Next Generation Sequencing Facilitates Quantitative Analysis of S. aureus subsp. aureus ST398 and ST239 transcriptomes

ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to investigate the significantly different pathways and genes between ST398 and ST239. Methods: mRNA profiles of ST398 and ST239 at mid-logarithmic growth phase (4h) were generated by deep sequencing, respectively in quadruplicate and duplicate samples, using the Hiseq2000 (Illumina, CA) sequencer. The four samples of ST398 are J-92 (Sample1), W-604 (Sample2), R-1025 (Sample3) and R-1089 (Sample4) and grouped to G1, while the two samples of ST239 are J-95 (Sample5) and J-99 (Sample6) and grouped to G2. The sequence reads of ST398 and ST239 that passed quality filters were respectively aligned to S. aureus subsp. aureus ST398 (RefSeq accession number AM990992) and S. aureus subsp. aureus TW20 (RefSeq accession number NC _017331) using the Burrows-Wheeler Alignment tool (BWA) followed by ANOVA (ANOVA). Only the consistent data between the four ST398 samples and two ST239 samples were reserved for further analysis. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, RNA-seq analyses revealed four types of significantly differentially expressed genes between ST398 and ST239 (G1 only, G2 only, G1/G2>2, G2/G1>2), and only the type of G1/G2>2 was included in this study. The type of G1/G2>2 included 164 genes in total, in which there are 14 top genes showing G1/G2>5 including essB gene. Conclusions: Our data provide new information to the signicantly different genes between ST239 and ST398, especially the highly expressed genes in ST398 compared to ST239 which might be closely related to the high virulence of ST398.

ORGANISM(S): Staphylococcus aureus CN79 Staphylococcus aureus subsp. aureus ST398

PROVIDER: GSE71516 | GEO | 2018/07/29

REPOSITORIES: GEO