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<p>In this study, we conducted whole-genome sequencing and comparative genomic analysis of two <i>Nocardia veterana</i> isolates (JJAEH1 and JJAEH2) from severe corneal ulcers to elucidate their pathogenic potential, antimicrobial resistance determinants, and genomic features associated with steroid–antibiotic interactions in keratitis. Genome assemblies, annotated with RAST and Prokka, ranged from 7.2 to 7.5&#xa0;Mb with a GC content of ~ 68.2%. Pan-genome analysis (Panaroo) revealed conserved virulence determinants, including <i>fbpA</i>, <i>fbpB</i>, and <i>fbpC</i> (fibronectin-binding mycolyltransferases), <i>stp</i> (serine/threonine phosphatase), type VII secretion system genes (<i>eccA3</i>, <i>eccB3</i>, <i>espG1</i>), and siderophore-associated iron acquisition genes (<i>mbtA</i>, <i>viuB</i>), indicating roles in host adherence, invasion, and immune evasion. Both isolates also harbored steroid-responsive genes (<i>choD</i>, <i>kstD</i>, <i>kshA/B</i>, <i>fadD</i>, <i>hsaA–D</i>) and two-component systems (<i>senX3–regX3</i>, <i>pdtaS</i>, <i>arlR</i>), linking metabolic adaptation to antibiotic tolerance. JJAEH1 exhibited broad susceptibility, whereas JJAEH2 was multidrug-resistant, carrying multiple efflux pumps (<i>mdtL</i>, <i>mdtH</i>). Heavy metal resistance determinants for mercury (merR) and arsenic (arsA, arsB, arsC, acr3) were present in both isolates, suggesting enhanced survival environments and co-selection of resistance traits. Average nucleotide identity analysis confirmed &gt; 99.99% similarity to <i>N. veterana</i>. In vitro assays demonstrated reduced amikacin susceptibility in the presence of prednisolone, suggesting potential corticosteroid-associated modulation. Overall, we provide genomic and phenotypic insights into virulence, antimicrobial resistance, and steroid responsiveness in ocular <i>N. veterana</i> and identify a modest decrease in amikacin inhibition in the presence of prednisolone in vitro, supporting further functional investigation of steroid–antibiotic interactions in nocardial keratitis.</p> Graphical abstract <p></p>

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Whole-genome sequencing and analysis of Nocardia veterana isolates from keratitis patients

  • 期刊论文

  • 发表日期：

    2026年3月17日

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  • Veena Radhakrishnan,
  • Lalitha Prajna,
  • Bharanidharan Devarajan,
  • Jeyaraman Jeyakanthan

摘要

In this study, we conducted whole-genome sequencing and comparative genomic analysis of two Nocardia veterana isolates (JJAEH1 and JJAEH2) from severe corneal ulcers to elucidate their pathogenic potential, antimicrobial resistance determinants, and genomic features associated with steroid–antibiotic interactions in keratitis. Genome assemblies, annotated with RAST and Prokka, ranged from 7.2 to 7.5 Mb with a GC content of ~ 68.2%. Pan-genome analysis (Panaroo) revealed conserved virulence determinants, including fbpA, fbpB, and fbpC (fibronectin-binding mycolyltransferases), stp (serine/threonine phosphatase), type VII secretion system genes (eccA3, eccB3, espG1), and siderophore-associated iron acquisition genes (mbtA, viuB), indicating roles in host adherence, invasion, and immune evasion. Both isolates also harbored steroid-responsive genes (choD, kstD, kshA/B, fadD, hsaA–D) and two-component systems (senX3–regX3, pdtaS, arlR), linking metabolic adaptation to antibiotic tolerance. JJAEH1 exhibited broad susceptibility, whereas JJAEH2 was multidrug-resistant, carrying multiple efflux pumps (mdtL, mdtH). Heavy metal resistance determinants for mercury (merR) and arsenic (arsA, arsB, arsC, acr3) were present in both isolates, suggesting enhanced survival environments and co-selection of resistance traits. Average nucleotide identity analysis confirmed > 99.99% similarity to N. veterana. In vitro assays demonstrated reduced amikacin susceptibility in the presence of prednisolone, suggesting potential corticosteroid-associated modulation. Overall, we provide genomic and phenotypic insights into virulence, antimicrobial resistance, and steroid responsiveness in ocular N. veterana and identify a modest decrease in amikacin inhibition in the presence of prednisolone in vitro, supporting further functional investigation of steroid–antibiotic interactions in nocardial keratitis.

Graphical abstract