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<p><i>Salmonella enterica</i> serovar Kentucky has emerged as a global human food-borne pathogen with a known phenotype of multidrug resistance. Whole-genome sequencing of the lab-isolated organism was performed to understand its genomic features using the Illumina platform. The assembled genome, utilizing short reads only, poses gaps that need to be resolved to completely close the genome. To improve the genome assembly, we developed a strategy that utilizes publicly available long reads produced by Nanopore sequencing of a similar strain for <i>de novo</i> hybrid assembly. This approach yielded one completely closed chromosome and three completely closed plasmids. The assembled genome showed the presence of antimicrobial-resistant genes on both chromosome as well as plasmid present in the isolate. Four prophage regions and one CRISPR cluster were also identified on the chromosome. The sequenced isolate of <i>S. enterica</i> serovar Kentucky belongs to sequence type ST198, exhibiting multidrug resistance, including to ciprofloxacin, that causes human non-typhoidal <i>Salmonella</i> infections. This study provides a simple workflow to improve the completeness of assembled genome, in the scenario where long reads of the same isolate are not available for genome assembly.</p>

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De novo hybrid genome assembly and analysis of Salmonella enterica serovar Kentucky of Indian origin

  • 期刊论文

  • 发表日期：

    2026年3月30日

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  • Dhruv Das,
  • A S Kakatkar,
  • A V S S Narayana Rao,
  • Ravindranath Shashidhar

摘要

Salmonella enterica serovar Kentucky has emerged as a global human food-borne pathogen with a known phenotype of multidrug resistance. Whole-genome sequencing of the lab-isolated organism was performed to understand its genomic features using the Illumina platform. The assembled genome, utilizing short reads only, poses gaps that need to be resolved to completely close the genome. To improve the genome assembly, we developed a strategy that utilizes publicly available long reads produced by Nanopore sequencing of a similar strain for de novo hybrid assembly. This approach yielded one completely closed chromosome and three completely closed plasmids. The assembled genome showed the presence of antimicrobial-resistant genes on both chromosome as well as plasmid present in the isolate. Four prophage regions and one CRISPR cluster were also identified on the chromosome. The sequenced isolate of S. enterica serovar Kentucky belongs to sequence type ST198, exhibiting multidrug resistance, including to ciprofloxacin, that causes human non-typhoidal Salmonella infections. This study provides a simple workflow to improve the completeness of assembled genome, in the scenario where long reads of the same isolate are not available for genome assembly.