Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

Daquigan, Ninalynn; Grim, Christopher J.; White, James R.; Hanes, Darcy E.; Jarvis, Karen G.

doi:10.3389/fmicb.2016.02103

Cited by 35 publications

(45 citation statements)

References 48 publications

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“…This method differed from those of previous studies that focused on optimized media to shorten target pathogen enrichment. For example, it was recently reported that nonselective preenrichment could reduce the levels of inoculated competitive bacteria, enabling an early Salmonella recovery (22). The shorter enrichment time enabled by IMS-MDA also helped address culture enrichment biases unfavorable for Salmonella detection, such as the microbiota shift from Proteobacteria, which includes Salmonella, to Firmicutes after extended (24 h) culturing (11,12,31).…”

Section: Discussionmentioning

confidence: 99%

“…SNP detection and phylogenetic analysis. Core-genome SNPs were identified using the CFSAN SNP pipeline v0.8.0 with default quality filters (22). Specifically, the minimum base quality was 20, the minimum mapping quality was 15, and the minimum fraction of reads for SNP calls was 0.6.…”

Section: Methodsmentioning

confidence: 99%

“…We have recently shown that IMS-MDA led to real-time PCR detection of low levels of Salmonella from raw chicken breast with no or shortened (4 h) culture enrichment (21). Unlike previous studies that were focused on optimizing culture enrichment prior to metagenomics sequencing (8)(9)(10)(11)(12)22), we aimed to reduce the need for culture enrichment via the alternative method of IMS-MDA. To differentiate it from conventional metagenomics sequencing without selective analyte concentration, the shotgun sequencing of IMS-MDA products was termed quasimetagenomics sequencing in this study.…”

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confidence: 99%

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Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

Hyeon

Mann

et al. 2018

Appl Environ Microbiol

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Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. Selective concentration of genomic DNA through immunomagnetic separation (IMS) and multiple displacement amplification (MDA) were shown to shorten culture enrichment of-spiked raw chicken breast samples by over 12 hours while permitting serotyping and high-fidelity single nucleotide polymorphisms (SNP) typing of the pathogen using short shotgun sequencing reads. The herein termed quasi-metagenomics approach was evaluated on -spiked lettuce and black peppercorn samples as well as retail chicken parts naturally contaminated with different serotypes of Between 8 and 24 h culture enrichment was required for detecting and subtyping naturally occurring from unspiked chicken parts compared with 4 to 12 h culture enrichment when-spiked food samples were analyzed, indicating the likely need for longer culture enrichment to revive low levels of stressed or injured cells in food. Further acceleration of the workflow was achieved by real-time nanopore sequencing. After 1.5 hours of analysis on a potable sequencer, sufficient data were generated from sequencing IMS-MDA product of a cultured-enriched lettuce sample to allow serotyping and robust phylogenetic placement of the inoculated isolate. Both culture enrichment and next-generation sequencing remain to be time-consuming processes for food testing where rapid methods for pathogen detection are widely available. Our study demonstrated substantial acceleration of the respective process through IMS-MDA and real-time nanopore sequencing. In one example, the combined use of the two methods delivered a less than 24 h turnaround time from a -contaminated lettuce sample to phylogenetic identification of the pathogen. Improved efficiency like this is important for further expanding the use of whole genome and metagenomics sequencing in microbial analysis of food. Our results suggest the potential of the quasi-metagenomics approach in areas where rapid detection and subtyping of foodborne pathogens is important, such as foodborne outbreak response and precision tracking and monitoring of foodborne pathogens in production environments and supply chains.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

Hyeon

Mann

et al. 2018

Appl Environ Microbiol

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“…It can be used to directly analyze the microorganisms within a sample by sequencing all the genomes in the sample and comparing the genomic data to those of known microorganisms [70][71][72][73][74][75]. In addition to identify the bacteria present in the sample, this method can also be used to analyze the genetic relationship among the organisms assessed, identify putative virulence factors and explore new or rare pathogens.…”

Section: Metagenomicsmentioning

confidence: 99%

Recent and the Latest Developments in Rapid and Efficient Detection of Salmonella in Food and Water

Hu¹,

Li²

2017

Adv Tech Biol Med

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Salmonella is a leading cause of foodborne diseases. Gastroenteritis caused by nontyphoid Salmonella is still a major infectious disease in the world. About 95% of Salmonella infections are caused by ingestion of contaminated food and water. Rapid, sensitive, and efficient detection and identification of Salmonella from foods and water are critical for minimizing the spread of outbreaks caused by this pathogen. These methods can be applied to track the food source of contamination or by early diagnosis of the infections in a clinical setting. Culture-based methods for detection of Salmonella are laborious and time-consuming, typically taking 5-7 days to obtain a pure culture and serovar identification. In the past few decades, molecular-based technologies have greatly shortened the time for detection and identification of bacterial pathogens from food and water, and drastically increased the specificity and sensitivity of the assays. In this review, we report an update on the development of rapid and efficient methods for the detection and identification of Salmonella in food and water, focusing on the approaches for concentration of Salmonella cells and viable cell detection, as well as the advantages and drawbacks of these methods.

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“…Therefore, rapid methods, such as polymerase chain reaction (PCR), have become more desirable (Ray & Bhunia, 2013). Furthermore, a pre-enrichment step prior to PCR has been shown to greatly increase its sensitivity and permit earlier detection compared to culture (Daquigan, Grim, White, Hanes, & Jarvis, 2016;Mohd Afendy & Son, 2015). For PCR detection of Salmonella spp., primers to amplify the invA gene have been used successfully (Anejo-Okopi et al, 2016;Galán, Ginocchio, & Costeas, 1992;Ohud, 2012;Rizzo, 2006;Salehi, Mahzounieh, & Saeedzadeh, 2005;Sharma, 2016;Suez et al, 2013).…”

mentioning

confidence: 99%

Bacteriological quality and the prevalence of Salmonella spp. and E. coli O157:H7 in ready‐to‐eat foods from Barbados, WI

Hull-Jackson

Mota‐Meira

Adesiyun

2019

Journal of Food Safety

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The bacteriological quality and safety of ready‐to‐eat (RTE) foods in Barbados were assessed in two separate studies conducted between 2014 and 2016. In Study 1, 206 food samples were processed for Salmonella spp. by conventional bacteriological methods. Polymerase chain reaction (PCR) and serotyping were used for confirmation. In Study 2, 120 food samples were processed for the total aerobic plate count (TAPC), coliform count, and E. coli count using conventional bacteriological methods. After a 24 hr pre‐enrichment, the food samples were screened for Salmonella spp. and E. coli O157:H7 by PCR. To validate the PCR screening method for use after pre‐enrichment, the detection limit was investigated in cooked chicken samples spiked with 10‐fold serial dilutions of an overnight culture of Salmonella Enteritidis. In Study 1, the prevalence of Salmonella Enteritidis was 1.5% (3/206). In Study 2, the prevalence of E. coli was 1.7%, and unsatisfactory TAPC (12.5%) and coliform counts (4.2%) were documented. The PCR screen detected DNA extracted from homogenates with as low as 6 CFU/mL, after a 24 hr pre‐enrichment. However, all samples screened negative (0.0%) for Salmonella spp. and E. coli O157:H7. Compared with other developing countries, the prevalence of pathogens in RTE foods in Barbados is low. Practical applications Salmonella and E.coli are major causes of food borne illness globally and antibiotic resistance among these bacteria have presented increasing challenges for clinicians. Studies demonstrate that bacterial contamination in ready‐to‐eat (RTE) foods have varied among developed and developing nations. While there are several published reports on the bacterial contamination of RTE foods from the developing Caribbean region, none have originated from Barbados. This study is the first to report a low prevalence of Salmonella, E. coli and other microbial contaminants in RTE foods sold in popular tourist districts in Barbados. This information can be applied to food safety considerations for public health and the tourism industry.

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Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

Cited by 35 publications

References 48 publications

Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

Recent and the Latest Developments in Rapid and Efficient Detection of Salmonella in Food and Water

Bacteriological quality and the prevalence of Salmonella spp. and E. coli O157:H7 in ready‐to‐eat foods from Barbados, WI

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