CRISPR-Cas–associated SCC mec Variants in Methicillin-resistant Staphylococcus aureus Evade Rapid Diagnostic Detection

Figures

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  Figure 1.. Structural comparison of SCCmec-associated III-A CRISPR-Cas elements in S. aureus. A, Comparison of six representative CRISPR-Cas elements from mecA-positive strains (90_005, 2_067, 6_063, 139_092 [index case], 22_044, 29_028), and 3 related clones (58_054, 43_003, 86_019). Subclones and related clones were selected based on SCCmec type, clonal complex, CRISPR-Cas subtype, and associated phage defense gene profiles (DefenseGroups A–F; Supplementary Table 1 and Supplementary Methods). Elements are ordered by overall similarity; gray shading highlights conserved regions. Annotations: SCCmec components (orange); CRISPR-Cas genes (blue); mecA (red); and SCCmec–orfX junction (red bars). Genomic regions spanning orfX to the CRISPR-Cas locus were defined by positional features, compared pairwise (blastn, default settings), and visualized with genoPlotR v0.8.11 (bit score <10 excluded). Junction sites and duplications were annotated via tblastn (query: GenBank ADC79452.1; PGAP CDS as subject; ≥95% query coverage) and blastn of the final 15 nt of orfX queried against the assembly (≥80% identity, 100% query coverage, word size 5, e value ≤100). Strains predicted in silico to evade…

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  Figure 2.. Maximum likelihood phylogeny of isolates carrying SCCmec-associated III-A CRISPR-Cas elements. The phylogeny includes one representative isolate per patient (n = 46), except for one patient from whom two distinct variants were recovered (43_003 and 44_029; see Supplementary Table 1). Sequence type (ST) and clonal complex (CC) were assigned by multilocus sequence typing; CCs are indicated when the ST is the recognized founder of that clonal complex (eg, CC5 for ST5). Colored blocks denote CC, putative transmission events (<20 SNPs with epidemiological link), predicted detectability by Xpert and BCID2, mecA status, SCCmec type, and CRISPR-Cas Class (light blue, Class 2; dark blue, Class 3). Scale bars indicate substitutions per site. Core genome size: 2 345 248 bp; variable sites 65 220 bp.