Rapid differentiation between livestock-associated and livestock-independent Staphylococcus aureus CC398 clades.
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.
Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark ; Translational Genomics Research Institute, Pathogen Genomics Division, Flagstaff, Arizona, United States of America.
Marc
M
Stegger
Cindy M
CM
Liu
Jesper
J
Larsen
Katerina
K
Soldanova
Maliha
M
Aziz
Tania
T
Contente-Cuomo
Andreas
A
Petersen
Stien
S
Vandendriessche
Judy N
JN
Jiménez
Caterina
C
Mammina
Alex
A
van Belkum
Saara
S
Salmenlinna
Frederic
F
Laurent
Robert L
RL
Skov
Anders R
AR
Larsen
Paal S
PS
Andersen
Lance B
LB
Price
D000820:Animal Diseases / Q000175:diagnosis* / Q000382:microbiology*; D000818:Animals; D005798:Genes, Bacterial; D006801:Humans; D058751:Livestock / Q000382:microbiology*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D013203:Staphylococcal Infections / Q000662:veterinary*; D013211:Staphylococcus aureus / Q000145:classification* / Q000235:genetics