P-1786. "The Cloacae Conundrum: Genomic and Phenotypic Trail of Novel Enterobacter cloacae "

TL;DR

This study identifies genomic and phenotypic traits of colistin-resistant Enterobacter cloacae, highlighting resistance mechanisms and testing challenges.

Contribution

The study reveals novel sequence types and resistance mechanisms in colistin-resistant E. cloacae, including efflux pumps and AMR gene profiles.

Findings

23.8% of E. cloacae isolates were colistin-resistant by BMD, with most from ICU patients.

WGS identified 103 AMR genes, no mcr genes, and universal oqxA/B and blaACT in resistant isolates.

VITEK 2 underestimated colistin MICs compared to BMD, showing testing discrepancies.

Abstract

This study examines colistin-resistant Enterobacter cloacae isolates, focusing on genomic and phenotypic resistance mechanisms, including chromosomal mutations and efflux pumps. It also addresses challenges in susceptibility testing and genotype-phenotype discordancePhylogenetic tree (SNP based) of E. cloacae

Phylogenetic tree (SNP based) of E. cloacae

From Aug 2023 to Apr 2025, 235 E.loacae isolates were collected from various clinical samples; 56 showed colistin resistance by BMD. AST for 13 antibiotics was performed using disk diffusion. Colistin MICs were compared between VITEK 2 and BMD. WGS was performed on 18 resistant isolates using Illumina and Oxford Nanopore. Hybrid assemblies were generated via Unicycler and annotated using pubMLST, Abricate, VariantFinder, and PlasmidFinder databases

Among 235 E. cloacae isolates, 56 (23.8%) were colistin-resistant by BMD. Most patients were ICU-admitted, median age 30 years, with 66% male. These 56 isolates showed 100% resistance to amoxicillin-clavulanate and 69% to cefuroxime, yet remained fully susceptible to 13 other antibiotics. VITEK 2 consistently underestimated colistin MICs compared to BMD (e.g., 0.5 vs. 32 µg/mL). WGS of 18 resistant isolates revealed genome sizes of 4.7–5.0 Mb, all with novel sequence types, 103 AMR genes (no mcr), and universal oqxA/B and blaACT. Plasmids were detected in 72.2% (13/18), predominantly IncFIB(K)_1_Kpn3. Universal virulence genes ompA and csgG suggest enhanced pathogenicity.

A study of 235 E. cloacae isolates found 56 (23.8%) were colistin-resistant by BMD. The median age was 30 years, with 66% male, and most isolates were from ICU patients. Antibiotic susceptibility testing showed 100% susceptibility to 13 antibiotics, including tigecycline and carbapenems, but 100% resistance to amoxicillin-clavulanate and 69% to cefuroxime. Colistin MICs showed discrepancies between VITEK 2 and BMD, with BMD reporting higher MICs (16– >32 µg/mL). WGS of 18 isolates revealed novel STs, 103 AMR genes, no mcr genes, and universal oqxA/B and blaACT. Plasmids (IncFIB(K)_1_Kpn3) were found in 72.2% of isolates, and virulence genes (ompA, csgG) were present in all, with entA and entB in 22.2%. These findings suggest genetically distinct, resistant strains,novel STs may drive heteroresistance and phenotypic-genotypic discordance.

All Authors: No reported disclosures

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