Genotypic and Phenotypic Characteristics of the Phylogenetic Groups of Escherichia Coli Isolates From Ostriches in Iran

Document Type : Research Article

Authors

• Mohammad Sadegh Edalatian Dovvom ¹
• Abolfazl Ghaniei ²
• Majid Jamshidian Mojaver ³
• Emadodin Tohidi ⁴

¹ Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.

² Department of Clinical Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran.

³ Mashhad Branch, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Mashhad, Iran.

⁴ Biotechnology Division, Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Iran.

10.22067/ijvst.2024.88886.1394

Abstract

Increased antibiotic use in the ostrich industry could lead to the emergence of virulent antibiotic-resistant bacterial strains transmissible to human. This study investigated the genotypic and phenotypic characteristics of the phylogenetic groups of Escherichia coli (E. coli) isolates from ostrich and reveal their health risk potential. One hundred twenty-nine confirmed presumptive commensal (44) and suspected pathogenic (85) E. coli isolates from ostrich flocks in Mashhad, Northeast Iran, were phylo-typed by the Clermont quadruplex polymerase chain reaction. The phylogenetic profile of the isolates was comparatively investigated based on antimicrobial susceptibility, resistance, and virulence gene profiles. Results indicated that both groups of presumptive commensal and pathogenic isolates were mostly distributed within phylogroups A (with proportions 31.81% and 32.94%, respectively) and B1 (with proportions 36.36% and 31.76%, respectively). Multi-drug resistance was highest within the phylogroup B2 (p ≥ 0.05). The phylogroup B1, typically known for commensal strains, unlike B2, showed the most negligible proportions of isolates which were devoid of resistance genes (p ≥ 0.05) and virulence genes (p ≥ 0.05). The findings of this study expanded the horizon of the genotypic and phenotypic characteristics of the phylogenetic groups of E. coli isolates from ostrich. Moreover, we indicated a complicated inconsistency between both characteristics. Therefore, more comprehensive and comparative studies on E. coli isolates from ostrich and human are favoured in future research.

Keywords

• Antimicrobial susceptibility
• Clermont quadruplex PCR
• MDR
• Resistance genes
• Virulence genes

Main Subjects

• Microbiology

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References

1.    Amani F, Hashemitabar G, Ghaniei A, et al. Antimicrobial resistance and virulence genes in the Escherichia coli isolates obtained from ostrich. Tropical Animal Health and Production. 2020; 52: 3501-8. Doi:10.1007/s11250-020-02384-6.
2.    Bagheri M, Ghanbarpour R, Alizade H. Shiga toxin and beta-lactamases genes in Escherichia coli phylotypes isolated from carcasses of broiler chickens slaughtered in Iran. International Journal of Food Microbiology. 2014; 177: 16-20. Doi:10.1016/j.ijfoodmicro.2014.02.003.
3.    Ibrahim RA, Cryer TL, Lafi SQ, et al. Identification of Escherichia coli from broiler chickens in Jordan, their antimicrobial resistance, gene characterisation and the associated risk factors. BMC Veterinary Research. 2019; 15:159-174. Doi:10.1186/s12917-019-1901-1.
4.    Pesciaroli M, Magistrali CF, Filippini G, et al. Antibiotic-resistant commensal Escherichia coli are less frequently isolated from poultry raised using non-conventional management systems than from conventional broiler. International Journal Food Microbiology. 2020; 314: 108391-402. Doi:10.1016/j.ijfoodmicro.2019.108391
5.    Subedi M, Luitel H, Devkota B, et al. Antibiotic resistance pattern and virulence genes content in avian pathogenic Escherichia coli (APEC) from broiler chickens in Chitwan, Nepal. BMC Veterinary Research. 2018; 14: 113-122. Doi:10.1186/s12917-018-1442-z.
6.    Mahmoud AT, Salim MT, Ibrahem RA, et al. Multiple drug resistance patterns in various phylogenetic groups of hospital-acquired uropathogenic E. coli isolated from cancer patients. Antibiotics. 2020; 9: 108-121. Doi:10.3390/antibiotics9030108.
7.    Saha O, Hoque MN, Islam OK, et al. Multidrug-resistant avian pathogenic Escherichia coli strains and association of their virulence genes in Bangladesh. Microorganisms. 2020; 8: 1135-1157. Doi:10.3390/microorganisms8081135.
8.    Sgariglia E, Mandolini NA, Napoleoni M, et al. Antibiotic resistance pattern and virulence genes in avian pathogenic Escherichia coli (APEC) from different breeding systems. Veterinaria Italiana. 2019; 55: 27-33. Doi:10.12834/VetIt.1617.8701.1.
9.    Javed S, Mirani ZA, Pirzada ZA. Phylogenetic group B2 expressed significant biofilm formation among drug resistant uropathogenic Escherichia coli. Libyan Journal of Medicine. 2021. 16: 1-7. Doi:10.1080/19932820.2020.1845444.
10.    Clermont O, Dixit OVA, Vangchhia B, et al. Characterisation and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environmental Microbiology. 2019; 21: 3107-3117. Doi:10.1111/1462-2920.14713.
11.    Abdi HA, Rashki A. Comparison of virulence factors distribution in uropathogenic E. coli isolates from phylogenetic groups B2 and D. International Journal Enteric Pathogens. 2014; 2: 1-5. Doi:10.17795/ijep21725.
12.    Adefioye OJ, Weinreich J, Rödiger S, et al. Phylogenetic characterisation and multilocus sequence typing of extended-spectrum beta lactamase-producing Escherichia coli from food-producing animals, beef, and humans in Southwest Nigeria. Microb. Drug Resistance. 2021; 27: 111-20. Doi:10.1089/mdr.2019.0397.
13.    Mohsenifard E, Asasi K, Sharifiyazdi H, et al. Phylotyping and ColV plasmid-associated virulence genotyping of E. coli isolated from broiler chickens with colibacillosis in Iran. Comparative Clinical Pathology. 2016; 25: 1035-42. Doi:10.1007/s00580-016-2303-4.
14.    Bhave S, Kolhe R, Mahadevaswamy R, et al. Phylogrouping and antimicrobial resistance analysis of extraintestinal pathogenic Escherichia coli isolated from poultry species. Turkish Journal of Veterinary and Animal Sciences. 2019; 43:117-26. Doi:10.3906/vet-1808-47. 
15.    Jeong J, Lee JY, Kang MS, et al. Comparative characteristics and zoonotic potential of avian pathogenic Escherichia coli (APEC) isolates from chicken and duck in South Korea. Microorganisms 2021; 9: 946-962. Doi:10.3390/microorganisms9050946.
16.    Murase T, Ozaki H. Relationship between phylogenetic groups of Escherichia coli and pathogenicity among isolates from chickens with colibacillosis and healthy chickens. Poultry Sciences. 2022; 101 (9): 102007-14.  Doi:10.1016/j.psj.2022.102007.
17.    Nardi AR, Salvadori MR, Coswig LT, et al. Type 2 heat-labile enterotoxin (LT-II)-producing Escherichia coli isolated from ostriches with diarrhea. Veterinary Microbiology. 2005; 105: 245-9. Doi:10.1016/j.vetmic.2004.11.005.
18.    Salari S, Hoseini A. The antibiogram profile of commensal Escherichia coli of the gastrointestinal tract of apparently healthy ostriches and diseased chickens with colibacillosis. Poultry Science Journal. 2021; 9: 121-129. Doi:10.22069/psj.2021.18892.1672
19.    Clermont O, Christenson JK, Denamur E, et al. The Clermont Escherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups. Environmental Microbiology Rep. 2013; 5: 58-65. Doi:10.1111/1758-2229.12019.
20.    CLSI, Performance Standards for Antimicrobial Susceptibility Testing, 28 ed. CLSI supplement M100, Wayne, PA: Clinical and Laboratory Standards Institute; 2018.
21.    Van TTH, Chin J, Chapman T, et al. Safety of raw meat and shellfish in Vietnam: an analysis of Escherichia coli isolations for antibiotic resistance and virulence genes. International Journal of Food Microbiology. 2008; 124: 217-223. Doi:10.1016/j.ijfoodmicro.2008.03.029.
22.    Ewers C, Janßen T, Kießling S, et al. Rapid detection of virulence-associated genes in avian pathogenic Escherichia coli by multiplex polymerase chain reaction. Avian Diseases. 2005; 49: 269-273. Doi:10.1637/7293-102604r.
23.    Ahumada-Santos YP, Báez-Flores ME, Díaz-Camacho SP, et al. Association of phylogenetic distribution and presence of integrons with multi-drug resistance in Escherichia coli clinical isolates from children with diarrhoea. Journal of Infection and Public Health. 2020; 13:767-72. Doi:10.1016/j.jiph.2019.11.019. 
24.    Iranpour D, Hassanpour M, Ansari H, et al. Phylogenetic groups of Escherichia coli strains from patients with urinary tract infection in Iran based on the new Clermont phylotyping method. BioMed Research International.  2015; 2015: 846219-27. Doi:10.1155/2015/846219.
25.    Mohamadi E, Alizade H, Askari N, et al. Antibiotic resistance profile in relation to phylogenetic background in Escherichia coli isolated from fecal samples of healthy ostrich. International Journal of Enteric Pathogens. 2015; 3: 6-9. Doi:/10.17795/ijep25366.
26.    Alizade H, Ghanbarpour R, Jajarami M, et al. Phylogenetic typing and molecular detection of virulence factors of avian pathogenic Escherichia coli isolated from colibacillosis cases in Japanese quail. Veterinary Research Forum. 2017; 8: 55-8. PMCID: PMC5413312 
27.    Ghanbarpour R, Daneshdoost S. Identification of shiga toxin and intimin coding genes in Escherichia coli isolates from pigeons (Columba livia) in relation to phylotypes and antibiotic resistance patterns. Tropical Animal Health and Production. 2012; 44: 307-12. Doi:10.1007/s11250-011-0021-0.
28.    Kocúreková T, Karahutová L, Bujňáková D. Antimicrobial susceptibility and detection of virulence-associated genes in Escherichia coli strains isolated from commercial broilers. Antibiotics. 2021; 10: 1303-16. Doi:10.3390/antibiotics10111303.
29.    Marazzato M, Aleandri M, Massaro MR, et al. Escherichia coli strains of chicken and human origin: Characterisation of antibiotic and heavy-metal resistance profiles, phylogenetic grouping, and presence of virulence genetic markers. Research in Veterinary Sciences. 2020; 132: 150-5. Doi:10.1016/j.rvsc.2020.06.012. 
30.    Meena RH, Mir IA, Maherchandani S, et al. Antibiotic resistance pattern and phylogenetic analysis of commensal Escherichia coli isolated from poultry. Journal of Pure Applied Microbiology. 2015; 9: 657-62. 
31.    Messaili C, Messaili Y, Bakour R. Virulence gene profiles, antimicrobial resistance and phylogenetic groups of fecal Escherichia coli strains isolated from broiler chickens in Algeria. Veterinaria Italiana 2019; 55: 35-46. Doi:10.12834/VetIt.799.3865.2.
32.    Obeng AS, Rickard H, Ndi O, et al. Antibiotic resistance, phylogenetic grouping and virulence potential of Escherichia coli isolated from the faeces of intensively farmed and free range poultry. Veterinary Microbiology. 2012; 154: 305-15. Doi:10.1016/j.vetmic.2011.07.010
33.    Amiri M, Ahmadi E. A comparative phylotyping analysis of E. coli originating from avian colibacillosis based on the Clermont triplex scheme and gyrA gene sequencing. Turkish Journal of Veterinary and Animal Sciences. 2019; 43: 212-7. Doi:10.3906/vet-1811-14
34.    Asadi A, Zahraei Salehi T, Jamshidian M, et al. ECOR phylotyping and determination of virulence genes in Escherichia coli isolates from pathological conditions of broiler chickens in poultry slaughter-houses of southeast of Iran. Veterinary Research Forum. 2018; 9: 211–216. Doi:10.30466/vrf.2018.30827.
35.    Goudarztalejerdi A, Mohammadzadeh A, Najafi SV, et al. Serogrouping, phylotyping, and virulence genotyping of commensal and avian pathogenic Escherichia coli isolated from broilers in Hamedan, Iran. Comparative Immunology Microbiology and Infectious Diseases. 2020; 73: 101558-67. Doi:10.1016/j.cimid.2020.101558.
36.    Kazemnia A, Ahmadi M, Dilmaghani M. Antibiotic resistance pattern of different Escherichia coli phylogenetic groups isolated from human urinary tract infection and avian colibacillosis. Iranian Biomedical Journal. 2014; 18: 219-224. Doi:10.6091%2Fibj.1394.2014. 
37.    Reddy CA, Beveridge TJ, Breznak JA, et al. American Society of Microbiology Press. Methods for general and molecular microbiology; 2007.
38.    Fazel F, Jamshidi A, Khoramian B. Phenotypic and genotypic study on antimicrobial resistance patterns of E. coli isolates from bovine mastitis. Microbiology Pathogens. 2019; 132: 355-61. Doi:10.1016/j.micpath.2019.05.018.