Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance.
OBJECTIVE
The purpose was to develop an analytical pipeline for specific gene analysis and biomarker discovery from next generation sequencing (NGS) data.


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.


CONCLUSIONS
The pipeline developed provides an effective bioinformatics tool for genetic diversity clarification and marker sequences discovery for pathogen characterization and surveillance.
Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
Weizhong
W
Zhao
Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
James J
JJ
Chen
Division of Microbiology, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
Steven
S
Foley
Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
Yuping
Y
Wang
Division of Animal & Food Microbiology, Office of Research, Center for Veterinary Medicine, US Food & Drug Administration, Laurel, MD 20993, USA.
Shaohua
S
Zhao
Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
John
J
Basinger
Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US Food & Drug Administration, 3900 NCTR Rd., Jefferson, AR 72079, USA.
Wen
W
Zou
D001426:Bacterial Proteins / Q000235:genetics; D015415:Biomarkers / Q000378:metabolism*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010802:Phylogeny; D019779:Salmonella enterica / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism
D001426:Bacterial Proteins; D015415:Biomarkers
Salmonella serotypes; bioinformatics pipeline; biomarker; fliC gene; gene diversity; next-generation sequencing analysis