Investigating a rare methicillin-resistant Staphylococcus aureus strain: first description of genome sequencing and molecular characterization of CC15-MRSA

Abstract

Purpose: Methicillin resistant Staphylococcus aureus CC15 strains (CC15-MRSA) have only been sporadically described in literature. This study was carried out to describe the genetic make-up for this rare MRSA strain.

Methods: Four CC15-MRSA isolates collected in Riyadh, Saudi Arabia, between 2013 and 2014 were studied. Two isolates were from clinical infection and 2 from retail meat products. Whole genome sequencing was carried out using Illumina HiSeq2500 genome analyzer.

Results: All the CC15-MRSA isolates had the multilocus sequence typing profile ST1535, 13-13-1-1-81-11-13, which is a single locus variant of ST15. Of the 6 contigs related to the SCC element, one comprised a recombinase gene ccrAA, ccrC-PM1, fusC and a helicase, another one included mvaS, dru, mecA and 1 had yobV and Q4LAG7. The SCC element had 5 transposase genes, namely 3 identical paralogs of tnpIS431 and 2 identical paralogs of tnpIS256. Two identical copies of a tnpIS256-based insertion element flank the aacA-aphD gene. Two copies of this insertion element were present with 1 located in the SCC element and another inserted into the sasC gene. A short 3 kb region, which lacks any bacteriophage structural genes and site-specific DNA integrase, was inserted into the hlb gene. The hsdM and the 5'-part of the hsdS gene are replaced by a copy of the hsdM/hsdS paralogs from νSaβ giving rise to a new chimeric paralog of hsdS in νSaα.

Conclusion: CC15-MRSA shows a novel SCCmecV/SCCfus composite element. Its variant of hsdM/hsdS probably facilitated uptake of foreign mobile genetic elements that promoted emergence of CC15-MRSA. Close surveillance is needed to monitor spread and emergence of further CC15 MRSA strains.

Keywords: MLST; MRSA; SCCmec; Saudi Arabia; clonal complex; whole genome sequencing.

Figure 1

CC15-MRSA SCC element. Notes: Six contigs related to the SCC element (MF185204 to MF185209). The first contig comprises the flanking orfX gene, and the last contig the flanking dusC gene. In between, four contigs are shown carrying genes typically found in SCC elements. Contig 2 has the fusidic acid resistance gene fusC and the SCC recombinase genes ccrAA and ccrC. Contig 3 comprises the mecA gene cluster with mecR1 truncated by tnpIS431. Contig 5 constitutes a true insertion element, where the bifunctional kanamycin resistance determinant aacAaphD is flanked by two copies of tnpIS256. Abbreviation: MRSA, methicillin-resistant Staphylococcus aureus.

Figure 2

The hlb-3kb-insert in CC15-MRSA. Notes: The hemolysin beta gene (hlb) is interrupted by a 3 kb insertion element in CC15-MRSA genomes. Abbreviation: MRSA, methicillin-resistant Staphylococcus aureus.

Figure 3

hsdM/hsdS recombination in CC15-MRSA. Notes: The Figure shows the contents of genomic islands νSaα and νSaβ in isolate RUH-2 (ST1535/CC15, MF185202, MF185203) and in ST20130938 (ST15/CC15, Genbank accession CP012972.1). The reference genome CP012972.1 comprises two distinct paralog of hsdM/hsdS in genomic islands alpha and beta. The mapping of the sequencing reads from isolate RUH-2 onto the reference sequence CP012972.1 reveals, that hsdM-alpha and the 5’-end of hsdS- alpha are missing in RUH-2, while the coverage of hsdM-beta and the 5′-end of hsdS-beta is doubled with respect to other chromosomal genes, indicating that this stretch of DNA is duplicated in RUH-2. We extracted the duplicated region of νSaβ from the SPAdes contigs and were able to link it to contigs mapping to νSaα. Abbreviation: MRSA, methicillin-resistant Staphylococcus aureus.