Supporting information for "Genomic signatures of virulence and resistance for Serratia marcescens revealed by analysis of clinical isolates from India"

Serratia marcescens is an opportunistic pathogen that is widely known to cause healthcare-associated infections with significant morbidity and mortality, particularly in high-risk settings. In this study, the genomic characteristics of S. marcescens isolates from an Indian tertiary care hospital outbreak of septicemia were investigated to better understand the genetic elements associated with pathogenicity and antibiotic resistance. Several mobile genetic elements, such as prophage sequences, genomic islands, and plasmid sequences, IncFIB(K), were present in the genome encoding various virulence and fitness traits, including FlhDC-ShlBA, Type Six Secretion System, pgaABCD operon, mannose-resistant (MR), and mannose-sensitive (MS) pilus. Phenotypic resistance to aminoglycoside group of antibiotics (gentamicin) was observed in 43% of the isolates analyzed, encoding aminoglycoside modifying enzymes, eight isolates that showed resistance to cefepime and aztreonam carried CTX-M-15, OXA-1, TEM-1 beta-lactamase resistance genes. Seven co-trimoxazole-resistant isolates harbored drfA14 and sul2 which confer resistance to trimethoprim and sulphonamide, respectively. None of the 16 S. marcescens isolates showed complete resistance to the fluoroquinolones tested in this study. Pan-genome analysis of 16 S. marcescens isolates identified 9601 genes, comprising 2476 core, 3488 shell, and 3637 cloud genes, demonstrating an open pan-genome shaped by horizontal gene transfer. Core genome phylogeny revealed vertical inheritance and close relatedness among isolates, while accessory gene-based clustering highlighted unit-specific adaptations and possible inter-unit transmission. Functional categorization showed core genes encoding essential metabolic functions, whereas accessory and unique genes contributed to motility, secretion, and niche-specific environmental interactions. The observations from this study highlight genetic versatility of the S. marcescens isolates.