Genome analysis of Uropathogenic Morganella morganii isolate from Sri Lanka

Abstract

Morganella morganii is an opportunistic Gram-negative pathogen increasingly implicated in both community and hospital-acquired infections.Though once considered relatively susceptible to conventional antimicrobials, the recent emergence of multidrug-resistant (MDR) M. morganii strains have raised significant clinical concern, particularly due to their ability to produce extended-spectrum beta-lactamases (ESBL) and AmpC beta-lactamases. The clinical management of M. morganii has become increasingly complicated as it continues to acquire additional resistance genes and virulence determinants via mobile genetic elements (MGEs). This study reports the first molecular characterisation of a uropathogenic M.moganii isolate from a hospital-acquired urinary tract infection in Sri Lanka, using whole genome sequencing and comparative genomics. Phenotypic testing for antimicrobial susceptibility was positive for ESBL production, AmpC β-lactamase activity, and carbapenemase production. Whole genome sequencing resulted in a draft genome, consisting of 71 contigs with a total length of 3,673,417 base pairs, GC content of 51.33%, and N50 value of 903,001 bp. Use of ResFinder and NCBI BLAST against the genomes revealed chromosomal ampC β-lactamase genes consistent with intrinsic resistance to ampicillin, amoxicillin, and early-generation cephalosporins. The phenotypic resistance to extended-spectrum beta-lactamases and carbapenems might be due to overexpression of AmpC β-lactamases, as well as alternative mechanisms like porin loss or efflux pump over-expression. A Virulence Factor screening using the Virulence Factor Database was negative for classical virulence factors such as urease subunits, hemolysins or fimbrial adhesins, indicating either yet uncharacterised virulence mechanisms or highly divergent gene sequences. Mobile genetic element studies showed that no plasmid replicons, integrons, and insertion sequences were detected, which suggested that the chromosomal localisation of resistance determinants. This study reveals the intricate discrepancy between phenotypic and genotypic profiles of M. morganii and demonstrates the need for implementing whole genomic analysis for precise virulence and antimicrobial resistance characterisation.