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Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput.

ConcepciĆ³n-Acevedo J, Weiss HN, Chaudhry WN, Levin BR - PLoS ONE (2015)

Bottom Line: The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes.Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day.This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Emory University, Atlanta, Georgia, United States of America.

ABSTRACT
The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes. Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day. Here we compare estimates of the relative fitness of antibiotic susceptible and resistant strains of E. coli, Pseudomonas aeruginosa and Staphylococcus aureus based on MP data obtained with automated multi-well plate readers with the results from pairwise competition experiments. This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

No MeSH data available.


Related in: MedlinePlus

Malthusian parameter and pairwise competition estimates of fitness for Pseudomonas aeruginosa ciprofloxacin susceptible and resistant mutants in LB and glucose-limited minimal medium.(A) Estimates of the absolute MP of WT and PA-CIP obtained with a Bioscreen (red bars) and BioTek (black bar) plate readers. (B) MP of PA-CIP of relative to wild type P. aeruginosa in glucose-limited minimal medium and LB, Bioscreen red and BioTek black. (C) Pairwise competition, ratio of PA-CIP strain relative to wild type in LB and minimal medium, mean and standard deviation of the ratios from three independent competition experiments. (D) Longer term changes in OD of CIP resistant and sensitive strains in minimal medium and LB, Bioscreen data.
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pone.0126915.g004: Malthusian parameter and pairwise competition estimates of fitness for Pseudomonas aeruginosa ciprofloxacin susceptible and resistant mutants in LB and glucose-limited minimal medium.(A) Estimates of the absolute MP of WT and PA-CIP obtained with a Bioscreen (red bars) and BioTek (black bar) plate readers. (B) MP of PA-CIP of relative to wild type P. aeruginosa in glucose-limited minimal medium and LB, Bioscreen red and BioTek black. (C) Pairwise competition, ratio of PA-CIP strain relative to wild type in LB and minimal medium, mean and standard deviation of the ratios from three independent competition experiments. (D) Longer term changes in OD of CIP resistant and sensitive strains in minimal medium and LB, Bioscreen data.

Mentions: Pseudomonas aeruginosa: In minimal media (Min) the absolute estimate of MP for PA obtained in the Bioscreen is significantly greater than that in the BioTek but not for PA-CIP. For both strains, the MP estimated in LB is significantly greater in the Bioscreen than the BioTek (Fig 4A). Based on the 99% Bootstrap estimates of the confidence intervals, in neither minimal medium nor broth is there a significant difference in MP for the CIP mutants relative to WT (Fig 4B). Whilst for the Bioscreen the 99% Bootstrap estimate of the MP for PA-CIP relative to WT predicts a fitness cost, an MP < 1.0, with this resistant mutant in minimal medium. No fitness difference is anticipated in minimal medium for the BioTek estimate of MP. These estimates of MP predict no fitness cost of the PA-CIP mutation in LB. However, the pairwise competition experiments demonstrate a fitness cost for ciprofloxacin resistance in both minimal medium and LB. At least part of the reason for the failure of the estimates of MP in LB to detect the lower relative fitness of the CIP-R mutant in pairwise competition with WT can be seen in Fig 4C. Although there is no initial difference, as time proceeds, the rate of growth (as measured by OD changes using the Bioscreen) of the CIP mutant declines at greater rate than the wild type (Fig 4D).


Malthusian Parameters as Estimators of the Fitness of Microbes: A Cautionary Tale about the Low Side of High Throughput.

ConcepciĆ³n-Acevedo J, Weiss HN, Chaudhry WN, Levin BR - PLoS ONE (2015)

Malthusian parameter and pairwise competition estimates of fitness for Pseudomonas aeruginosa ciprofloxacin susceptible and resistant mutants in LB and glucose-limited minimal medium.(A) Estimates of the absolute MP of WT and PA-CIP obtained with a Bioscreen (red bars) and BioTek (black bar) plate readers. (B) MP of PA-CIP of relative to wild type P. aeruginosa in glucose-limited minimal medium and LB, Bioscreen red and BioTek black. (C) Pairwise competition, ratio of PA-CIP strain relative to wild type in LB and minimal medium, mean and standard deviation of the ratios from three independent competition experiments. (D) Longer term changes in OD of CIP resistant and sensitive strains in minimal medium and LB, Bioscreen data.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4482697&req=5

pone.0126915.g004: Malthusian parameter and pairwise competition estimates of fitness for Pseudomonas aeruginosa ciprofloxacin susceptible and resistant mutants in LB and glucose-limited minimal medium.(A) Estimates of the absolute MP of WT and PA-CIP obtained with a Bioscreen (red bars) and BioTek (black bar) plate readers. (B) MP of PA-CIP of relative to wild type P. aeruginosa in glucose-limited minimal medium and LB, Bioscreen red and BioTek black. (C) Pairwise competition, ratio of PA-CIP strain relative to wild type in LB and minimal medium, mean and standard deviation of the ratios from three independent competition experiments. (D) Longer term changes in OD of CIP resistant and sensitive strains in minimal medium and LB, Bioscreen data.
Mentions: Pseudomonas aeruginosa: In minimal media (Min) the absolute estimate of MP for PA obtained in the Bioscreen is significantly greater than that in the BioTek but not for PA-CIP. For both strains, the MP estimated in LB is significantly greater in the Bioscreen than the BioTek (Fig 4A). Based on the 99% Bootstrap estimates of the confidence intervals, in neither minimal medium nor broth is there a significant difference in MP for the CIP mutants relative to WT (Fig 4B). Whilst for the Bioscreen the 99% Bootstrap estimate of the MP for PA-CIP relative to WT predicts a fitness cost, an MP < 1.0, with this resistant mutant in minimal medium. No fitness difference is anticipated in minimal medium for the BioTek estimate of MP. These estimates of MP predict no fitness cost of the PA-CIP mutation in LB. However, the pairwise competition experiments demonstrate a fitness cost for ciprofloxacin resistance in both minimal medium and LB. At least part of the reason for the failure of the estimates of MP in LB to detect the lower relative fitness of the CIP-R mutant in pairwise competition with WT can be seen in Fig 4C. Although there is no initial difference, as time proceeds, the rate of growth (as measured by OD changes using the Bioscreen) of the CIP mutant declines at greater rate than the wild type (Fig 4D).

Bottom Line: The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes.Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day.This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Emory University, Atlanta, Georgia, United States of America.

ABSTRACT
The maximum exponential growth rate, the Malthusian parameter (MP), is commonly used as a measure of fitness in experimental studies of adaptive evolution and of the effects of antibiotic resistance and other genes on the fitness of planktonic microbes. Thanks to automated, multi-well optical density plate readers and computers, with little hands-on effort investigators can readily obtain hundreds of estimates of MPs in less than a day. Here we compare estimates of the relative fitness of antibiotic susceptible and resistant strains of E. coli, Pseudomonas aeruginosa and Staphylococcus aureus based on MP data obtained with automated multi-well plate readers with the results from pairwise competition experiments. This leads us to question the reliability of estimates of MP obtained with these high throughput devices and the utility of these estimates of the maximum growth rates to detect fitness differences.

No MeSH data available.


Related in: MedlinePlus