A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium

Gand, Mathieu; Mattheus, Wesley; Roosens, Nancy; Dierick, Katelijne; Marchal, Kathleen; Bertrand, Sophie; Keersmaecker, Sigrid C. J. De

doi:10.1016/j.fm.2020.103534

Cited by 12 publications

(4 citation statements)

References 32 publications

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“…The genus Salmonella , the causative agent of foodborne salmonellosis, can infect both animals and humans, leading to public health problems and economic loss ( Gand M. et al, 2020a ). Most Salmonella infections are caused by consuming contaminated water or food ( Kasturi, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

“…Currently, Salmonella is divided into two species and six subspecies. Serotypes are further classified into more than 2,600 serovars following the White–Kauffman–Le Minor scheme, using antigenic agglutination reactions to three cell-surface antigens of somatic O, and flagellar H antigens denoted as H1 and H2 ( Grimont and Weill, 2007 ; Yachison et al, 2017 ; Zhang et al, 2019 ; Gand M. et al, 2020a ). As a reliable surveillance protocol is critical for detecting outbreaks or preventing their spread, using a differential serotyping method that identifies serogroups and serovars of Salmonella isolates from causative agents is important ( Kasturi, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis

Yang

Kim

et al. 2021

Front. Microbiol.

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An accurate diagnostic method for Salmonella serovars is fundamental to preventing the spread of associated diseases. A diagnostic polymerase chain reaction (PCR)-based method has proven to be an effective tool for detecting pathogenic bacteria. However, the gene markers currently used in real-time PCR to detect Salmonella serovars have low specificity and are developed for only a few serovars. Therefore, in this study, we explored the novel unique gene markers for 60 serovars that share similar antigenic formulas and show high prevalence using pangenome analysis and developed a real-time PCR to detect them. Before exploring gene markers, the 535 Salmonella genomes were evaluated, and some genomes had serovars different from the designated serovar information. Based on these analyses, serovar-specific gene markers were explored. These markers were identified as genes present in all strains of target serovar genomes but absent in strains of other serovar genomes. Serovar-specific primer pairs were designed from the gene markers, and a real-time PCR method that can distinguish between 60 of the most common Salmonella serovars in a single 96-well plate assay was developed. As a result, real-time PCR showed 100% specificity for 199 Salmonella and 29 non-Salmonella strains. Subsequently, the method developed was applied successfully to both strains with identified serovars and an unknown strain, demonstrating that real-time PCR can accurately detect serovars of strains compared with traditional serotyping methods, such as antisera agglutination. Therefore, our method enables rapid and economical Salmonella serotyping compared with the traditional serotyping method.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis

Yang

Kim

et al. 2021

Front. Microbiol.

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“…Considering that ONT has recently introduced R10.4.1 flow cells with similar sequencing accuracy to Illumina sequencing for DNA ( 21 , 71 ), ONT sequencing could be an alternative sequencing technique in bacterial genomics. While in silico serotyping based on Illumina WGS data is applied on a routine basis in some laboratories ( 72 ), ONT sequencing may become more integrated in public health laboratories. This study, in line with other studies in bacterial genomics, shows the potential of ONT sequencing for routine laboratories ( 73 – 76 ).…”

Section: Discussionmentioning

confidence: 99%

Oxford nanopore technologies—a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella

2023

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Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.

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“…Similar to the GeXP system, bead-based multiplex assays are applicable for high throughput and can simultaneously analyze up to 50-500 different targets within a single sample depending on the instrument and assay applied. In diagnosing poultry infectious agents bead-based multiplex PCRs were used in (i) parallel detection of different pathogens and (ii) typing of pathogens [218][219][220][221][222]. The clear advantage of both GeXP-analyzer-and Luminex-based methods is the much higher number of targets that can be detected in a single reaction as compared to real-time PCR or conventional PCR, which speeds up the diagnostics process.…”

Section: Molecular Diagnosticsmentioning

confidence: 99%

Diagnosing Infectious Diseases in Poultry Requires a Holistic Approach: A Review

Liebhart

Bilić

Grafl

et al. 2023

Poultry

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Controlling infectious diseases is vital for poultry health and diagnostic methods are an indispensable feature to resolve disease etiologies and the impact of infectious agents on the host. Although the basic principles of disease diagnostics have not changed, the spectrum of poultry diseases constantly expanded, with the identification of new pathogens and improved knowledge on epidemiology and disease pathogenesis. In parallel, new technologies have been devised to identify and characterize infectious agents, but classical methods remain crucial, especially the isolation of pathogens and their further characterization in functional assays and studies. This review aims to highlight certain aspects of diagnosing infectious poultry pathogens, from the farm via the diagnostic laboratory and back, in order to close the circle. By this, the current knowledge will be summarized and future developments will be discussed in the context of applied state-of-the-art techniques. Overall, a common challenge is the increasing demand for infrastructure, skills and expertise. Divided into separate chapters, reflecting different disciplines, daily work implies the need to closely link technologies and human expertise in order to improve bird health, the production economy and to implement future intervention strategies for disease prevention.

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A genoserotyping system for a fast and objective identification of Salmonella serotypes commonly isolated from poultry and pork food sectors in Belgium

Cited by 12 publications

References 32 publications

Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis

Rapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis

Oxford nanopore technologies—a valuable tool to generate whole-genome sequencing data for in silico serotyping and the detection of genetic markers in Salmonella

Diagnosing Infectious Diseases in Poultry Requires a Holistic Approach: A Review

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