A screening algorithm for diagnosing bacterial gastroenteritis by real-time PCR in combination with guided culture

Lint, Philippe Van; Witte, Evy De; Ursi, J. P.; Herendael, Bruno Van; Schaeren, J. Van

doi:10.1016/j.diagmicrobio.2016.03.017

Cited by 27 publications

(33 citation statements)

References 21 publications

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“…Similarly, 100% sensitivity was reported for bone marrow samples that tested positive for Salmonella (125), and successful results (95.4% sensitivity) have also been reported for the efficacy of nested PCR targeting the flagellin gene (fliC) to detect S. Typhi in urine (126) and blood (127) samples. Other useful Salmonella-specific genes that were used for Salmonella detection in clinical samples include the S. Typhi Vi capsular gene viaB (128), hilA (a regulatory gene controlling the expression of SPI-1 genes) (129), the tetrathionate genes ttrC-ttrA (130,131), the 23S rRNA gene (132), and the CS54 island-borne gene ratA (133).…”

Section: Pcr-based Molecular Methods For Salmonella Detectionmentioning

confidence: 99%

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

2018

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SUMMARY The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica. Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.

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Section: Pcr-based Molecular Methods For Salmonella Detectionmentioning

confidence: 99%

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

2018

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“…As these tests become more prevalent in clinical microbiology laboratories, it is essential that adequate evaluation of molecular tests for the diagnosis of gastrointestinal infections is undertaken. Recent evaluation studies demonstrate that the use of molecular-based diagnostics increases the sensitivity of testing for some enteric pathogens, with overall high negative predictive values [4][5][6][7][8][9][10]. However, the UK National Institute for Health and Care Excellence (NICE) published their diagnostics guidance in January 2017 [11], based on a Diagnostic Assessment Report commissioned by the National Institute of Health Research (NIHR) Health Technology Assessment (HTA) Programme [12].…”

Section: Evidence To Support Molecular-based Diagnostic Testingmentioning

confidence: 99%

“…The introduction of molecular technologies into a clinical microbiology laboratory, such as multiplex polymerase chain reaction (PCR) assays, can benefit the diagnosis of gastrointestinal infection by facilitating simultaneous detection of pathogens (bacterial, parasitic and viral) directly from faeces. Molecular-based diagnosis gives a laboratory the potential to increase sample throughput, increase the amount of information obtained from a single test and decrease sample turnaround times [4][5][6][7][8][9][10]. Additionally, simple workflows and a reduction in the need for technical expertise are appealing attributes of these diagnostic methods.…”

Section: Introductionmentioning

confidence: 99%

Molecular versus culture-based testing for gastrointestinal infection

Macfarlane-Smith

Ahmed

Wilcox

2018

Current Opinion in Gastroenterology

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Molecular techniques are capable of replacing culture in the diagnosis of gastrointestinal infections. Whether all positive results, however, represent true infection is still debateable, as is the clinical significance of identifying more than one pathogen. As it currently stands, microbiological culture remains vital for public health surveillance, monitoring antibiotic resistance and managing outbreaks.

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“…The sensitivity of the culturing of Shigella spp. and EIEC is low [12]. Additionally, most laboratories perform a molecular prescreening based on the ipaH gene, which is present in both Shigella spp and EIEC.…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, most laboratories perform a molecular prescreening based on the ipaH gene, which is present in both Shigella spp and EIEC. From approximately half of fecal samples positive in the molecular prescreening an isolate cannot be obtained in culture [12,13]. Shigellosis cases that are diagnosed purely by molecular procedures are not notifiable.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

et al. 2020

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Background: We investigated the association of symptoms and disease severity of shigellosis patients with genetic determinants of infecting Shigella and entero-invasive Escherichia coli (EIEC), because determinants that predict disease outcome per individual patient could be used to prioritize control measures. For this purpose, genome wide association studies (GWAS) were performed using presence or absence of single genes, combinations of genes, and k-mers. All genetic variants were derived from draft genome sequences of isolates from a multicenter cross-sectional study conducted in the Netherlands during 2016 and 2017. Clinical data of patients consisting of binary/dichotomous representation of symptoms and their calculated severity scores were also available from this study. To verify the suitability of the methods used, the genetic differences between the genera Shigella and Escherichia were used as control. Results: The isolates obtained were representative of the population structure encountered in other Western European countries. No association was found between single genes or combinations of genes and separate symptoms or disease severity scores. Our benchmark characteristic, genus, resulted in eight associated genes and > 3,000,000 k-mers, indicating adequate performance of the algorithms used. Conclusions: To conclude, using several microbial GWAS methods, genetic variants in Shigella spp. and EIEC that can predict specific symptoms or a more severe course of disease were not identified, suggesting that disease severity of shigellosis is dependent on other factors than the genetic variation of the infecting bacteria. Specific genes or gene fragments of isolates from patients are unsuitable to predict outcomes and cannot be used for development, prioritization and optimization of guidelines for control measures of shigellosis or infections with EIEC.

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A screening algorithm for diagnosing bacterial gastroenteritis by real-time PCR in combination with guided culture

Cited by 27 publications

References 21 publications

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae

Molecular versus culture-based testing for gastrointestinal infection

Genome-wide association studies of Shigella spp. and Enteroinvasive Escherichia coli isolates demonstrate an absence of genetic markers for prediction of disease severity

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