Genetic Diversity of <i>Salmonella enterica</i> subsp. <i>enterica</i> Serovar Enteritidis from Human and Non-Human Sources in Portugal
Célia Leão,
Leonor Silveira,
Ana Usié,
Joana Gião,
Lurdes Clemente,
Patricia Themudo,
Ana Amaro,
Angela Pista
Affiliations
Célia Leão
Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal
Leonor Silveira
National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
Ana Usié
Department of Animal Genomics and Bioinformatics, Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal
Joana Gião
Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal
Lurdes Clemente
Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal
Patricia Themudo
Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal
Ana Amaro
Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal
Angela Pista
National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the leading causes of foodborne infections associated with broilers and laying hens. Portugal has had the lowest notification rates of salmonellosis in recent years, due to the vaccinations of layer and breeder flocks and strict compliance with biosecurity measures. However, data about the genetic diversity of S. Enteritidis in Portugal are scarce. In this study, 102 S. Enteritidis isolates selected from human (n = 63) and non-human sources (n = 39) were characterized by serotyping, antimicrobial susceptibility, and whole genome sequencing. The S. Enteritidis population was mainly resistant to fluoroquinolones, and a sole isolate showed resistance to extended-spectrum cephalosporins. ST11 was the most frequent sequence type, and three novel STs from human isolates (ST9236, ST4457, and ST9995) were assigned. Several Salmonella pathogenic islands (SPI) and Putative SPI were present in the genomes, namely SPI-1, 2, 3, 4, 5, 9, 10, 12, 13, and 14, C63PI, CS54_island, and 170 virulence genes were identified. The phylogenetic analysis revealed that strains from Portugal are genetically heterogeneous regarding sample type, collection date, and genetic content. This study increases the available data, essential to a better characterization of strains in a global context.
