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Volume 11, Issue 7

Genomic features of three major diarrhoeagenic pathotypes in India Open Access

Abstract

Diarrhoea remains a major threat to children in developing nations, with diarrhoeagenic (DEC) being the primary causative agent. Characterizing prevalent DEC strains is crucial, yet comprehensive genomic analyses of major DEC strains, including enteropathogenic (EPEC), enteroaggregative (EAEC) and enterotoxigenic (ETEC), are lacking in India.

We sequenced 24 EAEC and 23 EPEC strains from Indian patients with diarrhoea and conducted an extensive database search for DEC human isolates from India. Detailed phylogenetic analyses, virulence gene subtyping and examinations of accessory virulence and antimicrobial resistance (AMR) genes were performed.

The analysed DEC strains included 32 EAEC, 25 EPEC, 32 ETEC and 1 each of the EPEC/ETEC-hybrid and ETEC/EAEC-hybrid pathotypes. These strains were predominantly classified into phylogroups A (35.2%) and B1 (41.8%) and dispersed within these phylogroups without pathotype-specific clustering. One ETEC strain was classified into cryptic clade 1. Subtypes of hallmark virulence genes varied substantially amongst strains in each pathotype, and 31 accessory virulence genes were detected either specifically within certain pathotypes or across multiple pathotypes at varying frequencies, indicating diversification of the virulence gene repertoire within each pathotype. Acquired AMR genes were found in 73.6% of the strains, with frequent identification of AMR genes for aminoglycosides (40.0%), -lactams (64.8%), sulphonamides (49.5%) and trimethoprim (42.9%). Known quinolone-resistant mutations were found in 74.7% of the strains, whereas AMR genes for macrolide (30.8%), phenicol (11.0%) and tetracycline (27.4%) were less frequent.

The diverse virulence potential and trends in AMR gene prevalence amongst major DEC strains in India are highlighted in this study. Continuous monitoring of DEC strain characteristics is essential for the effective control and treatment of DEC infections in India.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , diarrhoeagenic Escherichia coli , genome , India and virulence gene
Funding
This study was supported by the:
  • Japan Agency for Medical Research and Development (Award JP24wm0225021)
    • Principal Award Recipient: YoshitoshiOgura
  • Japan Agency for Medical Research and Development (Award JP24wm0125004)
    • Principal Award Recipient: Shin-ichiMiyoshi
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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References

  1. Collaborators GBDDD. Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: a systematic analysis for the global burden of disease study 2016. Lancet Infect Dis 2018; 18:1211–1228
     [Google Scholar]
  2. Black RE, Perin J, Yeung D, Rajeev T, Miller J et al. Estimated global and regional causes of deaths from diarrhoea in children younger than 5 years during 2000-21: a systematic review and bayesian multinomial analysis. Lancet Glob Health 2024; 12:e919–e928 [View Article] [PubMed]
     [Google Scholar]
  3. Dutta S, Guin S, Ghosh S, Pazhani GP, Rajendran K et al. Trends in the prevalence of diarrheagenic Escherichia coli among hospitalized diarrheal patients in Kolkata, India. PLoS One 2013; 8:e56068 [View Article] [PubMed]
     [Google Scholar]
  4. Nataro JP, Kaper JB. Diarrheagenic Escherichia coli. Clin Microbiol Rev 1998; 11:142–201 [View Article] [PubMed]
     [Google Scholar]
  5. Ghosh D, Chowdhury G, Samanta P, Shaw S, Deb AK et al. Characterization of diarrhoeagenic Escherichia coli with special reference to antimicrobial resistance isolated from hospitalized diarrhoeal patients in Kolkata (2012-2019), India. J Appl Microbiol 2022; 132:4544–4554 [View Article] [PubMed]
     [Google Scholar]
  6. Khan A, Yamasaki S, Sato T, Ramamurthy T, Pal A et al. Prevalence and genetic profiling of virulence determinants of non-O157 shiga toxin-producing Escherichia coli isolated from cattle, beef, and humans, Calcutta, India. Emerg Infect Dis 2002; 8:54–62 [View Article] [PubMed]
     [Google Scholar]
  7. Gomes TAT, Elias WP, Scaletsky ICA, Guth BEC, Rodrigues JF et al. Diarrheagenic Escherichia coli. Braz J Microbiol 2016; 47 Suppl 1:3–30 [View Article] [PubMed]
     [Google Scholar]
  8. Tobe T, Beatson SA, Taniguchi H, Abe H, Bailey CM et al. An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Proc Natl Acad Sci USA 2006; 103:14941–14946 [View Article] [PubMed]
     [Google Scholar]
  9. Sanchez-Garrido J, Ruano-Gallego D, Choudhary JS, Frankel G. The type III secretion system effector network hypothesis. Trends Microbiol 2022; 30:524–533 [View Article] [PubMed]
     [Google Scholar]
  10. Sarantuya J, Nishi J, Wakimoto N, Erdene S, Nataro JP et al. Typical enteroaggregative Escherichia Coli is the most prevalent pathotype among E. coli strains causing diarrhea in mongolian children. J Clin Microbiol 2004; 42:133–139 [View Article] [PubMed]
     [Google Scholar]
  11. Boisen N, Scheutz F, Rasko DA, Redman JC, Persson S et al. Genomic characterization of enteroaggregative Escherichia coli from children in Mali. J Infect Dis 2012; 205:431–444 [View Article] [PubMed]
     [Google Scholar]
  12. Panchalingam S, Antonio M, Hossain A, Mandomando I, Ochieng B et al. Diagnostic microbiologic methods in the GEMS-1 case/control study. Clin Infect Dis 2012; 55 Suppl 4:S294–302 [View Article] [PubMed]
     [Google Scholar]
  13. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–8 [View Article] [PubMed]
     [Google Scholar]
  14. Croxen MA, Finlay BB. Molecular mechanisms of Escherichia coli pathogenicity. Nat Rev Microbiol 2010; 8:26–38 [View Article] [PubMed]
     [Google Scholar]
  15. Kaper JB, Nataro JP, Mobley HL. Pathogenic Escherichia coli. Nat Rev Microbiol 2004; 2:123–140 [View Article] [PubMed]
     [Google Scholar]
  16. Pakbin B, Brück WM, Rossen JWA. Virulence Factors of Enteric Pathogenic Escherichia coli: a Review. Int J Mol Sci 2021; 22:9922 [View Article] [PubMed]
     [Google Scholar]
  17. López-Vélez R, Lebens M, Bundy L, Barriga J, Steffen R. Bacterial travellers’ diarrhoea: a narrative review of literature published over the past 10 years. Travel Med Infect Dis 2022; 47:102293 [View Article]
     [Google Scholar]
  18. Barr W, Smith A. Acute diarrhea. Am Fam Physician 2014; 89:180–189 [PubMed]
     [Google Scholar]
  19. Riddle MS, DuPont HL, Connor BA. ACG clinical guideline: diagnosis, treatment, and prevention of acute diarrheal infections in adults. Am J Gastroenterol 2016; 111:602–622 [View Article] [PubMed]
     [Google Scholar]
  20. Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2020; 27:dsaa014 [View Article] [PubMed]
     [Google Scholar]
  21. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
     [Google Scholar]
  22. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  23. Zhou Z, Alikhan NF, Mohamed K, Fan Y, Agama Study G et al. The enterobase user’s guide, with case studies on Salmonella transmissions, yersinia pestis phylogeny, and escherichia core genomic diversity. Genome Res 2020; 30:138–152
     [Google Scholar]
  24. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article] [PubMed]
     [Google Scholar]
  25. Okuno M, Arimizu Y, Miyahara S, Wakabayashi Y, Gotoh Y et al. Escherichia cryptic clade I is an emerging source of human intestinal pathogens. BMC Biol 2023; 21:81 [View Article] [PubMed]
     [Google Scholar]
  26. Arimizu Y, Kirino Y, Sato MP, Uno K, Sato T et al. Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains. Genome Res 2019; 29:1495–1505 [View Article] [PubMed]
     [Google Scholar]
  27. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014; 58:212–220 [View Article] [PubMed]
     [Google Scholar]
  28. Carattoli A, Hasman H. PlasmidFinder and in silico pMLST: identification and typing of plasmid replicons in whole-genome sequencing (WGS). Methods Mol Biol 2020; 2075:285–294 [View Article] [PubMed]
     [Google Scholar]
  29. Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J et al. AMRFinderPlus and the reference gene catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021; 11:12728 [View Article] [PubMed]
     [Google Scholar]
  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  31. Page AJ, Taylor B, Delaney AJ, Soares J, Seemann T et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom 2016; 2:e000056 [View Article] [PubMed]
     [Google Scholar]
  32. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019; 35:4453–4455 [View Article] [PubMed]
     [Google Scholar]
  33. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
     [Google Scholar]
  34. Csárdi GN. The igraph software package for complex network research. Int J Complex Syst 2006; 1695:1–9
     [Google Scholar]
  35. Zhang WL, Köhler B, Oswald E, Beutin L, Karch H et al. Genetic diversity of intimin genes of attaching and effacing Escherichia coli strains. J Clin Microbiol 2002; 40:4486–4492 [View Article] [PubMed]
     [Google Scholar]
  36. Boisen N, Østerlund MT, Joensen KG, Santiago AE, Mandomando I et al. Redefining enteroaggregative Escherichia coli (EAEC): genomic characterization of epidemiological EAEC strains. PLoS Negl Trop Dis 2020; 14:e0008613 [View Article]
     [Google Scholar]
  37. Hazen TH, Donnenberg MS, Panchalingam S, Antonio M, Hossain A et al. Genomic diversity of EPEC associated with clinical presentations of differing severity. Nat Microbiol 2016; 1:15014 [View Article] [PubMed]
     [Google Scholar]
  38. Hernandes RT, Hazen TH, Dos Santos LF, Richter TKS, Michalski JM et al. Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil. PLoS Negl Trop Dis 2020; 14:e0008373 [View Article] [PubMed]
     [Google Scholar]
  39. Rasko DA, Del Canto F, Luo Q, Fleckenstein JM, Vidal R et al. Comparative genomic analysis and molecular examination of the diversity of enterotoxigenic Escherichia coli isolates from Chile. PLoS Negl Trop Dis 2019; 13:e0007828 [View Article]
     [Google Scholar]
  40. von Mentzer A, Connor TR, Wieler LH, Semmler T, Iguchi A et al. Identification of enterotoxigenic Escherichia coli (ETEC) clades with long-term global distribution. Nat Genet 2014; 46:1321–1326 [View Article]
     [Google Scholar]
  41. Iguchi A, Takemura T, Ogura Y, Nguyen TTH, Kikuchi T et al. Genomic characterization of endemic diarrheagenic Escherichia coli and Escherichia albertii from infants with diarrhea in Vietnam. PLoS Negl Trop Dis 2023; 17:e0011259 [View Article] [PubMed]
     [Google Scholar]
  42. Khairy RMM, Fathy ZA, Mahrous DM, Mohamed ES, Abdelrahim SS. Prevalence, phylogeny, and antimicrobial resistance of Escherichia coli pathotypes isolated from children less than 5 years old with community acquired- diarrhea in Upper Egypt. BMC Infect Dis 2020; 20:908 [View Article] [PubMed]
     [Google Scholar]
  43. Modgil V, Mahindroo J, Narayan C, Kalia M, Yousuf M et al. Comparative analysis of virulence determinants, phylogroups, and antibiotic susceptibility patterns of typical versus atypical enteroaggregative E. coli in India. PLoS Negl Trop Dis 2020; 14:e0008769 [View Article] [PubMed]
     [Google Scholar]
  44. Denamur E, Clermont O, Bonacorsi S, Gordon D. The population genetics of pathogenic Escherichia coli. Nat Rev Microbiol 2021; 19:37–54 [View Article] [PubMed]
     [Google Scholar]
  45. Escobar-Páramo P, Clermont O, Blanc-Potard A-B, Bui H, Le Bouguénec C et al. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Mol Biol Evol 2004; 21:1085–1094 [View Article] [PubMed]
     [Google Scholar]
  46. Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M et al. Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 2009; 106:17939–17944 [View Article] [PubMed]
     [Google Scholar]
  47. Reid SD, Herbelin CJ, Bumbaugh AC, Selander RK, Whittam TS. Parallel evolution of virulence in pathogenic Escherichia coli. Nature 2000; 406:64–67 [View Article] [PubMed]
     [Google Scholar]
  48. Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5:e1000344 [View Article] [PubMed]
     [Google Scholar]
  49. Okeke IN, Wallace-Gadsden F, Simons HR, Matthews N, Labar AS et al. Multi-locus sequence typing of enteroaggregative Escherichia coli isolates from nigerian children uncovers multiple lineages. PLoS One 2010; 5:e14093 [View Article] [PubMed]
     [Google Scholar]
  50. Llorente MT, Escudero R, Ramiro R, Remacha MA, Martínez-Ruiz R et al. Enteroaggregative Escherichia coli as etiological agent of endemic diarrhea in Spain: a prospective multicenter prevalence study with molecular characterization of isolates. Front Microbiol 2023; 14:1120285 [View Article] [PubMed]
     [Google Scholar]
  51. Shabana II, Zaraket H, Suzuki H. Molecular studies on diarrhea-associated Escherichia coli isolated from humans and animals in Egypt. Vet Microbiol 2013; 167:532–539 [View Article] [PubMed]
     [Google Scholar]
  52. Irenge LM, Ambroise J, Bearzatto B, Durant J-F, Chirimwami RB et al. Whole-genome sequences of multidrug-resistant Escherichia coli in South-Kivu Province, democratic republic of congo: characterization of phylogenomic changes, virulence and resistance genes. BMC Infect Dis 2019; 19:137 [View Article] [PubMed]
     [Google Scholar]
  53. Vidal RM, Muhsen K, Tennant SM, Svennerholm A-M, Sow SO et al. Colonization factors among enterotoxigenic Escherichia coli isolates from children with moderate-to-severe diarrhea and from matched controls in the global enteric multicenter study (GEMS). PLoS Negl Trop Dis 2019; 13:e0007037 [View Article] [PubMed]
     [Google Scholar]
  54. Nishi J, Sheikh J, Mizuguchi K, Luisi B, Burland V et al. The export of coat protein from enteroaggregative Escherichia coli by a specific ATP-binding cassette transporter system. J Biol Chem 2003; 278:45680–45689 [View Article] [PubMed]
     [Google Scholar]
  55. Santiago AE, Ruiz-Perez F, Jo NY, Vijayakumar V, Gong MQ et al. A large family of antivirulence regulators modulates the effects of transcriptional activators in gram-negative pathogenic bacteria. PLoS Pathog 2014; 10:e1004153 [View Article] [PubMed]
     [Google Scholar]
  56. Sheikh J, Czeczulin JR, Harrington S, Hicks S, Henderson IR et al. A novel dispersin protein in enteroaggregative Escherichia coli. J Clin Invest 2002; 110:1329–1337 [View Article] [PubMed]
     [Google Scholar]
  57. Blanco M, Schumacher S, Tasara T, Zweifel C, Blanco JE et al. Serotypes, intimin variants and other virulence factors of eae positive Escherichia coli strains isolated from healthy cattle in Switzerland. Identification of a new intimin variant gene (eae-η2). BMC Microbiol 2005; 5:23 [View Article]
     [Google Scholar]
  58. Michel PA, Kase JA. Genetic profiles of Shiga toxin and intimin genes found in stool broth cultures: a 2-year reference laboratory study. Diagn Microbiol Infect Dis 2009; 65:85–92 [View Article] [PubMed]
     [Google Scholar]
  59. Xu Y, Bai X, Zhao A, Zhang W, Ba P et al. Genetic diversity of intimin gene of atypical enteropathogenic Escherichia coli isolated from human, animals and raw meats in China. PLoS One 2016; 11:e0152571 [View Article]
     [Google Scholar]
  60. Bielaszewska M, Mellmann A, Bletz S, Zhang W, Köck R et al. Enterohemorrhagic Escherichia coli O26:H11/H-: a new virulent clone emerges in Europe. Clin Infect Dis 2013; 56:1373–1381 [View Article] [PubMed]
     [Google Scholar]
  61. Bielaszewska M, Mellmann A, Zhang W, Köck R, Fruth A et al. Characterisation of the Escherichia coli strain associated with an outbreak of haemolytic uraemic syndrome in Germany, 2011: a microbiological study. Lancet Infect Dis 2011; 11:671–676 [View Article] [PubMed]
     [Google Scholar]
  62. Ingle DJ, Levine MM, Kotloff KL, Holt KE, Robins-Browne RM. Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nat Microbiol 2018; 3:1063–1073 [View Article] [PubMed]
     [Google Scholar]
  63. Chen K, Yang C, Dong N, Xie M, Ye L et al. Evolution of ciprofloxacin resistance-encoding genetic elements in Salmonella. mSystems 2020; 5: [View Article]
     [Google Scholar]
  64. Hong Y-P, Wang Y-W, Huang I-H, Liao Y-C, Kuo H-C et al. Genetic relationships among multidrug-resistant Salmonella enterica serovar Typhimurium strains from humans and animals. Antimicrob Agents Chemother 2018; 62: [View Article]
     [Google Scholar]
  65. Li Z, Jia C, Hu Z, Jin Y, Li T et al. Antimicrobial resistance and genomic characteristics of Escherichia coli strains isolated from the poultry industry in Henan Province, China. Microorganisms 2024; 12:575 [View Article]
     [Google Scholar]
  66. Zhou W, Lin R, Zhou Z, Ma J, Lin H et al. Antimicrobial resistance and genomic characterization of Escherichia coli from pigs and chickens in Zhejiang, China. Front Microbiol 2022; 13:1018682 [View Article] [PubMed]
     [Google Scholar]
  67. Lee KY, Schlesener CL, Aly SS, Huang BC, Li X et al. Whole genome sequence analysis reveals high genomic diversity and potential host-driven adaptations among multidrug-resistant Escherichia coli from pre-weaned dairy calves. Front Microbiol 2024; 15:1420300 [View Article] [PubMed]
     [Google Scholar]
  68. Prasad AK, Lyngdoh WV, Devi TS, Durairaj E. Presence of resistant DEC strains in a tertiary healthcare center in North East India in children under 18 Years. J Lab Physicians 2022; 14:278–283 [View Article] [PubMed]
     [Google Scholar]
  69. Salleh MZ, Nik Zuraina NMN, Hajissa K, Ilias MI, Deris ZZ. Prevalence of multidrug-resistant diarrheagenic Escherichia coli in Asia: a systematic review and meta-analysis. Antibiotics 2022; 11:1333 [View Article] [PubMed]
     [Google Scholar]
  70. Hooper DC, Jacoby GA. Mechanisms of drug resistance: quinolone resistance. Ann N Y Acad Sci 2015; 1354:12–31 [View Article] [PubMed]
     [Google Scholar]
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Genomic features of three major diarrhoeagenic Escherichia coli pathotypes in India
M Gen 11, 001430 (2025); https://doi.org/10.1099/mgen.0.001430
/content/journal/mgen/10.1099/mgen.0.001430
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