Data from: Resistance gene carriage predicts growth of natural and clinical Escherichia coli isolates in the absence of antibiotics

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.