3 Biotech

, 10:63 | Cite as

Evaluation of genetic diversity among aquatic and fecal isolates of Escherichia coli using multilocus variable number of tandem repeat analysis

  • Neha Khare
  • Megha Kaushik
  • Sanjay Kumar
  • Pooja GulatiEmail author
Original Article


In developing countries like India, fecal pollution of surface waters is a major threat to public and environmental health. The aim of the study was to assess serological, phylogenetic and molecular diversity among aquatic Escherichia coli isolates from Yamuna river and their comparison with the animal fecal isolates. A total of 97 E. coli isolates from Yamuna river and domesticated animals were characterized by multilocus variable number tandem repeat analysis (MLVA) using four VNTR loci. The pathogenicity of these strains by serological and phylogenetic analysis was also determined. E. coli strains were differentiated into 53 distinct MLVA types with high discriminatory power, Simpson's index of 0.95 (95% CI 0.923–0.978). Cluster analysis and population modeling using minimum spanning tree suggested a possible epidemiological linkage among aquatic and fecal isolates. The study also reported the presence of highly diverse and pathogenic serotypes belonging to STEC and EPEC strains, particularly O157 and high prevalence of pathogenic phylogroups (phylogroup, B2 and D). The presence of such a high molecular heterogeneity among aquatic and fecal E. coli isolates emphasizes upon the need to develop proper fecal pollution abatement strategies for Indian natural bodies.


E. coli Serotype Phylogroup VNTR MLVA Clonal relationship 



The present study was carried out with the financial support provided by UGC-RGNF [F1-17.1/2016-17/RGNF-2015-17-SC-HAR-18413/(SA-III/Website)] and UGC major research project (Grant No. UGC-41-1172/2012). NK and MK thank Maharshi Dayanand University for providing University Research Scholarship. MK expresses sincere gratitude to CSIR for Senior Research Fellowship (No. 09/382(0212)/19-EMR-I). The authors also wish to acknowledge FIST Grant funded by Department of Science and Technology (No. 1196 SR/FST/LS-I/2017/4) for improvement of infrastructural facilities. The authors are also grateful to National Salmonella and Escherichia Centre, Central Research Institute, Kasauli, Himachal Pradesh, India for serotyping E. coli isolates.

Author contribution

P.G. conceived and planned the experiments. N.K. carried out the experiments. P.G., N.K. and M.K. contributed to the interpretation of the results. All the authors provided critical feedback and helped shape the research, analysis and manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.


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Copyright information

© King Abdulaziz City for Science and Technology 2020

Authors and Affiliations

  1. 1.Medical Microbiology and Bioprocess Technology Laboratory, Department of MicrobiologyMaharshi Dayanand UniversityRohtakIndia

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