Genomic analysis revealed a novel genotype of methicillin-susceptible Staphylococcus aureus isolated from a fatal sepsis case in dengue patient

Soo Tein Ngoi,Cindy Shuan Ju Teh,Yee Wan Lee,Wen Kiong Niek,Sazaly Abubakar

doi:10.1038/s41598-021-83661-8

Soo Tein Ngoi, Cindy Shuan Ju Teh + Show 3 more

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https://doi.org/10.1038/s41598-021-83661-8

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Abstract

Staphylococcus aureus (S. aureus) is an opportunistic pathogen capable of causing serious health implications in susceptible individuals once it invades the host’s protective barriers. Methicillin-susceptible S. aureus (MSSA) often receives lesser attention although it has been frequently associated with serious infections in human. We aim to investigate the genomic features of a highly virulent yet pan susceptible MSSA strain (coded as HS-MSSA) which caused concurrent bacteraemia in a dengue patient, ultimately resulted in sepsis death of the patient. Whole genome sequence analysis was performed. The draft genome of HS-MSSA is approximately 2.78 Mb (GC content = 32.7%) comprising of 2637 predicted coding sequences. In silico genotyping of the HS-MSSA strain revealed a novel combined genotype (t091/ST2990). The HS-MSSA carries a SaPIn1-like pathogenicity island that harbours the staphylococcal enterotoxin and enterotoxin-like genes (sec3 and selL). The strain-specific β-lactamase (blaZ)-bearing plasmid region was identified in HS-MSSA. Core genome phylogeny showed that the HS-MSSA strain shared a common ancestry with the European MRSA clone. We report herein the genomic features of an MSSA lineage with novel genotype previously not reported elsewhere.

Highlights

Staphylococcus aureus isolated from a fatal sepsis case in dengue patient Soo Tein Ngoi1*, Wen Kiong Niek[1], Yee Wan Lee[2], Sazaly AbuBakar1,3 & Cindy Shuan Ju Teh1*
The size of the HS-Methicillinsusceptible S. aureus (MSSA) draft genome is approximately 2.78 Mb (GC content = 32.7%), of which 2,740,810 bp belongs to the genomic region that corresponds to the chromosome of S. aureus NCTC 8325
We report a novel genotype of MSSA (t091/ST2990) of community origin that caused severe sepsis in the human host

Summary

Introduction

Staphylococcus aureus isolated from a fatal sepsis case in dengue patient Soo Tein Ngoi1*, Wen Kiong Niek[1], Yee Wan Lee[2], Sazaly AbuBakar1,3 & Cindy Shuan Ju Teh1*. Since the emergence of methicillin-resistant S. aureus (MRSA) in the 1960s, this organism has been notorious for its ability to cause severe forms of infection in hospital settings and has eventually spread to the community after 30 years of evolution, most probably due to the transfer of the AMR gene cassette SCCmec to local methicillin-susceptible lineages[6]. This evolutionary theory for the emergence of MRSA lineage has recently been strengthened by whole genome sequence a nalysis[7]. A slow epidemic shift was observed in S. aureus infections worldwide

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