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<p>The genus <i>Enterobacter</i> includes several clinically relevant species associated with a wide range of healthcare-associated infections. However, accurate species-level identification within this genus remains challenging because of taxonomic complexity and the limited resolution of routine phenotypic methods. In this study, we performed comprehensive genomic characterization of <i>Enterobacter</i> strain MG-EB028, isolated from a cerebrospinal fluid (CSF) sample from a nosocomial meningitis patient at Songklanagarind Hospital, Thailand. Genomic DNA was sequenced using both MGISEQ-2000 and Oxford Nanopore Technologies, and a high-quality hybrid assembly was generated for taxonomic and comparative genomic analyses. Pairwise comparisons using average nucleotide identity (ANI) and in silico DNA–DNA hybridization (<i>is</i>DDH) showed that MG-EB028 was most closely related to <i>Enterobacter</i> strain 93, sharing 98.73% ANI and 90.2% <i>is</i>DDH, whereas comparisons with other currently assigned <i>Enterobacter nematophilus</i> strains yielded lower values of approximately 94.98–95.01% ANI and 60.4–60.5% <i>is</i>DDH. Consistently, phylogenetic analyses supported these findings, showing that MG-EB028 and strain 93 formed a distinct clade separate from other closely related <i>Enterobacter</i> lineages, including the remaining <i>E. nematophilus</i> genomes. Together, these results support that MG-EB028 is genomically closest to <i>E. nematophilus</i> strain 93 and separated from the <i>E. nematophilus</i> type-strain-associated group. This study highlights the value of whole-genome analysis for resolving taxonomic ambiguity in clinically relevant <i>Enterobacter</i> isolates.</p>

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Genomic evidence that Enterobacter strain MG-EB028 and Enterobacter nematophilus strain 93 form a lineage distinct from Enterobacter nematophilus sensu stricto

  • 期刊论文

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  • 发表日期：

    2026年7月28日

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  • Thitaporn Dechathai,
  • Ratchara Kalawong,
  • Nonthawat Thepsimanon,
  • Thunchanok Yaikhan,
  • Wuthiwat Ruangchai,
  • Bharkbhoom Jaemsai,
  • Chollachai Klaysubun,
  • Mingkwan Yingkajorn,
  • Kamonnut Singkhamanan,
  • Rattanaruji Pomwised,
  • Monwadee Wonglapsuwan,
  • Sarunyou Chusri,
  • Prasit Palittapongarnpim,
  • Komwit Surachat

摘要

The genus Enterobacter includes several clinically relevant species associated with a wide range of healthcare-associated infections. However, accurate species-level identification within this genus remains challenging because of taxonomic complexity and the limited resolution of routine phenotypic methods. In this study, we performed comprehensive genomic characterization of Enterobacter strain MG-EB028, isolated from a cerebrospinal fluid (CSF) sample from a nosocomial meningitis patient at Songklanagarind Hospital, Thailand. Genomic DNA was sequenced using both MGISEQ-2000 and Oxford Nanopore Technologies, and a high-quality hybrid assembly was generated for taxonomic and comparative genomic analyses. Pairwise comparisons using average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) showed that MG-EB028 was most closely related to Enterobacter strain 93, sharing 98.73% ANI and 90.2% isDDH, whereas comparisons with other currently assigned Enterobacter nematophilus strains yielded lower values of approximately 94.98–95.01% ANI and 60.4–60.5% isDDH. Consistently, phylogenetic analyses supported these findings, showing that MG-EB028 and strain 93 formed a distinct clade separate from other closely related Enterobacter lineages, including the remaining E. nematophilus genomes. Together, these results support that MG-EB028 is genomically closest to E. nematophilus strain 93 and separated from the E. nematophilus type-strain-associated group. This study highlights the value of whole-genome analysis for resolving taxonomic ambiguity in clinically relevant Enterobacter isolates.