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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 E. coli antibiotic sensitive and resistant mutants and transconjugants in LB and glucose-limited minimal medium.(A) Estimates of the MP in minimal medium (left panel) and broth (right panel), Bioscreen (BS, red bar) and BioTek (BT, black bar). (B) Relative to WT growth rates of BAM-Nal and BAM-JCA in minimal and broth. (C) Ratio of antibiotic sensitive (WT) and resistant mutants in pairwise competition; BAM-Nal and WT (blue) and BAM-JCA and WT (black). Mean and standard error for 3 independent cultures from the same initial mixture.
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pone.0126915.g005: Malthusian parameter and pairwise competition estimates of fitness for E. coli antibiotic sensitive and resistant mutants and transconjugants in LB and glucose-limited minimal medium.(A) Estimates of the MP in minimal medium (left panel) and broth (right panel), Bioscreen (BS, red bar) and BioTek (BT, black bar). (B) Relative to WT growth rates of BAM-Nal and BAM-JCA in minimal and broth. (C) Ratio of antibiotic sensitive (WT) and resistant mutants in pairwise competition; BAM-Nal and WT (blue) and BAM-JCA and WT (black). Mean and standard error for 3 independent cultures from the same initial mixture.

Mentions: E. coli: The MP estimated from the BioTek data is significantly lower than that obtained with the Bioscreen in both Minimal medium and LB (Fig 5A). There is no machine-associated difference in the ratio of the MP of the Nal-R (BAM-NAL) mutants and pJCA transconjugants (BAM-JCA) relative to WT (BAM) in LB, or an anticipated fitness cost of these mutants and transconjugants in LB (Fig 5A). On the other hand, in accord with the bootstrap estimates of the 99% confidence intervals, there is a highly significant difference in this ratio for the estimates of the MPs of these strains in minimal medium. Most critically, whilst the BioTek data predict no fitness cost for the resistant strains in minimal media, a substantial fitness cost of these resistant mutants and transconjugants is anticipated in minimal medium from the Bioscreen date but not in LB (Fig 5B). The pairwise competition experiments between these resistant clones and WT reveal a fitness cost for the BAM-Nal mutant and BAM-JCA transconjugants in both minimal media and broth (Fig 5C).


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 E. coli antibiotic sensitive and resistant mutants and transconjugants in LB and glucose-limited minimal medium.(A) Estimates of the MP in minimal medium (left panel) and broth (right panel), Bioscreen (BS, red bar) and BioTek (BT, black bar). (B) Relative to WT growth rates of BAM-Nal and BAM-JCA in minimal and broth. (C) Ratio of antibiotic sensitive (WT) and resistant mutants in pairwise competition; BAM-Nal and WT (blue) and BAM-JCA and WT (black). Mean and standard error for 3 independent cultures from the same initial mixture.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482697&req=5

pone.0126915.g005: Malthusian parameter and pairwise competition estimates of fitness for E. coli antibiotic sensitive and resistant mutants and transconjugants in LB and glucose-limited minimal medium.(A) Estimates of the MP in minimal medium (left panel) and broth (right panel), Bioscreen (BS, red bar) and BioTek (BT, black bar). (B) Relative to WT growth rates of BAM-Nal and BAM-JCA in minimal and broth. (C) Ratio of antibiotic sensitive (WT) and resistant mutants in pairwise competition; BAM-Nal and WT (blue) and BAM-JCA and WT (black). Mean and standard error for 3 independent cultures from the same initial mixture.
Mentions: E. coli: The MP estimated from the BioTek data is significantly lower than that obtained with the Bioscreen in both Minimal medium and LB (Fig 5A). There is no machine-associated difference in the ratio of the MP of the Nal-R (BAM-NAL) mutants and pJCA transconjugants (BAM-JCA) relative to WT (BAM) in LB, or an anticipated fitness cost of these mutants and transconjugants in LB (Fig 5A). On the other hand, in accord with the bootstrap estimates of the 99% confidence intervals, there is a highly significant difference in this ratio for the estimates of the MPs of these strains in minimal medium. Most critically, whilst the BioTek data predict no fitness cost for the resistant strains in minimal media, a substantial fitness cost of these resistant mutants and transconjugants is anticipated in minimal medium from the Bioscreen date but not in LB (Fig 5B). The pairwise competition experiments between these resistant clones and WT reveal a fitness cost for the BAM-Nal mutant and BAM-JCA transconjugants in both minimal media and broth (Fig 5C).

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