1. Epidemiology and Global Health
  2. Microbiology and Infectious Disease
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Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure

  1. Stephen Baker  Is a corresponding author
  2. Pham Thanh Duy
  3. Tran Vu Thieu Nga
  4. Tran Thi Ngoc Dung
  5. Voong Vinh Phat
  6. Tran Thuy Chau
  7. A Keith Turner
  8. Jeremy Farrar
  9. Maciej F Boni
  1. Wellcome Trust Major Overseas Programme, Vietnam
  2. University of Oxford, United Kingdom
  3. The London School of Hygeine and Tropical Medicine, United Kingdom
  4. The Wellcome Trust Sanger Institute, United Kingdom
Research Article
Cite this article as: eLife 2013;2:e01229 doi: 10.7554/eLife.01229
6 figures, 1 table and 1 additional file

Figures

Comparing two methods for calculation of allele frequencies.

(A) Pyrosequencing-measured allele frequencies (y-axis) of a range of S83F/parent strain dilutions plotted against enumeration-measured frequencies (x-axis) (n = 198). A linear regression between the two variables (solid black line) explains 90% of the variation in the relationship between these two measurements. (B) The same 198 data points (y-axis) are shown plotted against the original bacterial dilution ratio (x-axis). The broken line is the diagonal highlighting where predicted frequency and measured frequency would be identical. 18 measurement replicates were performed for each predicted frequency of S83F from 0.0 to 1.0.

https://doi.org/10.7554/eLife.01229.004
Likelihood profiles for the selection coefficients from 12 competition experiments.

Data generated by competing 12 S. Typhi mutants (labeled at the top of each panel) against the parent S. Typhi strain over approximately 150 generations. Open circles correspond to likelihood values over the entirety of the experiment (primary y-axis); the filled gray circles correspond to the maximum likelihood estimates (MLE) for the variance parameter σ (secondary y-axis), describing the 24-hourly variance in both process and measurement. The MLE selection coefficient (s^) is shown in the top right of each panel. Vertical dashed lines demark the 95% confidence intervals for the MLE s^. Note the compressed x-axis scale in the bottom-right panel.

https://doi.org/10.7554/eLife.01229.005
Fitness coefficients computed from 5 and 15 days of bacterial competition.

Black boxes show fitness coefficients computed across the entire 15-day competition. White boxes show fitness coefficients computed from the first 5 days only. The ΔaroC F10T mutation is that of the control strain. Horizontal lines are 95% confidence intervals. In a situation of compensatory evolution, we would expect to see the white box to the left of the black box.

https://doi.org/10.7554/eLife.01229.006
Likelihood profiles for the epistasis coefficient (ε^) from the four double mutant competition experiments.

Open circles correspond to likelihood values; the filled gray circles correspond to the maximum likelihood estimate (MLE) for the variance parameter σ, describing the 24-hourly variance in both process and measurement. The MLE epistasis coefficient ε^ is shown in the top right of each panel. Vertical dashed lines demark the 95% confidence intervals for the MLE ε^.

https://doi.org/10.7554/eLife.01229.007
Relationships among MICs, selection coefficients and epistasis parameters of S. Typhi mutants.

Diagram depicts the interactions among MLE selection coefficients (s^) (x-axis), MICs to ciprofloxacin (y-axis), and MLE epistasis coefficients ε^. Black circles denote S. Typhi strains that have been isolated clinically, while gray circles denote S. Typhi strains that have not been isolated clinically. Lines correspond to epistatic interactions of the four double mutants, two of which have been isolated clinically (black lines and ε^ value) and two of which have not (gray lines and ε^ value). The grayed upper half of graph highlights the current MIC breakpoint indicative of resistance and increasing risk of treatment failure (>0.125 μg/ml).

https://doi.org/10.7554/eLife.01229.008
Likelihood profiles for the epistasis coefficient (ε^) of three possible epistatic interactions that could have generated the triple-mutant S83F-D87G-S80I.

The interaction types are described on the top of each panel. The left panel shows the epistatic interaction among three single mutations. The middle and right panels show the epistatic interaction between a single mutation and a double mutation (joined by a hyphen). Open circles correspond to likelihood values; the filled gray circles correspond to the maximum likelihood estimate (MLE) for the variance parameter σ, describing the 24-hourly variance in both process and measurement. The MLE epistasis coefficient ε^ is shown in the top right of each panel. Vertical dashed lines demark the 95% confidence intervals for the MLE ε^.

https://doi.org/10.7554/eLife.01229.009

Tables

Table 1

S. Typhi mutants constructed for this study

https://doi.org/10.7554/eLife.01229.003
S. Typhi strainGenotypeMinimum inhibitory concentrations (μg/ml)
Nalidixic acidNorfloxacinOfloxacinCiprofloxacinGatifloxacinLevofloxacin
Parent BRD948ΔaroA, ΔaroC, ΔhtrA1.50.0640.0470.0080.0080.012
DPT001SNP in ΔaroC (codon 10)1.50.0640.0470.0080.0080.012
S83YSNP in gyrA (codon 83)2560.50.250.1250.1250.125
S83FSNP in gyrA (codon 83)2560.750.380.1250.1250.125
D87ASNP in gyrA (codon 87)480.750.190.0940.0640.064
D87NSNP in gyrA (codon 87)480.750.250.1250.1250.125
D87GSNP in gyrA (codon 87)480.750.250.1250.1250.25
S80ISNP in parC (codon 80)30.190.0470.0160.0160.016
D87G-S80ISNP in gyrA (codon 87) and SNP in parC (codon 80)25610.250.1250.0940.094
S83F-D87G2 SNPs in gyrA (codons 83 and 87)25610.380.190.250.25
S83F-D87A2 SNPs in gyrA (codons 83 and 87)1921.50.380.250.380.25
S83F-D87N2 SNPs in gyrA (codons 83 and 87)640.750.380.190.190.19
S83F-D87G-S80I2 SNP in gyrA (codons 83 & 87) and SNP in parC (codon 80)2562416823

Additional files

Supplementary file 1

Oligonucleotides used in this study.

https://doi.org/10.7554/eLife.01229.010

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