Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing

Nature. 2016 Jun 30;534(7609):693-6. doi: 10.1038/nature18313. Epub 2016 Jun 22.


In 1943, Luria and Delbrück used a phage-resistance assay to establish spontaneous mutation as a driving force of microbial diversity. Mutation rates are still studied using such assays, but these can only be used to examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing, may be skewed by mutational ‘hot’ or ‘cold’ spots. Both approaches are affected by numerous caveats. Here we devise a method, maximum-depth sequencing (MDS), to detect extremely rare variants in a population of cells through error-corrected, high-throughput sequencing. We directly measure locus-specific mutation rates in Escherichia coli and show that they vary across the genome by at least an order of magnitude. Our data suggest that certain types of nucleotide misincorporation occur 10(4)-fold more frequently than the basal rate of mutations, but are repaired in vivo. Our data also suggest specific mechanisms of antibiotic-induced mutagenesis, including downregulation of mismatch repair via oxidative stress, transcription–replication conflicts, and, in the case of fluoroquinolones, direct damage to DNA.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology
  • DNA Damage / genetics
  • DNA Mismatch Repair / drug effects
  • DNA Mismatch Repair / genetics
  • DNA Replication / genetics
  • Escherichia coli / drug effects
  • Escherichia coli / genetics*
  • Escherichia coli / physiology
  • Evolution, Molecular*
  • Fluoroquinolones / pharmacology
  • Genetic Loci / drug effects
  • Genetic Loci / genetics
  • Genetic Variation / drug effects
  • Genetic Variation / genetics*
  • Genome, Bacterial / drug effects
  • Genome, Bacterial / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • INDEL Mutation / genetics
  • Mutagenesis / drug effects
  • Mutagenesis / genetics*
  • Mutation Rate*
  • Nucleotides / genetics
  • Nucleotides / metabolism
  • Oxidative Stress / genetics
  • Transcription, Genetic / genetics


  • Anti-Bacterial Agents
  • Fluoroquinolones
  • Nucleotides