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Updated: Mar 31, 2026

Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance
Weizhong Zhao1, James J Chen1, Steven Foley2
1Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
Aim:
The purpose was to develop an analytical pipeline for specific gene analysis and biomarker discovery from next generation sequencing (NGS) data.
Materials & Methods:
As a test case, the fliC gene reference sequences of 24 Salmonella enterica strains of 13 serotypes and NGS reads of 32 serovar Newport, 48 Montevideo and 115 Enteritidis outbreak isolates were retrieved from the National Center for Biotechnology Information database.
Results:
Establishment of an analytical pipeline consisting of four steps: reference sequences retrieval and template sequence determination; NGS sequence reads retrieval; multiple sequence alignments and phylogenetic analysis; data mining and biomarker discovery.
Conclusion:
The pipeline developed provides an effective bioinformatics tool for genetic diversity clarification and marker sequences discovery for pathogen characterization and surveillance.
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