Comparative Genomic Analysis Exposes Conserved Antimicrobial Resistance Elements and Diverse Secretion Systems in Serratia proteamaculans

Serratia proteamaculans is an environmentally widespread member of the genus Serratia isolated from aquatic animals, food products, plants, insects, environmental habitats and clinical sources. Ecologically broadly distributed, little is known about its genomic diversity and factors associated with antimicrobial resistance and virulence. The present study reports a comparative genomic analysis of 38 publicly available S. proteamaculans genomes to explore genomic diversity, antimicrobial resistance determinants, integrons, and bacterial secretion systems. Genome sizes were 4.99–5.93 Mb with GC contents of 54.5–55.5%. Pairwise average nucleotide identity (ANI) values of 97.0-99.9% confirmed that all genomes belonged to the same species, while rpoB-based phylogenetic analysis revealed moderate intraspecies diversity. None of the genomes had any integrons. Comparative resistome analysis identified 260 predicted antimicrobial resistance elements, including a conserved core resistome mainly composed of multidrug efflux pumps, aminoglycoside-modifying enzymes, regulatory proteins and chromosomally encoded β-lactamase-associated genes, and a variable accessory resistome likely acquired through horizontal gene transfer. Analysis of secretion systems revealed that the Type I secretion system (T1SS), Type IVa pili (T4aP), Type V secretion system (T5SS), and the flagellar export apparatus were present in all genomes, while the Type II secretion system (T2SS), Type VI secretion system (T6SS), Type IV secretion systems (T4SSs), Type IVb pili (T4bP), and Tight adherence (Tad) systems were present in a variable manner. These results suggest a conserved genomic backbone with accessory traits which are variable and probably responsible for ecological adaptation, environmental persistence and strain-specific functional diversity in S. proteamaculans.