Department Surface Waters - Research and Management

ResistFlow: Wastewater resistome gene expression and exchange


Biological wastewater treatment plants (WWTP) have been under extensive scrutiny over their central role in the dissemination of antibiotic resistance genes (ARGs) of human origin. However, resistance gene expression, environmental selection, as well as mechanisms underpinning resistance exchange and dissemination among bacteria remain unknown. In the ResistFlow project we combine quantitative metatranscriptomes, metagenome assembly, amplicon sequencing, and qPCR to quantify the resistome in 12 Swiss WWTPs over four treatment stages: primary clarifier, nitrification, denitrification and secondary clarifier.
Overall, we find that wastewater and activated sludge bacterial communities harbored ∼108 to 1012 transcripts per liter derived from tens of thousands of ARGs that confer resistance to over 20 classes of antibiotics including five classes of last-resort antbiotics. We demonstrate that biological factors including horizontal gene transfer and bacterial community composition play a dominant role in shaping resistome structure, and provide evidence for the exchange of resistance gene between WWTPs and human pathogens, which highlights the clincial relevance of wastewater resistome. In addition, we showed that wastewater treatment greatly affects the resistome composition and selectively enriches certain types of antibiotic resistance genes in the clarified effluent.

Research papers

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      originalId => protected23259 (integer)
      authors => protected'Yuan, L.; Wang, Y.; Zhang, L.; Palomo, A.; Zhou, J.
         ; Smets, B. F.; Bürgmann, H.; Ju, F.
' (133 chars) title => protected'Pathogenic and indigenous denitrifying bacteria are transcriptionally active
          and key multi-antibiotic-resistant players in wastewater treatment plants
' (150 chars) journal => protected'Environmental Science and Technology' (36 chars) year => protected2021 (integer) volume => protected55 (integer) issue => protected'15' (2 chars) startpage => protected'10862' (5 chars) otherpage => protected'10874' (5 chars) categories => protected'antibiotic resistance; wastewater treatment plant; denitrifying and pathogen
         ic bacteria; genome-centric metatranscriptomics; metagenome-assembled genome
' (152 chars) description => protected'The global rise and spread of antibiotic resistance greatly challenge the tr
         eatment of bacterial infections. Wastewater treatment plants (WWTPs) harbor
         and discharge antibiotic resistance genes (ARGs) as environmental contaminan
         ts. However, the knowledge gap on the host identity, activity, and functiona
         lity of ARGs limits transmission and health risk assessment of the WWTP resi
         stome. Hereby, a genome-centric quantitative metatranscriptomic approach was
          exploited to realize high-resolution qualitative and quantitative analyses
         of bacterial hosts of ARGs (i.e., multiresistance, pathogenicity, activity,
         and niches) in the 12 urban WWTPs. We found that ∼45% of 248 recovered gen
         omes expressed ARGs against multiple classes of antibiotics, among which bac
         itracin and aminoglycoside resistance genes in Proteobacteria were the most
         prevalent scenario. Both potential pathogens and indigenous denitrifying bac
         teria were transcriptionally active hosts of ARGs. The almost unchanged rela
         tive expression levels of ARGs in the most resistant populations (66.9%) and
          the surviving ARG hosts including globally emerging pathogens (e.g., <em>Al
         iarcobacter cryaerophilus</em>) in treated WWTP effluent prioritize future e
         xamination on the health risks related to resistance propagation and human e
         xposure in the receiving environment.
' (1329 chars) serialnumber => protected'0013-936X' (9 chars) doi => protected'10.1021/acs.est.1c02483' (23 chars) uid => protected23259 (integer) _localizedUid => protected23259 (integer)modified _languageUid => protectedNULL _versionedUid => protected23259 (integer)modified pid => protected124 (integer)
1 => Snowflake\Publications\Domain\Model\Publicationprototypepersistent entity (uid=17645, pid=124) originalId => protected17645 (integer) authors => protected'Ju,&nbsp;F.; Beck,&nbsp;K.; Yin,&nbsp;X.; Maccagnan,&nbsp;A.; McArdell,&nbsp
         ;C.&nbsp;S.; Singer,&nbsp;H.&nbsp;P.; Johnson,&nbsp;D.&nbsp;R.; Zhang,&nbsp;
         T.; Bürgmann,&nbsp;H.
' (174 chars) title => protected'Wastewater treatment plant resistomes are shaped by bacterial composition, g
         enetic exchange, and upregulated expression in the effluent microbiomes
' (147 chars) journal => protected'ISME Journal' (12 chars) year => protected2019 (integer) volume => protected13 (integer) issue => protected'2' (1 chars) startpage => protected'346' (3 chars) otherpage => protected'360' (3 chars) categories => protected'' (0 chars) description => protected'Wastewater treatment plants (WWTPs) are implicated as hotspots for the disse
         mination of antibacterial resistance into the environment. However, the in s
         itu processes governing removal, persistence, and evolution of resistance ge
         nes during wastewater treatment remain poorly understood. Here, we used quan
         titative metagenomic and metatranscriptomic approaches to achieve a broad-sp
         ectrum view of the flow and expression of genes related to antibacterial res
         istance to over 20 classes of antibiotics, 65 biocides, and 22 metals. All c
         ompartments of 12 WWTPs share persistent resistance genes with detectable tr
         anscriptional activities that were comparatively higher in the secondary eff
         luent, where mobility genes also show higher relative abundance and expressi
         on ratios. The richness and abundance of resistance genes vary greatly acros
         s metagenomes from different treatment compartments, and their relative and
         absolute abundances correlate with bacterial community composition and bioma
         ss concentration. No strong drivers of resistome composition could be identi
         fied among the chemical stressors analyzed, although the sub-inhibitory conc
         entration (hundreds of ng/L) of macrolide antibiotics in wastewater correlat
         es with macrolide and vancomycin resistance genes. Contig-based analysis sho
         ws considerable co-localization between resistance and mobility genes and im
         plies a history of substantial horizontal resistance transfer involving huma
         n bacterial pathogens. Based on these findings, we propose future inclusion
         of mobility incidence (M%) and host pathogenicity of antibiotic resistance g
         enes in their quantitative health risk ranking models with an ultimate goal
         to assess the biological significance of wastewater resistomes with regard t
         o disease control in humans or domestic livestock.
' (1798 chars) serialnumber => protected'1751-7362' (9 chars) doi => protected'10.1038/s41396-018-0277-8' (25 chars) uid => protected17645 (integer) _localizedUid => protected17645 (integer)modified _languageUid => protectedNULL _versionedUid => protected17645 (integer)modified pid => protected124 (integer)
Yuan, L.; Wang, Y.; Zhang, L.; Palomo, A.; Zhou, J.; Smets, B. F.; Bürgmann, H.; Ju, F. (2021) Pathogenic and indigenous denitrifying bacteria are transcriptionally active and key multi-antibiotic-resistant players in wastewater treatment plants, Environmental Science and Technology, 55(15), 10862-10874, doi:10.1021/acs.est.1c02483, Institutional Repository
Ju, F.; Beck, K.; Yin, X.; Maccagnan, A.; McArdell, C. S.; Singer, H. P.; Johnson, D. R.; Zhang, T.; Bürgmann, H. (2019) Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes, ISME Journal, 13(2), 346-360, doi:10.1038/s41396-018-0277-8, Institutional Repository