scholarly journals Mobile Colistin Resistance Genetic Determinants of Non-typhoid Salmonella enterica Isolates from Russia

2021 ◽  
Author(s):  
K. V. Kuleshov ◽  
A. S. Pavlova ◽  
E. D. Shedko ◽  
Y. V. Mikhaylova ◽  
G. Margos ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Diarrheal Disease ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Colistin Resistance ◽  
Oxford Nanopore ◽  
Susceptible Isolate ◽  
Long Read

Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently pose a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carries mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n=586). mcr-1 genes were detected using a previously developed qPCR assay and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological background.

scholarly journals Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia

2021 ◽  
Vol 9 (12) ◽  
pp. 2515
Author(s):  
Konstantin V. Kuleshov ◽  
Anastasia S. Pavlova ◽  
Elizaveta D. Shedko ◽  
Yulia V. Mikhaylova ◽  
Gabriele Margos ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Diarrheal Disease ◽  
Whole Genome ◽  
Genetic Determinants ◽  
Colistin Resistance ◽  
Oxford Nanopore ◽  
Susceptible Isolate ◽  
Long Read

Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently poses a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carrying mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n = 586). mcr-1 genes were detected using a previously developed qPCR assay, and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates, including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans, carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene-carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological backgrounds.

scholarly journals Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
S. Wesley Long ◽  
Sarah E. Linson ◽  
Matthew Ojeda Saavedra ◽  
Concepcion Cantu ◽  
James J. Davis ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Clinical Isolate ◽  
Genome Sequencing ◽  
Novel Species ◽  
Whole Genome ◽  
The Novel ◽  
Short Read ◽  
Oxford Nanopore ◽  
Long Read

ABSTRACT In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all recognized Klebsiella spp. We closed the genome of strain KPN1705 using a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For this novel species, we propose the name Klebsiella quasivariicola sp. nov.

scholarly journals DNA Extraction Method Optimized for Nontuberculous Mycobacteria Long-Read Whole Genome Sequencing

2018 ◽  
Author(s):  
Jennifer M. Bouso ◽  
Paul J. Planet
Keyword(s):  
Whole Genome Sequencing ◽  
Dna Extraction ◽  
Genome Sequencing ◽  
Nontuberculous Mycobacteria ◽  
Systemic Disease ◽  
Matrix Material ◽  
Whole Genome ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractNontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques, including the advent of Oxford Nanopore Technologies, provide new opportunities to sequence complete NTM genomes at a fraction of the previous cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to their slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA. Our refined method was compared to 6 other methods with variations in timing of mechanical and enzymatic digestion, quantity of matrix material, and reagents used in extraction and precipitation. We also demonstrate the ability of our optimized protocol to produce sufficient DNA to yield near-complete NTM genome assemblies using Oxford Nanopore Technologies long-read sequencing.

Evaluation of Whole Genome Sequencing for outbreak detection of Salmonella enterica serovar Enteritidis

2020 ◽  
Author(s):  
Ainhoa Arrieta-Gisasola ◽  
Aitor Atxaerandio Landa ◽  
Javier Garaizar ◽  
Joseba Bikandi ◽  
José Karkamo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Salmonella Enterica Serovar Enteritidis

scholarly journals Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e87991 ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Eva M. Nielsen ◽  
Rolf S. Kaas ◽  
Ole Lund ◽  
Frank M. Aarestrup
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome

Generating 1200bp tiled Amplicons for SARS-CoV2 Whole Genome Sequencing v2

2022 ◽  
Author(s):  
jason.nguyen not provided ◽  
Tracy Lee ◽  
Rebecca Hickman ◽  
Natalie Prystajecky ◽  
John Tyson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Oxford Nanopore ◽  
Sequencing Platforms

This procedure provides instructions for how to generate amplicons across the entire SARS-CoV-2 genome to be used for downstream whole genome sequencing applications, including Illumina MiSeq/NextSeq or Oxford Nanopore MinION sequencing platforms. The steps involved in this protocol were derived from version 3 of Freed et al protocol nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon)V.3 available at https://dx.doi.org/10.17504/protocols.io.bgggjttw

Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

2018 ◽  
Vol 64 (3) ◽  
pp. 191-197 ◽  
Author(s):  
Takeshi Mizuguchi ◽  
Tomoko Toyota ◽  
Hiroaki Adachi ◽  
Noriko Miyake ◽  
Naomichi Matsumoto ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Repeat Expansion ◽  
Whole Genome ◽  
Smrt Sequencing ◽  
Long Read

Identifying Genetic Determinants of Atopic Dermatitis and Bacterial Colonization Using Whole Genome Sequencing

2015 ◽  
Vol 135 (2) ◽  
pp. AB391 ◽  
Author(s):  
Rasika A. Mathias ◽  
Sameer Chavan ◽  
Kruthika R. Iyer ◽  
Nicholas M. Rafaels ◽  
Meher Boorgula ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Colonization ◽  
Whole Genome ◽  
Genetic Determinants
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