of 16S rRNA gene amplicons.(A) Relative abundance of potential pathogens at genus level. The effective pyrosequencing reads were classified using MEGAN. Rare genera refer to the taxa with maximum abundance <1% in any sample, including Bacillus, Campylobacter, Helicobacter, Klebsiella, Leptospira, Neisseria and Serratia. (B) Sequence number of potential pathogens at species level under the same sequencing depth (6200 reads). (C) Relative abundance of potential pathogens at species level. All the effective sequences identified as potentially pathogenic species were aligned using the local BLASTN tool. The relative abundance was obtained by normalizing the sequence number of each pathogenic taxon to the total number of all pathogenic taxa in one sample.
Mentions: Pyrosequencing of 16S rRNA gene amplicons revealed that the bacterial community shifted greatly along the treatment processes (S2 Fig). At genus level, the relative number of the sequences assigned to known pathogens was 3,428 (55.33%) for SI, 3,883 (62.63%) for PE, 102 (1.65%) for AS, 76 (1.23%) for SE, 83 (1.34%) for FFE and 56 (0.90%) for FRE (S5 Table), and a total of 20 genera containing potentially pathogenic species were detected in the six samples (Fig 1A). Among the genera identified, Acrobacter had the highest abundance in each of SI, PE, AS, SE and FFE, accounting for 43.42%-97.37% of all pathogenic sequences, and the genus also occupied 14.29% in FRE (Fig 1A). At species level, pyrosequencing showed that 1,422 (6 species, 22.95%), 1,302 (7 species, 21.00%), 23 (7 species, 0.37%), 23 (4 species, 0.37%), 21 (7 species, 0.34%) and 6 (4 species, 0.10%) sequences were closely related (with similarity over 97%) to known pathogens in SI, PE, AS, SE, FFE and FRE, respectively (Fig 1B), demonstrating that the sewage treatment processes can effectively reduce the relative abundance of the pathogens. In absolute terms, over 99% of the potential pathogens in SI (2.68×104 sequences per milliliter) were eliminated by the treatment processes (S6 Table). Among the species identified, Arcobacter butzleri had the highest abundance in the STP, and the relative abundance ranged from 33.33% to 94.87% of total pathogenic bacteria in the six samples (Fig 1C). Additionally, Aeromonas hydrophila was also found prevalent in SE and FRE (Fig 1C).

Bottom Line: However, presence of the residual A. butzleri in the final effluent still deserves more concerns.The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment.Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.

ABSTRACT
This study used 454 pyrosequencing, Illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (STP) applying both conventional and advanced treatment processes. Pyrosequencing and Illumina sequencing consistently demonstrated that Arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the STP. At species level, potential pathogens Arcobacter butzleri, Aeromonas hydrophila and Klebsiella pneumonia dominated in raw sewage, which was also confirmed by quantitative real time PCR. Illumina sequencing also revealed prevalence of various types of pathogenicity islands and virulence proteins in the STP. Most of the potential pathogens and virulence factors were eliminated in the STP, and the removal efficiency mainly depended on oxidation ditch. Compared with sand filtration, magnetic resin seemed to have higher removals in most of the potential pathogens and virulence factors. However, presence of the residual A. butzleri in the final effluent still deserves more concerns. The findings indicate that sewage acts as an important source of environmental pathogens, but STPs can effectively control their spread in the environment. Joint use of the high-throughput sequencing technologies is considered a reliable method for deep and comprehensive overview of environmental bacterial virulence.

No MeSH data available.


Related in: MedlinePlus