Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Comparative Genomic Analyses of E. coli ST2178 Strains Originated from Wild Birds in Pakistan

  • Jung Hun Lee (National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University) ;
  • Abdul Rauf Tareen (Department of Microbiology, Quaid-i-Azam University) ;
  • Nam-Hoon Kim (Department of Life Sciences, Jeonbuk National University) ;
  • Chanyeong Jeong (National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University) ;
  • Byeonghyeon Kang (National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University) ;
  • Gwangje Lee (National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University) ;
  • Dae-Wi Kim (Department of Life Sciences, Jeonbuk National University) ;
  • Rabaab Zahra (Department of Microbiology, Quaid-i-Azam University) ;
  • Sang Hee Lee (National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University)
  • Received : 2024.07.17
  • Accepted : 2024.08.14
  • Published : 2024.10.28
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Abstract

The emergence and spread of multidrug-resistance (MDR) pathogenic Escherichia coli due to horizontal gene transfer of antibiotic resistance genes (ARGs) and virulence factors (VFs) is a global health concern, particularly in developing countries. While numerous studies have focused on major sequence types (STs), the implication of minor STs in ARG dissemination and their pathogenicity remains crucial. In this study, two E. coli strains (PEC1011 and PEC1012) were isolated from wild bird feces in Pakistan and identified as ST2178 based on their complete genome sequences. To understand this minor ST, 204 genome assemblies of ST2178 were comparatively analyzed with the isolates' genomes. The phylogenetic analyses revealed five subclades of ST2178. Subclade E strains were predominantly isolated from human specimens, whereas subclades A and B strains including strains PEC1011 and PEC1012, respectively, were frequently isolated from animal. Mobile genetic elements (MGEs) exhibited the positive correlation with ARGs but not with VFs in this ST. Plasmid-borne ARGs exhibited higher correlation with plasmid-borne MGEs, indicating the role of diverse mobile plasmid structures in ARG transmission. Subclade E exhibited diverse plasmid-borne ARG repertoires correlated with MGEs, marking it as a critical surveillance target. In the case of VFs, they exhibited phylogeny-dependent profiles. Strain PEC1012 harbored various plasmid-borne ARGs, which are similar with conserved ARG repertoires in subclade A. The presence of unique ARG insertion in pPEC1012 highlights the importance of subclade A in ARG dissemination. This study comprehensively elucidates the landscape of ST2178, identifying critical phylogenetic subclades and their characteristics in ARG and VF occurrence.

Keywords

Acknowledgement

This work was supported by research grants from the National Research Foundation of Korea (NRF) funded by the Ministry of Science, Information and Communications Technology (MSIT; grant Nos. NRF-2021R1A2C3004826 and NRF-2019R1C1C1008615).

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