GENOMIC DIVERSITY AND RESISTOME PROFILING OF MULTI-DRUG RESISTANT SALMONELLA ENTERICA SUBSP. ENTERICA ISOLATED IN BANGLADESH

Abstract

Intro: The Salmonella enterica cause 21.6 49 million illnesses and 216,000 deaths worldwide during 2000 and remains a substantial global health concern. Multidrug-resistance (MDR) in Salmonella is increasing but its whole-genome sequence (WGS) based resistome profile was merely evaluated in Bangladesh. In this study, we aimed to identify the key genomic features of MDR Salmonella. Methods: Both Salmonella strains (Z12888 and Z13019) were isolated from diarrheal patients and subjected to WGS analysis based on their antimicrobial resistant (AMR) profiles to the five different classes of antibiotics (Macrolides, Penicillins, Tetracycline, Quinolones and Cephems). Genomes were sequenced on Illumina MiSeq platform and analyzed using several bioinformatics approaches. Findings: The MDR Z12888 strain was resistant to all five groups of antibiotics and its genome was substantially rich with AMR genes, virulence factors and mobile genetic elements (MGEs). Five different types of plasmid (IncHI2, IncN, IncQ1, Col440I and ColpVC) were identified in Z12888 strain. It also possessed 17 AMR genes (against 7 classes of antibiotics) of which seven genes were plasmid-borne. The AMR genes were arrayed as resistance gene cassettes like int1-aacC-aadA7-qacEdelta1-sul1 in an integron region, and sul2-aph (3) Ib and ant (2) Ia-dfrA14 were in plasmids. We found 117 MGEs in the MDR strain Z12888 of which 31 were plasmid borne. Fimbrial protein encoding genes (faeC-F and faeH), secretion system effector genes (sseK1 and steB), and flagellar chemotaxis associated gene tsr were uniquely found virulence factors in Z12888 strain. Additionally, 6 phage integrations were detected in Z12888. On the other hand, non-MDR Salmonella enterica Z13019 was harboring one IncX3 family plasmid with quinolone resistant gene qnrB7. Three phages and 68 MGEs (5 plasmid borne MGEs) were also detected in Z13019. Conclusion: The AMR genes were originated as pathogenicity islands in chromosome or MGEs. Epidemiological mapping of AMR profiles in large population may guide the current treatment strategy more precisely and effectively.