Genomic profiling of Morganella morganii: insights into antibiotic resistance genes, pathogenicity islands, and toxin-antitoxin systems.

Morganella morganii is an opportunistic pathogen affecting immunocompromised and hospitalized intensive care patients. It colonizes diverse environments and exhibits multidrug resistance. Its genome encodes factors that impart pathogenicity and resistance to multiple antibiotics. This study provided insights into the resistome, mobilome, and toxin-antitoxin systems of M. morganii strains from human clinical samples, food, animals, and wastewater. The pangenome predicted 2,852 core genes shared by >99% of the strains, with >30% of coding sequences annotated as hypothetical proteins co-localizing with virulence factors on mobile genetic elements (MGEs). M. morganii carried 1-3 plasmids and up to 71 diverse MGEs, independent of strain source. The strains shared unique 13-33 GI clusters (10-167 kb) in chromosomes and plasmids harboring transposable elements, phage-associated proteins, toxin-antitoxins (TAs), and additional virulence determinants. Diverse antimicrobial resistance genes, including aac(3)-lld, blaKPC, and blaNDM, were identified. A total of 24 distinct TA families were identified, predominantly belonging to the type II group, and three were identified as types IV and VII. The hha-tomB, higBA, mazEF, vapBC, and doc-phd TAs were the most prevalent, typically occurring as a single copy (hha-tomB) or multiple copies (higBA) in all strains. Although the presence or absence of plasmid and other mobile genetic elements influences the number of resistance genes, it has less of an effect on toxin-antitoxin system distribution. These findings emphasize the significance of MGEs in the evolution and propagation of antimicrobial resistance genes and virulence factors within M. morganii, highlighting their contribution to bacterial adaptation and survival in hostile environments.IMPORTANCEMorganella morganii, an emerging opportunistic pathogen, has garnered increasing attention in recent years due to its role in nosocomial infections and rising antimicrobial resistance (AMR). This study provides a comprehensive genomic analysis of M. morganii strains from diverse sources, revealing how mobile genetic elements (MGEs) drive the spread of AMR genes and virulence factors. By mapping the resistome, mobilome, and toxin-antitoxin (TA) systems across the pangenome, we uncover the conserved and variable genomic features that enable M. morganii to thrive in clinical and environmental niches. Our findings offer novel insights into the potential genomic determinants of persistence, adaptation, and multidrug resistance in an understudied and emerging opportunistic pathogen, informing surveillance strategies and the development of targeted interventions. This study shows that M. morganii encodes chromosomal and mobile genetic element-mediated virulence factors. Resistance and virulence determinants in M. morganii are comparable to those of other known pathogenic bacteria; hence, they should be given significant research attention.