Wastewater surveillance reveals the prevalence of last-resort antibiotic-resistant Escherichia coli and their multidrug resistance characteristics

Abstract

Antimicrobial resistance (AMR) imposes a substantial burden on global public health. Given the critical importance of last-resort antibiotics (LRAs) in clinical practice, comprehensive surveillance of LRA-related resistance is of paramount public health significance. As an emerging tool, wastewater surveillance (WS) has the potential to effectively complement existing clinical surveillance systems for LRA resistance at the population level. However, the extremely low abundance of LRA-resistant bacteria in wastewater hinders sensitive detection by conventional culture-based or molecular methods. In this study, using Escherichia coli (E. coli) as the target organism, we monitored resistance levels to three typical LRAs (tigecycline (TIG), meropenem (MEM), and colistin (CT)) in wastewater samples collected from wastewater treatment plants and manholes in Beijing, China. Our results demonstrated that the simultaneous species-resistance selection strategy significantly improved the detection of LRA-resistant E. coli, and the resistance rates in wastewater showed a certain correlation with clinical resistance rates. Further analysis revealed that the typical LRA-resistant isolates exhibited pronounced multidrug resistance (MDR) characteristics, with high resistance rates to clinical first-line antibiotics. Moreover, we identified dual LRA-resistant E. coli and a high-risk IncHI1 plasmid co-harboring blaNDM-5, mcr-1.1, and more than 12 antibiotic resistance genes, warranting further investigation. This study validates the feasibility of monitoring the prevalence of LRA resistance through WS and provides methodological support and key monitoring targets for future efforts.

Graphical abstract

Keywords

Antimicrobial resistance / Wastewater surveillance / Last-resort antibiotics / Escherichia coli

Highlight

	● Simultaneous species-resistance selection enables sensitive detection of LRA-resistant E. coli .
	● Resistance rates of E. coli in wastewater to LRAs correlate with the clinical results.
	● LRA-resistant E. coli in wastewater displays pronounced MDR characteristics.
	● A high prevalence of MEM/CT co-resistant E. coli in wastewater was observed.
	● IncHI1 plasmid co-harboring bla NDM-5 and mcr -1.1 poses a serious public health risk.

References

[1] Aarestrup F M , Woolhouse M E J . (2020). Using sewage for surveillance of antimicrobial resistance. Science, 367(6478): 630–632

[2] Abdelgalel R R , Ibrahem R A , Mohamed D S , Ahmed A B F . (2025). Multidrug-resistant E. Coli in wastewater sources: a comparative study and identification of resistance hotspots. BMC Microbiology, 25(1): 498

[3] Antimicrobial Resistance Collaborators . (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet, 399(10325): 629–655

[4] Che Y , Xu X Q , Yang Y , Břinda K , Hanage W , Yang C , Zhang T . (2022). High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria. Microbiome, 10(1): 16

[5] Feng J , Jia M , Zhuang Y , Xu Z , Chen Y , Fei J Y , Xia J H , Hong L , Zhang J , Wu H Y . et al. (2024a). Prevalence, transmission and genomic epidemiology of mcr-1-positive colistin-resistant Escherichia coli strains isolated from international airplane waste, local resident fecal and wastewater treatment plants. Science of the Total Environment, 957: 177556

[6] Feng J , Pan M , Zhuang Y , Luo J Y , Chen Y , Wu Y T , Fei J Y , Zhu Y Q , Xu Z , Yuan Z G . et al. (2024b). Genetic epidemiology and plasmid-mediated transmission of mcr-1 by Escherichia coli ST155 from wastewater of long-term care facilities. Microbiology Spectrum, 12(3): e03707–23

[7] GBD 2021 Antimicrobial Resistance Collaborators . (2024). Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. The Lancet, 404(10459): 1199–1226

[8] Gomi R , Matsumura Y , Yamamoto M , Tanaka M , Komakech A J , Matsuda T , Harada H . (2024). Genomic surveillance of antimicrobial-resistant Escherichia coli in fecal sludge and sewage in Uganda. Water Research, 248: 120830

[9] Grassly N C , Shaw A G , Owusu M . (2025). Global wastewater surveillance for pathogens with pandemic potential: opportunities and challenges. The Lancet Microbe, 6(1): 100939

[10] Hayashi W , Tanaka H , Taniguchi Y , Iimura M , Soga E , Kubo R , Matsuo N , Kawamura K , Arakawa Y , Nagano Y . et al. (2019). Acquisition of mcr-1 and cocarriage of virulence genes in avian pathogenic Escherichia coli isolates from municipal wastewater influents in Japan. Applied and Environmental Microbiology, 85(22): e01661–19

[11] Ho C S , Wong C T H , Aung T T , Lakshminarayanan R , Mehta J S , Rauz S , Mcnally A , Kintses B , Peacock S J , de la Fuente-Nunez C . et al. (2025). Antimicrobial resistance: a concise update. The Lancet Microbe, 6(1): 100947

[12] Hornsey M , Phee L , Wareham D W . (2011). A novel variant, NDM-5, of the New Delhi Metallo-β-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrobial Agents and Chemotherapy, 55(12): 5952–5954

[13] Huang J W , Lv C , Li M , Rahman T , Chang Y F , Guo X K , Song Z , Zhao Y N , Li Q T , Ni P H . et al. (2024). Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe. Communications Biology, 7(1): 51

[14] Huizer M , ter Laak T L , de Voogt P , van Wezel A P . (2021). Wastewater-based epidemiology for illicit drugs: a critical review on global data. Water Research, 207: 117789

[15] Knight M E , Webster G , Perry W B , Baldwin A , Rushton L , Pass D A , Cross G , Durance I , Muziasari W , Kille P . et al. (2024). National-scale antimicrobial resistance surveillance in waste-water: a comparative analysis of HT qPCR and metagenomic approaches. Water Research, 262: 121989

[16] Kong H F , Hu Z D , Zhang L T , Chen Q Q , Yang L , Li J , Tian B , Chai Y M , Feng X Q . (2024). Clinical risk factors and outcomes of carbapenem-resistant Escherichia coli nosocomial infections in a Chinese teaching hospital: a retrospective study from 2013 to 2020. Microbiology Spectrum, 12(7): e04228–23

[17] Liu Y Y , Wang Y , Walsh T R , Yi L X , Zhang R , Spencer J , Doi Y , Tian G B , Dong B L , Huang X H . et al. (2016). Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. The Lancet Infectious Diseases, 16(2): 161–168

[18] Mbanga J , Abia A L K , Amoako D G , Essack S Y . (2021). Longitudinal surveillance of antibiotic resistance in Escherichia coli and Enterococcus spp. from a wastewater treatment plant and its associated waters in KwaZulu-Natal, South Africa. Microbial Drug Resistance, 27(7): 904–918

[19] Mondal A H , Khare K , Saxena P , Debnath P , Mukhopadhyay K , Yadav D . (2024). A review on colistin resistance: an antibiotic of last resort. Microorganisms, 12(4): 772

[20] Mukherjee M , Laird E , Gentry T J , Brooks J P , Karthikeyan R . (2021). Increased antimicrobial and multidrug resistance downstream of wastewater treatment plants in an urban watershed. Frontiers in Microbiology, 12: 657353

[21] Nazir A , Nazir A , Zuhair V , Aman S , Sadiq S U R , Hasan A H , Tariq M , Rehman L U , Mustapha M J , Bulimbe D B . (2025). The global challenge of antimicrobial resistance: mechanisms, case studies, and mitigation approaches. Health Science Reports, 8(7): e71077

[22] Singer A C , Thompson J R , Filho C R M , Street R , Li X Q , Castiglioni S , Thomas K V . (2023). A world of wastewater-based epidemiology. Nature Water, 1(5): 408–415

[23] Sun J , Chen C , Cui C Y , Zhang Y , Liu X , Cui Z H , Ma X Y , Feng Y J , Fang L X , Lian X L . et al. (2019). Plasmid-encoded tet(X) genes that confer high-level tigecycline resistance in Escherichia coli. Nature Microbiology, 4(9): 1457–1464

[24] Wang D , Zou H Y , Zhao L , Li Q , Meng M , Li X W , Berglund B . (2023). High prevalence of Escherichia coli co-harboring conjugative plasmids with colistin- and carbapenem resistance genes in a wastewater treatment plant in China. International Journal of Hygiene and Environmental Health, 250: 114159

[25] Wang Q , Jin L Y , Sun S J , Yin Y Y , Wang R B , Chen F N , Wang X J , Zhang Y W , Hou J , Zhang Y M . et al. (2022). Occurrence of high levels of cefiderocol resistance in carbapenem-resistant Escherichia coli before its approval in China: a report from China CRE-network. Microbiology Spectrum, 10(3): e02670–21

[26] Wang Y , Xu C Y , Zhang R , Chen Y Q , Shen Y B , Hu F P , Liu D J , Lu J Y , Guo Y , Xia X . et al. (2020). Changes in colistin resistance and mcr-1 abundance in Escherichia coli of animal and human origins following the ban of colistin-positive additives in China: an epidemiological comparative study. The Lancet Infectious Diseases, 20(10): 1161–1171

[27] Wu Y N , Zhu L , Li N , Lu C Z , Zhang C D , Wang M Z . (2026). Antibiotic resistance genes against “last-resort” antibiotics within the One Health framework: dissemination, mechanisms, and AI-driven opportunities. Journal of Hazardous Materials, 504: 141296

[28] Wu Z Q , Che Y , Dang C Y , Zhang M , Zhang X Y , Sun Y H , Li X , Zhang T , Xia Y . (2022). Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body. Water Research, 226: 119282

[29] Xu X Q , Lin Y Q , Deng Y , Liu L , Wang D , Tang Q L , Wang C X , Chen X , Che Y , Wyrsch E R . et al. (2025). Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong. Nature Communications, 16(1): 7319

[30] Zhang Q Y , Xie X H , Tao L X , Wang J , Shi Y , Sheng H F , Liu C L , Zhao H W , Liu M H , Feng J . (2026). Characterization of an Escherichia coli ST156 isolate harboring an IncHI2-type plasmid Co-carrying bla_NDM-5 and mcr-1.1 genes from urban wastewater treatment plants in Fengxian, Shanghai. Antibiotics, 15(3): 275

[31] Zhang R , Li Y , Chen J W , Liu C C , Sun Q L , Shu L B , Chen G X , Wang Z Q , Wang S L , Li R C . (2023). Population genomic analysis reveals the emergence of high-risk carbapenem-resistant Escherichia coli among ICU patients in China. Journal of Infection, 86(4): 316–328

[32] Zhang W T , Zhang T F , Wang C , Liang G X , Lu Q , Wen G Y , Guo Y Q , Cheng Y L , Wang Z , Shao H B . et al. (2022). Prevalence of colistin resistance gene mcr-1 in Escherichia coli isolated from chickens in central China, 2014 to 2019. Journal of Global Antimicrobial Resistance, 29: 241–246

Rights & permissions

Higher Education Press 2027