Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity

Zeyu Zhu, Defne Surujon, Juan C. Ortiz-Marquez, Wenwen Huo, Ralph R. Isberg, José Bento and Tim van Opijnen ()
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Zeyu Zhu: Boston College
Defne Surujon: Boston College
Juan C. Ortiz-Marquez: Boston College
Wenwen Huo: Tufts University School of Medicine
Ralph R. Isberg: Tufts University School of Medicine
José Bento: Boston College
Tim van Opijnen: Boston College

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: Abstract Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.

Date: 2020
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DOI: 10.1038/s41467-020-18134-z

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