Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant

Schlueter, Andreas, Krause, Lutz, Szczepanowski, Rafael, Goesmann, Alexander and Puehler, Alfred (2008) Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. Journal of Biotechnology, 136 1-2: 65-76. doi:10.1016/j.jbiotec.2008.03.017


Author Schlueter, Andreas
Krause, Lutz
Szczepanowski, Rafael
Goesmann, Alexander
Puehler, Alfred
Title Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant
Journal name Journal of Biotechnology   Check publisher's open access policy
ISSN 0168-1656
1873-4863
Publication date 2008-08-31
Sub-type Article (original research)
DOI 10.1016/j.jbiotec.2008.03.017
Open Access Status Not Open Access
Volume 136
Issue 1-2
Start page 65
End page 76
Total pages 12
Place of publication Amsterdam, Netherlands
Publisher Elsevier
Language eng
Formatted abstract
Plasmid metagenome nucleotide sequence data were recently obtained from wastewater treatment plant (WWTP) bacteria with reduced susceptibility to selected antimicrobial drugs by applying the ultrafast 454-sequencing technology. The sequence dataset comprising 36,071,493 bases (346,427 reads with an average read length of 104 bases) was analysed for genetic diversity and composition by using a newly developed bioinformatic pipeline based on assignment of environmental gene tags (EGTs) to protein families stored in the Pfam database. Short amino acid sequences deduced from the plasmid metagenome sequence reads were compared to profile hidden Markov models underlying Pfam. Obtained matches evidenced that many reads represent genes having predicted functions in plasmid replication, stability and plasmid mobility which indicates that WWTP bacteria harbour genetically stabilised and mobile plasmids. Moreover, the data confirm a high diversity of plasmids residing in WWTP bacteria. The mobile organic peroxide resistance plasmid pMAC from Acinetobacter baumannii was identified as reference plasmid for the most abundant replication module type in the sequenced sample. Accessory plasmid modules encode different transposons, insertion sequences, integrons, resistance and virulence determinants. Most of the matches to Transposase protein families were identified for transposases similar to the one of the chromate resistance transposon Tn5719. Noticeable are hits to β-lactamase protein families which suggests that plasmids from WWTP bacteria encode different enzymes possessing β-lactam-hydrolysing activity. Some of the sequence reads correspond to antibiotic resistance genes that were only recently identified in clinical isolates of human pathogens. EGT analysis thus proofed to be a very valuable method to explore genetic diversity and composition of the present plasmid metagenome dataset.
Keyword Replication initiation
Stabilisation
Mobilisation
Conjugative transfer
Antibiotic resistance
Virulence
454-Pyrosequencing
Plasmid metagenome
Environmental gene tag analysis
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
 
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