The Antimicrobial Resistance Plasmid Mobilome of Salmonella enterica and Related Enteric Species and Factors that Influence the Transfer Efficiency.

The dynamic distribution of antimicrobial resistance genes in Salmonella enterica is considered a public health risk. S. enterica is one of the most important etiological agents of foodborne illness and has a critical impact on global human health. In S. enterica and related species, mobile genetic elements (MGEs) serve as primary vehicles for the dissemination of antibiotic resistance genes in the bacterial evolution. This dissemination can be impacted by different selective pressures that leads to diverse antibiotic response phenotypes. This project focusses on the dynamics of antimicrobial resistance genes, particularly exploring the transfer efficiency of multidrug resistance plasmids in S. enterica using a combination of in silico and in vitro techniques. Plasmid physiology is part of an essential genetic engineering tool has mediated the dynamic transfer and spread of antimicrobial resistance in Salmonella isolates. Several phenotypic and molecular techniques were selected in these studies to better understand the molecular biology and epidemiology of resistance plasmids. These methods included whole genome sequencing (WGS) analyses, replicon (incompatibility; Inc) typing and conjugation studies of plasmids from S. enterica and related species. Multiple in silico analyses were used to evaluate WGS and plasmid sequencing data to examine the distribution of MGEs, AMR, biocide, disinfectant, and heavy metal resistance genes across the different plasmid types and to develop a plasmid characterization database. The database supported the development of the computational algorithms to process the WGS data from S. enterica isolates and is very useful for identifying the plasmid Inc types and their specific conjugal transfer systems, which are valuable to study the diversity and dissemination of plasmids associated with AMR in S. enterica and other Enterobacteriaceae. In vitro studies explored the impact of different antimicrobial exposures on conjugal transfer potential of plasmids. For some S. enterica strains, exposure to different concentrations of tetracycline or chloramphenicol led to differences in the efficiency of AMR plasmid transfer. These data help to better understand the distribution of resistance genes and provide a useful method for a comprehensive molecular studies of plasmid transfer dynamics. The impact of these findings clarifies the role of the conjugation dynamics in the dissemination of antimicrobial resistance in S. enterica and related species, which can potentially impact the transfer of resistance genes within the gastrointestinal microbiome. Further studies are required to identify the underlying genetic mechanisms for Salmonella resistance plasmid transfer using approaches like RNA-sequencing methods to extend the understanding of the regulation of genetic pathways during conjugal transfer. Overall, the research study expands our knowledge of plasmid transfer dynamic and the provides tools that can be used to better understand AMR gene transfer among Salmonella enterica isolates which can have an impact in clinical and diagnostic laboratories as well as in epidemiological surveillance

In silico analyses of diversity and dissemination of antimicrobial resistance genes and mobile genetics elements, for plasmids of enteric pathogens

IntroductionThe antimicrobial resistance (AMR) mobilome plays a key role in the dissemination of resistance genes encoded by mobile genetics elements (MGEs) including plasmids, transposons (Tns), and insertion sequences (ISs). These MGEs contribute to the dissemination of multidrug resistance (MDR) in enteric bacterial pathogens which have been considered as a global public health risk.MethodsTo further understand the diversity and distribution of AMR genes and MGEs across different plasmid types, we utilized multiple sequence-based computational approaches to evaluate AMR-associated plasmid genetics. A collection of 1,309 complete plasmid sequences from Gammaproteobacterial species, including 100 plasmids from each of the following 14 incompatibility (Inc) types: A/C, BO, FIA, FIB, FIC, FIIA, HI1, HI2, I1, K, M, N, P except W, where only 9 sequences were available, was extracted from the National Center for Biotechnology Information (NCBI) GenBank database using BLAST tools. The extracted FASTA files were analyzed using the AMRFinderPlus web-based tools to detect antimicrobial, disinfectant, biocide, and heavy metal resistance genes and ISFinder to identify IS/Tn MGEs within the plasmid sequences.Results and DiscussionIn silico prediction based on plasmid replicon types showed that the resistance genes were diverse among plasmids, yet multiple genes were widely distributed across the plasmids from enteric bacterial species. These findings provide insights into the diversity of resistance genes and that MGEs mediate potential transmission of these genes across multiple plasmid replicon types. This notion was supported by the observation that many IS/Tn MGEs and resistance genes known to be associated with them were common across multiple different plasmid types. Our results provide critical insights about how the diverse population of resistance genes that are carried by the different plasmid types can allow for the dissemination of AMR across enteric bacteria. The results also highlight the value of computational-based approaches and in silico analyses for the assessment of AMR and MGEs, which are important elements of molecular epidemiology and public health outcomes