Mobile element-mediated carbapenem resistance in Enterobacter hormaechei in a Nigerian intensive care unit

Carbapenem-resistant Gram-negative bacteria pose a critical public health threat. The role of mobile genetic elements in driving their transmission and persistence remains poorly defined. In 2022, we investigated a suspected outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) in a Nigerian adult intensive care unit (ICU), using short-read whole genome sequencing (WGS) of carbapenem-resistant clinical and environmental isolates during the cluster period. Mobile element dynamics were then inferred from hybrid assemblies of Illumina and Oxford Nanopore reads. The suspected CRAB outbreak was ruled out by WGS but a carbapenem-resistant Enterobacter hormaechei ST114 bloodstream isolate was fund to be indistinguishable from two environmental isolates, all recovered during the Acinetobacter surge. Hybrid assemblies revealed a strikingly conserved approx. 19 Kb resistance island shared across all ST114 genomes. The island contained a blaNDM-5 cassette alongside many other antimicrobial resistance genes, within class 1 integrons and flanked by insertion sequences, located on a 46,176 bp plasmid. Using the ST114 plasmid’s hybrid assembly as scaffold, the same plasmid was identified int he genome of a Klebsiella pneumoniae ST15 isolate from the ICU environment during the same period. Additionally, re-interrogation of genomic surveillance data uncovered four clonal 2020 ST109 Enterobacter bloodstream isolates from the same facility that carried the resistance genes in the same context on a large 267,242 plasmid. Carbapenem resistance in hosptial Enterobacterales is driven by both clonal expansion and horizontal spread of mobile resistance elements. These findings underscore the need to track mobile elements alongside bacterial lineages to inform evidence-based infection control, especially in low-resource settings.