Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages

Abstract

Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). As the most prominent community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major clones characterized as PVL-negative SCCmec IV (carrying the staphylococcal cassette chromosome mec IV but Panton-Valentine leukocidin-negative) and PVL-positive SCCmec V (5C2&5). We investigated the drug resistance, phylogeny and the distribution and sequence variation of SCCmec, staphylococcal bacteriophage φSA3, genomic island νSaβ and MES (an enterococcal mobile genetic element conferring multidrug resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping revealed that all of the CC59/SCCmec V (5C2&5) MRSA strains had acquired MESPM1 or its segregants, and obtained a φSA3-related fragment in νSaβ. In contrast, MES6272-2 and MES4578, which showed gentamicin resistance that was not encoded by MESPM1, were dominant in SCCmec IVg MRSA. Translocation of a whole φSA3 into νSaβ instead of only a φSA3-related fragment was common in SCCmec IVg MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is the major) still carried MES and νSaβ structures similar to those in SCCmec V (5C2&5) MRSA. A minimum spanning tree constructed by multiple-locus variable-number tandem repeat analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA grouped respectively in two major clades. The CC59 MSSA was equally distributed among the two clades, while the non-subtype-g SCCmec IV MRSA mostly clustered with SCCmec V (5C2&5) MRSA. Our findings strongly suggest that CC59 MSSA acquired divergent mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The evolutionary history of CC59 S. aureus explains how mobile genetic elements increase the antimicrobial resistance and virulence and contribute to the success of CA-MRSA in Taiwan.

The Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain

“…Previous studies have demonstrated that ST59 is becoming the predominant MRSA sequence type isolated from hospitalized patients in China (Chuang and Huang, 2013;Yang et al, 2017;Li et al, 2018). There are two distinct clones within the ST59 sequence type, AP, which is PVL-negative/SAK-positive, and TW, which is PVLpositive/SAK-negative (Hung et al, 2016). Both of these clones were identified in our analysis (Figure 1); however, both clones underwent significant genetic changes.…”

Staphylococcus aureus ST59: Concurrent but Separate Evolution of North American and East Asian Lineages

“…Previous studies have suggested that ST59 evolved concurrently in both North America (NA), previously referred to as the United States lineage and East Asia (EA), with strains from each region belonging to separate and distinct sub-lineages ( Ward et al, 2016 ), with mobile genetic elements playing a part ( Hung et al, 2016 ). For a more detailed look into the evolution of the ST59 lineage, a Bayesian inference phylogenomic tree, comprised of both the monomorphic SNPs and insertions/deletions identified by snippy, was generated incorporating our isolates (red font), as well as select isolates from the Ward et al (2016) (blue font) and Pang et al (2020) (green font) studies, and ST59 sequences downloaded from NCBI (black font).…”

“…Previous studies have attempted to explain evolution of the lineage, not only identifying separate sub-lineages, but also identifying factors that contributed to expansion and success of the each of the sub-lineage. Studies by Hung et al (2016) and Pang et al (2020) focused on ST59 success on a local scale, investigating the lineage in Taiwan and mainland China, respectively, while a study by Ward et al (2016) examined evolution of the lineage on the global scale. All studies noted that acquisition of mobile genetic elements such as IEC, MES, SCC mec , and PVL contributed to diversification of the lineage.…”

“…A second mobile genetic element is the immune Evasion Complex (IEC), which carries genes such as chp (encoding the chemotaxis inhibitory protein), scn (encoding staphylococcal complement inhibitor) and sak (encoding staphylokinase), and is responsible for protecting the bacteria from the host’s immune response. Differing combinations of the IEC genes are suggested to be present in the differing lineages of ST59, and can be carried on ϕSa3 as in the Asian-Pacific clone, or on νSaβ as in the Taiwan clone ( Hung et al, 2016 ). Finally, a large study encompassing more widespread global isolates determined that, unlike the theory that the lineage evolved in either North America or Asia and then spread, distinct clades of ST59 emerged concurrently in East Asia and the United States, occupying distinct geographical niches ( Ward et al, 2016 ).…”

Fatal case of ST8/SCCmecIVl community-associated methicillin-resistant Staphylococcus aureus infection in Japan

“…It is characterized by the genotype ST1/SCC mec IVa, Panton-Valentine leukocidin (PVL) genes and lower multidrug resistance than HA-MRSA. Global examples of CA-MRSA include the genotypes ST8/SCC mec IV (particularly USA300, which has caused serious outbreaks [1] , [2] , [4] , [5] , [6] ), ST30/SCC mec IV, ST59/SCC mec V [7] and ST80/SCC mec IV (particularly in Europe [8] ). Although SCC mec IV (like SCC mec V) is common among CA-MRSA strains [2] , its role in the pathogenesis of MRSA remains unclear.…”