Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis

Abstract

Background: Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) Sequence Type 398 (ST398) isolate has emerged worldwide. Although there have been reports of invasive disease in humans, MRSA ST398 colonization is much more common in livestock and demonstrates especially high prevalence rates in pigs and calves. The aim of this study was to compare the genome sequence of an ST398 MRSA isolate with other S. aureus genomes in order to identify genetic traits that may explain the success of this particular lineage. Therefore, we determined the whole genome sequence of S0385, an MRSA ST398 isolate from a human case of endocarditis.

Results: The entire genome sequence of S0385 demonstrated considerable accessory genome content differences relative to other S. aureus genomes. Several mobile genetic elements that confer antibiotic resistance were identified, including a novel composite of an type V (5C2&5) Staphylococcal Chromosome Cassette mec (SCCmec) with distinct joining (J) regions. The presence of multiple integrative conjugative elements combined with the absence of a type I restriction and modification system on one of the two nuSa islands, could enhance horizontal gene transfer in this strain. The ST398 MRSA isolate carries a unique pathogenicity island which encodes homologues of two excreted virulence factors; staphylococcal complement inhibitor (SCIN) and von Willebrand factor-binding protein (vWbp). However, several virulence factors such as enterotoxins and phage encoded toxins, including Panton-Valentine leukocidin (PVL), were not identified in this isolate.

Conclusions: Until now MRSA ST398 isolates did not cause frequent invasive disease in humans, which may be due to the absence of several common virulence factors. However, the proposed enhanced ability of these isolates to acquire mobile elements may lead to the rapid acquisition of determinants which contribute to virulence in human infections.

Figure 1

Structure and comparative analysis of SCCmec element of S0385. The SCCmec element of S0385 contains a mec and ccr gene complex with a nearly identical structure compared to type V SCCmec, and two variable non-essential regions that include J1 and J3, the latter which contains a second solitary ccrC gene complex [19]. A pseudo-SCC element (ψSCC) is integrated upstream in tandem with the SCCmec element. Asterisks indicate the three direct repeat containing integration site sequences. The S0385 SCCmec element appears to be composed of gene clusters that have been previously described for other SCC elements. Shown is an alignment of the S0385 SCCmec element with the other SCC elements (i.e. S. aureus SCCHg, strain85/2082 and type V SCCmec, strain WIS; S. epidermidis SCCpbp4, strain ATCC12228; S. hominis SCC12263, strain GIFU12263 and S. aureus type II SCCmec, strain JCSC6826). Arrows represent ORFs and their direction of transcription. The homologous clusters of ORFs are indicated with similar colors. Red: solitary ccrC gene complex; blue: SCCmec type V mec and ccrC gene complex; green: cluster containing copA gene; aqua: metallo-hydrolase gene complex; orange: integrative conjugative element; yellow: IS431; black: orfX; grey: ORFs with no homology to the other SCC elements shown.

Figure 2

Compairison of the integrative conjugative elements. Amino acid matches from the six-frame translations (TBLASTX) of integrative conjugative elements of S. aureus S0385 (ICESa2 and ICESa1), B. subtilis (ICEBs1) [GenBank: AL009126 ] and L. monocytogenes (ICELm1) [GenBank: AARQ] dislayed using ACT http://www.sanger.ac.uk/software/ACT. ORFs are represented by coloured boxes. The red bars indicate TBLASTX matches between the elements. There are six proteins that are conserved among all ICEs (SAPIG0075, 0076, 0077 and 0079-0081), which include the FtsK/spoIII and replication initiation proteins.

Figure 3

Compairison of the SaPI. Nucleotide matches of SaPIbov, SaPI-S0385 and SaPI5 of S. aureus ET3, S0385 and USA300 FPR3757, respectivly dislayed using ACT. ORFs are represented by coloured boxes. The red bars indicate BLASTN matches between the elements, which mainly concern regions encoding genes that are essential for SAPI replication. The unique region in SaPI-S0385 contains the scn and vwb genes.