Epidemiologia genômica e determinantes da resistência antimicrobiana de isolados de Salmonella Typhimurium em Peru

Abstract

Salmonella Typhimurium is among the main serovars causing foodborne illness in Peru and worldwide. The high epidemiological record of cases of gastroenteritis, diarrhea and outbreaks transmitted by food are influenced by severe problems in the country, such as lack of access to drinking water, sanitation and deficiencies in the food sector. Regarding animal hosts, guinea pigs are an important nutritional and economic resource for the Andean region. However, they are reservoirs of the pathogen, and their production is affected by high mortality rates due to Salmonellosis and uncontrolled use of antibiotics. In 2017, the World Health Organization added Salmonella to the list of priority antibiotic-resistant bacteria. In addition, in Peru, a high profile of antimicrobial resistance has been reported in the most prevalent serovars, but the populations that are circulating and the genetic mechanisms that are associated with antimicrobial resistance are unknown. Thus, this thesis work aimed to contribute to the genomic and phenotypic surveillance system of S. Typhimurium in Peru from most clinical cases from different cities in Peru between the years 2000 and 2017. In collaboration with the National Institute of Health, it was 90 strains sequenced using Illumina technology and antimicrobial susceptibility testing was carried out in parallel with diffusion discs for ten antibiotics. The Peruvian diversity was obtained by comparing nucleotide, accessory genes, phylogeny and population with 46 global genomes of S. Typhimurium. Antimicrobial resistance (AMR) analyses were carried out with the prediction of genes and AMR mutations present in the chromosome and plasmids, genotype-phenotype correspondence and GWAS analysis to predict new genetic determinants. At least ten populations of diverse content of accessory genes are circulating in Peru, with two emerging clonal populations and three populations containing a mosaic of transmissible plasmids containing antimicrobial resistance genes. In addition, the diffusion disk test identified moderate multidrug resistance to first-line antibiotics (nalidixic acid, ampicillin, tetracycline) with genotypic correspondence, except for nitrofurantoin. Genomic analysis as a predictor of antimicrobial resistance was inconclusive due to low sensitivity values. On the other hand, six strains of S. Typhimurium were sequenced with Illumina for the analysis of guinea pig isolates, and another 20 genomes are public from food and breeding guinea pigs in Ecuador and Peru. Analysis of diversity, phylogeny and cgMLST identified at least three subpopulations (HC50_9757, HC50_67422, HC100_9460) circulating in Peru and a population (HC100_41507) of isolates from food in Ecuador, differentiated by the content of Single Nucleotide Polymorphisms (SNPs) and genes. We also identified reduced resistance from the Peruvian populations associated with transmissible plasmids and insertion sequences and AMR mutation genes associated with moderate resistance to nalidixic acid. Identifying strains from guinea pigs for breeding and food belonging to the same population or sharing transmissible resistance elements was impossible. It is concluded that there is reduced to moderate resistance to first-line antibiotics and reduced resistance to current treatment antibiotics. Antimicrobial resistance is associated with plasmids, insertion sequence, genes and populations circulating in human and guinea pig husbandry. These studies allow promoting the surveillance of reservoir sites of critical Salmonella serovars and antimicrobial resistance