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Searched keyword : Annotation
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search for transcrition factors upregulating Tgfb1 expression in FHL2-/- cells
Transfert annotations
Regulation by phase variation and attenuation: looking for leader peptides containing repeats in the intergenic regions of streptococcal genomes
A reference panel of dengue vector genomes
Yeast comparative genomics
The Physiological Consequences of Altering Bacterial Cell Wall Synthesis
Characterization of the specific TCR repertoire preferentially expressed in spontaneously controlled HIV infection
Discovery of non-annotated transcripts in RNAseq data from Aedes Aegypti
Evaluation of the GO annotation of the Leishmania donovani genome
Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia
Extended spectrum β-lactamase (ESBL) genes encode resistance to penicillins and cephalosporins and can be horizontally transferred among Enterobacteriaceae. More than 60% of healthy humans living in southeast Asia are faecal carriers of ESBL-producing Enterobacteriaceae (ESBL-PE), compared to <10% in Western Europe, suggesting diverse exposure routes. In Cambodia, meat and fish consumption is high and food safety is poorly enforced. Thus, we hypothesized that meat and fish could be a source of exposure to ESBL-PE. From Sept-Nov 2016, we conducted a meat sampling study in Phnom Penh in collaboration with the BIRDY program (http://www.birdyprogram.org/), an ongoing study of neonatal health in low-income countries. We evaluated ESBL-PE contamination among pork, fish, and chicken from two markets and collected survey data from BIRDY mothers. We performed whole genome sequencing on 87 ESBL-producing E. coli recovered from meat and fish and from 91 BIRDY mothers who provided faecal swabs less than one year prior. Now, we will conduct a two-step exploratory analysis of these WGS data:
- First, we will estimate the pairwise evolutionary distance between E. coli isolates, in order to infer a phylogenetic tree. We will use this tree to investigate such epidemiological questions as “Do E. coli sequences from women who reported eating poultry 3+ times/week cluster more closely with E. coli recovered from poultry samples, compared to women who reported never eating poultry?” This phylogenetic tree may be re-constructed using a finer resolution, as needed.
- Second, we will annotate all E. coli genomes in order to identify genomic islands related to antibiotic resistance. We will subsequently use logistic regression to model associations between BIRDY mothers’ reported dietary patterns (i.e. exposure) and the presence or absence of these genomic islands among the ESBL-E. coli they were colonized with (i.e., outcome).