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Project: PRJNA292667

Whole genome sequencing of foodborne pathogens as part of the US Department of Agriculture surveillance project for NARMS.

Organism:

Escherichia coli (E. coli)

Secondary Study Accession:

SRP066916

Study Title:

FSIS NARMS Escherichia coli

Center Name:

FDA

Study Name:

Escherichia coli

ENA-REFSEQ:

PROJECT-ID:

292667

ENA-FIRST-PUBLIC:

2015-08-18

ENA-LAST-UPDATE:

2025-03-07

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Study Accession	Sample Accession	Experiment Accession	Run Accession	Tax Id	Scientific Name	Download All Generated FASTQ files: FTP	Download All Submitted files: FTP	Download All SRA files: FTP	Download All Bam files: FTP
PRJNA292667	SAMN12662346	SRX6784121	SRR10049720	562	Escherichia coli	SRR10049720_1.fastq.gz SRR10049720_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049720	N/A
PRJNA292667	SAMN12662345	SRX6784140	SRR10049739	562	Escherichia coli	SRR10049739_1.fastq.gz SRR10049739_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049739	N/A
PRJNA292667	SAMN12662349	SRX6784142	SRR10049741	562	Escherichia coli	SRR10049741_1.fastq.gz SRR10049741_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049741	N/A
PRJNA292667	SAMN12662343	SRX6784152	SRR10049751	562	Escherichia coli	SRR10049751_1.fastq.gz SRR10049751_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049751	N/A
PRJNA292667	SAMN12662367	SRX6784154	SRR10049753	562	Escherichia coli	SRR10049753_1.fastq.gz SRR10049753_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049753	N/A
PRJNA292667	SAMN12662368	SRX6784155	SRR10049754	562	Escherichia coli	SRR10049754_1.fastq.gz SRR10049754_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049754	N/A
PRJNA292667	SAMN12662366	SRX6784157	SRR10049756	562	Escherichia coli	SRR10049756_1.fastq.gz SRR10049756_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049756	N/A
PRJNA292667	SAMN12662370	SRX6784163	SRR10049762	562	Escherichia coli	SRR10049762_1.fastq.gz SRR10049762_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10049762	N/A
PRJNA292667	SAMN12850985	SRX6907504	SRR10186982	562	Escherichia coli	SRR10186982_1.fastq.gz SRR10186982_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10186982	N/A
PRJNA292667	SAMN12850992	SRX6907511	SRR10186989	562	Escherichia coli	SRR10186989_1.fastq.gz SRR10186989_2.fastq.gz	N/ASubmitted files are only available for data submitted via ENA	SRR10186989	N/A

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Accession	Title/Description
PRJNA12319	A well-studied enteric bacterium <b><i>Escherichia coli</i></b>. This organism is typically present in the lower intestine of humans,... See more
PRJNA290865	National Antimicrobial Resistance Monitoring System (NARMS) Contains whole genome sequencing data acquired from bacterial isolates as part of NARMS, an interage... See more

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<b><i>Escherichia coli</i></b>. This organism is typically present in the lower intestine of humans, where it is the dominant facultative anaerobe present, but it is only one minor constituent of the complete intestinal microflora. E.coli is easily grown in a laboratory setting and is readily amenable to genetic manipulation making it one of the most studied prokaryotic model organisms. E.coli K-12 is the most widely studied strain of E. coli and serves as a reference for this species. E. coli is also one of the most diverse microbial species, containing both pathogenic and non-pathogenic strains. Pathogenic E. coli can cause urinary tract infections, neonatal meningitis, and many, often severe, intestinal diseases. Pathogenic strains often have virulence factors encoded on extrachromosomal plasmids or within bacteriophages and distinct DNA segments termed pathogenicity islands (PAIs). PAIs are likely to have been transferred horizontally and may even have integrated into the chromosome through bacteriophage or plasmid integration or transposition. These virulence factors have often been transferred from closely related, highly pathogenic, Shigella species. Among other virulence factors, enteroinvasive E. coli share an invasion plasmid with Shigella. Reference strains from the pathogenic E. coli are the urinary tract pathogens Escherichia coli IAI39 and Escherichia coli UMN026, Escherichia coli O157:H7 str. Sakai which causes hemorrhagic colitis, Escherichia coli O83:H1 str. NRG 857C which is implicated in Crohn's Disease, and Escherichia coli O104:H4 str. 2011C-3493 which cause hemolytic uremic syndrome.

Contains whole genome sequencing data acquired from bacterial isolates as part of NARMS, an interagency surveillance program that monitors antimicrobial resistance of foodborne pathogens.

SRR10049720_1.fastq.gz

SRR10049720_2.fastq.gz

SRR10049739_1.fastq.gz

SRR10049739_2.fastq.gz

SRR10049741_1.fastq.gz

SRR10049741_2.fastq.gz

SRR10049751_1.fastq.gz

SRR10049751_2.fastq.gz

SRR10049753_1.fastq.gz

SRR10049753_2.fastq.gz

SRR10049754_1.fastq.gz

SRR10049754_2.fastq.gz

SRR10049756_1.fastq.gz

SRR10049756_2.fastq.gz

SRR10049762_1.fastq.gz

SRR10049762_2.fastq.gz

SRR10186982_1.fastq.gz

SRR10186982_2.fastq.gz

SRR10186989_1.fastq.gz

SRR10186989_2.fastq.gz

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Project: PRJNA292667

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