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Volume 66, Issue 11

Investigation of next-generation sequencing data of using web-based tools Free

Abstract

Rapid identification and characterization of multidrug-resistant strains is necessary due to the increasing frequency of severe infections in patients. The decreasing cost of next-generation sequencing enables us to obtain a comprehensive overview of genetic information in one step. The aim of this study is to demonstrate and evaluate the utility and scope of the application of web-based databases to next-generation sequenced (NGS) data.

The whole genomes of 11 clinical isolates were sequenced using Illumina MiSeq. Selected web-based tools were used to identify a variety of genetic characteristics, such as acquired antimicrobial resistance genes, multilocus sequence types, plasmid replicons, and identify virulence factors, such as virulence genes, cps clusters, urease-nickel clusters and efflux systems.

Using web-based tools hosted by the Center for Genomic Epidemiology, we detected resistance to 8 main antimicrobial groups with at least 11 acquired resistance genes. The isolates were divided into eight sequence types (ST11, 23, 37, 323, 433, 495 and 562, and a new one, ST1646). All of the isolates carried replicons of large plasmids. Capsular types, virulence factors and genes coding AcrAB and OqxAB efflux pumps were detected using BIGSdb-Kp, whereas the selected virulence genes, identified in almost all of the isolates, were detected using CLC Genomic Workbench software.

Applying appropriate web-based online tools to NGS data enables the rapid extraction of comprehensive information that can be used for more efficient diagnosis and treatment of patients, while data processing is free of charge, easy and time-efficient.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): BIGSdb-Kp , Klebsiella pneumoniae , MLST , next generation sequencing , PlasmidFinder and ResFinder
© 2017 The Authors
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2017-11-01
2024-04-18
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Investigation of next-generation sequencing data of Klebsiella pneumoniae using web-based tools
J. Med. Microbiol. 66, 1673 (2017); https://doi.org/10.1099/jmm.0.000624
/content/journal/jmm/10.1099/jmm.0.000624
/content/journal/jmm/10.1099/jmm.0.000624
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