Neb monarch genomic purification kit

Manufactured by New England Biolabs

Sourced in United States

The NEB Monarch Genomic Purification Kit is a laboratory product designed for the efficient purification of genomic DNA from a variety of sample types. It utilizes a silica-based membrane technology to selectively bind and purify DNA, while removing impurities and inhibitors.

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Lab products found in correlation

Smrtbell express template prep kit 2, by Pacific Biosciences (2 mentions) Pacbio sequel iie system, by Pacific Biosciences (1 mentions) Smrt link software version 9, by Pacific Biosciences (1 mentions) Sequencing platform, by Illumina (1 mentions) Miseq instrument, by Illumina (1 mentions) Pacbio sequel 2 system, by Pacific Biosciences (1 mentions)

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NEB Monarch Genomic DNA Purification Kit Monarch kits NEB kits

3 protocols using neb monarch genomic purification kit

Molecular Typing of mcr-1 E. coli Isolates

Cited 1 time

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For nine mcr-1 positive E. coli isolated from human stool (n = 2) and porcine feces (n = 7) of six different farms, molecular typing using whole-genome sequencing (WGS) was performed. Genomic DNA (gDNA) was extracted using the NEB Monarch Genomic Purification Kit (New England Biolabs, Ipswich, Massachusetts, USA). Isolates were sequenced on a PacBio Sequel IIe system (Pacific Biosciences, Menlo Park, California, USA) using a 20 kb insert size library and the SMRTbell® Express Template Prep Kit 2.0. Raw sequences were de novo assembled using the hierarchical genome assembly process (HGAP) and analyzed using the SMRTLink software suite v9 with default parameters for microbial assembly. Final assembly contigs were extracted in FASTA format.
For genotyping of isolates, allelic profiles were created using a task template based on 2325 cgMLST targets of E. coli Sakai [19 (link)] in Ridom SeqSphere⁺ v7.0.1 (Ridom GmbH, Münster, Germany). A minimum spanning tree was created from these profiles using the ‘missing values are own category’ option in SeqSphere⁺. The contigs containing the mcr genes, presumably reflecting plasmids, were determined using ResFinder v3.2 [20 (link)]. Subsequently, the respective contigs were checked for complete circularization and uploaded to PlasmidFinder v2.1 [21 (link)] to predict the plasmid replicon type.

Effelsberg N., Kobusch I., Linnemann S., Hofmann F., Schollenbruch H., Mellmann A., Boelhauve M., Köck R, & Cuny C. (2021). Prevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms. One Health, 13, 100354.

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Whole Genome Sequencing of Bcg Isolates

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All isolates that arrived at the laboratory before or on 08/21/2020 were sequenced on the Illumina sequencing platform on a single MiSeq instrument (Illumina, San Diego, CA, USA). WGS library preparation, sequencing and subsequent data analysis were performed as described in [23 (link)]. Briefly, resulting fastq files were de novo assembled using SKESA. Isolates that arrived after 08/21/2020 were sequenced using the PacBio Sequel II system (Pacific Biosciences Inc., Menlo Park, CA, USA). WGS library preparation, sequencing and subsequent data analysis were performed as described recently [24 (link)] with minor modifications. After DNA extraction using the NEB Monarch Genomic Purification Kit (New England Biolabs, Ipswich, Massachusetts, USA), we constructed the sequence library using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences Inc.) in accordance with the manufacturer’s recommendations. After the 15 h-sequencing run on the Sequel II system, the resulting long reads were assembled by applying the “Microbial Assembly” pipeline within the SMRT Link software version 9 (Pacific Biosciences Inc.) using default parameters except for the genome size, which was adopted to 5.4 Mb to reflect the anticipated genome size of Bcg. More details regarding sequencing results are provided in Additional file 6: Table S6.

Tönnies H., Heep A., Herrmann J., Lange M., Mellmann A, & Hamprecht A. (2024). Investigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing. Antimicrobial Resistance and Infection Control, 13, 1.

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Molecular Detection of Filarial Parasites

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DNA was extracted from a 25 µl pellet using NEB Monarch Genomic Purification Kit (NEB). Sample lysis was performed according to the animal tissue protocol provided by the manufacturer. Incubation was increased to 3 h at 56°C to improve the yield. DNA was eluted with 50 µl elution buffer. Loa loa infection as well as coinfection with either M. perstans or Mansonella sp “DEUX” based on the internal transcribed spacer region (ITS1 region) was excluded by qPCR according to previously published protocols (Sandri et al., 2021 (link)). These procedures resulted in three eligible samples, named mperst1, mdeux2 and mdeux3.

Rodi M., Gross C., Sandri T.L., Berner L., Marcet-Houben M., Kocak E., Pogoda M., Casadei N., Köhler C., Kreidenweiss A., Agnandji S.T., Gabaldón T., Ossowski S, & Held J. (2023). Whole genome analysis of two sympatric human Mansonella: Mansonella perstans and Mansonella sp “DEUX”. Frontiers in Cellular and Infection Microbiology, 13, 1159814.

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