Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

Abstract

Rodrigues et al. AMR Salmonella From Brazil frequency rates of antimicrobial resistance genes and predicted resistance phenotypes in the 2000s and the 2010s when compared with the 1980s and 1990s. The results presented herein contributed significantly to the understanding of the strategic use of WGS associated with in silico analysis and the predictions for the determination of AMR in Salmonella from Brazil.

Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

“…Full resistance is usually exhibited by isolates that bear multiple quinolone resistance genes, including mutations within the quinolone-resistance-determining regions (QRDR) of the gyrA , gyrB , parC and parE genes [ 47 ]. Nonetheless, NAL and CIP-resistant S. Schwarzengrund isolates that possess qnrB19 , but lack QRDR mutations, have been isolated from chicken by-products in Brazil [ 48 ].…”

Antimicrobial Resistance Gene Detection Methods for Bacteria in Animal-Based Foods: A Brief Review of Highlights and Advantages

“…With greater awareness of the risks of indiscriminate use of these antimicrobials, future problems in the treatment of pathogens can be mitigated. [28,75,80,93]…”

“…Some of these techniques have great advantages, such as the fast execution time of qPCR and the identification of all resistomes in a sample using metagenomics. Each technique also has particular limitations, e.g., execution time, low reproducibility of results, instability of the RNA molecule, specific equipment, technicians capable of executing it, and bioinformatics expertise, most of them required for greater reliability of results [28,31,32] This brief review aims to compile the techniques for detection of antimicrobial resistance (AMR) using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results in addressing some of the technical aspects, and then to discuss the application of these techniques for specific purposes.…”

“…The existence of viable non-cultivable microorganisms, or the long time that certain microorganisms may have to multiply in the environment, ends up being an obstacle to some researches [ 14 , 25 , 26 , 27 ]. On the other hand, molecular methods are essentially based on the amplification of target genes (i.e., PCR, real-time PCR (qPCR), multiplex PCR, random amplified polymorphic DNA (RAPD), PCR combined with restriction fragment length polymorphism (PCR–RFLP)), whole-genome sequencing and metagenomics [ 28 , 29 , 30 ]. Although more expensive than traditional cultivation, they are essential tools for the study of multiple microbiomes.…”

“…Some of these techniques have great advantages, such as the fast execution time of qPCR and the identification of all resistomes in a sample using metagenomics. Each technique also has particular limitations, e.g., execution time, low reproducibility of results, instability of the RNA molecule, specific equipment, technicians capable of executing it, and bioinformatics expertise, most of them required for greater reliability of results [ 28 , 31 , 32 ]…”