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Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

https://doi.org/10.1101/2019.12.20.884395
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s11157-017-9457-7openalex-snapshot
Quaternary ammonium compounds in soil: implications for antibiotic resistance development
inferredcites →https://doi.org/10.1016/j.ijantimicag.2015.06.005openalex-snapshot
Use of colistin-containing products within the European Union and European Economic Area (EU/EEA): development of resistance in animals and possible impact on human and animal health
inferredcites →https://doi.org/10.1016/j.mib.2019.06.004openalex-snapshot
The evolution and transmission of multi-drug resistant Escherichia coli and Klebsiella pneumoniae: the complexity of clones and plasmids
inferredcites →https://doi.org/10.1016/j.prevetmed.2012.03.001openalex-snapshot
Prophylactic and metaphylactic antimicrobial use in Belgian fattening pig herds
inferredcites →https://doi.org/10.1016/j.prevetmed.2015.07.005openalex-snapshot
Antimicrobial usage in 60 Swedish farrow-to-finish pig herds
inferredcites →https://doi.org/10.1016/j.tim.2018.06.007openalex-snapshot
Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context
inferredcites →https://doi.org/10.1016/j.vetmic.2009.12.013openalex-snapshot
Assessing the antimicrobial susceptibility of bacteria obtained from animals
inferredcites →https://doi.org/10.1016/s1473-3099(15)00424-7openalex-snapshot
Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study
inferredcites →https://doi.org/10.1017/s1466252317000020openalex-snapshot
Types and prevalence of extended–spectrum beta–lactamase producing Enterobacteriaceae in poultry
inferredcites →https://doi.org/10.1038/nbt.3103openalex-snapshot
MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island
inferredcites →https://doi.org/10.1038/s41467-018-02974-xopenalex-snapshot
No evidence that carotenoid pigments boost either immune or antioxidant defenses in a songbird
inferredcites →https://doi.org/10.1038/s41467-018-03205-zopenalex-snapshot
The global distribution and spread of the mobilized colistin resistance gene mcr-1
inferredcites →https://doi.org/10.1038/s41587-020-0422-6openalex-snapshot
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
inferredcites →https://doi.org/10.1038/s41598-017-00095-xopenalex-snapshot
Genetic Analysis of the IncX4 Plasmids: Implications for a Unique Pattern in the mcr-1 Acquisition
inferredcites →https://doi.org/10.1038/s41598-019-52424-xopenalex-snapshot
Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology
inferredcites →https://doi.org/10.1089/vbz.2012.1164openalex-snapshot
Humans and Cattle: A Review of Bovine Zoonoses
inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot
Prokka: rapid prokaryotic genome annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btw152openalex-snapshot
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/gigascience/gix043openalex-snapshot
Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer
inferredcites →https://doi.org/10.1093/gigascience/giz043openalex-snapshot
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
inferredcites →https://doi.org/10.1093/gigascience/giz104openalex-snapshot
Comparison of single-nucleotide variants identified by Illumina and Oxford Nanopore technologies in the context of a potential outbreak of Shiga toxin–producing Escherichia coli
inferredcites →https://doi.org/10.1093/jac/dkw149openalex-snapshot
Colistin resistance inSalmonellaandEscherichia coliisolates from a pig farm in Great Britain
inferredcites →https://doi.org/10.1093/jac/dkw411openalex-snapshot
Genetic characterization of mcr-1 -bearing plasmids to depict molecular mechanisms underlying dissemination of the colistin resistance determinant
inferredcites →https://doi.org/10.1093/jac/dkx327openalex-snapshot
Identification of a novel transposon-associated phosphoethanolamine transferase gene, mcr-5, conferring colistin resistance in d-tartrate fermenting Salmonella enterica subsp. enterica serovar Paratyphi B
inferredcites →https://doi.org/10.1093/jac/dky292openalex-snapshot
Molecular epidemiology of isolates with multiple mcr plasmids from a pig farm in Great Britain: the effects of colistin withdrawal in the short and long term
inferredcites →https://doi.org/10.1093/nar/gkw1328openalex-snapshot
Rapid resistome mapping using nanopore sequencing
inferredcites →https://doi.org/10.1098/rstb.2009.0133openalex-snapshot
Livestock infectious diseases and zoonoses
inferredcites →https://doi.org/10.1101/167015openalex-snapshot
Using MinION ™ to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach
inferredcites →https://doi.org/10.1101/180406openalex-snapshot
Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics
inferredcites →https://doi.org/10.1101/435750openalex-snapshot
Yersiniabactin, Colibactin and Wider Resistome Contribute to Enhanced Virulence and Persistence of KPC-2-Producing Klebsiella pneumoniae CG258 in South America
inferredcites →https://doi.org/10.1101/456905openalex-snapshot
Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome
inferredcites →https://doi.org/10.1101/530725openalex-snapshot
Genomes of a major nosocomial pathogen Enterococcus faecium are shaped by adaptive evolution of the chromosome and plasmidome
inferredcites →https://doi.org/10.1101/585067openalex-snapshot
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
inferredcites →https://doi.org/10.1101/768630openalex-snapshot
Plasmid transmitted small multidrug resistant (SMR) efflux pumps differ in gene regulation and enhance tolerance to quaternary ammonium compounds (QAC) when grown as biofilms
inferredcites →https://doi.org/10.1101/gr.214270.116openalex-snapshot
Fast and accurate de novo genome assembly from long uncorrected reads
inferredcites →https://doi.org/10.1101/gr.2289704openalex-snapshot
Mauve: Multiple Alignment of Conserved Genomic Sequence With Rearrangements
inferredcites →https://doi.org/10.1128/jcm.37.8.2479-2482.1999openalex-snapshot
PCR and Blood Culture for Detection of Escherichia coli Bacteremia in Rats
inferredcites →https://doi.org/10.1128/mbio.00543-17openalex-snapshot
Novel Plasmid-Mediated Colistin Resistance Gene mcr-3 in Escherichia coli
inferredcites →https://doi.org/10.1128/mbio.02693-18openalex-snapshot
One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock
inferredcites →https://doi.org/10.1128/msphere.00130-19openalex-snapshot
Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts
inferredcites →https://doi.org/10.1128/msphere.00316-19openalex-snapshot
Diverse Commensal Escherichia coli Clones and Plasmids Disseminate Antimicrobial Resistance Genes in Domestic Animals and Children in a Semirural Community in Ecuador
inferredcites →https://doi.org/10.1136/vropen-2013-000002openalex-snapshot
Survey of quantitative antimicrobial consumption per production stage in farrow‐to‐finish pig farms in Spain
inferredcites →https://doi.org/10.1186/s13059-015-0677-2openalex-snapshot
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
inferredcites →https://doi.org/10.1186/s13756-017-0250-8openalex-snapshot
Key features of mcr-1-bearing plasmids from Escherichia coli isolated from humans and food
inferredcites →https://doi.org/10.1186/s40168-017-0336-9openalex-snapshot
Profiling bacterial communities by MinION sequencing of ribosomal operons
inferredcites →https://doi.org/10.12688/f1000research.16817.1openalex-snapshot
Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon
inferredcites →https://doi.org/10.1371/journal.pcbi.1005595openalex-snapshot
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
inferredcites →https://doi.org/10.1371/journal.pone.0119114openalex-snapshot
Cross-Sectional Study on Antibiotic Usage in Pigs in Germany
inferredcites →https://doi.org/10.2807/1560-7917.es.2016.21.27.30280openalex-snapshot
Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016
inferredcites →https://doi.org/10.2807/1560-7917.es.2017.22.31.30586openalex-snapshot
Co-occurrence of colistin-resistance genes mcr-1 and mcr-3 among multidrug-resistant Escherichia coli isolated from cattle, Spain, September 2015
inferredcites →https://doi.org/10.2807/1560-7917.es.2017.22.31.30589openalex-snapshot
Novel plasmid-mediated colistin resistance mcr-4 gene in Salmonella and Escherichia coli, Italy 2013, Spain and Belgium, 2015 to 2016
inferredcites →https://doi.org/10.2807/1560-7917.es.2018.23.50.1800228openalex-snapshot
Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
inferredcites →https://doi.org/10.2807/1560-7917.es.2018.23.6.17-00672openalex-snapshot
Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes
inferredcites →https://doi.org/10.3389/fmicb.2016.01789openalex-snapshot
Colistin in Pig Production: Chemistry, Mechanism of Antibacterial Action, Microbial Resistance Emergence, and One Health Perspectives
inferredcites →https://doi.org/10.3389/fmicb.2018.00331openalex-snapshot
Fitness Advantage of mcr-1–Bearing IncI2 and IncX4 Plasmids in Vitro
inferredcites →https://doi.org/10.3389/fmicb.2018.00803openalex-snapshot
Comparing Microbiome Sampling Methods in a Wild Mammal: Fecal and Intestinal Samples Record Different Signals of Host Ecology, Evolution
inferredcites →https://doi.org/10.7717/peerj.6800openalex-snapshot
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

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inferred← citeshttps://doi.org/10.3390/vetsci12090862openalex-snapshot
From Farm to Fork: Antimicrobial-Resistant Bacterial Pathogens in Livestock Production and the Food Chain
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.