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10,667 E. coli and Shigella Genomes

Data from: What can we learn from over 100,000 Escherichia coli genomes? Kaleb Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Dave W. Ussery bioRxiv 708131; doi: https://doi.org/10.1101/708131

June 21 19Y

CampyIBS - pseD

pseD single gene tree + laboratory phenotypes

June 7 19Y

Icelandic epidemic S. zooepidemicus

Data from the publication: 'Genomic dissection of an Icelandic epidemic of respiratory disease in horses and associated zoonotic cases'

April 12 19Y

MersTest

WHO Proof of principle

March 26 19Y

Streptococcus pyogenes global diversity

Global population genomics of Streptococcus pyogenes (group A Streptococcus, GAS, Strep A) as per Davies et al 2019., Nature Genetics. http://dx.doi.org/10.1038/s41588-019-0417-8

March 26 19Y

WGCAC Peru 2019 Cholera Outbreak Confirmed Clinical Cases

Microreact Exercise designed for the WGCAC Genomics and Epidemiological Surveillance of Bacterial Pathogens (Lima, Peru) 03 - 08 March 2019

February 27 19Y

WGCAC Peru 2019 Cholera Outbreak Final

Microreact Exercise designed for the WGCAC Genomics and Epidemiological Surveillance of Bacterial Pathogens (Lima, Peru) 03 - 08 March 2019

February 26 19Y

CC8

RAxML tree, 24,258 SNPs

January 17 19Y

High Level Azithromycin Resistant Neisseria gonorrhoeae outbreak

High Level Azithromycin Resistant Neisseria gonorrhoeae outbreak

January 4 19Y

CC5

RAxML tree

January 4 19Y

Campylobacter IBS-GWAS

Genome-wide association study of Campylobacter from IBS patients and control patients

November 16 18Y

SKA S. aureus SNP Pipeline tree

Tree of the S. aureus outbreak dataset from Harris et al. 2013 with the addition of 10 isolates from Coll et al. 2017/Toleman et al. 2016. This tree was created using IQ-Tree with a GTR+G+ASC model on an alignment created by SNP Pipeline using a realistic reference genome (HO 5096 0412).

October 25 18Y

SKA S. aureus ska align tree

Tree of the S. aureus outbreak dataset from Harris et al. 2013 with the addition of 10 isolates from Coll et al. 2017/Toleman et al. 2016. This tree was created using IQ-Tree with a GTR+G+ASC model on an alignment of variable sites from ska align.

October 25 18Y

SKA S. aureus gold standard tree

Gold standard tree of the S. aureus outbreak dataset from Harris et al. 2013 with the addition of 10 isolates from Coll et al. 2017/Toleman et al. 2016. This tree was created using IQ-Tree with a GTR+G+ASC model on a manually curated alignment based on a SNP Pipeline alignment against a PacBio reference of one of the outbreak isolates (GCA_001369415.1).

October 25 18Y

Southampton NTHi vs H. haemolyticus in COPD

Core genome alignment of Haemophilus spp identifying groups of interest.

October 3 18Y

SKA E. coli example

Results of SKA analysis of the E. coli outbreak dataset from Timme RE et al. 2017. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ, Volume 5, pages e3893.

October 2 18Y

SKA S. enterica example

Results of SKA analysis of the S. enterica outbreak dataset from Timme RE et al. 2017. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ, Volume 5, pages e3893.

October 2 18Y

SKA L. monocytogenes example

Results of SKA analysis of the L. monocytogenes outbreak dataset from Timme RE et al. 2017. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ, Volume 5, pages e3893.

October 2 18Y

Aeromonas salmonicida vapA

Biogeography of the fish pathogen Aeromonas salmonicida inferred by vapA genotyping

October 2 18Y

SKA C. jejuni example

Results of SKA analysis of the C. jejuni outbreak dataset from Timme RE et al. 2017. Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance. PeerJ, Volume 5, pages e3893.

October 2 18Y

ST258-KPC-UH-Leipzig-Outbreak-2010-2013 (short-reads)

From 2010 to 2013 the biggest outbreak of Carbapenem Resistant Enterobacteriaceae (CRE) happened in Germany. In this special case with K.pneumoniae ST258 at the University Hospital Leipzig (UHL). Tree was generated using short read Illumina data sets.

August 29 18Y

Salmonella enterica BAPS/PopPUNK comparison

Comparison between PopPUNK and RhierBAPS clusters on Salmonella enterica

June 18 18Y

Fleming Regional

Activities between IVI/WHONET/BDI

June 10 18Y

Neisseria gonorrhoeae BAPS/PopPUNK comparison

Comparison between results from BAPS and PopPUNK

June 9 18Y

NIHR Global Health Research

List of Global Health Research Units and Groups

March 5 18Y

S. aureus isolates from orthopedic device related infections

S. aureus isolates from orthopedic device related infections categorized by patient treatment outcome. n=86 + reference collection (Meric et al 2014); ML tree; PANINI clustering...

January 17 18Y

Thai Salmonella biofilm GWAS

We conducted a sampling survey isolating Salmonella from various stages of the pork production process in Thailand. In total, 126 isolates were collected and whole genome sequences used in a bacterial paired-isolate, pan-genome-wide association study (pGWAS). Isolates with differential biofilm-forming abilities were compared and survival-associated genetic elements identified.

January 12 18Y

Genetic bottlenecks in the evolution of an agriculture-associated disease causing clade of Streptococcus suis in SE Asia

We investigated the evolutionary history of S. suis using whole genome sequence data from healthy and diseased pigs sampled in Northern Thailand in addition to publicly available S. suis genomes from human infection in SE Asia.

January 9 18Y

SJ Dolphin Watch

A citizen science project which uses the Epicollect5 app to get sightings of marine mammals from around the British Channel Islands.

December 26 17Y

Molecular epidemiology and comparative genomics of Campylobacter concisus

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease [doi:10.1038/s41598-018-20135-4] https://www.nature.com/articles/s41598-018-20135-4

December 17 17Y

Peruvian peadiatric Campylobacter_Peru only

Symptomatic and asymptomatic Campylobacter isolates from Peruvian children in the Amazon.

December 12 17Y

Global cholera

Combined analysis of seventh pandemic cholera isolates from Weill et al (2017), Domman et al (2017), and Weill et al (2019)

October 25 17Y

GPSC23

Gladstone, Lo et al 2019. International Genomic Definition of Pneumococcal Lineages to Contextualise Disease, Antibiotic Resistance and Vaccine Impact: A Whole Genome Sequencing Study

October 16 17Y

A day in the life: the domestication of Campylobacter jejuni NCTC11168

Comparison of Campylobacter laboratory strains

October 2 17Y

GPSC103

Gladstone, Lo et al 2019. International Genomic Definition of Pneumococcal Lineages to Contextualise Disease, Antibiotic Resistance and Vaccine Impact: A Whole Genome Sequencing Study

September 28 17Y

Pneumococcal multiLocusNFDS

Combination of four pneumococcal genomic datasets from Massachusetts (Croucher et al (2013) Nat. Genet. 45(6):656-63), Southampton (Gladstone et al (2017) Microb Genomics 3:119), Nijmegen (Cremers et al (2015) Sci. Rep. 5:14952) and the Maela refugee camp (Chewapreecha et al (2014) Nat. Genet. 46(3):306-309). Analysed using a model of multilocus negative frequency dependent selection by Corander et al (2017).

August 5 17Y

microreact-project-CR2017

A7, A8, B4, B8

July 13 17Y

ANdrea y Soledad

dgggbg

July 13 17Y

West African Ebola epidemic (2013-2016)

Phylogeographic reconstruction of the West African Ebola epidemic based 1610 complete genomes (Dudas et al., Nature, 2017, doi:10.1038/nature22040).

April 13 17Y

SNP Genotypes Nepal

Data from DOI10.1371/journal.pntd.0005420 PlosNTD 11(3): e0005420 (Rai et al. 2017)

March 1 17Y

Zika virus in the Americas

Rodrigues Faria, N. et al. 2016. Zika virus in the Americas: Early epidemiological and genetic findings. Science 352(6283):345-9.

November 21 16Y

Fully_sequenced_IncA/C_plasmids

Phylogeny, temporal and spatial distribution of 82 completely sequenced IncA/C plasmids available from NCBI genbank (May 9th 2016).

October 27 16Y

Microreact Example

A hypothetical dataset to illustrate the basic features of Microreact

September 20 16Y

Serotype 1 ST217 Phylogeny

Understanding pneumococcal serotype 1 biology through population genomic analysis

May 5 16Y

Southampton pneumococcal carriage

Gladstone et al. Pre-vaccine serotype composition within a lineage signposts its serotype replacement – a carriage study over seven years following pneumococcal conjugate vaccine use in the UK. MGEN. 2017

April 8 16Y

ESBL-Kp-ST307

ESBL-Kp outbreak

March 17 16Y

Cuni_distribution

Worldwide distribution of C

March 10 16Y

BSAC EMRSA-16

BSAC EMRSA-16 collection, 2001-2010 colour scheme ERY: orange ermA, red ermA+ermC, others: blue absent, red present, purple overlapping phenotypes at location

February 8 16Y

BSAC EMRSA-15

BSAC EMRSA-15 collection, 2001-2010 colour scheme: blue absent, red present, purple overlapping phenotypes at location

February 8 16Y

Typhi Haplotypes

Global Typhi collection, with haplotypes

November 12 15Y

Klebsiella pneumoniae

Data accompanying Holt et al, PNAS 2015. http://www.pnas.org/content/early/2015/06/17/1501049112.abstract

September 28 15Y

The microevolution of Renibacterium salmoninarum

DOI: 10.1038/ismej.2013.186

July 20 15Y

Norovirus

Cotten M, et al. 2004. Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting. J Virol. 88(19):11056.

June 26 15Y

Microevolution of Renibacterium salmoninarum

Evidence for intercontinental dissemination of R. salmoninarum associated with fish movements.

June 26 15Y

SPARC: 2001-2007

Whole genome sequences of 616 Streptococcus pneumoniae isolates from Massachusetts, as described in Croucher et al (2013) Nat. Genet. 45:656–663, Croucher et al (2014) Nat. Comm. 5:5471, and Croucher et al (2015) PLoS Genet. 11(3): e1005095. All bacteria were isolated from nasopharyngeal carriage following the introduction of the seven-valent polysaccharide conjugate vaccine.

June 26 15Y

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system: ST22 population

Global context of Singaporean ST22 MRSA population described by Hsu et al., (2015) Genome Biology 16(1):81

June 12 15Y

CC30 McAdam

CC30 study from PNAS

June 11 15Y

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