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multiple antibiotic resistance coliform bacteria was isolated from influent of Shatin WWTP treating domestic wastewater in Hong Kong. 96 randomly picked coliform colonies were pooled together for resistome quantification based on Illumina and Nanopore sequencing platforms

Identifiers: SRA: ERP022895
BioProject: PRJEB20722
shuixia100: ena-STUDY-shuixia100-04-05-2017-08:50:14:052-594
Study Type: 
Other
Abstract: Wastewater treatment plants functioned as the intersection between the human society and the nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistancet genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION nNanopore sequencing to quantify the resistancet genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples. Our pipeline could deliver the results within 30 hours from sample collection and the resistome quantification was consistent to that based on the Illumina platform. Additionally, the long Nanopore reads not only enabled a simultaneous identification of the carrier populations of ARGs detected, but also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of environmental resistance gene obtained by plasmid exchange with a porcine pathogen. This study demonstrated the utilization of MinION sequencing in real-time monitoring and simultaneous phylogenetic tracking of environmental ARGs to address potential health risk associated with them.
Description: Wastewater treatment plants functioned as the intersection between the human society and the nature environment, are receiving increasingly more attention on risk assessment of the acquisition of environmental antibiotic resistancet genes (ARGs) by pathogenetic populations during treatment. However, because of the general lack of robust resistome profiling methods, genotype and resistance phenotype is still poorly correlated in human pathogens of sewage samples. Here we applied MinION nNanopore sequencing to quantify the resistancet genes of multiple antibiotic resistant (MAR) coliform bacteria, a common indicator for human enteric pathogens in sewage samples. Our pipeline could deliver the results within 30 hours from sample collection and the resistome quantification was consistent to that based on the Illumina platform. Additionally, the long Nanopore reads not only enabled a simultaneous identification of the carrier populations of ARGs detected, but also facilitated the genome reconstruction of a representative MAR strain, from which we identified an instance of chromosomal integration of environmental resistance gene obtained by plasmid exchange with a porcine pathogen. This study demonstrated the utilization of MinION sequencing in real-time monitoring and simultaneous phylogenetic tracking of environmental ARGs to address potential health risk associated with them.

Related SRA data

Experiments:
2 ( 2 samples )
Runs:
2 (3.7Gbp; 1.8Gb)
Additional objects:
File type count
fastq 2
nanopore 1
realign to de-novo assembly 1
WGMLST signature 1