Identifying Enteric Pathogens and Assessing Their Health Risks in Urban Environments of Dhaka, Bangladesh Open Access

Abstract

In densely populated urban environments such as Dhaka, Bangladesh, frequent exposure to fecal contamination may cause a high risk of enteric infections and diarrheal diseases. Children and adults are frequently exposed to ubiquitous open drains and canals in their immediate environment, which serve as outlets for wastewater and feces disposal in Dhaka city. A cross- sectional study was conducted to detect and quantify pathogens in open drains and canals and estimate monthly risks of infection from exposure to these hazards. This study was conducted in two densely populated areas of Mirpur, Dhaka from April 2019 to October 2019. Selected enteric pathogens, Norovirus Genogroup II (GII), Vibrio cholerae, Giardia, Shigella, and Salmonella Typhi, were quantified in environmental samples using ultrafiltration, polyethylene glycol precipitation (PEG), total nucleic acid (TNA) extraction, and polymerase chain reaction (PCR) methods. Monthly risks of pathogen-specific infections in adults and children from open drain and canal exposure were estimated by quantitative microbial risk assessment (QMRA) using Monte Carlo simulations. The average concentration of pathogens ranged from 0.54 log10 genomic copies/100 mL of Giardia in canal samples to 4.16 log10 genomic copies/100 mL of Shigella in drain samples. The highest monthly risks of infection from exposure to open drains in adults and children were associated with Norovirus GII and the lowest with Salmonella Typhi. The probability of pathogen-specific infection from canal exposure was highest for adults and children for Vibrio cholerae and the lowest for Giardia. Because of the high concentrations of pathogens detected in both open drain and canal water samples, any contact with open drains or canals will likely result in a high level of exposure to fecal contamination and therefore an increased risk of infection by enteric pathogens. The results from this study should be used to guide public health communications and the development of targeted interventions to reduce exposure to fecal contamination in open drains and canals in Dhaka, Bangladesh. 

Table of Contents

TABLE OF CONTENTS

CHAPTER I: BACKGROUND ....................................................................................................................1

A. THE GLOBAL BURDEN OF DIARRHEAL DISEASE ......................................................................................1

B. THE BURDEN OF DIARRHEAL DISEASE CAUSED BY ENTERIC PATHOGENS IN BANGLADESH...................7

C. SANITATION CHALLENGES IN URBAN ENVIRONMENTS .........................................................................13

D. SANITATION IN DHAKA, BANGLADESH: THE ROLE OF CANALS AND OPEN DRAINS..............................15

E. DETECTION METHODS FOR ENVIRONMENTAL ENTERIC PATHOGENS ....................................................17

F. ENTERIC PATHOGENS IN THE ENVIRONMENT .........................................................................................19

G. QUANTITATIVE MICROBIAL RISK ASSESSMENT ....................................................................................25

H. STUDY OBJECTIVES ...............................................................................................................................28

CHAPTER II: MANUSCRIPT ...................................................................................................................30

A. TITLE, AUTHORS, ABSTRACT.................................................................................................................30

B. INTRODUCTION ......................................................................................................................................30

C. METHODS...............................................................................................................................................33

i. Study Site Selection...........................................................................................................................34

ii. Environmental Sample Collection....................................................................................................34

iii. Data Collection................................................................................................................................35

iv. Laboratory Methods.........................................................................................................................37

v. Statistical Methods............................................................................................................................40

vi. Exposure Assessment ......................................................................................................................41

D. RESULTS ................................................................................................................................................46

i. Enteric Pathogen Positive Rates in Open Drains and Canals ............................................................46

ii. Enteric Pathogen Concentrations in Open Drains and Canals..........................................................48

iii. Exposure Assessment ......................................................................................................................50

E. DISCUSSION............................................................................................................................................52

i. Enteric Pathogen Concentrations in Ultrafiltration and Grab Samples: Implications for Detection Methods.................................................................................................................................................52

ii. Open Drain and Canal Exposure Models .........................................................................................55

iii. Open Drain and Canal Exposure Data: Implications for Quantitative Microbial Risk Assessment ...............................................................................................................................................................60

iv. Strengths and Limitations ................................................................................................................62

F. REFERENCES ......................................................................................................................................66

G. TABLES................................................................................................................................................82

H. FIGURES ..............................................................................................................................................93

CHAPTER III: SUMMARY, PUBLIC HEALTH IMPLICATIONS, POSSIBLE FUTURE DIRECTIONS ...............................................................................................................................................99

A. SUMMARY AND PUBLIC HEALTH IMPLICATIONS ...................................................................................99

B. RECOMMENDATIONS............................................................................................................................100

C. FUTURE DIRECTIONS............................................................................................................................101

TABLES

TABLE 2.1. PRIMERS AND PROBES PROFILES USED IN THE QPCR ASSAYS IN THIS STUDY ........................82

TABLE 2.2. PATHOGEN CONCENTRATIONS (LOG10 GENOMIC COPIES/100ML)A IN ENVIRONMENTAL SAMPLES FROM URBAN NEIGHBORHOODS, DHAKA, BANGLADESH 2019 ..................................................83

TABLE 2.3. SURVEY DATA USED TO ESTIMATE MONTHLY EXPOSURE TO CANALS AND DRAINS ..............84

TABLE 2.4. DOSE RESPONSE PARAMETERS USED TO TRANSLATE DOSE INTO INFECTION RISK.................85

TABLE 3.1 ENTERIC PATHOGEN POSITIVE RATES IN ENVIRONMENTAL SAMPLES FROM AN URBAN NEIGHBOURHOOD, DHAKA, BANGLADESH.................................................................................................86

TABLE 3.2. COMPARISON BETWEEN ENTERIC PATHOGEN POSITIVE RATES BETWEEN DRAIN SAMPLES AND CANAL SAMPLES ................................................................................................................................87

TABLE 3.3. COMPARISON BETWEEN ENTERIC PATHOGEN POSITIVE RATES BETWEEN GRAB SAMPLES AND ULTRAFILTRATION SAMPLES......................................................................................................................88

TABLE 3.4. COMPARISON BETWEEN PATHOGEN CONCENTRATIONS (LOG10 GENOMIC COPIES/100 ML)A BETWEEN DRAIN SAMPLES AND CANAL SAMPLES.....................................................................................89

TABLE 3.5. COMPARISON BETWEEN PATHOGEN CONCENTRATIONS (LOG10 GENOMIC COPIES/100 ML)A BETWEEN GRAB SAMPLES AND ULTRAFILTRATION SAMPLES ...................................................................90

TABLE 3.6. ESTIMATED MONTHLY RISKS OF PATHOGEN INFECTION FOR CHILDREN FROM CANAL AND DRAIN EXPOSURES .....................................................................................................................................91

TABLE 3.7. ESTIMATED MONTHLY RISKS OF PATHOGEN INFECTION FOR ADULTS FROM CANAL AND DRAIN EXPOSURES .....................................................................................................................................92

FIGURES

FIGURE 2.1. SAMPLING LOCATIONS IN URBAN NEIGHBORHOODS..............................................................93

FIGURE 2.2. FLOW DIAGRAMS FOR ENVIRONMENTAL SAMPLE PROCESSING PROCEDURES FOR LARGE VOLUME (20 L) AND SMALL VOLUME (400 ML) SAMPLES ........................................................................94

FIGURE 3.1. DISTRIBUTION OF ESTIMATED MONTHLY RISKS OF PATHOGEN-SPECIFIC INFECTIONS IN ADULTS FROM OPEN DRAIN EXPOSURE .....................................................................................................95

FIGURE 3.2. DISTRIBUTION OF ESTIMATED MONTHLY RISKS OF PATHOGEN-SPECIFIC INFECTIONS IN CHILDREN FROM OPEN DRAIN EXPOSURE..................................................................................................96

FIGURE 3.3. DISTRIBUTION OF ESTIMATED MONTHLY RISKS OF PATHOGEN-SPECIFIC INFECTIONS IN ADULTS FROM CANAL EXPOSURE ..............................................................................................................97

FIGURE 3.4. DISTRIBUTION OF ESTIMATED MONTHLY RISKS OF PATHOGEN-SPECIFIC INFECTIONS IN CHILDREN FROM CANAL EXPOSURE...........................................................................................................98 

About this Master's Thesis

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School	Rollins School of Public Health
Department	Epidemiology
Subfield / Discipline	Global Epidemiology - MPH & MSPH
Degree	M.P.H.
Submission	Master's Thesis
Language	English
Research Field	Health Sciences, Public Health Health Sciences, Epidemiology Environmental Health
Keyword	Canals Giardia Shigella Vibrio cholerae Wastewater Quantitative Microbial Risk Assessment (QMRA) Ultrafiltration WASH Salmonella Typhi Urban Health Open Drains Norovirus
Committee Chair / Thesis Advisor	Christine Moe, Emory University
Committee Members	Pengbo Liu, Emory University

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