Real-Time PCR Assay for Differentiation of Typhoidal and Nontyphoidal
            <i>Salmonella</i>

Nair, Satheesh; Patel, Vineet; Hickey, Tadgh; Maguire, C.; Greig, David R.; Lee, Winnie W Y; Godbole, Gauri; Grant, Kathie; Chattaway, Marie Anne

doi:10.1128/jcm.00167-19

Cited by 46 publications

(43 citation statements)

References 21 publications

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“…The test provides a reliable alternative to serotyping and can be integrated into a continuous routine workflow because of its simple performance and low hands-on time. Because many NTS can harbour single genes that are normally characteristic for TS, cross-reactions cannot fully be excluded when single genes are used [15]. In silico blast analysis predicted a low number of cross-reactions of the TS primer sets with some NTS serovars and they were technically confirmed.…”

Section: Discussionmentioning

confidence: 97%

“…However, these approaches are expensive and not applicable for rapid diagnosis in a routine laboratory. By using a set of specific target genes TS can be identified by PCR [15]. As an alternative molecular technique, loopmediated isothermal amplification (LAMP) is increasingly being used in diagnostics because of its very easy handling and fast amplification [16][17][18].…”

Section: Introductionmentioning

confidence: 99%

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Simple differentiation of Salmonella Typhi, Paratyphi and Choleraesuis from Salmonella species using the eazyplex TyphiTyper LAMP assay

Rödel

Edel

Ehricht

et al. 2020

Journal of Medical Microbiology

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Introduction. Identification of typhoidal Salmonella (TS) serovars and their discrimination from non-typhoidal Salmonella (NTS) is conventionally performed by seroagglutination. This method is labour-intensive, requires technical experience and can be inconclusive in some cases. Molecular assays may be reliable alternative diagnostic tools. Aim. This study was designed to evaluate the eazyplex TyphiTyper based on loop-mediated isothermal amplification (LAMP) for fast identification of TS and S. Choleraesuis in culture. Methodology. A total of 121 Salmonella strains and 33 isolates of other Enterobacterales species were tested by the eazyplex TyphiTyper. Simulated and clinical blood cultures (BCs) were used to examine the performance of the assay for diagnosis of systemic infection. Sample preparation took about 5 min and the test running time was 20 min. Amplification was measured by real-time fluorescence detection. Results. All TS and S. Choleraesuis strains were correctly identified. The most common NTS S. Typhimurium (n=34) and S. Enteritidis (n=15) were detected as Salmonella species without any false positive result for TS targets. Cross-reactions of NTS with TS were only rarely observed. Direct testing of positive BCs gave correct results. Sensitivities and specificities of the assay were as follows: 100 and 99.3 % for S. Typhi, 100 and 98.7 % for S. Paratyphi A, 100 and 97.3 % for S. Paratyphi B, 100 and 100 % for S. Paratyphi C, 100 and 100 % for S. Choleraesuis, and 100 and 100 % for Salmonella species, respectively. Conclusion. The eazyplex TyphiTyper is very easy to perform and allows the rapid identification of TS and S. Choleraesuis isolates.

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Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 99%

Simple differentiation of Salmonella Typhi, Paratyphi and Choleraesuis from Salmonella species using the eazyplex TyphiTyper LAMP assay

Rödel

Edel

Ehricht

et al. 2020

Journal of Medical Microbiology

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“…The simplification of sample processing also reduces the potential for laboratory errors and minimizes staff exposure to pathogens thereby improving safety practices. In addition, we have utilized the sequence data generated through routine testing to develop specific, rapid real-time PCR tests to assist in the management of patients including for the rapid differential diagnoses of typhoidal from non-typhoidal Salmonella (39) and to detect azithromycin resistant infections (in house assay). This has had a direct clinical impact as same day testing can be provided for urgent clinical cases.…”

Section: Discussionmentioning

confidence: 99%

“…Additional limitations include the necessity of pure cultures required for DNA extraction as contamination will interfere with bioinformatic outputs including accurate sequence typing, fine typing results of SNP analysis and correct calling of AMR gene determinants. Batch processing of samples is still required for sequencing to improve efficiency and maintain cost-effective operations; as a result, TATs are typically in excess of 7 days and in urgent typhoidal cases, PCR (39) is still required to provide a preliminary identification.…”

Section: Discussionmentioning

confidence: 99%

The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Chattaway

Dallman

Larkin

et al. 2019

Front. Public Health

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100

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The use of whole genome sequencing (WGS) as a method for supporting outbreak investigations, studying Salmonella microbial populations and improving understanding of pathogenicity has been well-described (1–3). However, performing WGS on a discrete dataset does not pose the same challenges as implementing WGS as a routine, reference microbiology service for public health surveillance. Challenges include translating WGS data into a useable format for laboratory reporting, clinical case management, Salmonella surveillance, and outbreak investigation as well as meeting the requirement to communicate that information in an understandable and universal language for clinical and public health action. Public Health England have been routinely sequencing all referred presumptive Salmonella isolates since 2014 which has transformed our approach to reference microbiology and surveillance. Here we describe an overview of the integrated methods for cross-disciplinary working, describe the challenges and provide a perspective on how WGS has impacted the laboratory and surveillance processes in England and Wales.

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“…Some studies have developed multiplex PCR methods or parallel methods for multiple targets to increase breadth and specificity of detection of S . Typhi and S. Paratyphi [ 54 ]. For example, primers targeting the fliC-d (phase-1 flagellin gene for d antigen H:d of Salmonella enterica serovar S .…”

Section: Environmental Surveillance Methods For S mentioning

confidence: 99%

Review of Methods Suitable for Environmental Surveillance of Salmonella Typhi and Paratyphi

Matrajt

Lillis

Meschke

2020

Clinical Infectious Diseases

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Typhoid fever is an enteric disease caused by the pathogens Salmonella Typhi and Salmonella Paratyphi. Clinical surveillance networks are lacking in many affected areas, thus presenting a need to understand transmission and population prevalence. Environmental surveillance (ES) has been suggested as a potentially effective method in the absence of (or in supplement to) clinical surveillance. This review summarizes methods identified in the literature for sampling and detection of typhoidal Salmonella from environmental samples including drinking water, wastewater, irrigation water, and surface waters. Methods described use a trap or grab sampling approach combined with various selective culture and molecular methods. The level to which the performance of identified methods is characterized for ES in the literature is variable, thus arguing for the optimization and standardization of ES techniques.

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Real-Time PCR Assay for Differentiation of Typhoidal and Nontyphoidal Salmonella

Cited by 46 publications

References 21 publications

Simple differentiation of Salmonella Typhi, Paratyphi and Choleraesuis from Salmonella species using the eazyplex TyphiTyper LAMP assay

Simple differentiation of Salmonella Typhi, Paratyphi and Choleraesuis from Salmonella species using the eazyplex TyphiTyper LAMP assay

The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Review of Methods Suitable for Environmental Surveillance of Salmonella Typhi and Paratyphi

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