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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 S. aureus ciprofloxacin and fusidic acid susceptible and resistant mutants (A) Growth rates estimates from three S. aureus strains using a Bioscreen (BS, red bar) and BioTek (BT, black bar) plate readers. SA is an antibiotic sensitive strain, SA-CIP is a ciprofloxacin resistant strain and SA-FUS is a fusidic acid resistant strain. (B) Malthusian parameters relative to wild type (SA), (Bioscreen red BioTek black) and Bootstrap-calculated confidence intervals. (C) Changes in the ratio of the antibiotic resistant mutants and SA WT in pairwise competition SA-CIP (black) and SA-FUS (blue), mean and standard deviation of the ratios from three independent competition experiments.
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pone.0126915.g003: Malthusian parameter and pairwise competition estimates of fitness for S. aureus ciprofloxacin and fusidic acid susceptible and resistant mutants (A) Growth rates estimates from three S. aureus strains using a Bioscreen (BS, red bar) and BioTek (BT, black bar) plate readers. SA is an antibiotic sensitive strain, SA-CIP is a ciprofloxacin resistant strain and SA-FUS is a fusidic acid resistant strain. (B) Malthusian parameters relative to wild type (SA), (Bioscreen red BioTek black) and Bootstrap-calculated confidence intervals. (C) Changes in the ratio of the antibiotic resistant mutants and SA WT in pairwise competition SA-CIP (black) and SA-FUS (blue), mean and standard deviation of the ratios from three independent competition experiments.

Mentions: S. aureus: For two of the three strains examined (SA and SA-FUS) the absolute value of the MP estimated in the Bioscreen is significantly greater than the corresponding estimate in the BioTek (Fig 3A). Considering the bootstrap 99% confidence intervals (Fig 3B) there are no statistically significant machine differences in the relative to WT MPs of the SA-FUS mutant. This was not the case for the SA-CIP mutant, where the relative to WT estimate of the MP in the BioTek is significantly greater than the corresponding estimate obtained with the Bioscreen. The estimates of the MP obtained with both machines predict a fitness cost for the fuscidic acid resistance mutant (SA-FUS). Our pairwise competition results support this prediction (Fig 3C, blue line). For the SA-CIP, the pairwise competition experiments predict little or no fitness cost for the ciprofloxacin resistance mutant (Fig 3C, black line). This is consistent with what is anticipated from the relative MP estimates obtained in the BioScreen (Fig 3B), whilst the BioTek relative growth rate difference suggests a fitness advantage for the Ciprofloxicin resistant mutant.


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 S. aureus ciprofloxacin and fusidic acid susceptible and resistant mutants (A) Growth rates estimates from three S. aureus strains using a Bioscreen (BS, red bar) and BioTek (BT, black bar) plate readers. SA is an antibiotic sensitive strain, SA-CIP is a ciprofloxacin resistant strain and SA-FUS is a fusidic acid resistant strain. (B) Malthusian parameters relative to wild type (SA), (Bioscreen red BioTek black) and Bootstrap-calculated confidence intervals. (C) Changes in the ratio of the antibiotic resistant mutants and SA WT in pairwise competition SA-CIP (black) and SA-FUS (blue), mean and standard deviation of the ratios from three independent competition experiments.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4482697&req=5

pone.0126915.g003: Malthusian parameter and pairwise competition estimates of fitness for S. aureus ciprofloxacin and fusidic acid susceptible and resistant mutants (A) Growth rates estimates from three S. aureus strains using a Bioscreen (BS, red bar) and BioTek (BT, black bar) plate readers. SA is an antibiotic sensitive strain, SA-CIP is a ciprofloxacin resistant strain and SA-FUS is a fusidic acid resistant strain. (B) Malthusian parameters relative to wild type (SA), (Bioscreen red BioTek black) and Bootstrap-calculated confidence intervals. (C) Changes in the ratio of the antibiotic resistant mutants and SA WT in pairwise competition SA-CIP (black) and SA-FUS (blue), mean and standard deviation of the ratios from three independent competition experiments.
Mentions: S. aureus: For two of the three strains examined (SA and SA-FUS) the absolute value of the MP estimated in the Bioscreen is significantly greater than the corresponding estimate in the BioTek (Fig 3A). Considering the bootstrap 99% confidence intervals (Fig 3B) there are no statistically significant machine differences in the relative to WT MPs of the SA-FUS mutant. This was not the case for the SA-CIP mutant, where the relative to WT estimate of the MP in the BioTek is significantly greater than the corresponding estimate obtained with the Bioscreen. The estimates of the MP obtained with both machines predict a fitness cost for the fuscidic acid resistance mutant (SA-FUS). Our pairwise competition results support this prediction (Fig 3C, blue line). For the SA-CIP, the pairwise competition experiments predict little or no fitness cost for the ciprofloxacin resistance mutant (Fig 3C, black line). This is consistent with what is anticipated from the relative MP estimates obtained in the BioScreen (Fig 3B), whilst the BioTek relative growth rate difference suggests a fitness advantage for the Ciprofloxicin resistant mutant.

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