Genomic surveillance captures resistance evolution in Salmonella enterica ST376 during prolonged disseminated infection in an immunocompromised patient from the United Arab Emirates.

BACKGROUND

Invasive non-typhoidal Salmonella infections represent a clinical challenge in immunocompromised patients, yet genomic data from the Middle East remain scarce. This study aimed to characterize Salmonella enterica sequence type 376 (ST376), reported for the first time in the United Arab Emirates (UAE), through clinical and genomic analysis of two isolates from blood and bone tissue.

METHODS

A 52-year-old woman with breast cancer developed disseminated salmonellosis with bacteremia, bilateral septic arthritis, and osteomyelitis. One isolate from bone tissue (SA1) and one from blood (SA2) underwent antimicrobial susceptibility testing and whole-genome sequencing to characterize resistance, virulence, and phylogenomic relationships.

RESULTS

Both isolates were identified as monophasic S. typhimurium ST376. The genomes were highly similar (average nucleotide identity >99%) and differed by 10 core SNPs. They shared an invasive virulence repertoire, including SPI-1, SPI-2, fimbrial, and spv genes, and both carried quinolone-resistance mutations and the tet(B) gene. The blood isolate (SA2) additionally harbored blaTEM-1A, floR, lnu(G), sul2, aac(3)-IIa, aph(3'')-Ib, and aph(6)-Id. Phylogenetic analysis placed these isolates within the global ST376 lineage, with closest relatedness to Middle Eastern isolates from Lebanon.

CONCLUSIONS

This is the first comprehensive genomic and clinical characterization of the rare monophasic S. typhimurium ST376 from the UAE. The genomic differences between the two closely related isolates may reflect within-host diversification; however, alternative explanations, including infection with multiple closely related strains, cannot be excluded. These findings highlight the importance of integrated genomic surveillance within a One Health framework to better understand the emergence of rare and antimicrobial-resistant Salmonella lineages.