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Uropathogenic Escherichia coli in India—an Overview on Recent Research Advancements and Trends


Urinary tract infection (UTI), a prevalent disease in India, also ranks among the most common infections in developing countries. The rapid emergence of antibiotic-resistant uropathogenic Escherichia coli (UPECs), the leading etiologic agent of UTI, in the last few years, led to an upsurge in the health care cost. This caused a considerable economic burden, especially in low-middle income country, India. This review aimed to provide an explicit overview of the recent advancements in E. coli–mediated UTI in India by incorporation of valuable information from the works published in PubMed and Google Scholar in the last six years (2015 to August, 2020). The literature survey demonstrated UPECs as the most predominant uropathogen in India, especially among females, causing both asymptomatic bacteriuria (ABU) and symptomatic UTI. An overall increasing national trend in resistance to penicillins, cephalosporins, aminoglycosides, fluoroquinolones, and sulfonamides was perceived irrespective of ABU and symptomatic UPECs during the aforementioned study period. High incidences of multidrug resistance, extended-spectrum β-lactamases, metallo β-lactamases, and AmpCs in UPECs were reported. Notable information on the pathogenic profiles, phylogroups, pathogenicity islands, and evidence of pathoadaptive FimH mutations was described. Alternative therapeutics and potential drug targets against UPECs were also reconnoitered. Therefore, the nationwide widespread occurrences of highly virulent MDR UPEC together with the limited availability of therapeutics highlighted the urgent need for promotion and invention of alternative therapeutics, search for which had already been started. Moreover, investigation of several mechanisms of UPEC infection and the search for potential drug targets might help to design newer therapeutics.

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  1. Karigoudar, R. M., Karigoudar, M. H., Wavare, S. M., & Mangalgi, S. S. (2019). Detection of biofilm among uropathogenic Escherichia coli and its correlation with antibiotic resistance pattern. Journal of Laboratory Physicians, 11 [01], 017-022.

  2. Ghosh, A., & Mukherjee, M. (2019). Incidence of multidrug resistance, pathogenicity island markers, and pathoadaptive FimH mutations in uropathogenic Escherichia coli isolated from asymptomatic hospitalized patients. Folia Microbiologica, 64(4), 587-600

  3. Paralikar, P., Ingle, A.P., Tiwari, V., Golinska, P., Dahm, H., & Rai, M. (2019). Evaluation of antibacterial efficacy of sulfur nanoparticles alone and in combination with antibiotics against multidrug-resistant uropathogenic bacteria. Journal of Environmental Science and Health, Part A, 54[5], 381-390.

  4. Gopichand, P., Agarwal, G., Natarajan, M., Mandal, J., Deepanjali, S., Parameswaran, S., & Dorairajan, L.N. (2019). In vitro effect of fosfomycin on multi-drug resistant gram-negative bacteria causing urinary tract infections. Infection and Drug Resistance, Volume 12, 2005-2013.

  5. Malik, S., Sidhu, P.K., Rana, J.S., & Nehra, K. (2019). Managing urinary tract infections through phage therapy: a novel approach. Folia Microbiologica, 65[2], 217-231.

  6. Prasada, S., Bhat, A., Bhat, S., Shenoy Mulki, S., & Tulasidas, S. (2019). Changing antibiotic susceptibility pattern in uropathogenic Escherichia coli over a period of 5 years in a tertiary care center. Infection and Drug Resistance, Volume 12, 1439-1443.

  7. Pullanhi, U., Khan, S., Vinod, V., Mohan, K., & Kumar, A. (2019). Outcome of acute urinary tract infections caused by uropathogenic Escherichia coli with phenotypically demonstrable virulence factors. Annals of African Medicine, 18[3], 138. .

  8. Kaza, P., Mahindroo, J., Veeraraghavan, B., Mavuduru, R. S., Mohan, B., & Taneja, N. (2019). Evaluation of risk factors for colistin resistance among uropathogenic isolates of Escherichia coli and Klebsiella pneumoniae: a case–control study. Journal of Medical Microbiology, 68[6], 837-847

  9. Mukherjee, S. K., & Mukherjee, M. (2019). Characterization and bio-typing of multidrug resistance plasmids from uropathogenic Escherichia coli isolated from clinical setting. Frontiers in Microbiology, 10.

  10. Bala Subramaniyan, S., Senthilnathan, R., Arunachalam, J., & Anbazhagan, V. (2019). Revealing the significance of the glycan binding property of Butea monosperma seed lectin for enhancing the antibiofilm activity of silver nanoparticles against uropathogenic Escherichia coli. Bioconjugate Chemistry, 31[1], 139-148.

  11. Rubini, D., Varthan, P. V., Jayasankari, S., Vedahari, B. N., & Nithyanand, P. (2020). Suppressing the phenotypic virulence factors of uropathogenic Escherichia coli using marine polysaccharide. Microbial Pathogenesis, 141, 103973

  12. Verma, V., Kumar, P., Gupta, S., Yadav, S., Dhanda, R.S., Thorlacius, H., & Yadav, M. (2020). α-Hemolysin of uropathogenic E. coli regulates NLRP3 inflammasome activation and mitochondrial dysfunction in THP-1 macrophages. Scientific Reports, 10[1]. doi:10.1038/s41598-020-69501-1

  13. Ghosh, B., & Mukherjee, M. (2016). Emergence of co-production of plasmid-mediated AmpC beta-lactamase and ESBL in cefoxitin-resistant uropathogenic Escherichia coli. European Journal of Clinical Microbiology & Infectious Diseases, 35(9), 1449-1454.

  14. Basu, S., & Mukherjee, M. (2019). Conjugal transfer of PMQR from uropathogenic E.coli under high ciprofloxacin selection pressure generates gyrA mutation. Microbial Pathogenesis, 132, 26-29.

  15. Gnanasekaran, A., Manikandan, P., Poongothai, P., Senthilkumar, P.K. (2019). In vitro screening of multidrug resistance uropathogenic Escherichia coli from the urban area of Namakkal district. Journal of Applied Pharmaceutical Science, 9(9), 84–91.

  16. Muraleetharan, M., Viswanathan, T., (2019). Genotyping and molecular characterization of extended-spectrum beta-lactamases-producing uropathogenic Escherichia coli in and around Coimbatore district, Tamil Nadu, India. Urological Science ; 30: 244

  17. Kammili, N., Rani, M., Styczynski, A., Latha, M., Pavuluri, P. R., Reddy, V., & Alsan, M. (2020). Plasmid-mediated antibiotic resistance among uropathogens in primigravid women—Hyderabad, India. Plos One, 15(5). doi:10.1371/journal.pone.0232710

  18. Siddaramappa, S., Pullela, K., Thimmappa, B., Devkota, R., Bajaj, R., Manivannan, B., . . . Pradeep, B. E. (2018). Characterization of blaCTX-M sequences of Indian origin and thirteen uropathogenic Escherichia coli isolates resistant to multiple antibiotics. BMC Research Notes, 11(1).

  19. Mehrishi, P., Faujdar, S.S., Kumar, S., Solanki, S., Sharma, A. (2019) Antibiotic susceptibility profile of uropathogens in rural population of Himachal Pradesh, India: where we are heading? Biomedical & Biotechnology Research Journal, 3:171-5

  20. Mittal, S., Sharma, M., & Chaudhary, U. (2015 a). Biofilm and multidrug resistance in uropathogenic Escherichia coli. Pathogens and Global Health, 109(1), 26-29.

  21. Miryala, S., Makala, H., Yadavali, S. P., Venkatasubramanian, U., Subbaiah, N., & Srinandan, C. (2020). Disperse red 15 (DR15) impedes biofilm formation of uropathogenic Escherichia coli. Microbial Pathogenesis, 138, 103772.

  22. Mittal, S., Sharma, M., & Chaudhary, U. (2015b). Fosfomycin use in multi drug resistant uropathogenic Escherichia coli. Infectious Disorders - Drug Targets, 15(3), 196-201.

  23. Singh, S. K., Seema, K., & Gupta, M. (2016). Detection of Amp C β-lactamase and adherence factors in uropathogenic Escherichia coli isolated from aged patients. Microbial Pathogenesis, 100, 293-298

  24. Vasudevan, S., Selvan, G. T., Bhaskaran, S., Hari, N., & Solomon, A. P. (2020). Reciprocal cooperation of type A procyanidin and nitrofurantoin against multi-drug resistant (MDR) UPEC: a pH-dependent study. Frontiers in Cellular and Infection Microbiology, 10.

  25. Mukherjee, M., Koley, S., Mukherjee, S. K., Basu, S., Ghosh, B., & Chakraborty, S. (2015). Phylogenetic background of E. coli isolated from asymptomatic pregnant women from Kolkata, India. The Journal of Infection in Developing Countries, 9(07), 720-724.

  26. Biswas, B., Bhushan, S., Rajesh, A., Suraj, S. K., Lu, Y., Meinhardt, A., & Yenugu, S. (2015). Uropathogenic Escherichia coli (UPEC) induced antimicrobial gene expression in the male reproductive tract of rat: evaluation of the potential of Defensin 21 to limit infection. Andrology, 3(2), 368-375.

  27. Manohar, P., Tamhankar, A. J., Lundborg, C. S., & Nachimuthu, R. (2019). Therapeutic characterization and efficacy of bacteriophage cocktails infecting Escherichia coli, Klebsiella pneumoniae, and Enterobacter species. Frontiers in Microbiology, 10.

  28. Shruti, S. R., & Rajasekaran, R. (2020). Identification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using in silico techniques. Journal of Biomolecular Structure and Dynamics, 38(15), 4407-4417

  29. Parra, G.I., Squires, R. B., Karangwa, C.K., Johnson, J.A., Lepore, C J , Sosnovtsev, S.V., & Green, K.Y. (2017). Static and evolving norovirus genotypes: implications for epidemiology and immunity. PLOS Pathog.2017 Jan 19; 13(1):e1006136.

  30. Yadav, S. (2018). Correlation analysis in biological studies. J Pract Cardiovasc Sci, 4:116-21.

  31. Akoglu, H.(2018). User’s guide to correlation coefficients. Turk J Emerg Med, 7; 18(3):91-93.

  32. Bhattacharyya, S., Sarfraz, A., Ansari, M.A.A., Jaiswal, N., (2015). Characterization and antibiogram of Uropathogenic Escherichia coli from a tertiary care hospital in Eastern India. Int J Curr Microbiol App Sci., 4(2): 701-705

  33. Wabale, V.R., Bharadwaj, R.S., Joshi, A.A., Chowdhary, A.S. (2015). Serotypes, Hemolysin production and drug resistance among uropathogenic Escherichia coli at a tertiary care hospital in Mumbai. International Journal of Current Research 7(07), 18596-18600

  34. Yadav, M., Khumanthem, S.V., Kshtrimayum, M.D. (2017). Antibiotic resistance trends of Uropathogenic Escherichia coli isolated from inpatients in a tertiary care hospital in north East India. International Journal of Recent Scientific Research. 8(7), 18496-18500

  35. Sukumaran,T.S., Mohan A.K. (2017). Antimicrobial resistance among uropathogenic bacteria in Rural Kerala, India. Int.J.Curr.Microbiol.App.Sci, 6(9): 2287-2296

  36. Mishra, M. P., Sarangi, R., & Padhy, R. N. (2016). Prevalence of multidrug resistant uropathogenic bacteria in pediatric patients of a tertiary care hospital in eastern India. Journal of Infection and Public Health, 9(3), 308-314.

  37. Tadepalli, S., Prudhivi, S., Myneni, R.B., Rao, S. (2016). Biofilm formation in uropathogenic Escherichia coli isolates and its association with extended betalactamase production and drug resistance. Saudi Journal of Pathology and Microbiology, 1(Iss-2), 60-64.

  38. Bandyopadhyay, D., & Mukherjee, M., (2020). Reactive oxygen species and uspA overexpession: an alternative bacterial response toward selection and maintenance of multidrug resistance in clinical isolates of uropathogenic E. coli. European Journal of Clinical Microbiology & Infectious Diseases, 39(9), 1753-1760

  39. Vysakh, A., Midhun, S. J., Jayesh, K., Jyothis, M., & Latha, M. (2018). Studies on biofilm formation and virulence factors associated with uropathogenic Escherichia coli isolated from patient with acute pyelonephritis. Pathophysiology, 25(4), 381-387.

  40. Bandyopadhyay D, Mukherjee M. (2017). Distribution of class D-oxacillinases amongst third generation cephalosporin resistant nosocomial uropathogenic Escherichia coli isolates, their phylogenetic background and clonal analysis International Journal of Current Research. 9(10) 59099-59106

  41. Singh, B. R. (2019). Quinolones and fluoroquinolones are useless to counter uropathogenic Escherichia coli infections (Letter). Infection and Drug Resistance, Volume 12, 2161-2162.

  42. Basu, S., & Mukherjee, M. (2018). Incidence and risk of co-transmission of plasmid-mediated quinolone resistance and extended-spectrum β-lactamase genes in fluoroquinolone-resistant uropathogenic Escherichia coli: a first study from Kolkata, India. Journal of Global Antimicrobial Resistance, 14, 217-223.

  43. Das, B., Mittal, N., Goswami, R., Adhana, D., & Rathore, N. (2018). Prevalence of multidrug resistance (MDR) and extended spectrum beta-lactamases (ESBLs) among uropathogenic Escherichia coli isolates from female patients in a tertiary care hospital in North India. International Journal of Reproduction, Contraception, Obstetrics and Gynecology, 7(12), 5031

  44. Patwardhan, V., Kumar, D., Goel, V., & Singh, S. (2017). Changing prevalence and antibiotic drug resistance pattern of pathogens seen in community-acquired pediatric urinary tract infections at a tertiary care hospital of North India. Journal of Laboratory Physicians, 9(04), 264-268.

  45. Thattil, S.J., & Santhosh, S. (2018). Prevalence of UTI in different age groups in a tertiary care hospital and their Antibiogram. International Journal of Contemporary Medical Research, 5(1), 2454-7379.

  46. Jena, J., Sahoo, R. K., Debata, N. K., & Subudhi, E. (2017). Prevalence of TEM, SHV, and CTX-M genes of extended-spectrum β-lactamase-producing Escherichia coli strains isolated from urinary tract infections in adults. 3 Biotech, 7(4).

  47. Narayan, A., Gopi, S., Fushman, D., & Naganathan, A. N. (2019). A binding cooperativity switch driven by synergistic structural swelling of an osmo-regulatory protein pair. Nature Communications, 10(1).

  48. Verma, V., Gupta, S., Kumar, P., Yadav, S., Dhanda, R.S., Gaind, R., Arora, R., Frimodt-Møller, N., & Yadav, M. (2019b). Involvement of NLRP3 and NLRC4 inflammasome in uropathogenic E. coli mediated urinary tract infections. Frontiers in Microbiology, 10. .

  49. Verma, V., Gupta, S., Kumar, P., Rawat, A., Singh Dhanda, R., & Yadav, M. (2019a). Efficient production of endotoxin depleted bioactive α-hemolysin of uropathogenic Escherichia coli. Preparative Biochemistry and Biotechnology, 49[6], 616-622.

  50. Pandey, N. K., Verma, G., Kushwaha, G. S., Suar, M., & Bhavesh, N. S. (2020). Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state. FEBS Letters, 594(18), 3057-3066.

  51. Zuberi, A., Ahmad, N., & Khan, A. U. (2017). CRISPRi induced suppression of fimbriae gene (fimH) of a uropathogenic Escherichia coli: an approach to inhibit microbial biofilms. Frontiers in Immunology, 8. doi:10.3389/fimmu.2017.01552

  52. Mukherjee, S., Mandal, R., Das, S., & Mukherjee, M. (2018). Effect of non-β-lactams on stable variants of inhibitor-resistant TEM β-lactamase in uropathogenic Escherichia coli: implication for alternative therapy. Journal of Applied Microbiology, 124(3), 667-681.

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The authors would like to express their sincere gratitude to Prof (Dr.) Pratip Kumar Kundu, Director, Calcutta School of Tropical Medicine, Kolkata West Bengal, India, for his kind support and cooperation.

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The study was supported by grants received from the Science and Engineering Research Board (SERB), Department of Science and Technology, Government of India, (Grant No. EMR/2016/001670 dated 22.08.17); Department of Higher Education, Science and Technology and Biotechnology, Government of West Bengal, India (Grant No. 62 (Sanc.)/BT/P/Budget/RD-60/2017 dated 12.03.2018); and the INSPIRE fellowship grant from Department of Science and Technology, New Delhi, Government of India, No.-DST/INSPIRE Fellowship/2016/ IF160069 (2016-2019).

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A. Ghosh, D. Bandyopadhyay, and S. Koley contributed equally in the data collection, compilation, and writing of this manuscript. M. Mukherjee participated in the preparation and correction of the manuscript.

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Correspondence to Mandira Mukherjee.

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Ghosh, A., Bandyopadhyay, D., Koley, S. et al. Uropathogenic Escherichia coli in India—an Overview on Recent Research Advancements and Trends. Appl Biochem Biotechnol 193, 2267–2296 (2021).

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