Evidence map›Paper›PMID 33030625›Full record

ArticleEuropean journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology2021

Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia.

Boutheina Ksibi, Sonia Ktari, Houcemeddine Othman, Kais Ghedira, Sonda Maalej, Basma Mnif, Mohamed Salah Abbassi, Laetitia Fabre, Faouzia Rhimi, Simon Le Hello and 1 more

Abstract readComparative Study
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In one paragraph

Article in European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Genetic Diversity ofPathogens (Basel, Switzerland) · 2024
    Article
  2. Article
  3. Review
  4. Article
  5. Antimicrobial Susceptibility ofFoods (Basel, Switzerland) · 2021
    Article
  6. Article
  7. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Boutheina KsibiHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia.
Sonia KtariHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia. sonia_ktari2002@yahoo.fr.ORCID http://orcid.org/0000-0002-8090-3140
Houcemeddine OthmanSydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Kais GhediraLaboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia.
Sonda MaalejHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia.
Basma MnifHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia.
Mohamed Salah AbbassiVeterinary Research, Tunis, Tunisia.
Laetitia FabreCentre National de Référence des Escherichia coli, Shigella and Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, 75015, Paris, France.
Faouzia RhimiHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia.
Simon Le HelloCentre National de Référence des Escherichia coli, Shigella and Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, 75015, Paris, France.
Adnene HammamiHabib Bourguiba University Hospital, Research Laboratory Microorganisms and Human Disease, University of Sfax, Sfax, Tunisia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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 whole-genome 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.

Indexed as

Molecular TypingWhole Genome SequencingAnimalsElectrophoresis, Gel, Pulsed-FieldFoodborne DiseasesGenetic VariationHumansMinisatellite RepeatsPhylogenyPolymorphism, Single NucleotideSalmonella enteritidisSalmonella InfectionsSerogroupTunisiaDiversity geneticMultiple locus variable-number tandem repeat analysisPulsed-field gel electrophoresisSalmonella enterica serovar EnteritidisSingle-nucleotide polymorphismWhole-genome sequencing

Identifiers

PMID33030625

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.