Draft genome sequence of human-associated streptogramin resistant Staphylococcus aureus

Authors: GUPTA, SUSHIM - Orise Fellow; SHARMA, POONAM - Orise Fellow; Barrett, John; Hiott, Lari; Woodley, Tiffanie; Frye, Jonathan; Jackson, Charlene

Submitted to: Journal of Global Antimicrobial Resistance
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/6/2018
Publication Date: 3/16/2019
Citation: Gupta, S., Sharma, P., Barrett, J.B., Hiott, L.M., Woodley, T.A., Frye, J.G., Jackson, C.R. 2019. Draft genome sequence of human-associated streptogramin resistant Staphylococcus aureus. Journal of Global Antimicrobial Resistance. https://doi.org/10.1016/j.jgar.2018.11.021.
DOI: https://doi.org/10.1016/j.jgar.2018.11.021

Interpretive Summary: Methicillin-resistant Staphylococcus aureus (MRSA) infections are difficult to treat because they are not only resistant to clinically relevant Beta-lactam antibiotics, but may also exhibit multidrug resistance. As MRSA clones emerged with decreased susceptibility to glycopeptides, the streptogramin compound, Quinupristin-Dalfopristin (Q/D), came into use. However, the streptogramin, virginiamycin, was used in food animal production for decades, and common resistance mechanisms for the two drugs from both human and animal sources is cause for concern. In this study, the genome sequence of a human-associated streptogramin resistant MRSA was analyzed to provide valuable insight into its resistome and virulence factors. The isolate was resistant to ampicillin, ceftriaxone, gentamicin, kanamycin, oxacillin, penicillin, Q/D, and tetracycline and contained resistance genes to the aminoglycosides, ß-lactams, fosfomycin, macrolides, streptogramins, and tetracycline. The isolate also harbored numerous plasmids and virulence genes. This data will provide a basis for comparison to Gram-positive bacteria of food animal origin which will be useful for researchers and policy makers as antimicrobial use in food animal production is evaluated.

Technical Abstract: Objectives: Staphylococcus aureus is one of the leading causes of nosocomial and community-acquired infections. Treatment of those infections with macrolide-lincosamide-streptogramin (MLS) antibiotics has led to resistance to those antibiotics through various mechanisms. S. aureus strain CIP108540, isolated from a human in France, has been previously shown to exhibit resistance to the streptogramins, Quinupristin and Dalfopristin; the presence of streptogramin resistance genes was verified by PCR. However, the extent of MLS resistance genes in this strain is unknown. This study analyzed the genome sequence of S. aureus CIP108540 to assess genes associated with resistance, including streptogramins. Methods: Genomic DNA of S. aureus CIP108540 was sequenced using Illumina MiSeq. The generated sequencing reads were de novo assembled using A5 miseq. Results: The draft genome size was 3, 014, 273bp with 32.72% GC content. The predicted coding sequences were 3,063 with 59 tRNA. Several antibiotic resistance genes were identified conferring resistance to various antibiotics. Conclusion: The draft genome sequence of S. aureus CIP108540 released here will provide valuable information for a better understanding of its genetic makeup and resistome.