2022
DOI: 10.4014/jmb.2211.11009
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Development and Evaluation of a Next-Generation Sequencing Panel for the Multiple Detection and Identification of Pathogens in Fermented Foods

Abstract: These days, bacterial detection methods have some limitations in sensitivity, specificity, and multiple detection. To overcome these, novel detection and identification method is necessary to be developed. Recently, NGS panel method has been suggested to screen, detect, and even identify specific foodborne pathogens in one reaction. In this study, new NGS panel primer sets were developed to target 13 specific virulence factor genes from five types of pathogenic Escherichia coli , … Show more

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Cited by 6 publications
(5 citation statements)
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“…Culture-based methods remain the reference methods for detecting foodborne pathogens despite the existence of other more modern methods [ 30 , 31 , 32 , 33 ]. These methods are premised on the ability of bacteria and fungi to grow on culture media, forming visible colonies which can then be subject to other downstream assays as required.…”
Section: Methods For Detecting Foodborne Pathogensmentioning
confidence: 99%
“…Culture-based methods remain the reference methods for detecting foodborne pathogens despite the existence of other more modern methods [ 30 , 31 , 32 , 33 ]. These methods are premised on the ability of bacteria and fungi to grow on culture media, forming visible colonies which can then be subject to other downstream assays as required.…”
Section: Methods For Detecting Foodborne Pathogensmentioning
confidence: 99%
“…A 2023 report estimated that in 2019 among 35 countries in the Americas there were 114,000 deaths associated with carbapenem resistant infections. Most of these deaths were attributed to infections with the following carbapeneum-resistant bacterial species (number of deaths): Acinetobacter baumannii (36,800), Pseudomonas aeruginosa (33,200), Streptococcus pneumoniae (18,100) and K. pneumoniae (16,500) (2). With our pipeline we identified only one A. baumannii and did not detect S. pneumoniae – but we did not use growth conditions specific for S. pneumoniae .…”
Section: Introductionmentioning
confidence: 99%
“…Research is ongoing to use next generation sequencing to detect foodborne pathogens in wastewater. The challenges include low sensitivity and false positive results at low concentrations – problems which are likely to occur in wastewater samples (26). Additionally, time and resource consuming culturing methods must be in place to select for relevant pathogens before undergoing molecular and genomic characterization, which makes practical implementation for public health surveillance daunting (24).…”
Section: Introductionmentioning
confidence: 99%
“…Accordingly, several genotyping schemes were developed and applied to describe the molecular epidemiology of E. coli in different regions and among various communities. The genotyping schemes include BOX PCR fingerprinting [5], pulsed-field gel electrophoresis [6], restriction fragment length polymorphism [7], 16S RNA sequencing [8] next-generation sequencing [9], and whole genome sequencing [10].…”
Section: Introductionmentioning
confidence: 99%