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Publications

Journal Article Case Reports Ppublish

PubMed: 42670169 DOI: 10.1155/tbed/5654145

Oxford Nanopore Sequencing of Clinical DNA for Identification and Comparative Genomic Analysis of Erysipelothrix piscisicarius.

Transbound Emerg Dis 2026(1):e5654145

Authors: Rattagan Kajeekul, Thidathip Wongsurawat, Worarat Kruasuwan, Phichaya Sawankatat, Pattaraporn Nimsamer, Tantip Arigul, Athita Riwlord, Piroon Jenjaroenpun, Anusak Kerdsin

Affiliations

  • Department of Medicine, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand, mnrh.go.th.
  • Medical Bioinformatics, Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand, mahidol.ac.th.
  • Special Research Unit for Tropical Zoonoses and Antimicrobial Resistance Surveillance (TZARS), Kasetsart University, Bangkok, Thailand, ku.ac.th.
  • Clinical Microbiology Laboratory, Department of Medical Technology, Maharat Nakhon Ratchasima Hospital, Nakhon Ratchasima, Thailand, mnrh.go.th.
  • Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand, ku.ac.th.
  • Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, chula.ac.th.
  • Center of Excellence for Food and Water Risk Analysis (FAWRA), Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand, chula.ac.th.

Abstract

The genus Erysipelothrix comprises facultative anaerobic, nonspore-forming, gram-positive bacteria that can cause skin infections and severe diseases such as septicemia and endocarditis in humans. Although E. rhusiopathiae is the primary pathogen, other species may also be involved, necessitating accurate identification. However, 16S rDNA sequencing lacks sufficient resolution to differentiate among Erysipelothrix species. In this study, we used Oxford Nanopore Technology (ONT) to directly sequence low-quality DNA extracted from heart valve tissue of a 66-year-old female patient with a fatal case of septicemia and aortic endocarditis. In contrast to 16S rDNA Illumina sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), which incorrectly identified the pathogen as E. rhusiopathiae, direct sequencing via ONT precisely identified E. piscisicarius as the cause of infection. About 1.47 Mb genome was retrieved from nanopore direct sequencing. Within the E. piscisicarius genome, we detected genes associated with virulence. Phylogenetic analysis showed that our strain clustered with a human-derived E. piscisicarius strain from China and swine-derived strains from Brazil. In conclusion, this study demonstrated that ONT can be used to sequence low-quality DNA extracted directly from patient specimens, obtain a draft bacterial genome, and reliably distinguish between pathogenic species.

MeSH

Genome, Endocarditis, Sepsis, Nanopore Sequencing, Bacteria, Dna, Erysipelothrix, Infections, Nanopores