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Volume 6, Issue 3

Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies Open Access

Abstract

Antimicrobial resistance (AMR) in is a pressing public health challenge with significant implications for the dairy industry, encompassing bovine mastitis concerns and potential zoonotic threats. To delve deeper into the resistance mechanisms of , this study employed a hybrid whole genome assembly approach that synergized the precision of Illumina with the continuity of Oxford Nanopore. A total of 62 isolates, collected from multiple sources from Vermont dairy farms, were sequenced using the GridION Oxford Nanopore R9.4.1 platform and the Illumina platform, and subsequently processed through our long-read first bioinformatics pipeline.

Our analyses showcased the hybrid-assembled genome’s superior completeness compared to Oxford Nanopore (R9.4.1)-only or Illumina-only assembled genomes. Furthermore, the hybrid assembly accurately determined multilocus sequence typing (MLST) strain types across all isolates. The comprehensive probe for antibiotic resistance genes (ARGs) using databases like CARD, Resfinder, and MEGARES 2.0 characterized AMR in isolates from Vermont dairy farms, and revealed the presence of notable resistance genes, including beta-lactam genes , , and . In conclusion, the hybrid assembly approach emerged as a tool for uncovering the genomic nuances of isolates collected from multiple sources on dairy farms. Our findings offer a pathway for detecting AMR gene prevalence and shaping AMR management strategies crucial for safeguarding human and animal health.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): folp gene , hybrid assembly , MLST , phenotype , resistance genes , spa type and whole-genome sequencing (WGS)
Funding
This study was supported by the:
  • National Institute of Food and Agriculture (Award VT-2023-AH01)
    • Principle Award Recipient: JohnBarlow
  • National Institute of Food and Agriculture (Award VT-AH02703)
    • Principle Award Recipient: JohnBarlow
  • National Institute of Food and Agriculture (Award VT-H02413MS)
    • Principle Award Recipient: JohnBarlow
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-03-25
2024-04-29
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Hybrid Illumina-Nanopore assembly improves identification of multilocus sequence types and antimicrobial resistance genes of Staphylococcus aureus isolated from Vermont dairy farms: comparison to Illumina-only and R9.4.1 nanopore-only assemblies
Access Microbiology 6, 000766.v3 (2024); https://doi.org/10.1099/acmi.0.000766.v3
/content/journal/acmi/10.1099/acmi.0.000766.v3
/content/journal/acmi/10.1099/acmi.0.000766.v3
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