Whole-Genome Analysis of an Extensively Drug Resistant Enterobacter Hormaechei Clinical Isolate from Mosul, Iraq

Vollständiger Abstract

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Background: Enterobacter hormaechei, a significant opportunistic pathogen, is associated with antimicrobial resistance including Urinary Tract Infections (UTIs). Limited genomic information is available from Iraqi clinical isolates of E. hormaechei. This research involved an investigation of the antimicrobial resistance genes and genomic-level determinants of a single E. hormaechei clinical isolate, recovered from a UTI patient in Mosul, Iraq. The isolate was initially identified through standard bacteriological testing and 16S rRNA gene sequencing. Whole-Genome Sequencing (WGS) was performed using the Illumina NovaSeq X platform after library preparation with the Illumina TruSeq Nano DNA Library Preparation Kit (350-bp insert size), generating 150-bp paired-end reads and the reads were assembled de novo using SPAdes. Genome annotation was performed using the RAST server, resistance genes were screened using CARD (v3.2.6) and phylogenomic placement was assessed using TYGS and MEGA-11. Results: The isolate, designated ESE.iq, was resistant to 13 of the 14 antibiotics tested, with meropenem remaining active. The isolate therefore met the XDR criterion based on the tested antimicrobial classes. The draft genome assembly comprised 63 contigs totaling 4,748,095 bp, with a G+C content of 55.25% and 4,544 Predicted Coding Sequences (CDSs). CARD identified 17 resistance-associated genes, including blaCTX-M-15, blaTEM-1B, blaOXA-1, qnrB1, fosA2, tet(A), sul2, dfrA14 and aac(6')-Ib-cr. Whole-genome phylogenomics placed ESE.iq closest to E. hormaechei subsp. xiangfangensis LMG 27195 (isDDH 93.8%). The BioProject accession is PRJNA1215288, whereas JBLHDI000000000 is the genome assembly accession. Conclusion: The ESE.iq draft genome contained diverse resistance-associated determinants that were consistent with the observed XDR phenotype. Genome-based analysis supported assignment of the isolate to E. hormaechei and identified multiple predicted resistance mechanisms. These isolate-specific findings provide genomic information from Mosul, Iraq and support continued surveillance of antimicrobial resistance in Enterobacter. Functional studies and comparative analyses of additional Iraqi isolates are needed to determine the broader epidemiological significance of these findings.