High-throughput Oxford Nanopore sequencing-based approach for the multilocus sequence typing analysis of large-scale avian Escherichia coli study in Mississippi.

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  • Additional Information
    • Source:
      Publisher: Elsevier Country of Publication: England NLM ID: 0401150 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1525-3171 (Electronic) Linking ISSN: 00325791 NLM ISO Abbreviation: Poult Sci Subsets: MEDLINE
    • Publication Information:
      Publication: 2020- : [Cambridge, UK] : Elsevier
      Original Publication: Champaign Il : Poultry Science Association
    • Subject Terms:
      Escherichia coli*/genetics ; Escherichia coli*/classification ; Escherichia coli*/isolation & purification ; Chickens* ; Multilocus Sequence Typing*/veterinary ; Multilocus Sequence Typing*/methods ; Poultry Diseases*/microbiology ; Escherichia coli Infections*/veterinary ; Escherichia coli Infections*/microbiology; Animals ; Nanopore Sequencing/methods ; Nanopore Sequencing/veterinary
    • Abstract:
      Avian pathogenic Escherichia coli (APEC) cause avian colibacillosis and accurately distinguishing infectious isolates is critical for controlling its transmission. Multilocus sequence typing (MLST) is an accurate and efficient strain identification method for epidemiological surveillance. This research aimed to develop a fast and high-throughput workflow that simultaneously sequences the Achtman typing scheme's 7 housekeeping genes of multiple E. coli isolates using the Oxford Nanopore Technologies (ONT) platform for large-scale APEC study. E. coli strains were isolated from poultry farms, the housekeeping genes were amplified, and amplicons were sequenced on an R9.4 MinION flow cell using the Nanopore GridION sequencer (ONT, Oxford, UK) following the initial workflow (ONT-MLST). Moreover, the workflow was revised by introducing large-scale DNA extraction and multiplex PCR into the ONT-MLST workflow and applied to 242 new isolates, 18 isolates from the previous workflow, and 5 ATCC reference strains using Flongle flow cell on the Nanopore MinION Mk1C sequencer (ONT, Oxford, UK). Finally, the sequence type (ST) results of the 308 isolates collected from infected chickens and poultry farm environments were reported and analyzed. Data indicated that E. coli belonging to ST159, ST8578, and ST355 have the potential to infect multiple organs in broiler. In addition, zoonotic STs, ST69, ST10, ST38, and ST131, were detected from poultry farms. With the advantages of the high throughput of ONT, this study provides a rapid workflow for large-scale E. coli typing and identified frequently isolated sequence types related to APEC infection in poultry.
      (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
    • Contributed Indexing:
      Keywords: Oxford Nanopore; avian Escherichia coli; field study; high-throughput; large-scale
    • Publication Date:
      Date Created: 20240727 Date Completed: 20240921 Latest Revision: 20240921
    • Publication Date:
      20240922
    • Accession Number:
      PMC11338106
    • Accession Number:
      10.1016/j.psj.2024.104067
    • Accession Number:
      39067129