Profiles of bacteria/phage-comediated ARGs in pig farm wastewater treatment plants in China: Association with mobile genetic elements, bacterial communities and environmental factors

2021 ◽  
Vol 404 ◽  
pp. 124149
Author(s):  
Yiwen Yang ◽  
Sicheng Xing ◽  
Yingxi Chen ◽  
Ruiting Wu ◽  
Yinbao Wu ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Environmental Factors ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Pig Farm ◽  
Farm Wastewater

scholarly journals Comparative Genomics of Multidrug-Resistant Enterococcus spp. isolated from Wastewater Treatment Plants

2019 ◽  
Author(s):  
Haley Sanderson ◽  
Rodrigo Ortega-Polo ◽  
Rahat Zaheer ◽  
Noriko Goji ◽  
Kingsley K. Amoako ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Comparative Genomics ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Multi Drug Resistance ◽  
Genetic Elements ◽  
Conventional Activated Sludge ◽  
Enterococcus Spp

Abstract Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Entercoccus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis (n=24), E. faecium (n=11), E. casseliflavus (n=2) and E. gallinarum (n=2), were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p < 0.001) and E. faecalis ( p < 0.001) and with the number of AMR genes in E. faecium ( p = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on source but not based on WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

Potential regulation of small RNAs on bacterial function activities in pig farm wastewater treatment plants

2020 ◽  
Vol 91 ◽  
pp. 292-300 ◽  
Author(s):  
Yiwen Yang ◽  
Sicheng Xing ◽  
Sumin Li ◽  
Yajing Niu ◽  
Cheng Li ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Small Rnas ◽  
Wastewater Treatment Plants ◽  
Pig Farm ◽  
Bacterial Function ◽  
Farm Wastewater

scholarly journals Comparative Genomics of Multidrug-Resistant Enterococcus spp. isolated from Wastewater Treatment Plants

2019 ◽  
Author(s):  
Haley Sanderson ◽  
Rodrigo Ortega-Polo ◽  
Rahat Zaheer ◽  
Noriko Goji ◽  
Kingsley K. Amoako ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Comparative Genomics ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Multi Drug Resistance ◽  
Genetic Elements ◽  
Conventional Activated Sludge ◽  
Enterococcus Spp

Abstract Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Entercoccus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis (n=24), E. faecium (n=11), E. casseliflavus (n=2) and E. gallinarum (n=2), were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p < 0.001) and E. faecalis ( p < 0.001) and with the number of AMR genes in E. faecium ( p = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on source but not based on WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

scholarly journals Comparative Genomics of Multidrug-Resistant Enterococcus spp. isolated from Wastewater Treatment Plants

2019 ◽  
Author(s):  
Haley Sanderson ◽  
Rodrigo Ortega-Polo ◽  
Rahat Zaheer ◽  
Noriko Goji ◽  
Kingsley K. Amoako ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Comparative Genomics ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Multi Drug Resistance ◽  
Genetic Elements ◽  
Conventional Activated Sludge ◽  
Enterococcus Spp

Abstract Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Entercoccus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis (n=24), E. faecium (n=11), E. casseliflavus (n=2) and E. gallinarum (n=2), were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p < 0.001) and E. faecalis ( p < 0.001) and with the number of AMR genes in E. faecium ( p = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on source but not based on WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

scholarly journals Comparative Genomics of Multidrug-Resistant Enterococcus spp. isolated from Wastewater Treatment Plants

2019 ◽  
Author(s):  
Haley Sanderson ◽  
Rodrigo Ortega-Polo ◽  
Rahat Zaheer ◽  
Noriko Goji ◽  
Kingsley K. Amoako ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Comparative Genomics ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Multi Drug Resistance ◽  
Genetic Elements ◽  
Conventional Activated Sludge ◽  
Enterococcus Spp

Abstract Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Entercoccus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis (n=24), E. faecium (n=11), E. casseliflavus (n=2) and E. gallinarum (n=2), were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p < 0.001) and E. faecalis ( p < 0.001) and with the number of AMR genes in E. faecium ( p = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on source but not based on WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

scholarly journals Comparative Genomics of Multidrug-Resistant Enterococcus spp. isolated from Wastewater Treatment Plants

2019 ◽  
Author(s):  
Haley Sanderson ◽  
Rodrigo Ortega-Polo ◽  
Rahat Zaheer ◽  
Noriko Goji ◽  
Kingsley K. Amoako ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Comparative Genomics ◽  
Virulence Genes ◽  
Wastewater Treatment Plants ◽  
Mobile Genetic Elements ◽  
Multidrug Resistant ◽  
Multi Drug Resistance ◽  
Genetic Elements ◽  
Conventional Activated Sludge ◽  
Enterococcus Spp

Abstract Background Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Entercoccus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted. Results VRE isolates, including E. faecalis (n=24), E. faecium (n=11), E. casseliflavus (n=2) and E. gallinarum (n=2), were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium ( p < 0.001) and E. faecalis ( p < 0.001) and with the number of AMR genes in E. faecium ( p = 0.005). Genes conferring vancomycin resistance, including van A and van M ( E. faecium ), van G ( E. faecalis ), and van C ( E. casseliflavus / E. gallinarum ), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium , E. faecalis , E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium , than E. casseliflavus and E. gallinarum . A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E. faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium . Phylogenetic analysis demonstrated differential clustering of isolates based on source but not based on WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers. Conclusions There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp .

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