Staphylococcal protein A Typing Protocol

Staphylococcal protein A (spa) typing was performed by amplifying the spa gene as described above. PCR products were sequenced by Eton Biosciences, Inc. (Research Triangle Park, NC). spa types were assigned using the Ridom Staph Type standard protocol (http://www.ridom.com) and the Ridom SpaServer (http://spa.ridom.de/index.shtml). To assess nasal carriage prevalence of CC398 and CC9, spa types were assigned to these clonal complexes based on the scientific literature and analyses of S. aureus isolates collected from our prior livestock worker studies in North Carolina (Nadimpalli et al. 2015 (link); Rinsky et al. 2013 (link)). The spa types classified as CC398 and CC9 are listed in the Supplemental Material in “Assignment of spa types to clonal complexes (CCs).” For within household concordance, spa types were assigned to multi-locus sequence types (MLSTs) based on the scientific literature, analyses of S. aureus isolates collected from our prior livestock worker studies in North Carolina (Nadimpalli et al. 2015 (link); Rinsky et al. 2013 (link)), and queries of the Ridom SpaServer.