Understanding how adaptation to a given antibiotic increases the sensitivity to other antibiotics is of great medical importance for the understanding of evolutionary trade-offs. Here, the first experimental map of such collateral sensitivity is presented, along with insights into the underlying mechanisms.

Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B.Molecular biology studies rely heavily on Escherichia coli for essential operations, ranging from the simple propagation of plasmid DNA to the creation of large clone libraries for wholegenome sequence determination. Among the strains developed as hosts for these everyday applications, DH10B (17) is commonly used across the research community, taking advantage of particularly useful properties exhibited by the strain. These include high transformation efficiency, the ability to take up and stably maintain large plasmids, the lack of methylation-dependent restriction systems (MDRS), and colony screening via lacZ-based ␣-complementation. However, analysis of sequenced bacterial artificial chromosome (BAC) clones derived from DH10B shows a high incidence of insertion sequence (IS) transposition from the chromosome into the cloned fragment (25).The genome of DH10B was constructed before the modern era of molecular biology, through a series of genetic manipulations (Fig. 1). The progenitors were all K-12 strains, with the exception of D7091F, in which a region surrounding the ⌬(araA-leu)7697 deletion had been derived from E. coli B SB3118 by P1 transduction (John Wertz, personal communication). Ultimately, MC1061 (9) served as a starting point for Hanahan and coworkers to replace alleles by using a series of P1 transductions that resulted in DH10B (17). Among the engineered gene replacements were recA1 ...

Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies.