Genome-scale analysis of s. aureus clinical isolates recovered from Lebanon. (c2018)

Abstract

The rising prevalence of multidrug resistant (MDR) Staphylococcus aureus is a worldwide threat. S. aureus is a Gram-positive bacterium that asymptomatically colonizes the nasal passages and the skin in 30% of the individuals. It is a major human pathogen that can cause a range of infections such as pneumonia, bacteremia, food poisoning, skin and soft tissue infections. This study was based on the molecular characterization of 23 S. aureus isolates collected from the American University of Beirut – Medical Center (AUB-MC). Six representative isolates were also sequenced. The initial assemblies produced an average genome length of 2,711,679 bp, G+C content of 32.6%, and 104 contigs. The majority of the isolates were Methicillin-resistant (MRSA), 85% were positive for the blaZ and 50% showed resistance to aminoglycosides. The multilocus sequence typing (MLST) revealed that the isolates belonged to various sequence types (ST97, ST5, ST6, ST44, ST291, ST1, ST121, ST80, ST45, ST2, and ST8), and were assigned to 12 different S. aureus protein A (spa) types (t267, t067, t304, t002, t3310, t1149, t386, t159, t044, t586, t711, and t008). SCCmec typing of MRSA revealed the prevalence of the mobile genetic element SCCmec type IV. Isolates were also assigned to three accessory gene regulator (agr) types: agr-type I (43%), agr-type II (31%) and agr-type III (26%), and 13 different phages were detected. The whole-genome based SNP phylogenetic analysis showed higher discriminatory power, compared to Pulsed-field Gel Electrophoresis (PFGE) fingerprinting and full chromosome comparison. This whole-genome based comparative analysis and the trends observed should stimulate initiatives to control MRSA at a national, regional, and hospital levels.