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

2018; Microbiology Society; Volume: 4; Issue: 10 Linguagem: Inglês

10.1099/mgen.0.000213

2057-5858

David R. Greig, Timothy J. Dallman, Katie L. Hopkins, Claire Jenkins,

Infections and bacterial resistance

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