Coexistence of bla_MIR-1 and bla_NDM-1 resistance genes with a novel ST type in Enterobacter roggenkampii from a stool sample: A genome sequencing study

Objective: The Enterobacter cloacae complex, known for causing infections in hospitalised patients, displays resistance to β-lactam antibiotics due to AmpC β-lactamase expression. This study emphasises the genome sequence of Enterobacter roggenkampii, which coexists with MIR-1 and NDM-1 genes, isolated from the stool of a hospitalised patient in China.

Methods: A faecal sample was diluted in Luria-Bertani broth and incubated overnight. Cultures were then spread on MacConkey agar containing meropenem and incubated for 18-24 h to select carbapenem-resistant Enterobacteriaceae. Individual colonies were isolated, and bacterial species were identified using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and 16S rRNA gene sequencing. Genomic DNA was extracted and sequenced via Illumina and Oxford Nanopore sequencing.

Results: Genomic analysis of E. roggenkampii L3897 revealed a 4 897 636 bp genome with 55.9% GC content and confirmed its classification as E. roggenkampii through average nucleotide identity-based analysis. A new sequence type distinct from ST2392, ST3014, with a unique rplB genotype was identified. Additionally, the genome harbours three antibiotic resistance genes and a newly discovered plasmid, pL3897_NDM, highlighting the need for surveillance of drug-resistant pathogens.

Conclusions: The discovery of a new sequence type and the presence of an antibiotic resistance gene in E. roggenkampii L3897 underscores the need for ongoing genomic surveillance to effectively manage multidrug-resistant pathogens.