MinION nanopore sequencing identifies the position and structure of bacterial antibiotic resistance determinants in a multidrug-resistant strain of enteroaggregative Escherichia coli

• DOI: 10.1099/mgen.0.000213
• Publication Date: 2018-09-20T17:12:47Z
• Authors: David R. Greig; Timothy J. Dallman; Katie L. Hopkins; Claire Jenkins
• Keywords: Minion; Salmonella enterica

The aim of this study was to use single-molecule, nanopore sequencing explore the genomic environment resistance determinants in a multidrug-resistant (MDR) strain enteroaggregative Escherichia coli serotype O51 : H30, sequence type (ST) 38. Sequencing performed on MinION Flow cell MIN-106 R9.4. Nanopore raw FAST5 reads were base-called using Albacore v1.2.1, converted FASTA and FASTQ formats Poretools v0.6.0, assembled Unicycler v0.4.2, combining long-read data with short-read produced by Illumina sequencing. genome interrogated against an antimicrobial (AMR) gene reference database blast . majority 12 AMR identified clustered together chromosome at three separate locations flanked integrases and/or insertion elements [region 1 – catA , bla OXA-1 aac(6′)-Ib- cr, tetA CTX-M-15 ; region 2 dfrA1 aadA1 3 TEM-1 sul2 ]. located outside these regions chromosomally encoded CMY-16 mutations gyrA parC two plasmid-encoded determinants, OXA-181 qnrS1 same IncX3 plasmid. Long-read analysis whole mobile genetic which revealed combination different co-located element. These contribute better understanding transmission MDR E. causing gastrointestinal extra-intestinal infections.