Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.

ABSTRACT: We report here the genome sequences of 55 strains belonging to the genus Escherichia from multiple animal and environmental sources. These strains include representatives of Escherichia albertii, Escherichia fergusonii, and six additional genetically distinct lineages of Escherichia spp., one of which is newly discovered and is being reported for the first time here.

SUBMITTER: Gangiredla J

PROVIDER: S-EPMC5940954 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Draft Genome Sequences of Escherichia albertii, Escherichia fergusonii, and Strains Belonging to Six Cryptic Lineages of Escherichia spp.

Gangiredla Jayanthi J Mammel Mark K MK Barnaba Tammy J TJ Tartera Carmen C Gebru Solomon T ST Patel Isha R IR Leonard Susan R SR Kotewicz Michael L ML Lampel Keith A KA Elkins Christopher A CA Lacher David W DW

Genome announcements 20180503 18

We report here the genome sequences of 55 strains belonging to the genus Escherichia from multiple animal and environmental sources. These strains include representatives of Escherichia albertii, Escherichia fergusonii, and six additional genetically distinct lineages of Escherichia spp., one of which is newly discovered and is being reported for the first time here. ...[more]

PMID: 29724828

Similar Datasets

Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii.

Project description:Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E. coli, 5 Shigella spp., 21 E. albertii, 12 E. fergusonii and 5 other species) and design primers for the following species-specific regions: a 212bp region of the cyclic di-GMP regulator gene (cdgR, AW869_22935 from genome K-12 MG1655, CP014225) for E. coli/Shigella; a 393bp region of the DNA-binding transcriptional activator of cysteine biosynthesis gene (EAKF1_ch4033 from genome KF1, CP007025) for E. albertii; and a 575bp region of the palmitoleoyl-acyl carrier protein (ACP)-dependent acyltransferase (EFER_0790 from genome ATCC 35469, CU928158) for E. fergusonii. We incorporated the species-specific primers into a conventional multiplex PCR assay and assessed its performance with a collection of 97 Enterobacteriaceae strains. The assay was 100% sensitive and specific for detecting the expected species and offers a quick and accurate strategy for identifying E. coli, E. albertii, and E. fergusonii in either a single reaction or by in silico PCR with sequence assemblies.

| S-EPMC5603207 | biostudies-literature

Draft Genome Sequences of Two Escherichia albertii Isolates Collected from Healthy Pets in Switzerland.

Project description:Here, we report the genome sequences of two Escherichia albertii isolates recovered from a healthy dog (KBD171i) and cat (KBK128i) in Switzerland in 2022. The genome sizes of KBK128i and KBD171i were 4.7 Mbp and 4.9 Mbp, respectively.

| S-EPMC10019296 | biostudies-literature

Draft Genome Sequences of Six Moroccan Helicobacter pylori Isolates Belonging to the hspWAfrica Group.

Project description:Helicobacter pylori affects up to 50% of people worldwide. Here, we present the draft genome sequences of six H. pylori strains isolated from Moroccan patients with different gastric diseases. Multilocus sequence typing analysis showed that all of the H. pylori isolates belonged to the hspWAfrica group.

| S-EPMC7545276 | biostudies-literature

Cryptic lineages of the genus Escherichia.

Project description:Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that E. coli and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all Escherichia lineages (named and unnamed) were evaluated, we found evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from E. coli that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical E. coli, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However, our sampling suggests that CIII, CIV, and CV represent environmentally adapted Escherichia lineages that may be more abundant outside the host gastrointestinal tract.

| S-EPMC2765150 | biostudies-literature

Whole-Genome Draft Sequences of Six Commensal Fecal and Six Mastitis-Associated Escherichia coli Strains of Bovine Origin.

Project description:The bovine gastrointestinal tract is a natural reservoir for commensal and pathogenic Escherichia coli strains with the ability to cause mastitis. Here, we report the whole-genome sequences of six E. coli isolates from acute mastitis cases and six E. coli isolates from the feces of udder-healthy cows.

| S-EPMC4966475 | biostudies-literature

Draft genome sequences of Escherichia spp. isolates from New Zealand environmental sources.

Project description:Escherichia coli is often used as a fecal indicator bacterium for water quality monitoring. We report the draft genome sequences of 500 Escherichia isolates including newly described Escherichia species, namely Escherichia marmotae, Escherichia ruysiae, and Escherichia whittamii, obtained from diverse environmental sources to assist with improved public health risk assessments.

| S-EPMC10927642 | biostudies-literature

Draft genome sequences of six Escherichia coli isolates from the stepwise model of emergence of Escherichia coli O157:H7.

Project description:Enterohemorrhagic Escherichia coli (EHEC) of serotype O157:H7 has been implicated in food-borne illnesses worldwide. An evolutionary model was proposed in which the highly pathogenic EHEC O157:H7 serotype arose from its ancestor, enteropathogenic E. coli (EPEC) O55:H7 (sorbitol fermenting [SOR(+)] and β-glucuronidase positive [GUD(+)]), through sequential gain of virulence, phenotypic traits, and serotype change. Here we report six draft genomes of strains belonging to this evolutionary model: two EPEC O55:H7 (SOR(+) GUD(+)) strains, two nonmotile EHEC O157:H(-) strains (SOR(+) GUD(+)) containing plasmid pSFO157, one EHEC O157:H7 (SOR(-) GUD(+)) strain, and one O157:H7 strain containing plasmid pSFO157 (SOR(+) GUD(+)).

| S-EPMC3133052 | biostudies-literature

Draft Genome Sequences of Six Yersinia kristensenii Strains.

Project description:Yersinia kristensenii is one of the Yersinia enterocolitica-like bacterial species, which are considered nonpathogenic to humans. In this work, we reported the draft genome sequences of six Yersinia kristensenii strains. These draft genomes will help to better characterize Yersinia kristensenii at the genomic level.

| S-EPMC8759387 | biostudies-literature

Draft Genome Sequences of 16 Strains of Escherichia Cryptic Clade II Isolated from Intertidal Sediment in Hong Kong.

Project description:The genus Escherichia includes several cryptic clades. Among them, the members of cryptic clade II have rarely been found, and their genome sequences remain largely uninvestigated. Here, we report the draft genome sequences of 16 strains of Escherichia cryptic clade II that were isolated from intertidal sediment in Hong Kong.

| S-EPMC6639607 | biostudies-literature

Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus.

Project description:The draft genomes of the alkaliphilic, anaerobic bacteria, Anaerobacillus arseniciselenatis, A. alkalidiazotrophicus, and A. alkalilacustris, and a novel closely related isolate of the Anaerobacillus genus are reported here. These assembled genomes will help identify, at the molecular level, the phenotypic differences between the species of this poorly characterized genus.

| S-EPMC5255918 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data