Characterization of multidrug resistant Salmonella enterica and antimicrobial resistance plasmids isolated from clinical and community sources using phenotypic testing and hybrid whole genome sequencing

Abstract

Introduction

Antimicrobial resistance (AMR) has emerged as a critical global health problem. Sharing of genetic materials, especially plasmids, plays a key role for the dissemination of AMR across bacterial genera. Identification of resistance plasmids in community and clinical bacteria remains a significant challenge for microbiology studies. The objective of this research was to characterize multidrug-resistant (MDR) S. enterica isolated from clinical and community sources focusing on phenotypic properties and molecular characterization, especially resistance plasmids, using conventional assays and hybrid whole genome sequencing.

Material and Methods

Two hundred twenty-one of S. enterica was collected from clinical samples in two hospitals (n=115) and community sources such as meat products from fresh markets (n=106) in Bangkok, Thailand. Phenotypic and molecular characterization tests were conducted to select bacterial candidates for hybrid whole genome sequencing (WGS) using Illumina and Oxford nanopore platforms and data analysis was performed.

Results

In total, 27.15% (60/221) of Salmonella isolates was classified as MDR, exhibiting resistance to tetracycline, sulphadiazine, ampicillin, etc. Thirty isolates were selected for WGS. Each candidate contained at least twenty-nine resistance genes and various mobile genetic elements (MGEs). For plasmid analysis, twenty-three contigs were characterized as antimicrobial resistance plasmids. At alignment score ≥ 70.00%, the plasmids could be divided into the five groups. One group demonstrated the linkage between clinical plasmids and plasmids from chicken meat with 98.00% coverage and 100% identity. In addition to resistance genes, both plasmids also contained high similar plasmid stability function, mobile genetic elements and genes associated with horizontal transfer.

Discussion

This study showed the evidence of AMR plasmid sharing between clinical and community isolates via food chain. Such information could promote awareness regarding the dissemination of MDR plasmids.