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Leão C, Silveira L, Usié A, Gião J, Clemente L, Themudo P, Amaro A, Pista A. Genetic Diversity of Salmonella enterica subsp. enterica Serovar Enteritidis from Human and Non-Human Sources in Portugal. Pathogens 2024; 13:112. [PMID: 38392849 PMCID: PMC10892295 DOI: 10.3390/pathogens13020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
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.
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Affiliation(s)
- Célia Leão
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, 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;
- MED—Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento & CHANGE–Global Change and Sustainability Institute, CEBAL, 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; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, 1300-477 Lisbon, 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; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal;
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Romero-Calle DX, Pedrosa-Silva F, Ribeiro Tomé LM, Fonseca V, Guimarães Benevides R, de Oliveira Santos LTS, de Oliveira T, da Costa MM, Alcantara LCJ, de Carvalho Azevedo VA, Brenig B, Venancio TM, Billington C, Góes-Neto A. Molecular Characterization of Salmonella Phage Wara Isolated from River Water in Brazil. Microorganisms 2023; 11:1837. [PMID: 37513009 PMCID: PMC10384808 DOI: 10.3390/microorganisms11071837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/07/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial resistance is increasing despite new treatments being employed, so novel strategies are required to ensure that bacterial infections remain treatable. Bacteriophages (phages; bacteria viruses) have the potential to be used as natural antimicrobial methods to control bacterial pathogens such as Salmonella spp. A Salmonella phage, Wara, was isolated from environmental water samples at the Subaé River Basin, Salvador de Bahia, Brazil. The basin has environmental impacts in its main watercourses arising from the dumping of domestic and industrial effluents and agricultural and anthropological activities. The phage genome sequence was determined by Oxford Nanopore Technologies (ONT) MinION and Illumina HiSeq sequencing, and assembly was carried out by Racon (MinION) and Unicycler (Illumina, Illumina + MinION). The genome was annotated and compared to other Salmonella phages using various bioinformatics approaches. MinION DNA sequencing combined with Racon assembly gave the best complete genome sequence. Phylogenetic analysis revealed that Wara is a member of the Tequintavirus genus. A lack of lysogeny genes, antimicrobial resistance, and virulence genes indicated that Wara has therapeutic and biocontrol potential against Salmonella species in healthcare and agriculture.
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Affiliation(s)
- Danitza Xiomara Romero-Calle
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | - Francisnei Pedrosa-Silva
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Luiz Marcelo Ribeiro Tomé
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Vagner Fonseca
- General Coordination of Public Health Laboratories/Secretariat of Health Surveillance, Ministry of Health, Brasília 70800-400, Brazil
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Raquel Guimarães Benevides
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
| | | | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mateus Matiuzzi da Costa
- Department of Biological Sciences, Federal University of the São Francisco Valley, Petrolina 56304-917, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
- Flavivirus Laboratory, Oswaldo Cruz Institute, Rio de Janeiro 21040-900, Brazil
| | | | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, 37073 Göttingen, Germany
| | - Thiago M Venancio
- Laboratory of Chemistry, Function of Proteins and Peptides, Center for Biosciences and Biotechnology, Darcy Ribeiro North Fluminense State University (UENF), Campos dos Goytacazes 28013-602, Brazil
| | - Craig Billington
- Health & Environment Group, Institute of Environmental Sciences and Research, Christchurch 8540, New Zealand
| | - Aristóteles Góes-Neto
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Av. Transnordestina S/N, Feira de Santana 44036-900, Brazil
- Molecular and Computational Biology of Fungi Laboratory, Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
- Department of Biological Sciences, Feira de Santana State University (UEFS), Feira de Santana 44036-900, Brazil
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