Genomic characterisation of a multidrug-resistant Escherichia coli strain carrying the mcr-1 gene recovered from a paediatric patient in China.

Abstract Objectives The global spread of carbapenem-resistant Enterobacterales has become a leading public health threat. The lack of effective treatment has resulted in the use of colistin as a last-resort therapeutic option for multidrug-resistant bacterial infections. Here, we report the complete genome sequence of a multidrug-resistant Escherichia coli strain carrying a plasmid-mediated colistin resistance gene mcr-1 recovered from a Chinese pediatric patient. Methods Whole genome sequence of E. coli strain 1506 was determined using both Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of both short Illumina reads and long MinION reads was performed using Unicycler. In silico Multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicons were identified from the genome sequence. The core genome multilocus sequence typing (cgMLST) analysis between E. coli 1506 and all of the ST48 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server. Results The complete genome sequence of E. coli 1506 consists of six contigs that comprised 4,849,058 bp, including one chromosome and five plasmids, and could be assigned to ST48. Fourteen antimicrobial resistance genes were identified, including mcr-1 that located on a 33,309 bp IncX4 plasmid. The closest relative of E. coli 1506 was another isolate originated from livestock in Australia, which differed by 614 cgMLST alleles. Conclusion Our study reports the genome sequence of a multidrug-resistant E. coli carrying mcr-1 gene isolated from a pediatric patient in China. These data may help to understand the antimicrobial resistance mechanisms, genomic features and to highlight the growing threat of antimicrobial resistance in Children.