Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enter
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ORIGINAL ARTICLE
Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia Boutheina Ksibi 1 & Sonia Ktari 1,2 & Houcemeddine Othman 3 & Kais Ghedira 4 & Sonda Maalej 1 & Basma Mnif 1 & Mohamed salah Abbassi 5 & Laetitia Fabre 6 & Faouzia Rhimi 1 & Simon Le Hello 6,7 & Adnene Hammami 1 Received: 5 May 2020 / Accepted: 30 September 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract 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. Keywords Salmonella enterica serovar Enteritidis . Diversity genetic . Pulsed-field gel electrophoresis . Multiple locus variable-number tandem repeat analysis . Whole-genome sequencing . Single-nucleotide polymorphism Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10096-020-04055-8) contains supplementary material, which is available to authorized users. * Sonia Ktari [email protected]
Mohamed salah Abbassi [email protected]
Boutheina Ksibi [email protected]
Laetitia Fabre [email protected]
Houcemeddine Othman [email protected]
Faouzia Rhimi [email protected]
Kais Ghedira [email protected]
Simon Le Hello [email protected]
Sonda Maalej [email protected] Basma Mnif [email protected]
Adnene
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