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microbial genomics

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Key links

AMRgen R pkg
AMRnet Dashboard
AMRrules: Interpretive Standards
KlebNET Genomic Surveillance
LSHTM AMR Centre
Typhoid Genomics Consortium

Nanopore seq

Assembling bacterial genomes – how to guide
BadRead: long read simulator
Basecalling accuracy paper
Basecalling comparison repo
Closing bacterial genomes
Deepbinner: De-barcoding raw nanopore reads
DNA extraction protocol
Genotyping Klebsiella using Nanopore data
Long-read assembly benchmarking
Polypolish: short read polishing of ONT assemblies
Recovering small plasmids from nanopore data
Trycycler: longread-only assembly
Unicycler: hybrid assembler

Papers: AMR

Acinetobacter plasmid typing
AMR drivers in E. coli
AMR evolution in Acinetobacter
AMR surveillance using routine data
AMRnet paper
Carbapenem resistance evolution during prolonged Acinetobacter infection
MDR Salmonella Kentucky
Review: Genomic insights into AMR evolution

Papers: BioRxiv

Ciprofloxacin resistance prediction in Kleb
Effect of reference DB choice on taxonomic assignment for metagenomics
Kleb pneumo LINcodes
Transmission dynamics of Klebsiella pneumoniae in a neonatal intensive care unit in Zambia before and after an infection control bundle
Transmission in neonatal units in Africa and South Asia
tRNA and genomic islands in Klebs

Papers: Klebsiella

AMR Klebsiella spread in hospitals
Bactabolize: high-throughput genome-scale metabolic modelling
Comparison of HGT dynamics in AMR/virulent Klebs clones
Differentiating Kleb species complex with MALDI-TOF
Diversity of Kleb oxytoca hospital isolates
Evolution of hypervirulent Klebs CG23
Genomic epi of hospital Kleb
Genomic Surveillance of Klebs in South & Southeast Asia
Genotyping Klebsiella using Nanopore data
Kaptive v2 – K/O typing for Klebsiella
Kaptive v3
Kleborate – genotyping Klebsiella
Klebs across niches in Norway
Klebs africana and pneumo in bats
Klebs metabolic atlas
Klebs metabolic modelling
Klebs plasmids encoding AMR & virulence
Klebs ST307 evolution & spread
Klebs virulence plasmids
Klebsiella carriage -> infection
Klebsiella Pathogenwatch
Klebsiella rmp (hypermucoidy) variation
Klebsiella Vaccine Value Profile
Linear plasmids in Klebsiella
MDR colonization & infection in ICU
National genomic surveillance of Klebs in Norway
Nitrofurantoin resistance
Online Klebs Capsule & O typing
Plasmid transfer contributing to ESBL Kleb infection burden
Recovering small plasmids from nanopore data
Review: Klebs as key trafficker of drug resistance
Review: Population Genomics of K. pneumoniae
Risk factors for Kleb carriage in the community
Seroepi of Klebs neonatal sepsis
SHV enzyme in Kleb pneumo
Yersiniabactin in Klebsiella

Papers: typhoid

Cip resistant typhoid in India
MDR typhoid in Africa
Pediatric typhoid in Nepal
Typhi genomics in Dhaka, Kathmandu & Blantyre (STRATAA)
Typhi Genotyper
TyphiNET dashboard
Typhoid Disease Primer
Typhoid genomes from PNG
Typhoid Genomics Consortium
Typhoid genomics consortium: 13k genomes
Typhoid genomics in Kenya
Typhoid in Bangladesh
Typhoid PathogenWatch
Typhoid sentinel traveller surveillance
Updates to GenoTyphi

Publications: other

Acinetobacter capsule typing
Airway microbiome from 0-5 yrs
AmpliconTyper
Assembling bacterial genomes – how to guide
Asthma/allergy development trajectories
CRISPR-Cas9 enriched seq of Enterobacterales
Data Sharing Comment
Elizabethkingia outbreak
Evolutionary dynamics of polysaccharide loci in Enterobacteriaceae
FastSpar (correlations for sparse microbiome data)
Fixing up legacy ref genomes of Acinetobacter
Haemophilus colonisation in CF children
Haemophilus influenzae serotyping
Identifying plasmid contigs with kraken
IS and convergent evolution of Shigella
Polypolish: short read polishing of ONT assemblies
Review: Capsule locus genetics
Royal Society Special Issue – Microbial Pathogens
Shigella sonnei genomic framework
Shigella sonnei reference panel
SNPPar – homoplasy detection
TB genomic epi in Vietnam
Trycycler: longread-only assembler

Posts by tag

act antibiotic resistance artemis bandage beginner's guide brig communities comparative genomics e. coli genomic epi ismapper klebsiella mauve microbiome mlst papers phylogenetics phylogeography populations resistance resistance genes shigella software spatial trees tutorial typhoid velvet vietnam visualisation

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