Identification and Genomic Analysis of the First Salmonella typhimurium Monophasic Variant 1,4,[5],12:i:- Isolate...

We report the first clinical strain of the monophasic variant of Salmonella typhimurium (serotype 1,4,[5],12:i:-) belonging to ST34 with chromosomally integrated bla_NDM-5. Although chromosomal integration of bla_NDM-5 has been described in other Enterobacterales and Salmonella serovars, this is the first such report in this high-risk clone. This study characterises the genomic and epidemiological background of this strain. The isolate (1111-90), obtained from a paediatric patient, was subjected to antimicrobial susceptibility testing, whole-genome sequencing and comparative genomic analysis against 674 complete bla_NDM-5-positive plasmids retrieved from the PlasmidScope database. The isolate exhibited a multidrug-resistant phenotype, including carbapenem resistance, while retaining susceptibility to tigecycline and aztreonam. It harboured 13 resistance genes distributed across the chromosome and two plasmids. The ~11 kb chromosomally integrated bla_NDM-5 segment is flanked by directly oriented IS26 elements, forming an IS26-bounded composite transposon with no canonical target-site duplication at its boundaries. Phylogenetic analysis suggested that this chromosomal segment likely originated from IncX3 or IncI1 plasmid lineages prevalent in China. Comparative genetic analysis highlighted the significant role of mobile genetic elements (IS26, IS5 and IS3000) in the spread of bla_NDM-5 within S. typhimurium. The chromosomal integration of an IS26-bounded bla_NDM-5 module in S. 1,4,[5],12:i:- ST34 suggests the emergence of a stable, high-risk carbapenem-resistant clone, underscoring the need for genomic surveillance to track IS26-mediated chromosomal integration events.