Genomic insights into a multidrug-resistant uropathogenic Escherichia coli ST131-H30 strain associated with a fatal healthcare-associated infection.

OBJECTIVE

Uropathogenic Escherichia coli (UPEC) poses a significant public health challenge due to increasing antimicrobial resistance (AMR) and severe infections. This study aimed to investigate the genetic heterogeneity and AMR mechanisms of a clinical UPEC strain associated with a fatal healthcare-associated infection.

METHODS

Whole-genome sequencing (WGS) was performed on a multidrug-resistant (MDR) UPEC strain isolated from a pediatric patient by using an Illumina Miseq platform. The genome was assembled using Unicycler v0.4.8 and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Genomic analysis included characterisation of the resistome, virulome, and phylogenetic profile using various bioinformatics tools such as ResFinder v4.7.2, VFDB, and PubMLST.

RESULTS

The isolate has a genome with a size of 4,681,240 bp, a GC content of 50.60% and harbour seven plasmids. Genomic analysis revealed multiple genetic determinants contributing to a multidrug-resistant profile, including efflux systems, enzymatic target alterations, and antibiotic transporter modifications. Adhesin genes (fimH, afaA-D, lpfA, fdeC, csgA), hemolysins (hlyE, hlyF), iron acquisition systems (iucC, iutA, sitA), and genes related to antimicrobial peptide degradation (ompT, traJ) and colicin production (cma, cvaC) were identified. Resistance to heavy metals (tellurium, copper/silver, arsenic) was also detected. These findings characterise the isolate as a highly virulent, multidrug-resistant, and environmentally resilient emerging UPEC clone.

CONCLUSIONS

This study highlights the convergence of virulence, AMR, and environmental adaptability in an ST131-H30 UPEC strain. The findings underscore the critical need for comprehensive genomic surveillance, infection control strategies to mitigate the public health impact of MDR E. coli.