2024-12-11
ENA first public
ERC000047
ENA-CHECKLIST
CMR
INSDC center name
public
INSDC status
ERS22355082
SRA accession
SRP300315_co1_11
Submitter Id
Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs
assembly quality
metaSPAdes;3.15.4;default
assembly software
coverage and kmer
binning parameters
MetaBAT2;2.15;default
binning software
aquatic
broad-scale environmental context
2018-02-15
collection date
100
%
completeness score
CheckM2;1.0.2;default
completeness software
0.12
%
contamination score
This sample represents a Third Party Annotation (TPA) Metagenome-assembled genome assembled from the metagenomic runs SRR13355620,SRR13355622 of study SRP300315.
description
aquatic
environmental medium
Cyprus
geographic location (country and/or sea)
35.150243
DD
geographic location (latitude)
33.391634
DD
geographic location (longitude)
metagenome-assembled genome
investigation type
wastewater metagenome
isolation_source
wastewater biome
local environmental context
wastewater metagenome
metagenomic source
uncultured Gammaproteobacteria bacterium
organism
Antibiotic resistance is an emerging global issue of utmost importance. Wastewater treatment plants are considered evolutionary hotspots for microbial multi-drug resistance of strains with known pathogenic potential, gradually depriving the arsenal of chemotherapeutic weapons. Membrane bioreactors (MBR) are good alternatives to conventional activated sludge (CAS) systems in reducing the load of antibiotic resistance genes (ARGs) and pathogens in treated effluents. So far, limited information is available regarding the removal of pathogens and ARGs, based mainly on bench-scale experimental setups. To this end, the performance of two full-scale urban wastewater treatment plants (UWTPs), a membrane bioreactor (MBR) and a conventional activated sludge (CAS) system, were investigated for the removal and ecological correlations of putative pathogenic bacteria, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs) and mobile genetic elements (MGEs), using a shotgun metagenomic approach. Total prokaryotic, eukaryotic and viral marker genes in the influent and effluent of the two full-scale systems were also analyzed. Vertical (along the treatment line) and horizontal (between UWTPs) comparisons determined the efficiency of the two systems. Correlation tests revealed links between identified putative pathogens and: (i) ARGs/BRGs/MGEs, denoting associations of clinical importance and inferring potential roles of MGEs in pathogen dispersal (ii) bacteriophages/protists/ predatory bacteria defining specific and significant predator-prey interactions, for the homeostasis of the engineered systems. A strong decline in the abundance of pathogen-containing taxa and ARGs was observed in the MBR-treated effluents compared with the CAS-treated ones. MBR treatment favored ARGs associated with the commonly found in urban wastewater triclosan or antimicrobials of natural occurrence like streptothricin. On the other hand, CAS effluents contained a diverse set of ARGs associated with antibiotics of clinical importance. The conducted correlation tests showed that: (i) opportunistic pathogens like Clostridia and Nocardia may be developing resistance against first-line treatments in the tested environments and (ii) that bacteriophages play an important role in controlling bacterial populations in such systems and thus may be considered as a natural mechanism for pathogen-specific removal in UWTPs. Overall, our findings reinforce the capacity of MBR systems of retaining pathogenic loads, hence reducing the potential health risks associated with the release or reuse of treated wastewaters.
project name
SAMN17167484,SAMN17167482
sample derived from
uncultured Gammaproteobacteria bacterium
scientific_name
Illumina HiSeq 2500
sequencing method
multi-marker approach
taxonomic identity marker
Metagenome-assembled genome: SRP300315_co1_11
title