Abstract
Staphylococcus aureus clonal complex 398 (CC398) isolates cluster into two distinct phylogenetic clades based on single-nucleotide polymorphisms (SNPs) revealing a basal human clade and a more derived livestock clade. The scn and tet(M) genes are strongly associated with the human and the livestock clade, respectively, due to loss and acquisition of mobile genetic elements. We present canonical single-nucleotide polymorphism (canSNP) assays that differentiate the two major host-associated S. aureus CC398 clades and a duplex PCR assay for detection of scn and tet(M). The canSNP assays correctly placed 88 S. aureus CC398 isolates from a reference collection into the human and livestock clades and the duplex PCR assay correctly identified scn and tet(M). The assays were successfully applied to a geographically diverse collection of 272 human S. aureus CC398 isolates. The simple assays described here generate signals comparable to a whole-genome phylogeny for major clade assignment and are easily integrated into S. aureus CC398 surveillance programs and epidemiological studies.
Highlights
Livestock has been considered the primary reservoir of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398); there is strong evidence of a livestockindependent S. aureus CC398 clade circulating in humans that predates the livestock clade [1,2,3,4]
Validation of the canonical single-nucleotide polymorphism (canSNP) Assays The canSNP assays correctly placed 99% (87/88) of the S. aureus CC398 reference isolates into the human clade (n = 19) and the livestock clade (n = 68)
We recently showed that the livestock-associated S. aureus CC398 clade evolved from the basal human clade, and that this human-to-livestock host jump was accompanied by the loss of a bacteriophage (WSa3) harboring scn and functionally related genes that encode modulators of human innate immunity (IEC) and acquisition of a Tn916-like transposon carrying the tet(M) gene that confers resistance to tetracycline, which is commonly used in livestock production [3]
Summary
Livestock has been considered the primary reservoir of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398); there is strong evidence of a livestockindependent S. aureus CC398 clade circulating in humans that predates the livestock clade [1,2,3,4].Epidemiological studies have shown that most livestockassociated MRSA CC398 (LA-MRSA CC398) strains colonize and transmit between humans to a lesser degree than other MRSA strains [5], they are an important cause of infection in persons having direct contact with livestock [6,7,8]. Livestock has been considered the primary reservoir of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398); there is strong evidence of a livestockindependent S. aureus CC398 clade circulating in humans that predates the livestock clade [1,2,3,4]. Livestock-associated S. aureus CC398 isolates carry a number of resistance determinants, including the staphylococcal cassette chromosome mec (SCCmec) and the tet(M) gene encoding methicillin and tetracycline resistance, respectively [3]. The existence of two major host-associated S. aureus CC398 clades emphasizes the need for rapid molecular genotyping methods in epidemiological investigations and source tracking of S. aureus CC398. We describe here two assays for defining the phylogenetic origin of S. aureus CC398 Using these assays, we were able to determine the sources of S. aureus CC398 recovered from humans and to demonstrate the existence of several scnpositive LA-MRSA CC398 isolates that may be readapting to humans
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