Complete genome sequence of a novel fimH32 variant Escherichia coli LD91-1 ST1737, recovered from a hepatitis B patient in Yangon, Myanmar.

OBJECTIVES: In this study, we report the complete genome sequence of a multidrug-resistant Escherichia coli LD91-1 recovered from a 57-year-old hepatitis B patient in Myanmar.

METHODS: E. coli LD91-1 was subjected to antimicrobial susceptibility testing. Extracted genomic DNA from the E. coli LD91-1 clone was sequenced using a Nanopore PromethION sequencer (ONT, UK) and the high-throughput Illumina HiSeq 2500 platform. The clean reads were de novo assembled using Flye (v.2.9). The complete genome was annotated using MLST, phylogeny, serotyping, plasmid replicons, fimH typing, chromosomal point mutations, antibiotic resistance, and virulence genes using web tools available at the Center for Genomic Epidemiology.

RESULTS: E. coli LD91-1 had a circular genome of 4,838,891 bp. In silico analysis revealed that E. coli LD91-1 comprised plasmid pLD91-1 and belonged to the ST1737-O22:H16 serotype carrying a fimH32 variant that had not been reported in such strains. Core genome phylogeny demonstrated clear divergence among major E. coli clades. Mutations in the quinolone resistance-determining regions gyrA, gyrB, parC, and parE conferred fluoroquinolone resistance; mutations in pmrA and pmrB conferred colistin resistance. Cephalosporin, fluoroquinolone, and tetracycline resistance genes were located on plasmid pLD91-1. Notably, several virulence genes, including 12 encoding yersiniabactin and yersiniabactin siderophores were also revealed in the E. coli LD91-1 genome.

CONCLUSIONS: To our knowledge, this is the first complete genome report of a new E. coli LD91-1 carrying the fimH32 variant in Myanmar. This MDR E. coli isolate may pose potential risks to human and animal health, highlighting the urgent need for control and preventive strategies.