Emergence of Resistance Mutations in Salmonella enterica Serovar Typhi Against Fluoroquinolones

BACKGROUND: Little is known about the evolutionary process and emergence time of resistance mutations to fluoroquinolone in Salmonella enterica serovar Typhi. METHODS: We analyzed S. Typhi isolates collected from returned travelers between 2001 and 2016. Based on ciprofloxacin susceptibility, isolates were categorized as highly resistant (minimum inhibitory concentration [MIC] ≥ 4 μg/mL [CIP(HR)]), resistant (MIC = 1–2 μg/mL [CIP(R)]), intermediate susceptible (MIC = 0.12–0.5 μg/mL [CIP(I])), and susceptible (MIC ≤ 0.06 μg/mL [CIP(S)]). RESULTS: A total of 107 isolates (33 CIP(HR), 14 CIP(R), 30 CIP(I), and 30 CIP(S)) were analyzed by whole-genome sequencing; 2461 single nucleotide polymorphisms (SNPs) were identified. CIP(S) had no mutations in the gyrA or parC genes, while each CIP(I) had 1 of 3 single mutations in gyrA (encoding Ser83Phe [63.3%], Ser83Tyr [33.3%], or Asp87Asn [3.3%]). CIP(HR) had the same 3 mutations: 2 SNPs in gyrA (encoding Ser83Phe and Asp87Asn) and a third in parC (encoding Ser80Ile). CIP(HR) shared a common ancestor with CIP(R) and CIP(I) isolates harboring a single mutation in gyrA encoding Ser83Phe, suggesting that CIP(HR) emerged 16 to 23 years ago. CONCLUSIONS: Three SNPs—2 in gyrA and 1 in parC—are present in S. Typhi strains highly resistant to fluoroquinolone, which were found to have evolved in 1993–2000, approximately 10 years after the beginning of the ciprofloxacin era. Highly resistant strains with survival advantages arose from strains harboring a single mutation in gyrA encoding Ser83Phe. Judicious use of fluoroquinolones is warranted to prevent acceleration of such resistance mechanisms in the future.