Combining a COI Mini-Barcode with Next-Generation Sequencing for Animal Origin Ingredients Identification in Processed Meat Product

For revealing animal species in complex or adulterated processed meat product, we presented a method combining a novel cytochrome oxidase I (COI) mini-barcode with next-generation sequencing (NGS), which identifies various animal species (swine, bovine, Caprinae, and some of fish, shrimp, and poultry) accurately and efficiently in processed meat products. We designed a universal primer based on 140 sequences from 51 edible animal species. A mixture of 12 species raw meat samples were identified with the clone sequencing and also with a mini-barcode- (136 bp) combined NGS method, respectively. The mini-barcode of these 12 species was 100% identical to the target species sequence by Sanger sequencing. Compared to the clone sequencing method, the NGS method is superior in accuracy, sensitivity, and detection efficiency. Various edible animal species were identified in the species level both in the mixed samples and the 7 heavily processed food products. Moreover, some unlabeled species and dubious contamination were detected as well.

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A universal primer-independent next-generation sequencing approach for investigations of norovirus outbreaks and novel variants

Scientific Reports ◽

10.1038/s41598-017-00926-x ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 9

Author(s):

Jannik Fonager ◽

Marc Stegger ◽

Lasse Dam Rasmussen ◽

Mille Weismann Poulsen ◽

Jesper Rønn ◽

...

Keyword(s):

Next Generation Sequencing ◽

Next Generation ◽

Universal Primer ◽

Novel Variants ◽

Generation Sequencing

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Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

PLoS ONE ◽

10.1371/journal.pone.0105592 ◽

2014 ◽

Vol 9 (8) ◽

pp. e105592 ◽

Cited By ~ 433

Author(s):

Shunsuke Takahashi ◽

Junko Tomita ◽

Kaori Nishioka ◽

Takayoshi Hisada ◽

Miyuki Nishijima

Keyword(s):

Next Generation Sequencing ◽

Simultaneous Analysis ◽

Next Generation ◽

Universal Primer ◽

Generation Sequencing

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Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

Biology ◽

10.3390/biology9050089 ◽

2020 ◽

Vol 9 (5) ◽

pp. 89 ◽

Cited By ~ 1

Author(s):

Carolina Sabença ◽

Telma de Sousa ◽

Soraia Oliveira ◽

Didier Viala ◽

Laetitia Théron ◽

...

Keyword(s):

Mass Spectrometry ◽

Next Generation Sequencing ◽

Charge Ratio ◽

Processed Meat ◽

Next Generation ◽

Intrinsic Resistance ◽

Maldi Tof ◽

Vancomycin Resistant Enterococci ◽

Vancomycin Resistant ◽

Generation Sequencing

Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6’)-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish Enterococcus faecium from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization.

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A highly efficient method for extracting next-generation sequencing quality RNA from adipose tissue of recalcitrant animal species

Journal of Cellular Physiology ◽

10.1002/jcp.25951 ◽

2017 ◽

Vol 233 (3) ◽

pp. 1971-1974 ◽

Cited By ~ 2

Author(s):

Davinder Sharma ◽

Naresh Golla ◽

Dheer Singh ◽

Suneel K. Onteru

Keyword(s):

Adipose Tissue ◽

Next Generation Sequencing ◽

Efficient Method ◽

Animal Species ◽

Next Generation ◽

Highly Efficient ◽

Sequencing Quality ◽

Generation Sequencing

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A comparison between next-generation sequencing and ASO-qPCR for minimal residual disease detection in multiple myeloma.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.8601 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 8601-8601

Author(s):

Hiroyuki Takamatsu ◽

Ryoichi Murata ◽

Jianbiao Zheng ◽

Martin Moorhead ◽

Yasushi Terasaki ◽

...

Keyword(s):

Multiple Myeloma ◽

Next Generation Sequencing ◽

Minimal Residual Disease ◽

Residual Disease ◽

Survival Rates ◽

Japanese Patients ◽

Next Generation ◽

Universal Primer ◽

Generation Sequencing ◽

Minimal Residual

8601 Background: Although molecular CR in multiple myeloma (MM) can be assessed by allele-specific oligonucleotide (ASO)-PCR, this technique requires preparation of clonotype-specific primers for each individual which is laborious and time-consuming. The usage of the LymphoSIGHT method, a next-generation sequencing (NGS)-based platform, may overcome these challenges and increase sensitivity and specificity. We compared the LymphoSIGHT approach with ASO-qPCR for minimal residual disease (MRD) detection in autografts in the autologous peripheral blood stem cell transplantation (ASCT) setting. Methods: Seventeen Japanese patients with newly diagnosed MM who received various induction regimens prior to ASCT were retrospectively analyzed. All patients had achieved a PR or CR after ASCT. Bone marrow (BM) slides from 13 MM patients and fresh BM cells from 4 MM patients at diagnosis as well as autografts were obtained for DNA extraction. Using universal primer sets, we amplified IGH variable (V), diversity (D), and joining (J) gene segments, IGH-DJ, and IGK from genomic DNA. Amplified products were subjected to deep sequencing using NGS. Reads were analyzed using standardized algorithms for clonotype determination. Myeloma-specific clonotypes were identified for each patient based on their high frequency in BM samples. The presence of the myeloma clonotype was then assessed in follow-up samples. Results: MRD in autografts was detected in 6 of 17 (35%) by ASO-qPCR and 13 of 17 (76%) by NGS. When MRD was assessed by NGS, 6 MRD (+) cases received post-ASCT therapy while 4 MRD (-) cases and 7 MRD (+) cases were followed without post-ASCT therapy. The MRD (-) cases tended to show a better PFS than the MRD (+) cases with post-ASCT therapy (P = 0.26) and those without post-ASCT therapy (P = 0.09) although overall survival rates were comparable among the three groups. There was no difference in PFS between MRD (-) and MRD (+) cases when MRD was assessed by ASO-qPCR (P = 0.6). These studies will be extended in 30 additional MM patients, and results will be presented. Conclusions: MRD-negativity in autografts revealed by NGS may be more closely associated with durable remission of MM than that revealed by ASO-qPCR.

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