Emergence of ceftriaxone resistant Salmonella Kentucky in India driven by multiple novel variants of Salmonella genomic island carrying blaCTX-M-55.

BACKGROUND

Salmonella enterica serovar Kentucky increasingly implicated in multidrug-resistant (MDR) gastroenteritis globally. While chromosomally encoded resistance mediated by Salmonella Genomic Islands (SGIs) is well established in this serovar, recent years have seen the emergence of diverse SGI backbone variants and associated resistance cassettes. However, the distribution, structural variability, and role of these SGIs particularly in ceftriaxone-resistant S. Kentucky remain poorly characterized.

METHODS

Between 2017 and 2021, 45 clinical S. Kentucky isolates were recovered from fecal samples, along with one isolate obtained from a patient with bloodstream infection (BSI). Isolates were confirmed via serotyping and MLST (all ST198), and antimicrobial susceptibility testing (AST) was performed per CLSI 2021 guidelines. Whole genome sequencing and in-depth comparative genome analyses were conducted to characterize antimicrobial resistance (AMR) determinants, SGI structures, and phylogenetic relationships.

RESULTS

All isolates belonged to the ciprofloxacin-resistant MDR clade ST198.2, specifically the ST198.2-4 sublineage. Resistance to ampicillin and ceftriaxone was widespread, driven by blaTEM-1 and blaCTX-M-55 integrated into novel SGI1-K variants. Structural analysis revealed four distinct SGI backbone configurations and extensive rearrangement within the multiple antibiotic resistance (MAR) region, including a "split" configuration in which resistance cassettes mobilized by Tn5393, Tn1721, Tn21, and an In4-type integron were translocated into the rbsK locus.

CONCLUSION

This study documents the emergence and diversification of ceftriaxone-resistant S. Kentucky in India, mediated by multiple novel chromosomal SGI1-K variants harbouring blaCTX-M-55. The dynamic rearrangement and integration of resistance determinants highlight an urgent need for ongoing genomic surveillance to limit the spread of MDR S. Kentucky in clinical settings.