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Genome-wide genetic marker analysis and genotyping of Escherichia fergusonii strain OTSVEF-60

  • Veterinary Microbiology - Research Paper
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Abstract

Poultry originated Escherichia fergusonii (POEF), an emerging bacterial pathogen, causes a wide range of intestinal and extra-intestinal infections in the poultry industry which incurred significant economic losses worldwide. Chromosomal co-existence of antibiotics and metal resistance genes has recently been the focal point of POEF isolates besides its pathogenic potentials. This study reports the complete genome analysis of POEF strain OTSVEF-60 from the poultry originated samples of Bangladesh. The assembled draft genome of the strain was 4.2 Mbp containing 4503 coding sequences, 120 RNA (rRNA = 34, tRNA = 79, ncRNA = 7), and three intact phage signature regions. Forty-one broad range antibiotic resistance genes (ARGs) including dfrA12, qnrS1, blaTEM-1, aadA2, tet(A), and sul-2 along with multiple efflux pump genes were detected, which translated to phenotypic resistant patterns of the pathogen to trimethoprim, fluoroquinolones, β-lactams, aminoglycoside, tetracycline, and sulfonamides. Moreover, 22 metal resistance genes were found co-existing within the genome of the POEF strain, and numerous virulence genes (VGs) coding for cit (AB), feo (AB), fep (ABCG), csg (ABCDEFG), fliC, ompA, gadA, ecpD, etc. were also identified throughout the genome. In addition, we detected a class I integron gene cassette harboring dfrA12, ant (3″)-I, and qacEΔ-sul2 genes; 42 copies of insertion sequence (IS) elements; and two CRISPR arrays. The genomic functional analysis predicted several metabolic pathways related to motility, flagellar assembly, epithelial cell invasion, quorum sensing, biofilm formation, and biosynthesis of vitamin, co-factors, and secondary metabolites. We herein for the first time detected multiple ARGs, VGs, mobile genetic elements, and some metabolic functional genes in the complete genome of POEF strain OTSVEF-60, which might be associated with the pathogenesis, spreading of ARGs and VGs, and subsequent treatment failure against this emerging avian pathogen with currently available antimicrobials.

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Acknowledgements

The authors would like to acknowledge Bangladesh Academy of Science–United States Department of Agriculture (BAS–USDA) for supporting this project. We would also like to acknowledge Bangabandhu Science & Technology Fellowship Trust for supporting Otun Saha as PhD student. We would like to further acknowledge University Grants Commission (UGC), Ministry of Science and Technology, Bangladesh for supporting reagents and equipment.

Funding

This work was supported by the grant from Bangladesh Academy of Science–United States Department of Agriculture (BAS–USDA) (Grant no: BAS -USDA PALS DU LSc-34).

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Authors and Affiliations

  1. Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh

    Otun Saha, M. Nazmul Hoque, Munawar Sultana & M. Anwar Hossain

  2. Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh

    Nadira Naznin Rakhi

  3. Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh

    M. Nazmul Hoque

  4. Jashore University of Science and Technology, Jashore, 7408, Bangladesh

    M. Anwar Hossain

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  1. Otun Saha
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Contributions

O.S. carried out the studies (sequencing, molecular and data analysis). O.S. and N.N.R. participated in drafting the manuscript. M.N.H edited and revised the final manuscript. M.S. and M.A.H. developed the hypothesis, supervised the whole work and helped to prepare and revise the manuscript. All authors read and approved the final manuscript.

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Correspondence to Munawar Sultana or M. Anwar Hossain.

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Ethical approval was granted from the Ethics Committee of the Faculty of Biological Sciences, University of Dhaka, Bangladesh who has approved the procedure under the Reference 71/Biol.Scs./2018-2019.

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Saha, O., Rakhi, N.N., Hoque, M.N. et al. Genome-wide genetic marker analysis and genotyping of Escherichia fergusonii strain OTSVEF-60. Braz J Microbiol 52, 989–1004 (2021). https://doi.org/10.1007/s42770-021-00441-2

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