Antimicrobial resistance is a major public health problem and is mainly due to the indiscriminate use of antimicrobials in human and veterinary medicine. The consumption of animal-based foods can contribute to the transfer of these genes between animal and human bacteria. Resistant and multi-resistant bacteria such as Salmonella spp. and Campylobacter spp. have been detected both in animal-based foods and in production environments such as farms, industries and slaughterhouses. This review aims to compile the techniques for detecting antimicrobial resistance using traditional and molecular methods, highlighting their advantages and disadvantages as well as the effectiveness and confidence of their results.

Salmonella Minnesota has emerged in Brazil as the predominant serovar in poultry and poultry products, along with Salmonella Heidelberg. To understand the emergence of Salmonella Minnesota over the last few years in Brazil, we performed a comparative analysis between 69 selected S . Minnesota genomes from Pathogen Detection database and 65 clonal emergent genomes isolated from Brazil. We demonstrate the presence of multidrug resistance genes against tetracycline [ tet (A)], sulfonamide ( sul2 ), and AmpC beta-lactamase ( bla _CMY-2 ) in emergent genomes, along with the carriage of a megaplasmid of resistance and virulence (~210 kb), designated pESM (plasmid for emergent Salmonella Minnesota). pESM is an IncC/A2 plasmid predicted to increase S . Minnesota environmental tolerance to mercury ( mer operon) and provide resistance to tetracycline and ampicillin due to the presence of tet (A) and bla _CMY-2 , respectively. Moreover, pESM carries the yersiniabactin siderophore (high-pathogenicity island of Yersinia ) related to the iron uptake. The temporal inference demonstrated that the most recent common ancestor dated from ~1978 and that the clonal emergent genomes carrying the pESM belong to a completely different lineage of S . Minnesota. Our results indicate that the presence of pESM likely contributes to the emergence of S . Minnesota and is precisely related to the successful spread of this particular clonal lineage in Brazil. IMPORTANCE: Salmonella Minnesota has emerged in Brazil as one of the leading serovars related to human and animal infection, presenting high virulence and antibiotic resistance to drugs classified as the highest priority for clinical treatment in humans. This study performed whole-genome sequencing, temporal analysis, and phylogenetics to understand the genetic insights related to the emergence of Salmonella Minnesota in Brazil. Long-read sequencing has led to the identification and characterization of a unique megaplasmid carrying virulence, antibiotic resistance, and heavy-metal tolerance genes, which may play a central role in S . Minnesota’s successful emergence in Brazil and possibly worldwide. The potentially high transmissibility of this plasmid between clones and serovars represents a risk to public health since its acquisition may increase Salmonella ’s fitness, virulence, resistance, and persistence. Understanding the genetic aspects related to the emergence of serovars can help devise measures to mitigate the spread of hazardous multidrug-resistant strains.

Salmonella Isangi is an infrequent serovar that has recently been reported in several countries due to nosocomial infections. A considerable number of reports indicate Salmonella Isangi multidrug resistance, especially to cephalosporins, which could potentially pose a risk to public health worldwide. Genomic analysis is an excellent tool for monitoring the emergence of microorganisms and related factors. In this context, the aim of this study was to carry out a genomic analysis of Salmonella Isangi isolated from poultry in Brazil, and to compare it with the available genomes from the Pathogen Detection database and Sequence Read Archive. A total of 142 genomes isolated from 11 different countries were investigated. A broad distribution of extended-spectrum beta-lactamase (ESBL) genes was identified in the Salmonella Isangi genomes examined (bla_CTX-M-15, bla_CTX-M-2, bla_DHA-1, bla_NDM-1, bla_OXA-10, bla_OXA-1, bla_OXA-48, bla_SCO-1, bla_SHV-5, bla_TEM-131, bla_TEM-1B), primarily in South Africa. Resistome analysis revealed predicted resistance to aminoglycoside, sulfonamide, macrolide, tetracycline, trimethoprim, phenicol, chloramphenicol, and quaternary ammonium. Additionally, PMQR (plasmid-mediated quinolone resistance) genes qnr19, qnrB1, and qnrS1 were identified, along with point mutations in the genes gyrA^D87N, gyrA^S83F, and gyrB^S464F, which confer resistance to ciprofloxacin and nalidixic acid. With regard to plasmids, we identified 17 different incompatibility groups, including IncC, Col(pHAD28), IncHI2, IncHI2A, IncM2, ColpVC, Col(Ye4449), Col156, IncR, IncI1(Alpha), IncFIB (pTU3), Col(B5512), IncQ1, IncL, IncN, IncFIB(pHCM2), and IncFIB (pN55391). Phylogenetic analysis revealed five clusters grouped by sequence type and antimicrobial gene distribution. The study highlights the need for monitoring rare serovars that may become emergent due to multidrug resistance.

Background: Staphylococcus aureus constitutes a significant public health threat due to its exceptional adaptability, antimicrobial resistance (AMR), and capacity to form biofilms, all of which facilitate its persistence in clinical and environmental settings. Methods: This study undertook an extensive in silico analysis of 44,069 S. aureus genomic sequences acquired from the NCBI database to assess the global distribution of biofilm-associated and resistance-associated genes. The genomes were categorized into human clinical and environmental groups, with clinical samples representing a predominant 96%. Results: The analysis revealed notable regional discrepancies in sequencing efforts, with Europe and North America contributing 76% of the genomes. Key findings include the high prevalence of the ica locus, which is associated with biofilm formation, and its robust correlation with other genes, such as sasG, which was exclusively linked to SCCmec type IIa. The AMR gene analysis revealed substantial genetic diversity within environmental samples, with genes like vga(E) and erm being identified as particularly prominent. The clonal complex analysis revealed ST8 (USA300) and ST5 as the predominant types in human clinical isolates, while ST398 and ST59 were most frequently observed in environmental isolates. SCCmec type IV was globally prevalent, with subtype Iva being strongly associated with ST8 in North America and subtype IVh with ST239 in Europe. Conclusions: These findings underscore the dynamic evolution of S. aureus via mobile genetic elements and highlight the necessity for standardized metadata in public genomic databases to improve surveillance efforts. Furthermore, they reinforce the critical need for a One Health approach in monitoring S. aureus evolution, particularly concerning the co-dissemination of biofilm and resistance genes across various ecological niches.

Whole-genome sequencing identified three previously unidentified multilocus sequence types of Campylobacter jejuni (ST-12332) and Campylobacter coli (ST-12333 and ST-12663), harboring resistance genes for multiple antimicrobial classes. The sources of isolation highlight the circulation of resistance strains within animals and humans, emphasizing the need for preventive measures.