Skip to main content
SpringerLink
Log in

Antibiotic resistance profiling and phylotyping of human-diarrheagenic Escherichia coli pathotypes detected from diarrheic and non-diarrheic calves in Iran

  • Original Article
  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Background

Escherichia coli (E. coli) serves as a common indicator of gut microbiota and is utilized for monitoring antimicrobial resistance determinants in food-producing animals. This study aimed to investigate antimicrobial resistance patterns in virulence gene-positive E. coli isolates obtained from 340 healthy and diarrheic calves.

Methods and results

A total of 340 fecal swab samples were obtained from diarrheic (n = 170) and healthy (n = 170) calves for 12 months from different farms in Kerman, Iran. The samples were phenotypically analyzed to detect E. coli isolates and antibiotic resistance. Also, antimicrobial resistance genes, diarrheagenic E. coli pathotypes, and phylogenetic background were screened by PCR. Fifteen percent (51/340) of E. coli isolates were positive for at least one of the examined virulence genes (VGs); the prevalence of VGs in E. coli isolates from healthy calves (36/170; 21.17%) was higher than that in diarrheic cases (15/170; 8.82%). Out of the 51 VG-positive isolates, six pathotypes including Shiga toxin-producing E. coli (STEC; 27.45%), enterotoxigenic E. coli (ETEC; 23.52%), enterohemorrhagic E. coli (EHEC; 19.6%), necrotoxigenic E. coli (NTEC; 19.6%), enteropathogenic E. coli (EPEC; 15.68%), enteroinvasive E. coli (EIEC; 1.96%) and three hybrid pathotypes including ETEC/STEC, ETEC/EHEC, and STEC/EIEC were detected among the strains. Antimicrobial resistance (AR) was observed in 98.03% of the VG-positive isolates, which was the same for both healthy and diarrheic calves. The maximum prevalence rate of AR was found against trimethoprim/sulfamethoxazole (49.01%; 3/51), while the minimum prevalence rate was against gentamycin (5.88%; 25/51). Among the VG-positives, phylotype A was found to be the most prevalent followed by B1 and D phylotypes.

Conclusions

The prevalence of VG-positive E. coli isolates was higher in healthy calves compared to diarrheic cases. AR was widespread among VG-positive isolates. These findings suggest that calves may serve as potential reservoirs of antimicrobial-resistant hybrid pathotypes of E. coli.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Data availability

All data supporting the findings of this study are available within the paper. This study lacks data related to DNA/RNA sequences/sequencing data, genetic polymorphisms, linked genotype/phenotype data, macromolecular structure, microarray data and crystallographic data for small molecules. As such, we have not data for deposition into a database or uploaded into a repository.

Abbreviations

AR:

Antimicrobial resistance

CTX:

Cefotaxime

CTC:

Cefotaxime/clavulanic acid

CAZ:

Ceftazidime

CZA:

Ceftazidime-clavulanic acid

NFX:

Enrofloxacin

EHEC:

Enterohemorrhagic E. coli

EIEC:

Enteroinvasive E. coli

EPEC:

Enteropathogenic E. coli

ETEC:

Enterotoxigenic E. coli

E. coli :

Escherichia coli

FF:

Florfenicol

GM:

Gentamycin

K:

Kanamycin

NTEC:

Necrotoxigenic E. coli

WHO:

World Health Organization

OIE:

Organization for animal health

STEC:

Shiga toxin-producing E. coli

SPT:

Spectinomycin

S:

Streptomycin

SMZ:

Sulfamethoxazole

TE:

Tetracycline

SXT:

Trimethoprim/sulfamethoxazole

VG:

Virulence gene

References

  1. Pokharel P, Dhakal S, Dozois CM (2023) The diversity of Escherichia coli pathotypes and vaccination strategies against this versatile bacterial pathogen. Microorganisms 11:344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Quinn PJ, Markey BK, Leonard FC et al (2011) Veterinary microbiology and microbial disease. Wiley, Hoboken

    Google Scholar 

  3. Kolenda R, Burdukiewicz M, Schierack P (2015) A systematic review and meta-analysis of the epidemiology of pathogenic Escherichia coli of calves and the role of calves as reservoirs for human pathogenic E. coli. Front Cell Infect Microbiol 5:23

    Article  PubMed  PubMed Central  Google Scholar 

  4. Peterson E, Kaur P (2018) Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front Microbiol 9:2928

    Article  PubMed  PubMed Central  Google Scholar 

  5. Carlos C, Hachich EM, Ottoboni LMM et al (2010) Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiol 10:161

    Article  PubMed  PubMed Central  Google Scholar 

  6. Clermont O, Christenson JK, Denamur E, Gordon DM (2013) The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 5:58–65. https://doi.org/10.1111/1758-2229.12019

    Article  CAS  PubMed  Google Scholar 

  7. Aminov RI, Mackie RI (2007) Evolution and ecology of antibiotic resistance genes. FEMS Microbiol Lett 271:147–161

    Article  CAS  PubMed  Google Scholar 

  8. Markey B, Leonard F, Archambault M et al (2013) Clinical veterinary microbiology E-Book. Elsevier, Amsterdam

    Google Scholar 

  9. Askari Badouei M, Jajarmi M, Mirsalehian A (2015) Virulence profiling and genetic relatedness of Shiga toxin-producing Escherichia coli isolated from humans and ruminants. Comp Immunol Microbiol Infect Dis 38:15–20. https://doi.org/10.1016/j.cimid.2014.11.005

    Article  PubMed  Google Scholar 

  10. Ghanbarpour R, Askari N, Ghorbanpour M et al (2017) Genotypic analysis of virulence genes and antimicrobial profile of diarrheagenic Escherichia coli isolated from diseased lambs in Iran. Trop Anim Health Prod 49:591–597

    Article  PubMed  PubMed Central  Google Scholar 

  11. Roschanski N, Fischer J, Guerra B, Roesler U (2014) Development of a multiplex real-time PCR for the rapid detection of the predominant beta-lactamase genes CTX-M, SHV, TEM and CIT-type AmpCs in Enterobacteriaceae. PLoS ONE 9:e100956

    Article  PubMed  PubMed Central  Google Scholar 

  12. Naderi Z, Ghanbarpour R, Sami M (2016) Antimicrobial resistance characteristics and phylogenetic groups of Escherichia coli isolated from diarrheic calves in southeast of Iran. Int J Enteric Pathog 4:1–7

    Article  Google Scholar 

  13. CLSI (2018) Performance standards for antimicrobial disk and dilution susceptibility tests for bacteria isolated from animals (CLSI supplement VET08), 4th edn. Clinical and Laboratory Standards Institute, Wayne

    Google Scholar 

  14. CLSI (2016) Performance Standards for Antimicrobial Susceptibility Testing (CLSI supplement M100S), 26th edn. Clinical and Laboratory Standards Institute, Wayne

    Google Scholar 

  15. Chekole WS, Adamu H, Sternberg-Lewrein S et al (2022) Occurrence of Escherichia coli pathotypes in diarrheic calves in a low-income setting. Pathogens 12:42

    Article  PubMed  PubMed Central  Google Scholar 

  16. Singh S, Singh R, Singh KP et al (2023) Molecular detection and patho-morphological study of enteric Escherichia coli pathotypes in diarrheic neonatal calves. Anim Biotechnol 34:3267–3273

    Article  CAS  PubMed  Google Scholar 

  17. Habets A, Engelen F, Duprez J-N et al (2020) Identification of Shigatoxigenic and enteropathogenic Escherichia coli serotypes in healthy young dairy calves in Belgium by recto-anal mucosal swabbing. Vet Sci 7:167

    Article  PubMed  PubMed Central  Google Scholar 

  18. Leomil L, Aidar-Ugrinovich L, Guth BEC et al (2003) Frequency of Shiga toxin-producing Escherichia coli (STEC) isolates among diarrheic and non-diarrheic calves in Brazil. Vet Microbiol 97:103–109

    Article  CAS  PubMed  Google Scholar 

  19. Coura FM, Diniz S de A, Silva MX et al (2019) Virulence factors and phylotyping of Escherichia coli isolated from non-diarrheic and diarrheic water buffalo calves. Ciência Rural. https://doi.org/10.1590/0103-8478cr20180998

    Article  Google Scholar 

  20. Ryu J-H, Kim S, Park J, Choi K-S (2020) Characterization of virulence genes in Escherichia coli strains isolated from pre-weaned calves in the Republic of Korea. Acta Vet Scand 62:1–7

    Article  Google Scholar 

  21. da Costa Custódio DA, Pereira CR, Gonçalves MS et al (2024) Antimicrobial resistance and public and animal health risks associated with pathogenic Escherichia coli isolated from calves. Comp Immunol Microbiol Infect Dis 107:102149

    Article  Google Scholar 

  22. Khawaskar DP, Sinha DK, Lalrinzuala MV et al (2022) Pathotyping and antimicrobial susceptibility testing of Escherichia coli isolates from neonatal calves. Vet Res Commun 46:353–362

    Article  PubMed  Google Scholar 

  23. Dall Agnol AM, Lorenzetti E, Leme RA et al (2021) Severe outbreak of bovine neonatal diarrhea in a dairy calf rearing unit with multifactorial etiology. Brazilian J Microbiol 52:2547–2553

    Article  CAS  Google Scholar 

  24. Umpiérrez A, Ernst D, Fernández M et al (2021) Virulence genes of Escherichia coli in diarrheic and healthy calves. Rev Argent Microbiol 53:34–38

    PubMed  Google Scholar 

  25. Srivani M, Reddy YN, Subramanyam KV, Lakshman M (2022) Association between virulence genes and serogroups of Escherichia coli isolates from calves. J Anim Res 12:439–446

    Article  Google Scholar 

  26. Borriello G, Lucibelli MG, De Carlo E et al (2012) Characterization of enterotoxigenic E. coli (ETEC), Shiga-toxin producing E. coli (STEC) and necrotoxigenic E. coli (NTEC) isolated from diarrhoeic Mediterranean water buffalo calves (Bubalus bubalis). Res Vet Sci 93:18–22

    Article  CAS  PubMed  Google Scholar 

  27. Kannaiyan K, Prabhakar K, Rajendran S et al (2010) Isolation of necrotoxigenic Escherichia coli from paediatric patients with acute diarrhoea. J Med Microbiol 59:503–504

    Article  Google Scholar 

  28. Pohl P, Oswald E, Van Muylem K et al (1993) Escherichia coli producing CNF1 and CNF2 cytotoxins in animals with different disorders. Vet Res 24:311–315

    CAS  PubMed  Google Scholar 

  29. Bako E, Kagambèga A, Traore KA et al (2017) Characterization of diarrheagenic Escherichia coli isolated in organic waste products (Cattle Fecal Matter, Manure and Slurry) from Cattle’s Markets in Ouagadougou, Burkina Faso. Int J Environ Res Public Health 14:1100

    Article  PubMed  PubMed Central  Google Scholar 

  30. Thiem VD, Sethabutr O, Von Seidlein L et al (2004) Detection of Shigella by a PCR assay targeting the ipaH gene suggests increased prevalence of shigellosis in Nha Trang. Vietnam J Clin Microbiol 42:2031–2035

    Article  CAS  Google Scholar 

  31. Bai X, Zhang J, Ambikan A et al (2019) Molecular characterization and comparative genomics of clinical hybrid Shiga toxin-producing and enterotoxigenic Escherichia coli (STEC/ETEC) strains in Sweden. Sci Rep 9:1–9

    Article  Google Scholar 

  32. de Mello Santos AC, Santos FF, Silva RM, Gomes TAT (2020) Diversity of hybrid-and hetero-pathogenic Escherichia coli and their potential implication in more severe diseases. Front Cell Infect Microbiol 10:339

    Article  Google Scholar 

  33. Askari Badouei M, Morabito S, Najafifar A, Mazandarani E (2016) Molecular characterization of enterohemorrhagic Escherichia coli hemolysin gene (EHEC-hlyA)-harboring isolates from cattle reveals a diverse origin and hybrid diarrheagenic strains. Infect Genet Evol 39:342–348. https://doi.org/10.1016/j.meegid.2016.02.002

    Article  CAS  PubMed  Google Scholar 

  34. Hazen TH, Michalski J, Luo Q et al (2017) Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic E. coli. Sci Rep 7:1–17

    Article  CAS  Google Scholar 

  35. Nyholm O, Halkilahti J, Wiklund G et al (2015) Comparative genomics and characterization of hybrid Shigatoxigenic and enterotoxigenic Escherichia coli (STEC/ETEC) strains. PLoS ONE 10:e0135936

    Article  PubMed  PubMed Central  Google Scholar 

  36. Nawaz Z, Aslam B, Zahoor MA et al (2021) Frequency of extended spectrum beta lactamase producing Escherichia coli in fresh and frozen meat. Pak Vet J 41:102–106

    Article  CAS  Google Scholar 

  37. Maciel JF, Matter LB, Tasca C et al (2019) Characterization of intestinal Escherichia coli isolated from calves with diarrhea due to rotavirus and coronavirus. J Med Microbiol 68:417–423

    Article  CAS  PubMed  Google Scholar 

  38. Shahrani M, Dehkordi FS, Momtaz H (2014) Characterization of Escherichia coli virulence genes, pathotypes and antibiotic resistance properties in diarrheic calves in Iran. Biol Res 47:28. https://doi.org/10.1186/0717-6287-47-28

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Sobhy NM, Yousef SGA, Aboubakr HA et al (2020) Virulence factors and antibiograms of Escherichia coli isolated from diarrheic calves of Egyptian cattle and water buffaloes. PLoS ONE 15:e0232890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Formenti N, Martinelli C, Vitale N et al (2021) Antimicrobial resistance of Escherichia coli in dairy calves: a 15-year retrospective analysis and comparison of treated and untreated animals. Anim an open access J from MDPI. https://doi.org/10.3390/ani11082328

    Article  Google Scholar 

  41. El-Seedy FR, Abed AH, Yanni HA, Abd El-Rahman SAA (2016) Prevalence of Salmonella and E. coli in neonatal diarrheic calves. Beni-Suef Univ J basic Appl Sci 5:45–51

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Waade J, Seibt U, Honscha W et al (2021) Multidrug-resistant enterobacteria in newborn dairy calves in Germany. PLoS ONE 16:e0248291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Astorga F, Navarrete-Talloni MJ, Miró MP et al (2019) Antimicrobial resistance in E. coli isolated from dairy calves and bedding material. Heliyon 5:e02773. https://doi.org/10.1016/j.heliyon.2019.e02773

    Article  PubMed  PubMed Central  Google Scholar 

  44. Cengiz S, Adiguzel MC (2020) Determination of virulence factors and antimicrobial resistance of E. coli isolated from calf diarrhea, part of eastern Turkey. Ankara Üniversitesi Vet Fakültesi Derg 67:365–371

    Article  Google Scholar 

  45. Nüesch-Inderbinen M, Hänni C, Zurfluh K et al (2022) Antimicrobial resistance profiles of Escherichia coli and prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in calves from organic and conventional dairy farms in Switzerland. Microbiologyopen 11:e1269

    Article  PubMed  PubMed Central  Google Scholar 

  46. Collignon PC, Conly JM, Andremont A et al (2016) World Health Organization ranking of antimicrobials according to their importance in human medicine: a critical step for developing risk management strategies to control antimicrobial resistance from food animal production. Clin Infect Dis 63:1087–1093

    Article  CAS  PubMed  Google Scholar 

  47. Salaheen S, Kim SW, Springer HR et al (2023) Genomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves. J Glob Antimicrob Resist 33:164–170

    Article  CAS  PubMed  Google Scholar 

  48. Blahna MT, Zalewski CA, Reuer J et al (2006) The role of horizontal gene transfer in the spread of trimethoprim–sulfamethoxazole resistance among uropathogenic Escherichia coli in Europe and Canada. J Antimicrob Chemother 57:666–672

    Article  CAS  PubMed  Google Scholar 

  49. Jia Y, Mao W, Liu B et al (2022) Study on the drug resistance and pathogenicity of Escherichia coli isolated from calf diarrhea and the distribution of virulence genes and antimicrobial resistance genes. Front Microbiol. https://doi.org/10.3389/fmicb.2022.992111

    Article  PubMed  PubMed Central  Google Scholar 

  50. Staji H, Tonelli A, Zahraei Salehi T et al (2018) Distribution of antibiotic resistance genes among the phylogroups of Escherichia coli in diarrheic calves and chickens affected by colibacillosis in Tehran. Iran Arch Razi Inst 73:131–137

    CAS  PubMed  Google Scholar 

  51. Kime L, Randall CP, Banda FI et al (2019) Transient silencing of antibiotic resistance by mutation represents a significant potential source of unanticipated therapeutic failure. MBio 10:e01755–e01819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Coura FM, de Araújo DS, Mussi JMS et al (2017) Characterization of virulence factors and phylogenetic group determination of Escherichia coli isolated from diarrheic and non-diarrheic calves from Brazil. Folia Microbiol (Praha) 62:139–144

    Article  CAS  PubMed  Google Scholar 

  53. Mohammadi F, Ebrahim-Saraie HS, Sinaei N, Karimi-Dehkordi M (2023) The prevalence of phylogenetic group of Shiga toxin-producing Escherichia coli strain isolated from farm animals in Iran: a meta-analysis study. Rev Res Med Microbiol 34:101–109

    Google Scholar 

Download references

Acknowledgements

The authors would like to express their gratitude to the employees of microbiology laboratory, faculty of veterinary medicine, Shahid Bahonar university of Kerman for their kind participation in this research.

Funding

The authors did not receive support from any organization for the submitted work.

Author information

Authors and Affiliations

  1. Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran

    Zahede Naderi, Maziar Jajarmi, Sanaz Dehdashti & Parvin Mohseni

  2. Molecular Microbiology Research Group, Shahid Bahonar University of Kerman, Kerman, Iran

    Reza Ghanbarpour

  3. Department of Food Science and Technology, Bardsir Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran

    Mahboube Bagheri

  4. Department of Basic Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran

    Neda Eskandarzade

  5. Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran

    Hesam Alizade

Authors
  1. Zahede Naderi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Reza Ghanbarpour
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maziar Jajarmi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sanaz Dehdashti
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Mahboube Bagheri
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Neda Eskandarzade
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Parvin Mohseni
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hesam Alizade
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Zahede Naderi, Maziar Jajarmi, Sanaz Dehdashti, Mahboube Bagheri, Neda Eskandarzade, Parvin Mohseni and Hesam Alizade. The first draft of the manuscript was written by Reza Ghanbarpour and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Reza Ghanbarpour.

Ethics declarations

Competing interests

The authors have no relevant financial or non-financial interests to disclose.

Ethical approval

This work presents research on animals that do not require ethical approval for their study; no human studies are presented in the work, no potentially identifiable images or data are presented in this study, and laboratory animals and human samples were not used in this study. All fecal samples were obtained from the calves with the consent of farm managers. All methods were carried out in accordance with relevant guidelines and regulations presented by Iran National Committee for Ethics in Biomedical Research.

Consent to participate

Informed consent was obtained from all individual participants (farm managers) included in the study.

Consent to publish

No human studies are presented in the work. No potentially identifiable images or data are presented in this study. All fecal samples were obtained from the calves with the consent of farm managers.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Naderi, Z., Ghanbarpour, R., Jajarmi, M. et al. Antibiotic resistance profiling and phylotyping of human-diarrheagenic Escherichia coli pathotypes detected from diarrheic and non-diarrheic calves in Iran. Mol Biol Rep 51, 494 (2024). https://doi.org/10.1007/s11033-024-09494-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11033-024-09494-6

Keywords

Search

Navigation