Fig 1.
XDR S. Typhi strains isolated from children ages 1–13 years old.
A, Illustration showing the geographical location that XDR S. Typhi characterized in this study was isolated compared to the location that the first case of XDR S. Typhi was reported. B, PCR reactions of 45 XDR isolates for typhoid toxin pltB. C, pltB sequences from all 45 XDR isolates (XDR, one representative is shown) were identical to typhoid toxin pltB sequence of S. Typhi ISP2825 (ISP). ISP, antibiotic-susceptible S. Typhi ISP2825, GenBank accession number CP080960. N, negative control containing all PCR components except for S. Typhi genomic DNA. See S1 and S2 Tables for sample information and antibiotic breakpoints.
Fig 2.
Molecular basis of resistance to first-line antibiotics among XDR S. Typhi isolates.
A, Sample information and antibiotic resistance profiles of select of XDR S. Typhi isolates for molecular characterization. See S3 Table for details. B, PCR reactions for blaTEM1. C, PCR reactions for dhfR7 and sul1. D, PCR reactions for catA1. ISP, antibiotic-susceptible S. Typhi ISP2825. N, negative control containing all PCR components except for S. Typhi genomic DNA. See S4 Table for details.
Fig 3.
Molecular basis of fluoroquinolone-resistance among XDR S. Typhi isolates.
A-E, PCR reactions for qnrS (A), gyrA (B), gyrB (C), parC (D), and parE (E). See S4 Table for details. ISP, antibiotic-susceptible S. Typhi ISP2825. N, negative control containing all PCR components except for S. Typhi genomic DNA. F, Representative sequencing chromatogram showing GyrA S83F mutation. G, Summary of PCR amplicon sequencing analysis for gyrA, gyrB, parC, and parE. See S6 Table for additional information. WT, wild type for the known mutations.
Fig 4.
Molecular basis of third-generation cephalosporin-resistance among XDR S. Typhi isolates.
PCR reactions for blaCTX-M-15. ISP, antibiotic-susceptible S. Typhi ISP2825. N, negative control containing all PCR components except for S. Typhi genomic DNA. Note that all XDR S. Typhi isolates are resistant to cephalosporin.
Fig 5.
macA and acrB sequence analysis among XDR S. Typhi isolates.
A-B, PCR reactions for macA (A) and acrB (B). acrB was split into two pieces for more productive PCR reaction outcomes (acrB-Nterm and acrB-Cterm). ISP, antibiotic-susceptible S. Typhi ISP2825. N, negative control containing all PCR components except for S. Typhi genomic DNA. See S4 Table for details. C, Summary of PCR amplicon sequencing analysis for macA and acrB. WT, wild type for the known mutations. S, susceptible to azithromycin.
Fig 6.
AcrR sequence analysis among XDR S. Typhi isolates.
A, AcrR amino acid sequence comparison analysis of the latest RefSeq dataset of the fully assembled complete genome of S. Typhi (107 in total) collected from NCBI as of Feb 26, 2021. Ty2, S. Typhi Ty2 (RefSeq assembly accession: GCF_000007545.1, assembly name: ASM754v1, strain: Ty2, submitter: University of Wisconsin). CT18, S. Typhi CT18 (RefSeq assembly accession: GCF_000195995.1, assembly name: ASM19599v1, strain: CT18, submitter: Sanger Institute). SGB92, S. Typhi SGB92 (RefSeq assembly accession: GCF_001121865.2, assembly name: 404Ty, strain name: SGB92, submitter: Wellcome Sanger Institute). 403Ty, S. Typhi 403Ty-sc-1979084 (RefSeq assembly accession: GCF_900205275.1, assembly name: 403Ty, isolate: 403Ty-sc-1979084, submitter: Wellcome Sanger Institute). See S5 Table for details. B, PCR reactions for acrR. ISP, antibiotic-susceptible S. Typhi ISP2825. N, negative control containing all PCR components except for S. Typhi genomic DNA. C, Summary of PCR amplicon sequencing analysis for acrR. WT, wild type for the known mutations. S, susceptible to azithromycin.