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Integrated Whole-Genome Sequencing and In Silico Characterization of Salmonella Cerro and Schwarzengrund from Brazil

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Udgivet i:Genes vol. 16, no. 8 (2025), p. 880-900
Hovedforfatter: Nunes Nathaly Barros
Andre forfattere: Castro Vinicius Silva, da Cunha-Neto Adelino, Carvalho, Fernanda Tavares, Carvalho Ricardo César Tavares, Figueiredo Eduardo Eustáquio de Souza
Udgivet:
MDPI AG
Fag:
Brazil
United States > US
Beef
Pathogens
Metadata
Phylogenetics
Virulence factors
Food
Salmonella
Animals
Genomes
Data processing
Antimicrobial resistance
Nucleotide sequence
Genes
Phylogeny
Virulence
Cattle
Drug resistance
Plasmids
Whole genome sequencing
Antimicrobial agents
Milk
Serotypes
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Resumen:Background: Salmonella is a bacterium that causes foodborne infections. This study characterized two strains isolated from cheese and beef in Brazil using whole-genome sequencing (WGS). Objectives: We evaluated their antimicrobial resistance profiles, virulence factors, plasmid content, serotypes and phylogenetic relationships. Methods: DNA was extracted and sequenced on the NovaSeq 6000 platform; the pangenome was assembled using the Roary tool; and the phylogenetic tree was constructed via IQ-TREE. Results and Discussion: For contextualization and comparison, 3493 Salmonella genomes of Brazilian origin from NCBI were analyzed. In our isolates, both strains carried the aac(6′)-Iaa_1 gene, while only Schwarzengrund harbored the qnrB19_1 gene and the Col440I_1 plasmid. Cerro presented the islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5 and SPI-9, while Schwarzengrund also possessed SPI-13 and SPI-14. Upon comparison with other Brazilian genomes, we observed that Cerro and Schwarzengrund represented only 0.40% and 2.03% of the national database, respectively. Furthermore, they revealed that Schwarzengrund presented higher levels of antimicrobial resistance, a finding supported by the higher frequency of plasmids in this serovar. Furthermore, national data corroborated our findings that SPI-13 and SPI-14 were absent in Cerro. A virulence analysis revealed distinct profiles: the cdtB and pltABC genes were present in the Schwarzengrund isolates, while the sseK and tldE1 family genes were exclusive to Cerro. The results indicated that the sequenced strains have pathogenic potential but exhibit low levels of antimicrobial resistance compared to national data. The greater diversity of SPIs in Schwarzengrund explains their prevalence and higher virulence potential. Conclusions: Finally, the serovars exhibit distinct virulence profiles, which results in different clinical outcomes.
ISSN:2073-4425
DOI:10.3390/genes16080880
Fuente:Biological Science Database