Abstract
Salmonella is a leading human pathogen and a significant public health concern worldwide. Massive food production and distribution have contributed to this pathogen dissemination, which, combined with antimicrobial resistance (AMR), creates new control challenges in food safety. The development of AMR is a natural phenomenon and can occur in the bacterial evolutionary process. However, the overuse and the misuse of antimicrobial drugs in humans and in animals have increased AMR selective pressure. In Brazil, there is an accuracy lack in AMR frequency in Salmonella because too many isolates are under-investigated for genetic and phenotypic AMR by the Brazilian health authorities and the research community. This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. The present study aimed to use bioinformatics tools for a rapid in silico screening of the genetic antimicrobial resistance profile of Salmonella through whole-genome sequences (WGS). A total of 930 whole-genome sequences of Salmonella were retrieved from the public database of the National Biotechnology Information Center (NCBI). A total of 65 distinct resistance genes were detected, and the most frequent ones were tet(A), sul2, and fosA7. Nine point mutations were detected in total, and parC at the 57 position (threonine → serine) was the highest frequent substitution (26.7%, 249/930), followed by gyrA at the 83 position (serine → phenylalanine) (20.0%, 186/930) and at the 87 position (aspartic acid → asparagine) (15.7%, 146/930). The in silico prediction of resistance phenotype showed that 58.0% (540/930) of the strains can display a multidrug resistance (MDR) profile. Ciprofloxacin and nalidixic acid were the antimicrobial drugs with the highest frequency rates of the predicted phenotype resistance among the strains. The temporal analysis through the last four decades showed increased 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.
Highlights
Salmonella is a frequent human pathogen, and salmonellosis is a global public health concern
The increasing frequency of the predicted AMR profiles among S. enterica reflected on the collected genomes over the last four decades represents a national public health concern, mainly due to the frequent cross-contamination between food, clinical, FIGURE 5 | (A) Temporal distribution of antimicrobial resistance genes within Salmonella whole-genome sequences (WGS) in Brazil from the 1980s to the 2010s. (B) Temporal distribution of the chromosomal mutations within Salmonella WGS in Brazil from the 1980s to the 2010s. (C) Temporal distribution of the predicted antimicrobial resistance phenotype by antimicrobial class within Salmonella WGS in Brazil from the 1980s to the 2010s
It is of concern that little epidemiological surveillance data of AMR is publicly available in Brazil
Summary
Salmonella is a frequent human pathogen, and salmonellosis is a global public health concern. Among the diarrheal and/or invasive agents, including bacteria, viruses, protozoa, helminths, and chemicals, Salmonella is among the 31 pathogens with a high capability of causing intestinal or systemic disease in humans (World Health Organization [WHO] (ed.), 2015). It is the third cause of death among food-transmitted diseases (World Health Organization [WHO] (ed.), 2015). The massive production and the broad distribution of food have contributed to the rapid dissemination of this pathogen worldwide, which, combined with the presence of antimicrobial resistance (AMR) strains, creates new control challenges in food safety and public health on a global scale (Majowicz et al, 2010). When the antimicrobials commonly used against the pathogenic bacteria are no longer effective, it is necessary to use drugs considered until the moment as “reserve” or “last resort” and these antimicrobials are often overpriced and/or can cause strong side effects (O’Neill, 2016)
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