DOI: 10.5061/dryad.d0q331t
title: Data from: Resistance gene carriage predicts growth of natural and clinical Escherichia coli isolates in the absence of antibiotics

description: Bacterial pathogens that carry antibiotic resistance alleles sometimes pay
 a cost in the form of impaired growth in antibiotic-free conditions. This
 cost of resistance is expected to be a key parameter for understanding how
 resistance spreads and persists in pathogen populations. Analysis of
 individual resistance alleles from laboratory evolution and natural
 isolates has shown they are typically costly, but these costs are highly
 variable and influenced by genetic variation at other loci. It therefore
 remains unclear how strongly resistance is linked to impaired
 antibiotic-free growth in bacteria from natural and clinical scenarios,
 where resistance alleles are likely to coincide with other types of
 genetic variation. To investigate this, we measured the growth of 92
 natural and clinical Escherichia coli isolates across three
 antibiotic-free environments. We then tested whether variation of
 antibiotic-free growth among isolates was predicted by their resistance to
 10 antibiotics, while accounting for the phylogenetic structure of the
 data. We found that isolates with similar resistance profiles had similar
 antibiotic-free growth profiles, but it was not simply that higher average
 resistance was associated with impaired growth. Next, we used whole-genome
 sequences to identify antibiotic resistance genes and found that isolates
 carrying a greater number of resistance gene types grew relatively poorly
 in antibiotic-free conditions, even when the resistance genes they carried
 were different. This suggests that the resistance of bacterial pathogens
 is linked to growth costs in nature, but it is the total genetic burden
 and multivariate resistance phenotype that predict these costs, rather
 than individual alleles or mean resistance across antibiotics. IMPORTANCE
 Managing the spread of antibiotic resistance in bacterial pathogens is a
 major challenge for global public health. Central to this challenge is
 understanding whether resistance is linked to impaired bacterial growth in
 the absence of antibiotics, because this determines whether resistance
 declines when bacteria are no longer exposed to antibiotics. We studied 92
 isolates of the key bacterial pathogen Escherichia coli; these isolates
 varied in both their antibiotic resistance genes and other parts of the
 genome. Taking this approach, rather than focusing on individual genetic
 changes associated with resistance as in much previous work, revealed that
 growth without antibiotics was linked to the number of specialized
 resistance genes carried and the combination of antibiotics to which
 isolates were resistant but was not linked to average antibiotic
 resistance. This approach provides new insights into the genetic factors
 driving the long-term persistence of antibiotic-resistant bacteria, which
 is important for future efforts to predict and manage resistance.
description: Data_FilesThe folder contains files needed perform the analysis described in “Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics”. As well as the data contained here, several data sets from a previous paper are used. This paper is titled "Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates", for which the data are freely available at https://doi.org/10.5061/dryad.gj318. Please see Readme file for more information.