Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken

• Published in: BMC microbiology 2024-11, Vol.24 (1), p.497-17, Article 497
• Main Authors: Bu, Xiangfeng, Wu, Yufan, Hong, Yi, Shi, Juping, Shao, Jingdong, Jia, Kai, Dong, Qingli, Wang, Xiang
• Format: Article
• Language: English
• Subjects: Acids; Analysis; Animals; Anopheles; Anti-Bacterial Agents - pharmacology; Antibacterial agents; Antibiotic resistance; Antibiotics; Antimicrobial agents; Antimicrobial resistance; beta-Lactamases - genetics; Care and treatment; Chickens; Chickens - microbiology; Colistin; Contamination; Diagnosis; Diseases; DNA sequencing; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Multiple, Bacterial - genetics; Food; Food chains; Foodborne diseases; Foodborne pathogens; Gene mutations; Gene sequencing; Genes; Genetic analysis; Genetic aspects; Genome, Bacterial; Genomes; Genomic analysis; Genomic islands; Genomic Islands - genetics; Genomics; Growth; Humans; Islands; Medical research; Medicine, Experimental; Microbial Sensitivity Tests; Mobile genetic elements; Multidrug resistance; Multidrug-resistant; Nucleotide sequencing; Pathogenicity; Pathogenicity islands; Pathogens; Phylogenetic analysis; Phylogenetics; Phylogeny; Plasmids; Plasmids - genetics; Point mutation; Polymyxin B; Poultry Diseases - microbiology; Prevention; Prophages; Public health; Risk factors; Salmonella; Salmonella Enteritidis; Salmonella enteritidis - drug effects; Salmonella enteritidis - genetics; Salmonella enteritidis - isolation & purification; Salmonella Infections - microbiology; Salmonella Infections, Animal - microbiology; Software; Sulbactam; Surveillance; Tetracycline; Tetracyclines; Transposons; Virulence; Virulence (Microbiology); Virulence factors; Whole Genome Sequencing; β Lactamase
• ISSN: 1471-2180; 1471-2180
• DOI: 10.1186/s12866-024-03651-4

Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including bla , bla , bla , aph(3')-IIa, aph(3'')-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain.