The Sanger Institute was funded to perform comparative sequencing of five Escherichia coli and Shigella strains in collaboration with Dr. Christoph Tang of the Centre for Molecular Microbiology and Infection, Imperial College, London, Prof. Mark Pallen and Dr. Ian Henderson of the Division of Immunity and Infection, University of Birmingham, UK Dr. Claude Parsot and Dr. Phillipe Sansonetti of the Unite de Pathologie Microbienne, Institut Pasteur, France, Dr. Gadi Frankel, of the Department of Biochemistry, Imperial College, London, and Dr. Stuart Knutton of the Institute of Child Health, Birmingham.
Published Genome Data
Published Sequence
E. coli E2348/69 is published and consists of a chromosome, with EMBL/GenBank accession FM180568, and two plasmids, with EMBL/GenBank accessions FM180569 and FM180570.
Shotgun and assembly data from this project are available from our FTP site.
E. coli 042 is published and consists of a chromosomal genome, with EMBL/GenBank accession FN554766 and a plasmid, with EMBL/GenBank accession FN554767.
Shotgun and assembly data from this project are available from our FTP site.
The chromosomal genomes ofE.coli chi7122 and E. coli IMT2125 are available in EMBL/GenBank with accessions HE962388 and HE964769 respectively.
Funded Sequencing
E. coli non-K1 which has been funded for sequencing.
Other Projects
Additionally, as part of a joint project investigating the genomics and population biology of Enterotoxigenic E. coli (ETEC), the Sanger Institute, funded by the BBSRC has sequenced the genome of an ETEC strain, H10407 This project was funded in collaboration with Dr. Ian Henderson and Prof. Mark Pallen of the Department of Immunity and Infection, University of Birmingham.
This genome is published and consists of a chromosome and 4 plasmids. The chromosome has EMBL/GenBank accession FN649414 and the plasmids have accessions FN649415, FN649416, FN649417 and FN649418
Shotgun and assembly data from this project are available from our FTP site.
BSAC Resistance Surveillance Project and Multi-Drug Resistance
This data is from bacterial isolates collected in the BSAC Resistance Surveillance Project. Please see bsacsurv.org for details and availability.
Studies
- E. coli MiniTn5 sequencing
- Retrospective 0157:H7 TraDIS from screen in calves
- ETEC wild types and attenuated vaccine strains
- Haemophilus parasuis genome comparisons
- Global phylogeny of enterotoxigenic Escherichia coli collection
- Diversity of MRSA
- CF negative Enterotoxigenic Escherichia coli
- Atypical enteropathogenic E. coli virulence markers
- Global diversity of Shigella species
- Relationship of MLST structure of Escherichia coli species to genomic organisation complexity
- Defining EPEC: evolution, global distribution and effector inventory
- Comparative genome sequence analysis of the globally disseminated Escherichia coli ST131 lineage
- Whole genome sequencing of naturally isolated Escherichia coli from nursing homes in Ireland
- Clostridium difficile 078 diversity
- Antimicrobial resistance modifiers studied by TraDIS
- HPACC Murray project
- Comparative analysis of the two pandemic CTX-M-15 ESBL-producing E. coli lineages ST131 and ST648 from various hosts
- Defining hidden traits of successful pathogenic E. coli lineages in Sequence type 10 strains
- Unravelling the influence of stx phage transduction on gene expression of atypical EPEC
- Variation of DNA damage and repair along a bacterial genome
- Pathogenesis of Escherichia coli prostatitis and oncogenesis
- Whole genome sequencing of 1200 bacterial strains isolated from healthy faecal transplant donors and recurrent C. difficile patients
- Escherichia coli (PHE & BSAC collections) sequencing
- Multi Drug Resistant Gram Negative Rods (MDR-GNR) sequencing study
- Escherichia coli (ETEC) samples from KEMRI
- TraDIS method optimisation and validation
- NCTC 3000
- Pacbio sequencing for TraDIS reference genomes
- Hospital acquired Klebsiella pneumoniae and the role of colonization and transmission (Australia)
- TraDIS to study T6SS in Pseudomonas aeruginosa
- Sequencing bacterial genomes
- TraDIS to study Escherichia coli PHE isolates
- Sequencing Gram negative bacteria (HICF)
- Sequencing RNA samples from ETEC strains
- Escherichia coli sequencing
- Genomic characterization of bladder bacteria from healthy and infected women
- AMR Enterobacteriaceae in Blantyre
- Bloodstream surveillence across Africas
- Pathogenic lineages of enteric bacteria in Nigeria
- Global population genomics of Campylobacter fetus
- VREC-water
- VRES-water
- VREC-farm
- VRES-farm
- Study of novel antibiotic targets
- Lung Culturomics
- WGS on UPEC strains for colicin study
- TraDIS on Escherichia coli MG1665
- Analysing the genomic difference between ETEC strains isolated from symptomatic and asymptomatic carriers
- European Survey of Carbapenemase producing Enterobacteriaceae (EuSCAPE) Sequencing Project
- Sequencing VRE bacteria (UKCRC)
- RNA-seq analysis of Escherichia coli (ETEC) samples
- Coliform bacteria from Thailand
- WGS on E. coli BL21 harbouring a MDR plasmid
- Scottish Healthcare Associated Infection Prevention Institute (SHAIPI)
- Whole genome approach to investigate the potential zoonotic transmission of Escherichia coli and their antimicrobial resistance genes in chickens and humans in Vietnam
- Differentiating the Molecular epidemiology of ESBL-carrying Enterobacteriaceae (ESBL-E) among neonates.
- Characterisation of anaerobic E. coli K12 by Tradis
- Human Gastrointestinal Microbiota Diversity
- Towards a new Enterotoxigenic Escherichia coli (ETEC) vaccine strategy
- Clostridium perfringens- Phylogenetic and virulence analysis of Clostridium species primarily from pre-term infantsI
- Whole genome sequencing of Shigella and Salmonella Typhi from Papua New Guinea
- VREC-hospital
- VRES-hospital
- The phylogeography of Klebsiella pneumoniae and Escherichia coli causing bloodstream infections in Asia and the role of siderophores and antimicrobial resistance genes in virulence.
- ETEC from a single hospital in Nepal.
- ETEC_transcriptomics
- Sequencing ESKAPE pathogens in Malawi
- Commensal bacterial genomes from health and disease
- PacBio sequencing Escherichia coli sequence type (ST)131 from nursing homes in Ireland
E. coli MiniTn5 sequencing
Sample | Strain | Run Accession |
---|---|---|
EcoliAPEC_input_pooled | Escherichia coli APEC O78 Chi7188 | ERR305882 |
EcoliAPEC_liver_pooled | Escherichia coli APEC O78 Chi7188 | ERR305883 |
EcoliAPEC_lung_pooled | Escherichia coli APEC O78 Chi7188 | ERR305884 |
Ecoli_MiniTn5_input1 | Escherichia coli APEC O78 Chi7188 | ERR305901 |
E_coli_MiniTn5_Liver1 | Escherichia coli APEC O78 Chi7248 | ERR305899 |
E_coli_MiniTn5_Liver1 | Escherichia coli APEC O78 Chi7248 | ERR305900 |
Retrospective 0157:H7 TraDIS from screen in calves
Sample | Strain | Run Accession |
---|---|---|
O157_Input | 0157:H7 | ERR022652 |
O157_Output | 0157:H7 | ERR022653 |
Haemophilus parasuis genome comparisons
Sample | Strain | Run Accession |
---|---|---|
121113_ec | Unknown | ERR225615 |
Global phylogeny of enterotoxigenic Escherichia coli collection
Diversity of MRSA
CF negative Enterotoxigenic Escherichia coli
Atypical enteropathogenic E. coli virulence markers
Relationship of MLST structure of Escherichia coli species to genomic organisation complexity
Defining EPEC: evolution, global distribution and effector inventory
Comparative genome sequence analysis of the globally disseminated Escherichia coli ST131 lineage
Whole genome sequencing of naturally isolated Escherichia coli from nursing homes in Ireland
Antimicrobial resistance modifiers studied by TraDIS
HPACC Murray project
Comparative analysis of the two pandemic CTX-M-15 ESBL-producing E. coli lineages ST131 and ST648 from various hosts
Defining hidden traits of successful pathogenic E. coli lineages in Sequence type 10 strains
Unravelling the influence of stx phage transduction on gene expression of atypical EPEC
Sample | Strain | Run Accession |
---|---|---|
14505A | Mu/07/0324/ | ERR366433 |
14505B | Mu/07/0324/ | ERR366434 |
14505C | Mu/07/0324/ | ERR366435 |
14505T1A | Unknown | ERR366436 |
14505T1B | Unknown | ERR366437 |
14505T1C | Unknown | ERR366438 |
19064A | 910/00 | ERR366427 |
19064B | 910/00 | ERR366428 |
19064C | 910/00 | ERR366429 |
19064T1A | Unknown | ERR366430 |
19064T1B | Unknown | ERR366431 |
19064T1C | Unknown | ERR366432 |
8073A | IMT8073 | ERR366439 |
8073yjQA | Unknown | ERR366442 |
8073yjQB | Unknown | ERR366443 |
8073yjQC | Unknown | ERR366444 |
8074B | IMT8073 | ERR366440 |
8075C | IMT8073 | ERR366441 |
Variation of DNA damage and repair along a bacterial genome
Sample | Strain | Run Accession |
---|---|---|
0mM_1 | E.coli K12 MG1655 | ERR376617 |
0mM_2 | E.coli K12 MG1655 | ERR376618 |
0mM_3 | E.coli K12 MG1655 | ERR376619 |
5mM_1 | E.coli K12 MG1655 | ERR376620 |
5mM_2 | E.coli K12 MG1655 | ERR376621 |
5mM_3 | E.coli K12 MG1655 | ERR376622 |
5mM_RP1 | E.coli K12 MG1655 | ERR376623 |
5mM_RP2 | E.coli K12 MG1655 | ERR376624 |
5mM_RP3 | E.coli K12 MG1655 | ERR376625 |
Pathogenesis of Escherichia coli prostatitis and oncogenesis
Sample | Strain | Run Accession |
---|---|---|
PWDP26 | P26 | ERR361030 |
RWD1617 | 1617 | ERR361034 |
RWD5011 | 5011 | ERR361033 |
RWDP14 | P14 | ERR361027 |
RWDP2 | P2 | ERR361023 |
RWDP21 | P21 | ERR361028 |
RWDP22 | P22 | ERR361029 |
RWDP28 | P28 | ERR361031 |
RWDP29 | P29 | ERR361032 |
RWDP4 | P4 | ERR361024 |
RWDP7 | P7 | ERR361025 |
RWDP9 | P9 | ERR361026 |
Escherichia coli (PHE & BSAC collections) sequencing
Multi Drug Resistant Gram Negative Rods (MDR-GNR) sequencing study
Escherichia coli (ETEC) samples from KEMRI
TraDIS method optimisation and validation
Sample | Strain | Run Accession |
---|---|---|
UPEC_base | NCTC 13441 | ERR555092 |
NCTC 3000
Pacbio sequencing for TraDIS reference genomes
Sample | Strain | Run Accession |
---|---|---|
3027STDY5771422 | NCTC 13441 | ERR581109 |
3027STDY5771422 | NCTC 13441 | ERR581110 |
Hospital acquired Klebsiella pneumoniae and the role of colonization and transmission (Australia)
TraDIS to study T6SS in Pseudomonas aeruginosa
Sample | Strain | Run Accession |
---|---|---|
P1_ECvsrSH1_1 | DH10B | ERR877650 |
P1_ECvsrSH1_1 | DH10B | ERR877659 |
P1_ECvsrSH1_2 | DH10B | ERR877651 |
P1_ECvsrSH1_2 | DH10B | ERR877660 |
P1_ECvsrS_1 | DH10B | ERR877648 |
P1_ECvsrS_1 | DH10B | ERR877657 |
P1_ECvsrS_2 | DH10B | ERR877649 |
P1_ECvsrS_2 | DH10B | ERR877658 |
P2_ECvsrSH1_1 | DH10B | ERR877654 |
P2_ECvsrSH1_1 | DH10B | ERR877663 |
P2_ECvsrSH1_2 | DH10B | ERR877655 |
P2_ECvsrSH1_2 | DH10B | ERR877664 |
P2_ECvsrS_1 | DH10B | ERR877652 |
P2_ECvsrS_1 | DH10B | ERR877661 |
P2_ECvsrS_2 | DH10B | ERR877653 |
P2_ECvsrS_2 | DH10B | ERR877662 |
Sequencing bacterial genomes
Sample | Strain | Run Accession |
---|---|---|
Eco216 | Unknown | ERR698917 |
TraDIS to study Escherichia coli PHE isolates
Sample | Strain | Run Accession |
---|---|---|
Base_phage | strain 9000 | ERR986952 |
Con1_ON_A | strain 9000 | ERR1144655 |
Con1_ON_B | strain 9000 | ERR1144656 |
Con2_ON_A | strain 9000 | ERR1144659 |
Con2_ON_B | strain 9000 | ERR1144660 |
Cont_0hr | strain 9001 | ERR986953 |
Cont_3hr | strain 9002 | ERR986954 |
Cont_6hr | strain 9003 | ERR986955 |
O12_200_3hr | strain 9009 | ERR986961 |
O12_200_6hr | strain 9011 | ERR986963 |
O12_50_3hr | strain 9008 | ERR986960 |
O12_50_6hr | strain 9010 | ERR986962 |
O13_200_3hr | strain 9013 | ERR986965 |
O13_200_6hr | strain 9015 | ERR986967 |
O13_50_3hr | strain 9012 | ERR986964 |
O13_50_6hr | strain 9014 | ERR986966 |
O7_200_3hr | strain 9005 | ERR986957 |
O7_200_6hr | strain 9007 | ERR986959 |
O7_50_3hr | strain 9004 | ERR986956 |
O7_50_6hr | strain 9006 | ERR986958 |
P13_1_ON_A | strain 9000 | ERR1144657 |
P13_1_ON_B | strain 9000 | ERR1144658 |
P13_2_ON_A | strain 9000 | ERR1144661 |
P13_2_ON_B | strain 9000 | ERR1144662 |
Sequencing Gram negative bacteria (HICF)
Sequencing RNA samples from ETEC strains
Sample | Strain | Run Accession |
---|---|---|
E1057_ETEC | Unknown | ERR862923 |
E1167_ETEC | Unknown | ERR862924 |
E1189_ETEC | Unknown | ERR862925 |
E1373_ETEC | Unknown | ERR862926 |
E1441_ETEC | Unknown | ERR862927 |
E1533_ETEC | Unknown | ERR862928 |
E1556_ETEC | Unknown | ERR862929 |
E1574_ETEC | Unknown | ERR862930 |
E1600_ETEC | Unknown | ERR862931 |
E1635_ETEC | Unknown | ERR862932 |
E1649_ETEC | Unknown | ERR862933 |
E1679_ETEC | Unknown | ERR862934 |
E1739_ETEC | Unknown | ERR862935 |
E1752_ETEC | Unknown | ERR862936 |
E1779_ETEC | Unknown | ERR862937 |
E2980_ETEC | Unknown | ERR862938 |
E36_ETEC | Unknown | ERR862917 |
E562_ETEC | Unknown | ERR862918 |
E616_ETEC | Unknown | ERR862919 |
E626_ETEC | Unknown | ERR862920 |
E806_ETEC | Unknown | ERR862921 |
E925_ETEC | Unknown | ERR862922 |
Escherichia coli sequencing
Sample | Strain | Run Accession |
---|---|---|
E2278Del | Unknown | ERR776115 |
H10407Bir | Unknown | ERR776114 |
Genomic characterization of bladder bacteria from healthy and infected women
Sample | Strain | Run Accession |
---|---|---|
3454STDY6077225 | Unknown | ERR1045825 |
3454STDY6077233 | Unknown | ERR1045830 |
3454STDY6077241 | Unknown | ERR1045836 |
3454STDY6633096 | Unknown | ERR1939955 |
AMR Enterobacteriaceae in Blantyre
Bloodstream surveillence across Africas
Pathogenic lineages of enteric bacteria in Nigeria
Sample | Strain | Run Accession |
---|---|---|
3534STDY6056170 | Unknown | ERR987290 |
3534STDY6056172 | Unknown | ERR987343 |
3534STDY6056173 | Unknown | ERR987344 |
3534STDY6056176 | Unknown | ERR987345 |
3534STDY6056178 | Unknown | ERR987346 |
3534STDY6056179 | Unknown | ERR987291 |