Project #8521
Step by step one goes very far

Logged as guest

Go Back to Project List
#8521 : Relationships between ESBL-producing Escherichia coli from food and healthy mothers in Phnom Penh, Cambodia
Topics :
Organisms :
Group :
Name of Applicant : Maya Nadimpalli
Date of application : 27-06-2017
Unit : Pharmacopepidemiology and Infectious Diseases
Location : Laveran 2ème , Bureau 8
Phone : 0637452557
@ Mail :
@ PI-Mail :

Project context and summary :

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 (, 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).

Related team publications :
Service Delivery
Project Manager :
Project Type : Short
Status : Closed
Publication : 10.3201/eid2501.180534
Global Satisfaction for this application : Excellent (5/5)

Go Back to Project List

Sorry. You must be logged in to view this form.