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Next generation sequencing allows identification of quantitave differential gene expression between four clinical strains of methicilin resistant Staphylococcus aureus

ABSTRACT: Staphylococcus aureus can cause a broad spectrum of diseases that vary widely in clinical presentation and disease severity[121]. Methicillin-Resistant S. aureus (MRSA) strains first described in the 1960’s[122] were hospital acquired (HA MRSA), however in the 1990’s, community-associated MRSA strains (CA MRSA) were identified and are considered to be more virulent[16]. Therapeutics and management of MRSA focuses on novel antibacterials and vaccines targeting virulence factors. To date no clinical trials for vaccines have succeeded[123] due to the poor understanding of the pathogenic mechanisms exhibited by S.aureus.We investigated the differential gene expression of four clinical MRSA strains in vitro, belonging to HA and CA MRSA, at the stationary and exponential growth phases, using RNA-seq on the Ion torrent next generation sequencing platform. This study reveals the high diversity of virulence trait expression among MRSA strains within strains as well as between different growth phases, and also suggests potential factors other than PVL that contributes to enhanced virulence in CA MRSA

ORGANISM(S): Staphylococcus aureus

PROVIDER: GSE70636 | GEO | 2020/01/07

REPOSITORIES: GEO

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Project description:Approximatively 75% of the genome of S. aureus (“core” genome) are highly conserved between strains, whereas the remaining 25% (“accessory” genome) are composed of variable regions that are mostly composed of mobile genetic elements (MGE), containing virulence and resistance genes. We have developed a composite DNA-microarray (StaphVar Array) which selectively targets 403 genes located on the accessory or core variable genome. Target genes encode antimicrobial resistance factors (35 %), virulence factors (28 %) and adhesins (31%). This microarray was validated with reference strains and used to characterize the genomic DNA of 13 community-acquired methicillin resistant S. aureus (CA-MRSA) strains representative of all the Multilocus Sequence Types (STs) described to date in Belgium. Analysis of gene content of 8 reference strains by the StaphVar Array matched 96 to 99% of the theoretical results. Analysis of CA-MRSA strains showed that 54.4 % of the genes tested were strain-dependent. Strains presented specific exotoxin, enterotoxin, cytolysin and adhesin gene profile by multi-locus sequence typing (MLST) lineage. One exception to these “lineage-specific” gene profile was the variable presence of the Arginin Catabolic Mobile Element (ACME, characteristic of the USA300 clone) within ST8 strains. In conclusion, this novel StaphVar array enables characterization of more than 400 variable resistance and virulence determinants in S. aureus strains. CA-MRSA strains from Belgium displayed extensive diversity in virulence and resistance profile. The presence of the USA 300 clone in our country was confirmed. Although mainly located on MGE, association of virulence genes were highly conserved within strains of the same MLST lineage. CGH microarray was performed on 13 epidemiologically distinct clinical isolates of methicillin resistant S. aureus. S. aureus labeled genomic DNA were hybridized to StaphVar arrays containing 1326 60mer oligonucleotide probes (Eurogentec, Belgium).

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Next generation sequencing allows identification of quantitave differential gene expression between four clinical strains of methicilin resistant Staphylococcus aureus

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