Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Comparison of different broth media for short-term enrichment of Escherichia coli and Salmonella at 42°C a

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Comparison

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: The capture efficiency (CE) of immunomagnetic (IMS) beads for individual pure culture suspensions of Escherichia coli, Salmonella, and nontarget bacterial strains. CE was determined by dividing the viable count recovered after plating IMS beads by the initial count mixed with the beads.

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Taxonomic classification tree identification of Escherichia coli (A) and Salmonella (B), individually inoculated to wheat flour at a minimum abundance cut-off ratio of 3% generated by EPI2ME after 1 h of sequencing in a nanopore sequencer. Flour samples were inoculated with 0.1 log CFU/g E. coli O157:H7 or Salmonella Typhimurium strains, enriched in tryptic soy broth at 42°C, and subjected to immunomagnetic separation and multiple displacement amplification before sequencing.

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Generated, Sequencing, Immunomagnetic Separation, Multiple Displacement Amplification

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Phylogenetic tree of wheat flour samples coinoculated with Escherichia coli and Salmonella with 0.1 CFU/g of each organism at a minimum abundance cut-off rate of 0.5% generated by EPI2ME after 1 h of sequencing in a nanopore sequencer. Flour samples were inoculated with 0.1 log CFU/g E. coli O157:H7 and Salmonella Typhimurium strains, enriched in tryptic soy broth at 42°C, and subjected to immunomagnetic separation and multiple displacement amplification before sequencing.

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Generated, Sequencing, Immunomagnetic Separation, Multiple Displacement Amplification

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Phylogenetic clustering of inoculated flour samples inoculated at 0.1 log CFU/g, subjected to nanopore sequencing on a MinIon device in a quasimetagenomic approach. (A) Phylogenetic tree of Salmonella Typhimurium (ATCC 14028) and its tight clustering with the reference strain obtained from a 1-h sequencing run of Salmonella individual inoculation, subjected to analysis. (B) Phylogenetic tree of E. coli O157:H7 (ATCC 43895) and its tight clustering with the reference strain obtained from a 1-h sequencing run of E. coli and Salmonella dual inoculation, subjected to analysis. Numbers correspond to the closest GenBank strains for reference. Additional data are in Table S1 in the supplemental material.

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Nanopore Sequencing, Sequencing

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Microbial abundance at the genus level for two different flour samples inoculated at 0.1 CFU/g with E. coli and Salmonella, respectively, resulting from nanopore sequencing using a Minion device followed by a conventional bioinformatics analysis pipeline. Additional data are in Table S2 in the supplemental material.

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Nanopore Sequencing

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Metagenomics analysis at different sequencing run times using conventional bioinformatics pipeline h

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Sequencing

Journal: Applied and Environmental Microbiology

Article Title: Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

doi: 10.1128/AEM.00097-20

Figure Lengend Snippet: Metagenomics analysis at different sequencing run times using conventional bioinformatics pipeline h

Article Snippet: Genomes of S. enterica Typhimurium strain SL1344 (ATCC 14028; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_016810.1","term_id":"378697983","term_text":"NC_016810.1"}} NC_016810.1 ) and E. coli O157:H7 Sakai (ATCC 43895; NCBI assembly accession no. {"type":"entrez-nucleotide","attrs":{"text":"NC_002695.2","term_id":"1447699251","term_text":"NC_002695.2"}} NC_002695.2 ) were used as reference genomes for reads mapping for Salmonella and E. coli , respectively.

Techniques: Sequencing

Journal: Data in Brief

Article Title: Data on selected antimalarial drug resistance markers in Zambia

doi: 10.1016/j.dib.2020.106650

Figure Lengend Snippet: Nucleotide sequence for PfKelch 13 and deduced amino acid sequences, showing the three samples that had mutations.

Article Snippet: Multiple nucleotide sequence alignments were analysed by MacVector (Cambridge, UK) using the 3D7 PfK13 sequence (GenBank accession no. XM001350122) as a reference to detect point mutations in the gene.

Techniques: Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Differential Cytokine Responses and the Clinical Severity of Adult and Pediatric Nephropathia Epidemica

doi: 10.3390/ijms24087016

Figure Lengend Snippet: The sites of orthohantavirus exposure. The green circles and names (PUUV strains Hu466, Hu475, Hu493, Hu497, Hu500, Hu505, Hu518, Hu520, Hu523, Hu546, Hu563, Hu566, Hu587, Hu599, Hu608, HU_611 and Hu614 from NE patients). The brown circles (Hu526, Hu545, Hu574, Hu 600 and Hu604 strains were closely related to PUUV strains from habitats of bank voles in the east and southeast suburbs of Kazan). The blue circles and names (Hu464, Hu549, Hu598 and HU_639 strains were closely related to PUUV strains from Mamadysh in the east of the Pre-Kama area). The red circles and names for (Hu465). The purple circles (PUUV HU_585, HU_626 and HU_627, Hu461, Hu471, Hu487, Hu488, Hu542, Hu578, Hu602, Hu603, Hu638 and Hu 624 strains).

Article Snippet: Multiple nucleotide sequences of the PUUV strains were first aligned using the MegAlign program (Clustal W algorithm) from the DNASTAR software v. 7.1.0 package Lasergene (DNASTAR, Madison, WI, USA; accessed on 12 February 2022 [ ], and then used for phylogenetic analysis with MEGA v6.0 [ ].

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: Differential Cytokine Responses and the Clinical Severity of Adult and Pediatric Nephropathia Epidemica

doi: 10.3390/ijms24087016

Figure Lengend Snippet: Phylogenetic tree. Sequencing and phylogenetic analysis of PUUV strains from humans and rodents.

Article Snippet: Multiple nucleotide sequences of the PUUV strains were first aligned using the MegAlign program (Clustal W algorithm) from the DNASTAR software v. 7.1.0 package Lasergene (DNASTAR, Madison, WI, USA; accessed on 12 February 2022 [ ], and then used for phylogenetic analysis with MEGA v6.0 [ ].

Techniques: Sequencing