"Time-kill curve analysis and pharmacodynamic functions for in vitro evaluation of antimicrobials against Neisseria gonorrhoeae"
Contains data and scripts to reproduce the figures of the paper:
Software Versions Used
R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200)
locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] censReg_0.5-20 maxLik_1.2-4 miscTools_0.6-16 magicaxis_1.9.4 sm_2.2-5.4 plotrix_3.5-12 metafor_1.9-7 Matrix_1.2-0 [9] XLConnect_0.2-11 XLConnectJars_0.2-9 drc_2.5-12 MASS_7.3-40
loaded via a namespace (and not attached): [1] Rcpp_0.12.0 nloptr_1.0.4 plyr_1.8.3 tools_3.2.0 lme4_1.1-8 nlme_3.1-120 lattice_0.20-31 mgcv_1.8-6 glmmML_1.0 [10] parallel_3.2.0 mvtnorm_1.0-3 SparseM_1.6 rJava_0.9-7 gtools_3.5.0 grid_3.2.0 nnet_7.3-9 survival_2.38-1 multcomp_1.4-1 [19] TH.data_1.0-6 minqa_1.2.4 car_2.0-25 scales_0.2.5 codetools_0.2-11 splines_3.2.0 pbkrtest_0.4-2 colorspace_1.2-6 quantreg_5.11 [28] sandwich_2.3-3 munsell_0.4.2 zoo_1.7-12
Figure 1
Example to illustrate the parameters of the pharmacodynamic function
Example to illustrate the parameters of the pharmacodynamic function
Figure 2
script Figure2.R fits linear regression to data from WHO G, WHO K, WHO L, WHO M, WHO N treated with 11 doubling concentrations of ciprofloxacin and untreated control.
Figure 3
script Figure3.R fits linear regression to one representative experiment of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline
Figure 4
A: script Figure4A.R fits linear regression to DOGK18 treated with cefixime. Regressions are shown as dotted lines.
B: script Figure4B.R fits pharmacodynamic function to DOGK18 treated with cefixime. Dotted line shows fit without outliers removed.
C: script Figure4C.R takes model parameters of plots from figure 2 from file singleplot_statistics_panel.xls and plots them as solid lines in different colors for comparison.
D: script Figure4D.R takes model parameters of plots from figure 3 from file summary_statistics_9AB (arithmetic mean of parameters from 2 replicates) and plots them as solid lines in different colors for comparison.
ABCD: Latex script to make panel from A,B,C,D
Table 1
script Pharmacodynamics_DOGK18 fits pharmacodynamic function to two independent experiments of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline. Table 1 shows the arithmetic mean of the parameters and resistance determinants as published elsewhere.
script Table1 means calculates the means of the two independent experiments.
Figure S1
script growthcurves_3curves.R fits gompertz model to Growth_GW_short.txt (data from decline phase removed, complete raw data in Growth_GW.txt)
Table S1
Pharmacodynamics_wt.R fits pharmacodynamic function to two independent experiments of DOGK18 treated with gentamicin, spectinomycin, azithromycin, benzylpenicillin, ceftriaxone, cefixime, chloramphenicole, tetracycline and summarizes parameter estimates and standard errors.
Table S2
Pharmacodynamics_panel.R fits pharmacodynamic function to to data from WHO G, WHO K, WHO L, WHO M, WHO N treated with 11 doubling concentrations of ciprofloxacin and untreated control and summarizes parameter estimates and standard errors.