TABLE 2

Panel of housekeeping genes with amino acid variants known to be associated with antimicrobial resistancea

Antimicrobial agentGeneAmino acid substitutionsbReference gene accession no. (nucleotide positions)
CiprofloxacingyrAS84L, E88K, G106D, S85P, E88G, E88LBX571857.1 (7005–9668)
grlAS80F, S80Y, E84K, E84G, E84V, D432G, Y83N, A116E, I45M, A48T, D79V, V41G, S108NBX571857.1 (1386869–1389271)
grlBR470D*, E422D*, P451S*, P585S*, D443E*, R444S*BX571857.1 (1384872–1386869)
Fusidic acidfusAA160V*, A376V, A655E, A655P*, A655V*, A67T*, A70V*, A71V*, B434N, C473S*, D189G*, D189V*, D373N*, D463G*, E233Q*, E444K, E444V*, E449K*, F441Y, F652S*, G451V, G452C, G452S, G556S, G617D, G664S, H438N, H457Q, H457Y, L430S*, L456F, L461K, L461S, M161I*, M453I, M651I, P114H, P404L, P404Q, P406L, P478S, Q115L, R464C, R464H, R464S, R659C, R659H, R659L, R659S, R76C*, S416F*, T385N, T387I*, T436I, T656K, V607I, V90A, V90I, Y654N*BX571857.1 (577685–579766)
RifampinrpoBA473T*, A477D, A477T*, A477V, D471G*, D471Y, D550G, H481D, H481N, H481Y, I527F, I527L*, I527 M*, ins 475H, ins G475*, L466S*, M470T*, N474K*, Q456K, Q468K, Q468L, Q468R, Q565R*, R484H, S463P, S464P, S486L, S529L*BX571857 (568813–572364)
TrimethoprimdfrBF99Y, F99S, F99I, H31N, L41F, H150R, L21V*, N60I*BX571857.1 (1464014–1464493)
  • a All housekeeping gene sequences were obtained from the genome of reference strain MSSA 476 (7).

  • b An asterisk indicates that the amino acid substitution was reported in association with other variants. For the expected effect of each variant/combination on MIC, please see the supplemental data. ins, insertion.