Abstract
Microbial indicators are often used to monitor microbial safety of aquatic environments. However, information regarding the correlation between microbial indicators and ecotoxicological factors such as potential pathogens and antibiotic resistance genes (ARGs) in anthropogenically impacted waters remains highly limited. Here, we investigated the bacterial community composition, potential pathogens, ARGs diversity, ARG hosts, and horizontal gene transfer (HGT) potential in urban river and wastewater samples from Chaohu Lake Basin using 16S rRNA and metagenomic sequencing. The composition of the microbial community and potential pathogens differed significantly in wastewater and river water samples, and the total relative abundance of fecal indicator bacteria was positively correlated with the total relative abundance of potential pathogens (p < 0.001 and Pearson’s r = 0.758). Network analysis indicated that partial ARG subtypes such as dfrE, sul2, and PmrE were significantly correlated with indicator bacteria (p < 0.05 and Pearson’s r > 0.6). Notably, Klebsiella was the indicator bacteria significantly correlated with 4 potential pathogens and 14 ARG subtypes. ARGs coexisting with mobile gene elements were mainly found in Thauera, Pseudomonas, Escherichia, and Acinetobacter. Next-generation sequencing (NGS) can be used to conduct preliminary surveys of environmental samples to access potential health risks, thereby facilitating water resources management.
Similar content being viewed by others
Data availability
The original sequencing data has been uploaded to NCBI Sequence Read Archive (SRA), study accession number: PRJNA672794.
References
Ahmed J, Wong LP, Chua YP et al (2020) Quantitative microbial risk assessment of drinking water quality to predict the risk of waterborne diseases in primary-school children. IJERPH 17:2774. https://doi.org/10.3390/ijerph17082774
Ahmed W, Harwood VJ, Nguyen K et al (2016) Utility of Helicobacter spp. associated GFD markers for detecting avian fecal pollution in natural waters of two continents. Water Research 88:613–622. https://doi.org/10.1016/j.watres.2015.10.050
Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. 10.13140/2.1.1341.1520
Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics 29:1165–1188
Bondarczuk K, Piotrowska-Seget Z (2019) Microbial diversity and antibiotic resistance in a final effluent-receiving lake. Science of The Total Environment 650:2951–2961. https://doi.org/10.1016/j.scitotenv.2018.10.050
Bush K, Courvalin P, Dantas G et al (2011) Tackling antibiotic resistance. Nat Rev Microbiol 9:894–896. https://doi.org/10.1038/nrmicro2693
Byappanahalli MN, Nevers MB, Korajkic A et al (2012) Enterococci in the environment. Microbiol Mol Biol Rev 76:685–706. https://doi.org/10.1128/MMBR.00023-12
Chen H, Chen R, Jing L et al (2019) A metagenomic analysis framework for characterization of antibiotic resistomes in river environment: application to an urban river in Beijing. Environmental Pollution 245:398–407. https://doi.org/10.1016/j.envpol.2018.11.024
Cheng Z, Chen M, Xie L et al (2015) Bioaugmentation of a sequencing batch biofilm reactor with Comamonas testosteroni and Bacillus cereus and their impact on reactor bacterial communities. Biotechnol Lett 37:367–373. https://doi.org/10.1007/s10529-014-1684-1
Chong WH, Saha BK, Ramani A, Chopra A (2021) State-of-the-art review of secondary pulmonary infections in patients with COVID-19 pneumonia. Infection. https://doi.org/10.1007/s15010-021-01602-z
Cui Q, Huang Y, Wang H, Fang T (2019) Diversity and abundance of bacterial pathogens in urban rivers impacted by domestic sewage. Environmental Pollution 249:24–35. https://doi.org/10.1016/j.envpol.2019.02.094
de Celis M, Belda I, Ortiz-Álvarez R et al (2020) Tuning up microbiome analysis to monitor WWTPs’ biological reactors functioning. Sci Rep 10:4079. https://doi.org/10.1038/s41598-020-61092-1
Di W, Hong-fang L, Feng L, et al (2019) Interception effect of ecological ditch on nitrogen transport in agricultural runoff in subtropical China.
Duan C, Cui Y, Zhao Y et al (2016) Evaluation of Faecalibacterium 16S rDNA genetic markers for accurate identification of swine faecal waste by quantitative PCR. Journal of Environmental Management 181:193–200. https://doi.org/10.1016/j.jenvman.2016.06.022
Fang T, Cui Q, Huang Y, et al (2018) Distribution comparison and risk assessment of free-floating and particle-attached bacterial pathogens in urban recreational water: implications for water quality management. Science of The Total Environment 613–614:428–438. https://doi.org/10.1016/j.scitotenv.2017.09.008
Figueras MJ, Borrego JJ (2010) New perspectives in monitoring drinking water microbial quality. IJERPH 7:4179–4202. https://doi.org/10.3390/ijerph7124179
Fu L, Niu B, Zhu Z et al (2012) CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28:3150–3152. https://doi.org/10.1093/bioinformatics/bts565
Guo J, Li J, Chen H et al (2017) Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. Water Research 123:468–478. https://doi.org/10.1016/j.watres.2017.07.002
Han M, Zhang L, Zhang N et al (2022) Antibiotic resistome in a large urban-lake drinking water source in middle China: dissemination mechanisms and risk assessment. Journal of Hazardous Materials 424:127745. https://doi.org/10.1016/j.jhazmat.2021.127745
Harwood VJ, Staley C, Badgley BD et al (2014) Microbial source tracking markers for detection of fecal contamination in environmental waters: relationships between pathogens and human health outcomes. FEMS Microbiol Rev 38:1–40. https://doi.org/10.1111/1574-6976.12031
Jia B, Raphenya AR, Alcock B et al (2017) CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45:D566–D573. https://doi.org/10.1093/nar/gkw1004
Johnson DR, Helbling DE, Lee TK et al (2015) Association of biodiversity with the rates of micropollutant biotransformations among full-scale wastewater treatment plant communities. Appl Environ Microbiol 81:666–675. https://doi.org/10.1128/AEM.03286-14
Kietsiri P, Muangnapoh C, Lurchachaiwong W, et al (2021) Characterization of Arcobacter spp. Isolated from human diarrheal, non-diarrheal and food samples in Thailand. PLoS ONE 16:e0246598. https://doi.org/10.1371/journal.pone.0246598
Kim S-K, Lee J-H (2016) Biofilm dispersion in Pseudomonas aeruginosa. J Microbiol 54:71–85. https://doi.org/10.1007/s12275-016-5528-7
Li D, Liu C-M, Luo R et al (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31:1674–1676. https://doi.org/10.1093/bioinformatics/btv033
Li J, Chen Q, Li H et al (2020) Impacts of different sources of animal manures on dissemination of human pathogenic bacteria in agricultural soils. Environmental Pollution 266:115399. https://doi.org/10.1016/j.envpol.2020.115399
Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714. https://doi.org/10.1093/bioinformatics/btn025
Liu S, Wang C, Wang P et al (2018) Variation of bacterioplankton community along an urban river impacted by touristic city: with a focus on pathogen. Ecotoxicology and Environmental Safety 165:573–581. https://doi.org/10.1016/j.ecoenv.2018.09.006
Lu X, Zhang X-X, Wang Z et al (2015) Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing. PLoS ONE 10:e0125549. https://doi.org/10.1371/journal.pone.0125549
Miran W, Jang J, Nawaz M et al (2018) Biodegradation of the sulfonamide antibiotic sulfamethoxazole by sulfamethoxazole acclimatized cultures in microbial fuel cells. Science of The Total Environment 627:1058–1065. https://doi.org/10.1016/j.scitotenv.2018.01.326
Mishra M, Arukha AP, Patel AK et al (2018) Multi-drug resistant coliform: water sanitary standards and health hazards. Front Pharmacol 9:311. https://doi.org/10.3389/fphar.2018.00311
Neher TP, Ma L, Moorman TB et al (2020) Seasonal variations in export of antibiotic resistance genes and bacteria in runoff from an agricultural watershed in Iowa. Science of The Total Environment 738:140224. https://doi.org/10.1016/j.scitotenv.2020.140224
Nnadozie CF, Odume ON (2019) Freshwater environments as reservoirs of antibiotic resistant bacteria and their role in the dissemination of antibiotic resistance genes. Environmental Pollution 254:113067. https://doi.org/10.1016/j.envpol.2019.113067
Noguchi H, Park J, Takagi T (2006) MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research 34:5623–5630. https://doi.org/10.1093/nar/gkl723
Oravcova V, Mihalcin M, Zakova J et al (2017) Vancomycin-resistant enterococci with vanA gene in treated municipal wastewater and their association with human hospital strains. Science of The Total Environment 609:633–643. https://doi.org/10.1016/j.scitotenv.2017.07.121
Partridge SR, Kwong SM, Firth N, Jensen SO (2018) Mobile genetic elements associated with antimicrobial resistance. Clin Microbiol Rev 31. https://doi.org/10.1128/CMR.00088-17
Piotrowska M, Popowska M (2015) Insight into the mobilome of Aeromonas strains. Front Microbiol 6. https://doi.org/10.3389/fmicb.2015.00494
Prezioso SM, Brown NE, Goldberg JB (2017) Elfamycins: inhibitors of elongation factor-Tu Molecular Microbiology 106:22–34. https://doi.org/10.1111/mmi.13750
Rodríguez EA, Ramirez D, Balcázar JL, Jiménez JN (2021) Metagenomic analysis of urban wastewater resistome and mobilome: a support for antimicrobial resistance surveillance in an endemic country. Environmental Pollution 276:116736. https://doi.org/10.1016/j.envpol.2021.116736
Schmeller DS, Loyau A, Bao K, et al (2018) People, pollution and pathogens—global change impacts in mountain freshwater ecosystems. Science of The Total Environment 622–623:756–763. https://doi.org/10.1016/j.scitotenv.2017.12.006
Shin SB, Lee JH, Lim CW et al (2019) Fecal source tracking based on fecal coliform concentration and bacterial community structure in the Bong stream, Korea. Environ Sci Pollut Res 26:5601–5612. https://doi.org/10.1007/s11356-018-3995-6
Talagrand-Reboul E, Jumas-Bilak E, Lamy B (2017) Aeromonas—the social life of Aeromonas through biofilm and quorum sensing systems. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.00037
Triggiano F, Calia C, Diella G et al (2020) The role of urban wastewater in the environmental transmission of antimicrobial resistance: the current situation in Italy (2010–2019). Microorganisms 8:1567. https://doi.org/10.3390/microorganisms8101567
Trimble MJ, Mlynárčik P, Kolář M, Hancock REW (2016) Polymyxin: alternative mechanisms of action and resistance. Cold Spring Harb Perspect Med 6:a025288. https://doi.org/10.1101/cshperspect.a025288
Valenstein P, Bardy GH, Cox CC, Zwadyk P (1983) Pseudomonas alcaligenes Endocarditis. American Journal of Clinical Pathology 79:245–247. https://doi.org/10.1093/ajcp/79.2.245
Vila-Costa M, Gioia R, Aceña J et al (2017) Degradation of sulfonamides as a microbial resistance mechanism. Water Research 115:309–317. https://doi.org/10.1016/j.watres.2017.03.007
Wattam AR, Abraham D, Dalay O et al (2014) PATRIC, the bacterial bioinformatics database and analysis resource. Nucl Acids Res 42:D581–D591. https://doi.org/10.1093/nar/gkt1099
World Health Organization (ed) (2011) Guidelines for drinking-water quality, 4th edn. World Health Organization, Geneva
Wu J, Long SC, Das D, Dorner SM (2011) Are microbial indicators and pathogens correlated? A statistical analysis of 40 years of research. Journal of Water and Health 9:265–278. https://doi.org/10.2166/wh.2011.117
Wu Y, Shukal S, Mukherjee M, Cao B (2015) Comamonas—involvement in denitrification is beneficial to the biofilm lifestyle of Comamonas testosteroni: a mechanistic study and its environmental implications. Environ Sci Technol 49:11551–11559. https://doi.org/10.1021/acs.est.5b03381
Yang X, Cui H, Liu X et al (2020) Water pollution characteristics and analysis of Chaohu Lake basin by using different assessment methods. Environ Sci Pollut Res 27:18168–18181. https://doi.org/10.1007/s11356-020-08189-2
Yang Y, Li B, Ju F, Zhang T (2013) Exploring variation of antibiotic resistance genes in activated sludge over a four-year period through a metagenomic approach. Environ Sci Technol 47:10197–10205. https://doi.org/10.1021/es4017365
Yang Z, Kong F, Zhang M (2016) Groundwater contamination by microcystin from toxic cyanobacteria blooms in Lake Chaohu. China. Environ Monit Assess 188:280. https://doi.org/10.1007/s10661-016-5289-0
Yue Y, Huang H, Qi Z et al (2020) Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets. BMC Bioinformatics 21:334. https://doi.org/10.1186/s12859-020-03667-3
Zahedi Bialvaei A, Rahbar M, Hamidi-Farahani R et al (2021) Expression of RND efflux pumps mediated antibiotic resistance in Pseudomonas aeruginosa clinical strains. Microbial Pathogenesis 153:104789. https://doi.org/10.1016/j.micpath.2021.104789
Zhang L, Fang W, Li X et al (2020) Linking bacterial community shifts with changes in the dissolved organic matter pool in a eutrophic lake. Science of The Total Environment 719:137387. https://doi.org/10.1016/j.scitotenv.2020.137387
Zhang Q-Q, Ying G-G, Pan C-G et al (2015) Comprehensive evaluation of antibiotics emission and fate in the river basins of China: source analysis, multimedia modeling, and linkage to bacterial resistance. Environ Sci Technol 49:6772–6782. https://doi.org/10.1021/acs.est.5b00729
Zhao R, Feng J, Liu J et al (2019) Deciphering of microbial community and antibiotic resistance genes in activated sludge reactors under high selective pressure of different antibiotics. Water Research 151:388–402. https://doi.org/10.1016/j.watres.2018.12.034
Acknowledgements
We thank the University Synergy Innovation Program of Anhui Province for supporting the high-throughput sequencing. The collection of the experimental samples was supported by Integration and Demonstration of Quality and Safety Control Technology for Green Ecological Livestock and Poultry Products Industry Chain. We thank International Science Editing (http://www.internationalscienceediting.com) for editing this manuscript.
Funding
This study was supported by the University Synergy Innovation Program of Anhui Province (Grant No. GXXT-2019-035) and Integration and Demonstration of Quality and Safety Control Technology for Green Ecological Livestock and Poultry Products Industry Chain (1604a0702033).
Author information
Authors and Affiliations
Contributions
KZQ and YS conceived the idea. ZQ, YS, and XJS collected the samples. XLZ, HH, and JT analyzed and interpreted the data. XLZ wrote the manuscript. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
This study was performed in accordance with the Chinese Laboratory Animal Administration Act of 1988. Before experiments, the research protocol was reviewed and approved by the Research Ethics Committee of Anhui Agricultural University. Permission was obtained from all managers on study farms before sampling.
Consent for publication
Not applicable.
Conflict of interest
The authors declare no competing interests.
Additional information
Responsible Editor: Diane Purchase
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Zhao, XL., Qi, Z., Huang, H. et al. Coexistence of antibiotic resistance genes, fecal bacteria, and potential pathogens in anthropogenically impacted water. Environ Sci Pollut Res 29, 46977–46990 (2022). https://doi.org/10.1007/s11356-022-19175-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11356-022-19175-1