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Genotypic diversity in multi-drug-resistant E. coli isolated from animal feces and Yamuna River water, India, using rep-PCR fingerprinting

Environmental Monitoring and Assessment volume 192, Article number: 681 (2020) Cite this article

Abstract

Genotypic diversity among multi-drug-resistant (MDR) aquatic E. coli isolated from different sites of Yamuna River was analyzed using repetitive element PCR (rep-PCR) methods viz. ERIC-PCR and (GTG)5-PCR and compared with the MDR animal fecal isolates. The 97 E. coli isolates belonging to different serotypes, phylogroups, and multi-drug resistance patterns were analyzed. High genetic diversity was observed by both the methods; however, (GTG)5 typing showed higher discriminating potential. Combination of ERIC types (E1–E32) and (GTG)5 types (G1–G46) generated 77 genotypes. The frequency of genotypes ranged from 0.013 to 0.065. The genotype composition of E. coli isolates was highly diverse at all the sampling sites across Yamuna River except at its entry site in Delhi. The sampling sites under the influence of high anthropogenic activities showed an increase in number of unique genotype isolates. These sites also exhibited high multiple antibiotic resistance (MAR) indexes (above 0.25) suggesting high risk of contamination. Principal coordinate analysis (PCoA) showed limited clustering of genotypes based on the sampling sites. The most frequent genotypes were grouped in the positive zone of both the principal coordinates (PC1 and PC2). The genotypes of most of the animal fecal isolates were unique and occupied a common space in the negative PC1 area forming a separate cluster. High genotypic diversity among the aquatic E. coli and the drain isolates, discharging the untreated municipal waste in the river, was observed, suggesting that the sewage effluents contribute substantially to contamination of this river system than animal feces. The presence of such a high diversity among the MDR E. coli isolates in the natural river systems is of great public health significance and highlights the need of an efficient surveillance system for better management of Indian natural water bodies.

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Acknowledgments

Financial assistance received from the University Grant Commission (UGC) (Major Research Project grant no. UGC-41-1172/2012) and the Department of Science and Technology (DST grant no. 1196 SR/FST/LS-I/2017/4) is duly acknowledged. NK and MK are grateful to Maharshi Dayanand University for providing University Research Scholarship. NK sincerely thanks UGC for RGNF grant (UGC-RGNF grant no. F1-17.1/2016-17/RGNF-2015-17-SC-HAR-18413/(SA-III/Website)) and MK thanks CSIR for the Senior Research Fellowship (no. 09/382(0212)/19-EMR-I). The authors also wish to acknowledge National Salmonella and Escherichia Centre, Central Research Institute, Kasauli, Himachal Pradesh, India, for serotyping E. coli isolates.

Funding

This study was funded by the University Grant Commission (UGC) (Major Research Project grant no. UGC-41-1172/2012) and the Department of Science and Technology (grant no. 1196 SR/FST/LS-I/2017/4).

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  1. Neha Khare and Megha Kaushik contributed equally to this work.

Affiliations

  1. Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India

    Neha Khare, Megha Kaushik & Pooja Gulati

  2. Departamento de Biotechnologia-Biología Vegetal, Escuela Técnica Superior de Ingenieria Agrónomica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2-4, 28040, Madrid, Spain

    Juan Pedro Martin

  3. Department of Botany, Gargi College, University of Delhi, Delhi, India

    Aparajita Mohanty

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  1. Neha Khare
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  2. Megha Kaushik
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Correspondence to Pooja Gulati.

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Supplementary Fig 1.

Representative gels showing (A) ERIC- fingerprints (Lane 1-17) and (B) (GTG)5- fingerprints (Lane 18-34) of E. coli obtained in the present study. (JPG 968 kb)

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Khare, N., Kaushik, M., Martin, J.P. et al. Genotypic diversity in multi-drug-resistant E. coli isolated from animal feces and Yamuna River water, India, using rep-PCR fingerprinting. Environ Monit Assess 192, 681 (2020). https://doi.org/10.1007/s10661-020-08635-1

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Keywords

  • E. coli
  • ERIC-PCR
  • (GTG)5-PCR
  • Molecular typing
  • Water management