1. Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia
- Author
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Mohamed Salah Abbassi, Boutheina Ksibi, Faouzia Rhimi, Kais Ghedira, Simon Le Hello, Adnene Hammami, Houcemeddine Othman, Basma Mnif, Sonia Ktari, Laetitia Fabre, Sonda Maalej, Université de Sfax - University of Sfax, Faculté de médecine - Faculty of Medicine [Sfax, Tunisie] (FMS), University of the Witwatersrand [Johannesburg] (WITS), Laboratoire de Bioinformatique, biomathématiques, biostatistiques (BIMS) (LR11IPT09), Université de Tunis El Manar (UTM)-Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Veterinary Research, Tunis, Tunisia, Bactéries pathogènes entériques (BPE), Institut Pasteur [Paris] (IP), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), and This work was supported financially by the Research Laboratory Microorganisms and Human Disease 'MPH LR03SP03' - Higher Education and Scientific Research in Tunisia.
- Subjects
0301 basic medicine ,Serotype ,[SDV]Life Sciences [q-bio] ,Minisatellite Repeats ,Foodborne Diseases ,0302 clinical medicine ,MESH: Animals ,MESH: Genetic Variation ,030212 general & internal medicine ,Pulsed-field gel electrophoresis ,MESH: Phylogeny ,Phylogeny ,Single-nucleotide polymorphism ,Genetics ,MESH: Molecular Typing ,MESH: Polymorphism, Single Nucleotide ,General Medicine ,Salmonella enterica serovar Enteritidis ,Subtyping ,Electrophoresis, Gel, Pulsed-Field ,MESH: Electrophoresis, Gel, Pulsed-Field ,Infectious Diseases ,Salmonella Infections ,MESH: Tunisia ,MESH: Whole Genome Sequencing ,Diversity genetic ,Microbiology (medical) ,Tunisia ,Salmonella enteritidis ,030106 microbiology ,Biology ,Multiple Loci VNTR Analysis ,Serogroup ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Animals ,Humans ,Typing ,MESH: Foodborne Diseases ,Whole genome sequencing ,Whole-genome sequencing ,MESH: Humans ,MESH: Salmonella Infections ,Whole Genome Sequencing ,Multiple locus variable-number tandem repeat analysis ,Genetic Variation ,Outbreak ,MESH: Serogroup ,bacterial infections and mycoses ,Molecular Typing ,MESH: Minisatellite Repeats ,MESH: Salmonella enteritidis - Abstract
International audience; We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtyping Salmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175 Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and wholegenome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-five Salmonella Enteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification of Salmonella Enteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey of Salmonella Enteritidis lineages in Tunisia using WGS.
- Published
- 2020