Complete Genome Sequence of a Canadian Klebsiella michiganensis Strain, Obtained Using Oxford Nanopore Technologies Sequencing

Abstract

Klebsiella michiganensis is a Gram-negative opportunistic pathogen that is associated with many hospital-acquired infections in humans. Here, we report the complete genome sequence of a K. michiganensis strain isolated from a Canadian wastewater treatment facility.

Complete Genome Sequence of a Listeria monocytogenes Strain Isolated from Sprouts and Carrying an Antimicrobial Resistance Gene

“…Nanopore sequencing was performed using a one-dimensional native barcoding gDNA protocol (EXP-NBD104 and SQK-LSK109; Oxford Nanopore Technologies, UK) without shearing followed by sequencing using a FLO-MIN106 (R9.4.1) flow cell on a MinION Mk1C device. Nanopore sequencing base calling was performed using Super Accuracy mode in Guppy v5.0.11, trimming using Porechop v0.2.3 ( 3 ), and filtration using Filtlong v0.2.1 ( 4 ). Assembly of the Nanopore long reads was performed using Flye v2.7 ( 5 ), corrected using Medaka v1.4.4, and polished with Illumina MiSeq reads using a combination of NextPolish v1.4.0, ntEdit v1.3.5, and Polypolish v0.5.0 after trimming/filtering with fastp v0.23.2.…”

Complete Genome Sequences of Three Listeria monocytogenes Strains from Microgreens Obtained with MinION and MiSeq Sequencing

“…Nanopore sequencing library was generated using the 1D Native barcoding gDNA protocol (EXP-NBD104 and SQK-LSK109) (Oxford Nanopore Technologies, UK), and sequenced using a FLO-MIN106 (R9.4.1) flow cell in MinION MK1C. Basecalling was performed using Super Accuracy mode in Guppy v5.0.11, trimming using Porechop v0.2.3 ( 3 ) and filtration using Filtlong v0.2.1 ( 4 ). Long reads assembly was performed using Flye v2.7 ( 5 ), corrected using Medaka v1.4.4 and polished with Illumina MiSeq reads using a combination of NextPolish v1.4.0, ntEdit v1.3.5 and Polypolish v0.5.0 after trimming/filtering with fastp v0.23.2.…”

Complete Genome Sequence of a Listeria monocytogenes Strain from a Sample of Kale Salad

“…FastQC v0.11.9 ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc ) and pycoQC v2.5.2 ( https://github.com/a-slide/pycoQC ) were used to assess read quality for Illumina and Nanopore reads, respectively. Long reads were trimmed and filtered with Porechop v0.2.3 ( 3 ) and Filtlong v0.2.1, respectively ( 4 ), and assembled with Flye v2.7 ( 5 ). The assembly was corrected using Medaka v1.4.4 ( https://github.com/nanoporetech/medaka ) and polished with short reads using a combination of NextPolish v1.4.0 ( 6 ), ntEdit v1.3.5 ( 7 ), and Polypolish v0.5.0 ( 8 ) after trimming/filtering with fastp v0.23.2 ( 9 ).…”