Nanopore sequencing elucidates in vivo development of meropenem resistance by insertion of a mobile genetic element in the porin gene ompC in E. coli

Abstract

An ESBL-producing E. coli isolate recovered from a patient undergoing long-term treatment developed resistance to meropenem without acquiring carbapenem-hydrolysing enzymes. We performed Nanopore and Illumina sequencing and subsequent full hybrid genome assembly of this isolate and the meropenem-susceptible isolate recovered almost 8 weeks prior. Whole genome MLST patterns did not differ between isolates. However, we found the insertion of an IS5-like element in the sequence of the ompC gene and an increase in the number of copies of the CTX-M-15 gene in the resistant isolate. These results show that E. coli can develop meropenem resistance under antibiotic pressure by mutations in ompC genes and increasing the copy number of ESBL genes, and the value of next generation sequencing to reveal resistance mechanisms not detected by conventional PCR.