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Dhaka and Matlab, Bangladesh

UC Berkeley

Site Institution: International Centre of Diarrhoeal Diseases, Bangladesh (iccddr,b)
U.S. Institution: UC Berkeley
Research Focus: Transmission Dynamics of Multi-Drug Resistant Uropathogenic E. Coli In Bangladesh

Site Description:
Dedicated to saving lives, icddr,b is a leading international health research organization located in Dhaka, Bangladesh. Through translation of research into treatment, training and policy advocacy, this organization addresses some of the most critical health concerns facing the world today. Research programs include nutrition, child health, reproductive health, chronic diseases, infectious diseases, vaccine sciences, health systems, HIV/AIDS and climate change. Alongside its extensive research agenda, icddr,b provides humanitarian services to some of Bangladesh’s most vulnerable people―160,000 of whom visit its clinical facilities every year. Drawing on over 40 years of experience, icddr,b’s hospitals and clinics have also become an invaluable training ground, not only for the routine treatment of diarrheal diseases, such as cholera, but also for its epidemic response teams, who use their expertise in the field, both in Bangladesh and abroad.

This is a collaborative project between Dr. Mohammad Aminul Islam (GHES Fellow 2012-2013) at International Center for Diarrheal Diseases Research, Bangladesh (icddr,b) and Dr. Lee Riley at UC, Berkeley, to study transmission dynamics of drug-resistant extraintestinal pathogenic Escherichia coli (ExPEC) that cause community-acquired urinary tract infections. A large proportion of community-acquired UTI in most regions of the world are caused by a limited set of multi-drug resistant E. coli strains belonging to related lineages, orE. coli strains that harbor drug-resistance genes shared by pathogenic and environmental Gram negative bacteria. Some MDR uropathogenic E. coli (UPEC) strains share the same genetic lineages with those isolated from food sources, indicating potential foodborne transmissions of antibiotic resistant UPEC. This project will examine the transmission dynamics of MDR UPEC in slum and non-slum communities of Dhaka, Bangladesh as a paradigm of how UPEC clonal lineages and their drug-resistance determinants disseminate in community as opposed to healthcare settings. Bangladesh and India appear to be an important reservoir of many multidrug-resistant Enterobacteriaceae organisms and lineages that are observed globally. This study will have 3 main aims: 1) determine the trend in prevalence of MDR E. coli in patients with UTI and identify risk factors associated with MDR UTI; 2) study the retail food and poultry sources for MDR UPEC; and 3) compare the antibiotic resistance profiles and genotypic characteristics of isolates from UTI and food sources to track mode of transmission of UPEC associated with community acquired UTI. Whole genome sequencing of isolates sharing their genetic lineages (based on PFGE and MLST data) will be used to assess direction of transmission. This project is designed to quantitatively determine the impact, if any, of food and food-producing animals as reservoirs for UPEC on a common community-acquired infection—UTI. Demonstration of such a mode of transmission will contribute to devising more focused public health interventions to prevent them.

The urban Dhaka and rural Matlab Hospitals at icddr,b provide the clinical services to complement the development of lifesaving solutions. Dhaka Hospital was set up in 1962 and quickly became a refuge for the neediest in Bangladesh, offering treatment that would otherwise be beyond their means. The hospital currently treats around 140,000 patients in a year and maintains extremely low mortality rates and a very low average treatment cost per patient- around 40,000 of them would have died if not efficiently treated. In addition to treating those immediately in need of care, the hospital provides the research opportunities and information scientists need to battle enteric diseases on a larger scale. The hospital has short stay, long stay, and special care units. The Short Stay Unit houses the Triage, Out-Patient Department, Short Stay Children’s Ward, BRAC Bank Short Stay Ward, Emergency Ward, Critical Care Cell, Immunization Cell, Surveillance Cell and the Breast Feeding Cell for counseling mothers to promote exclusive breastfeeding. It is called the Short Stay Unit as the average duration of stay is 12-24 hours. Over 100,000 patients are seen every year.

If there are any complications like pneumonia, severe pneumonia, persistent diarrhea, meningitis, hyperthermia, febrile convulsions, severe protein energy malnutrition, electrolyte imbalance or sepsis, clients are admitted to the Longer Stay Unit or the Special Care Unit, or referred to any hospital outside the centre as per admission and referral criteria of Dhaka Hospital. The Longer Stay Unit consists of General Ward, HIV/AIDS ward, Nutrition Ward and facilities for follow up of severely malnourished children at the Out Patient Department after their discharge from the hospital. About 4-5% of the patients who seek care at icddr,b are admitted into the Long Stay Unit. Ninety percent of the admitted patients are under 5 children and most of them are from Dhaka and surrounding areas. The most common diseases among the admitted patients are pneumonia, severe pneumonia, typhoid fever, persistent diarrhea, meningitis, hyperthermia, febrile convulsions, severe protein energy malnutrition, electrolyte imbalance, sepsis and hypoglycemia. About 5-6% of the patients admitted to the General Ward become critical during their treatment and those are referred to Special Care Unit for more intensive treatment and observation. The Special Care Unit provides specialized personnel and resources for the care of the critically ill infants, children and adults. The Special Care Unit combines the Special Care Ward and the recently established Isolation Room with negative-pressure system. On average, 1,600 patients are provided care in the Special Care Unit every year, and 81% of them are children under the age of 5 years.

The Matlab Hospital is one of the richest, most comprehensive and longest running, longitudinal data resources in the developing world, producing regular accurate demographic and health data for rural Bangladesh. With over 45 years of continuous demographic information on a population of over 200,000 people, Matlab is the major rural field site, and a major public health resource for the world. The Health and Demographic Surveillance System at Matlab covers a population of about 225,000, providing data necessary to plan, conduct, and evaluate various types of public-health intervention research. The surveillance system's key role is to monitor population exposure accurately over time to derive health and demographic rates and ratios and assess impacts of health and social interventions. Structured interviews are conducted to register birth, death, marriage, divorce, migration, internal movement and household split every two months in all households in the 142 villages. Periodic socioeconomic surveys also collect information on occupation and household assets.

The mandate of icddr,b’s laboratories is to adopt, develop and use the best scientific technology to address infectious diseases, nutritional, and related health problems of disadvantaged populations in partnership with other national, regional and international institutions that share our commitment to maintain healthy populations. The large and modern laboratories provide facilities for basic and applied research, and extend services to both the rest of icddr,b and the general community. Researchers collaborate with national and international research and educational institutions and participate in conferences, workshops, symposia, and training programs worldwide. The laboratories are additionally used for HIV surveillance, voluntary counseling and testing, and other research projects for investigating the dynamics of a possible HIV epidemic involve laboratory sciences. There are several state-of-the-art laboratories including laboratories for: enteric and respiratory microbiology; environmental microbiology; immunology; molecular genetics; nutritional biochemistry; parasitology; reproductive tract microbiology; tuberculosis; virology; and clinical diagnostics.

Tuberculosis Lab: Established in June 2001, this lab is equipped with adequate instruments for conducting the following procedures: rapid culture using mycobacteria growth indicator tube and conventional culture, and susceptibility testing; PCR- based deletion analysis for identification of Mycobacterium spp.; spoligotyping; mycobacterial interspersed repetitive units typing; rapid immunological diagnostic test of pulmonary tuberculosis; and laboratory diagnosis of paediatric tuberculosis, using gastric aspirate. The laboratory collaborates with the other icddr,b scientific centres in the hospital. It is working with the National TB Reference Laboratory of the National TB Control Programme and the National Institute of Diseases of Chest and Hospital, Dhaka for routine conventional cultures (Lowenstein-Jensen medium-based) and antimicrobial susceptibility testing of M. tuberculosis isolated from sputum samples of TB patients. In 2003, 506 sputa samples were cultured. Senior staff members of the Laboratory are also associated with the national programme for training laboratory technicians and assessment of laboratories of nongovernmental organizations working with the National TV Control Programme.