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Open AccessArticle

Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital

1
Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, 11562 Cairo, Egypt
2
Microbiology and Infection Control Department, Dar Al-Fouad Hospital, 11562 Cairo, Egypt
3
Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian-Russian University, 11829 Badr City, Egypt
4
Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt
5
Center for Genome and Microbiome Research, Cairo University, 11562 Cairo, Egypt
*
Author to whom correspondence should be addressed.
Genes 2020, 11(10), 1219; https://doi.org/10.3390/genes11101219
Received: 2 September 2020 / Revised: 13 October 2020 / Accepted: 14 October 2020 / Published: 17 October 2020
(This article belongs to the Special Issue Genetics of Antimicrobial Resistance)
Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype–phenotype–clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton–Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases. View Full-Text
Keywords: next-generation sequencing (NGS); whole-genome sequencing (WGS); methicillin- resistant Staphylococcus aureus (MRSA); virulome; resistome next-generation sequencing (NGS); whole-genome sequencing (WGS); methicillin- resistant Staphylococcus aureus (MRSA); virulome; resistome
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Soliman, M.S.; Soliman, N.S.; El-Manakhly, A.R.; ElBanna, S.A.; Aziz, R.K.; El-Kholy, A.A. Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital. Genes 2020, 11, 1219.

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