Detection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 Strain Phylogroup A: ST167 from a Poultry Farm in Egypt.

This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes and are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (), trimethoprim (), β-lactams (), aminoglycosides (, , , , and ), tetracycline ((A)), and chloramphenicol (). It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding includes IS-IS---F-1-2-IS. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (IS) are critical vehicles for the dissemination of and its related variants. To our knowledge, this is the first genomic report of a /IncX3-carrying isolate of animal origin globally.