Phenotypic and Genotypic Analysis of a Novel 4th Generation Cephalosporin Resistant Salmonella Enterica Ser. Typhi Clinical Isolate

Abstract

A case of Typhoid fever was reported at a tertiary care hospital in Rawalpindi that was caused by an extended spectrum β-lactamase (ESBL) producing Salmonella enterica serovar Typhi (S. typhi) exhibiting resistance to ceftriaxone (3rd generation cephalosporin). Phenotypic analysis by antimicrobial susceptibility assay using KB Disk Diffusion and MIC assay by Broth Microdilution revealed the isolate to be exhibiting resistance to all commonly used antibiotics for treatment of Typhoid fever. The isolate showed susceptibility to Carbapenem class of antibiotics and was resistant to the rest of clinically prescribed antibiotics including Cefepime (4th generation Cephalosporin) and several fluroquinolone antibiotics suggesting the isolate to be classified as Extensively Drug Resistant (XDR). Genotypic analysis was done by identification of β-lactamases by PCR revealing the presence of blaCTX-M. Alkaline Lysis and Plasmid Curing Assay confirmed the isolate to be lacking plasmids. Whole Genome Sequencing and downstream analysis was employed for further genotypic analyses. Whole Genome Annotation revealed the genome to be ~4.8Mb having 4,975 CDSs, 69 tRNA genes and 4 rRNA genes. Further downstream analysis revealed the presence of a putative novel resistance island harboring numerous resistance genes (incl. blaCTX-M, blaTEM, qnrS1), insertion elements and mobile element proteins without presence of an independent plasmid along with S83F gyrA mutation along with other resistance genes that provide resistance to aminoglycosides, sulfonamides, macrolides, isoniazid and mupirocin. These genetic elements explain for the increased antimicrobial resistance by the current bacterial isolate.