Enteric Pathogen Diversity in Infant Foods in Low-Income Neighborhoods of Kisumu, Kenya

Effect of exclusive breastfeeding and other infant and young child feeding practices on childhood morbidity outcomes: associations for infants 0-6 months in 5 South Asian countries using Demographic and Health Survey data

BACKGROUND

Despite growing evidence of the impacts of exclusively breastfeeding infants during the first 6 months of life on preventing childhood infections and ensuring optimal health, only a small number of studies have quantified this association in South Asia.

METHODS

We analyzed data from the Demographic and Health Surveys in Afghanistan (2015; n = 3462), Bangladesh (2017-2018; n = 1084), India (2019-2021; n = 26,101), Nepal (2022; n = 581), and Pakistan (2017-2018; n = 1,306), including babies aged 0-6 months. Multivariate logistic regression models were used to determine the association between exclusive breastfeeding in the last 24 h and diarrhoea, acute respiratory infections, and fever in the two weeks before the survey. We also examined the association between other infant and young feeding indicators and these outcomes.

RESULTS

Infants who were exclusive breastfed had decreased odds of diarrhoea in Afghanistan (AOR: 0.49, 95% CI 0.35, 0.70), India (AOR: 0.80, 95% CI 0.70, 0.91), and Nepal (AOR: 0.42, 95% CI 0.20, 0.89). Compared with infants who were not exclusive breastfed, infants who were exclusively breastfed were less likely to have fever in Afghanistan (AOR: 0.36, 95% CI 0.26, 0.50) and India (AOR: 0.75, 95% CI 0.67, 0.84). Exclusive breastfeeding was associated with lower odds of acute respiratory infections in Afghanistan (AOR: 0.57, 95% CI 0.39, 0.83). Early initiation of breastfeeding was protective against diarrhoea in India. Bottle feeding was a risk factor for diarrhoea in India and for fever in Afghanistan and India. Bottle feeding was also a risk factor for acute respiratory infection in Afghanistan and India.

CONCLUSIONS

Not exclusive breastfeeding is a risk factor for diarrhoea, acute respiratory infections, and fever in some South Asian countries. These findings could have substantial implications for global and national efforts to increase exclusive breastfeeding rates. More support, advocacy, and action are required to boost breastfeeding rates as a crucial public health measure.

Risk factors for food contamination among children discharged from community management of acute malnutrition programmes in South Sudan: A cross-sectional study and hazard analysis critical control point approach

Children under-5 years of age are particularly vulnerable to severe acute malnutrition (SAM), and the risk factors associated with relapse to SAM are poorly understood. Possible causes are asymptomatic or symptomatic infection with enteric pathogens, with contaminated food as a critical transmission route. This cross-sectional study comprised a household survey with samples of child food (n = 382) and structured observations of food preparation (n = 197) among children aged 6-59 months that were discharged from treatment in community management of acute malnutrition (CMAM) programmes in South Sudan. We quantified Escherichia coli and total coliforms (TCs), measured in colony forming units per g of food (CFU/g), as indicators of microbial contamination of child food. A modified hazard analysis critical control point (HACCP) approach was utilised to determine critical control points (CCPs) followed by multivariate logistic regression analysis to understand the risk factors associated with contamination. Over 40% (n = 164) of samples were contaminated with E. coli (43% >0 E. coli CFU/g, 95% CI 38%-48%), and 90% (n = 343) had >10 TCs (CFU/g) (>10 TC CFU/g, 95% CI 87%-93%). Risk factors associated (p < 0.05) with child food contamination included if the child fed themselves (9.05 RR, 95% CI [3.18, 31.16]) and exposure to animals (2.63 RR, 95% CI [1.33, 5.34]). This study highlights the risk factors and potential control strategies that can support interventions that reduce food contamination exposure in young children and help further protect those that are highly vulnerable to recurrent exposure to enteric pathogens.

Enterococcus contamination of infant foods and implications for exposure to foodborne pathogens in peri-urban neighbourhoods of Kisumu, Kenya

We collected infant food samples from 714 households in Kisumu, Kenya, and estimated the prevalence and concentration of Enterococcus, an indicator of food hygiene conditions. In a subset of 212 households, we quantified the change in concentration in stored food between a morning and afternoon feeding time. In addition, household socioeconomic characteristics and hygiene practices of the caregivers were documented. The prevalence of Enterococcus in infant foods was 50% (95% confidence interval: 46.1 - 53.4), and the mean log10 colony-forming units (CFUs) was 1.1 (SD + 1.4). No risk factors were significantly associated with the prevalence and concentration of Enterococcus in infant foods. The mean log10 CFU of Enterococcus concentration was 0.47 in the morning and 0.73 in the afternoon foods with a 0.64 log10 mean increase in matched samples during storage. Although no factors were statistically associated with the prevalence and the concentration of Enterococcus in infant foods, household flooring type was significantly associated with an increase in concentration during storage, with finished floors leading to 1.5 times higher odds of concentration increase compared to unfinished floors. Our study revealed high prevalence but low concentration of Enterococcus in infant food in low-income Kisumu households, although concentrations increased during storage implying potential increases in risk of exposure to foodborne pathogens over a day. Further studies aiming at investigating contamination of infant foods with pathogenic organisms and identifying effective mitigation measures are required to ensure infant food safety.

Protocol for the PATHOME study: a cohort study on urban societal development and the ecology of enteric disease transmission among infants, domestic animals and the environment

INTRODUCTION

Global morbidity from enteric infections and diarrhoea remains high in children in low-income and middle-income countries, despite significant investment over recent decades in health systems and water and sanitation infrastructure. Other types of societal development may be required to reduce disease burden. Ecological research on the influence of household and neighbourhood societal development on pathogen transmission dynamics between humans, animals and the environment could identify more effective strategies for preventing enteric infections.

METHODS AND ANALYSIS

The 'enteric pathome'-that is, the communities of viral, bacterial and parasitic pathogens transmitted from human and animal faeces through the environment is taxonomically complex in high burden settings. This integrated cohort-exposure assessment study leverages natural socioeconomic spectrums of development to study how pathome complexity is influenced by household and neighbourhood infrastructure and hygiene conditions. We are enrolling under 12-month-old children in low-income and middle-income neighbourhoods of two Kenyan cities (Nairobi and Kisumu) into a 'short-cohort' study involving repeat testing of child faeces for enteric pathogens. A mid-study exposure assessment documenting infrastructural, behavioural, spatial, climate, environmental and zoonotic factors characterises pathogen exposure pathways in household and neighbourhood settings. These data will be used to inform and validate statistical and agent-based models (ABM) that identify individual or combined intervention strategies for reducing multipathogen transmission between humans, animals and environment in urban Kenya.

ETHICS AND DISSEMINATION

The protocols for human subjects' research were approved by Institutional Review Boards at the University of Iowa (ID-202004606) and AMREF Health Africa (ID-ESRC P887/2020), and a national permit was obtained from the Kenya National Commission for Science Technology and Innovation (ID# P/21/8441). The study was registered on Clinicaltrials.gov (Identifier: NCT05322655) and is in pre-results stage. Protocols for research on animals were approved by the University of Iowa Animal Care and Use Committee (ID 0042302).

Exploration of Infant Food Microbial Composition from Formal and Informal Settings Using Viable Counts and 16S rRNA Gene Amplicon Sequencing in Johannesburg, South Africa

Diarrhoea is a considerable agent of disease and loss of life in children below age five in South Africa. Soweto, South Africa is an urban township in Johannesburg, with most of its population living in informal settlements. Informal settlements in areas such as Soweto are often impoverished communities that do not get water easily, inadequate sanitation is pervasive, and poor hygiene common (risk factors for diarrhoeal diseases). Among the age groups, infants are most vulnerable to diarrhoeal infection, mainly through the ingestion of food and water. The presence of undesirable microbiota is a food safety and health challenge. This study investigated the microbiome of infant food samples collected from formal (n = 19) and informal (n = 11) households in Soweto. A non-culture-dependent technique was used to characterise the bacterial diversity and composition of the infant food samples. The results indicated that household type did not influence microbial diversity and composition in Soweto. South Africa. Firmicutes, Proteobacteria, Cyanobacteria, and Tenericutes dominated the phyla rank in food samples from formal and informal households. Potential pathogens of public health significance, including diarrhoeal disease agents such as Salmonella spp., E. coli, and Campylobacter spp., were detected within the foods. We concluded that the infant food samples showed rich bacterial diversity, and the presence of potential pathogens of public health significance suggests a disease risk that infants may face upon consuming the foods.

Bacteriological quality and safety of bottle food and associated factors among bottle-fed babies attending pediatric outpatient clinics of Government Health Institutions in Arba Minch, southern Ethiopia

BACKGROUND

Microbial contamination of baby bottle food has been identified as a significant public health concern, especially in developing countries, but it remains overlooked. Therefore, this study aimed to determine microbiological hazards, compliance with hygiene practices, and critical control points of contamination in baby bottle food in Arba Minch, southern Ethiopia.

OBJECTIVE

To evaluate the bacteriological quality and prevalence of foodborne pathogens in baby bottle food and to identify associated factors among bottle-fed babies attending three government health institutions in Arba Minch, southern Ethiopia.

METHODS

A cross-sectional study was conducted between February 24 and March 30, 2022. A total of 220 food samples, comprising four types prepared with different sources of materials, were collected from systematically selected bottle-fed babies attending health facilities. The data on sociodemographic characteristics, food hygiene, and handling practices were solicited by face-to-face interview using a semi-structured questionnaire. Food samples (10 mL) were quantitatively analyzed for total viable counts (TVC) and total coliform count (TCC) and qualitatively for the presence of common foodborne bacterial pathogens. Data were analyzed using SPSS; ANOVA and multiple linear regression analyses were done to identify factors influencing microbial counts.

RESULTS

Results revealed that the means and standard deviations of TVC and TCC were 5.3 ± 2.3 log₁₀ colony forming units (CFU)/mL and 4.1 ± 2.6 log₁₀ CFU/mL, respectively. Of the various food samples analyzed, 57.3 and 60.5% had a TVC and TCC above the maximum acceptable limits, respectively. The result of the ANOVA showed that there was a significant difference in the mean score of TCV and TCC among the four types of food samples (p < 0.001). Enterobacteriaceae were found in the majority of positive food samples (79.13%), followed by Gram-positive cocci (20.8%). Salmonella spp., diarrheagenic Escherichia coli, and Staphylococcus aureus were the common foodborne pathogens detected in 8.6% of tested foods. The regression result revealed that the type of baby food, hand washing practices of mothers or caregivers, and sterilizing and disinfecting procedures of feeding bottles are independent determinants of bacterial contamination (p < 0.001).

CONCLUSION

The high microbial load and the presence of potential foodborne bacterial pathogens in the bottle food samples analyzed indicate unsanitary practices and the potential risk of exposure to foodborne pathogens in bottle-fed babies. Thus, interventions such as educating parents about proper hygiene practices, sterilizing feeding bottles and limiting bottle feeding practices are critical to reducing the risk of foodborne to bottle-fed infants.

A Mixed Methods Process Evaluation of a Food Hygiene Intervention in Low-Income Informal Neighbourhoods of Kisumu, Kenya

OBJECTIVES

Diarrhoea is a leading cause of infant mortality with the main transmission pathways being unsafe water and contaminated food, surfaces and hands. The 'Safe Start' trial evaluated a food hygiene intervention implemented in a peri-urban settlement of Kisumu, Kenya, with the aim of reducing diarrhoeagenic enteric infections among infants. Four food hygiene behaviours were targeted: handwashing with soap before preparation and feeding, boiling infant food before feeding, storing infant food in sealed containers, and exclusive use of designated utensils during feeding.

METHODS

A process evaluation of the intervention was guided by a theory of change describing the hypothesised implementation and receipt of the intervention, mechanisms of change, and the context. These were assessed by qualitative and quantitative data that included debriefing sessions with the delivery teams and Community Health Volunteers (CHVs), and structured observations during food preparation.

RESULTS

The intervention achieved high coverage and fidelity with over 90% of 814 eligible caregivers participating in the intervention. Caregivers in the intervention arm demonstrated an understanding of the intervention messages, and had 1.38 (95% CI: 1.02-1.87) times the odds of washing hands before food preparation and 3.5 (95% CI: 1.91-6.56) times the odds of using a feeding utensil compared to caregivers in the control group. Contextual factors, especially the movement of caregivers within and outside the study area and time constraints faced by caregivers influenced uptake of some intervention behaviours.

CONCLUSION

Future interventions should seek to explicitly target contextual factors such as secondary caregivers and promote food hygiene interventions as independent of each other.

Environmental and behavioural exposure pathways associated with diarrhoea and enteric pathogen detection in 5-month-old, periurban Kenyan infants: a cross-sectional study

OBJECTIVES

The aim of this study was to test whether household environmental hygiene and behavioural conditions moderated associations between diarrhoea and enteric pathogen detection in infants 5 months of age in Kenya and pathogen sources, including latrine access, domestic animal co-habitation and public food sources.

DESIGN

Cross-sectional study utilising enrolment survey data of households participating in the Safe Start cluster-randomised controlled trial .

SETTING

Kisumu, Kenya.

PARTICIPANTS

A total of 898 caregivers with 5-month (22 week ± 1 week) aged infants were enrolled in the study and completed the enrolment survey.

PRIMARY AND SECONDARY OUTCOME MEASURES

Outcomes were (1) caregiver-reported 7-day diarrhoea prevalence and (2) count of types of enteric viruses, bacteria and parasites in infant stool. Exposures and effect modifiers included water access and treatment, cohabitation with domestic animals, sanitation access, handwashing practices, supplemental feeding, access to refrigeration and flooring.

RESULTS

Reported handwashing after handling animals (adjusted odds ratio (aOR)=0.20; 95% CI=0.06 to 0.50) and before eating (aOR=0.44; 95% CI=0.26 to 0.73) were strongly associated with lower risk of caregiver-reported diarrhoea, while cohabitation with animals (aOR=1.54; 95% CI=1.01 to 2.34) living in a household with vinyl-covered dirt floors (aOR=0.60; 95% CI=0.45 to 0.87) were strongly associated with pathogen codetection in infants. Caregiver handwashing after child (p=0.02) or self-defecation (p=0.03) moderated the relationship between shared sanitation access and infant exposure to pathogens, specifically private latrine access was protective against pathogen exposure of infants in households, where caregivers washed hands after defecation. In the absence of handwashing, access to private sanitation posed no benefits over shared latrines for protecting infants from exposure.

CONCLUSION

Our evidence highlights eliminating animal cohabitation and improving flooring, postdefecation and food-related handwashing, and safety and use of cow milk sources as interventions to prevent enteric pathogen exposure of young infants in Kenya.

TRIAL REGISTRATION NUMBER

NCT03468114.

Determinants of food preparation and hygiene practices among caregivers of children under two in Western Kenya: a formative research study

INTRODUCTION

Diarrhea is a leading cause of child morbidity and mortality worldwide and is linked to early childhood stunting. Food contamination from improper preparation and hygiene practices is an important transmission pathway for exposure to enteric pathogens. Understanding the barriers and facilitators to hygienic food preparation can inform interventions to improve food hygiene. We explored food preparation and hygiene determinants including food-related handwashing habits, meal preparation, cooking practices, and food storage among caregivers of children under age two in Western Kenya.

METHODS

We used the Capabilities, Opportunities, and Motivations model for Behavior Change (COM-B) framework in tool development and analysis. We conducted 24 focus group discussions with mothers (N = 12), fathers (N = 6), and grandmothers (N = 6); 29 key informant interviews with community stakeholders including implementing partners and religious and community leaders; and 24 household observations. We mapped the qualitative and observational data onto the COM-B framework to understand caregivers' facilitators and barriers to food preparation and hygiene practices.

RESULTS

Facilitators and barriers to food hygiene and preparation practices were found across the COM-B domains. Caregivers had the capability to wash their hands at critical times; wash, cook, and cover food; and clean and dry utensils. Barriers to food hygiene and preparation practices included lack of psychological capability, for instance, caregivers' lack of knowledge of critical times for handwashing, lack of perceived importance of washing some foods before eating, and not knowing the risks of storing food for more than four hours without refrigerating and reheating. Other barriers were opportunity-related, including lack of resources (soap, water, firewood) and an enabling environment (monetary decision-making power, social support). Competing priorities, socio-cultural norms, religion, and time constraints due to work hindered the practice of optimal food hygiene and preparation behaviors.

CONCLUSION

Food hygiene is an underexplored, but potentially critical, behavior to mitigate fecal pathogen exposure for young children. Our study revealed several knowledge and opportunity barriers that could be integrated into interventions to enhance food hygiene.

Key Food Hygiene Behaviors to Reduce Microbial Contamination of Complementary Foods in Rural Bangladesh

Microbial contamination of complementary foods puts young children at risk of developing intestinal infections and could be reduced by improved handwashing and food hygiene practices. We aimed to identify which promoted food hygiene practices are associated with reduced complementary food contamination in a rural population in Bangladesh. We collected cross-sectional data on reported and observed maternal food hygiene behaviors and measured Escherichia coli counts as an indicator of microbial contamination in complementary food samples from 342 children of women enrolled in the Food and Agricultural Approaches to Reducing Malnutrition trial in Sylhet, Bangladesh. We used multivariable logistic regression to examine associations of food hygiene behaviors with food contamination. Approximately 46% of complementary food samples had detectable levels of E. coli. Handwashing with soap at critical times and fresh preparation of food before feeding were strongly associated with reduced odds of food sample contamination (odds ratio [OR]: 0.8, 95% confidence interval [CI]: 0.6-0.9 and OR: 0.3, 95% CI: 0.1-0.7, respectively); in contrast, there was no or only weak evidence that reheating of stored food, safe food storage, and cleanliness of feeding utensils reduced contamination. Reduction in food contamination could be more than halved only when several food hygiene behaviors were practiced in combination. In conclusion, single food hygiene practices showed limited potential and a combined practice of multiple food hygiene behaviors may be needed to achieve a substantial reduction of complementary food contamination.

Milk Product Safety and Household Food Hygiene Influence Bacterial Contamination of Infant Food in Peri-Urban Kenya

Background

Milk is a common infant food in peri-urban Kenya that can transmit diarrhea-causing enteric pathogens. Little is known about how contamination of milk at point of purchase and household handling of milk-based infant foods contribute to infant exposure to enteric pathogens.

Objective

To compare the prevalence and concentrations of bacterial indicator organisms and enteric pathogens in unpackaged, fresh pasteurized, and ultra-high temperature (UHT) treated milk at purchase and assess the influence of the type of milk used to prepare infant food on contamination of this food.

Methods

Paired samples of purchased milk and infant food prepared with this milk were obtained from 188 households in low-income neighborhoods in Kisumu, Kenya. Samples were cultured on selective media to isolate Salmonella enterica, Shigella spp., Klebsiella aerogenes, Proteus spp., and Escherichia coli, with pathogens validated by PCR. Probability of detection of these bacteria was compared by milk product treatment and packaging method, and between milk at point of purchase vs. food at point of infant consumption.

Results

Unpackaged milk was most contaminated at point of purchase, but bacterial contamination was also present in pasteurized and UHT milk at purchase. Presence of bacteria in UHT and fresh pasteurized milk at purchase predicted presence of the same bacteria type in infant food. Prevalence of bacterial contamination and concentration level for bacterial indicators generally increased between point of purchase and consumption in UHT and fresh pasteurized milk-based food but decreased in unpackaged milk-based food. Prevalence of the four fecal bacteria were similar in infant foods prepared with each type of milk.

Conclusion

Both pre-market contamination and post-purchase handling influence the likelihood of infants ingesting foods contaminated by diarrheal pathogens.

Bacteroides Microbial Source Tracking Markers Perform Poorly in Predicting Enterobacteriaceae and Enteric Pathogen Contamination of Cow Milk Products and Milk-Containing Infant Food

Consumption of microbiologically contaminated food is one of the leading causes of diarrheal diseases. Understanding the source of enteric pathogens in food is important to guide effective interventions. Enterobacteriaceae bacterial assays typically used to assess food safety do not shed light on the source. Source-specific Bacteroides microbial source tracking (MST) markers have been proposed as alternative indicators for water fecal contamination assessment but have not been evaluated as an alternative fecal indicator in animal-derived foods. This study tested various milk products collected from vendors in urban Kenyan communities and infant foods made with the milk (n = 394 pairs) using conventional culture methods and TaqMan qPCR for enteric pathogens and human and bovine-sourced MST markers. Detection profiles of various enteric pathogens and Bacteroides MST markers in milk products differed from that of milk-containing infant foods. MST markers were more frequently detected in infant food prepared by caregivers, indicating recent contamination events were more likely to occur during food preparation at home. However, Bacteroides MST markers had lower sensitivity in detecting enteric pathogens in food than traditional Enterobacteriaceae indicators. Bacteroides MST markers tested in this study were not associated with the detection of culturable Salmonella enterica and Shigella sonnei in milk products or milk-containing infant food. The findings show that while Bacteroides MST markers could provide valuable information about how foods become contaminated, they may not be suitable for predicting the origin of the enteric pathogen contamination sources.

Effectiveness of hygiene kit distribution to reduce cholera transmission in Kasaï-Oriental, Democratic Republic of Congo, 2018: a prospective cohort study

INTRODUCTION

Household contacts of cholera cases are at a greater risk of Vibrio cholerae infection than the general population. There is currently no agreed standard of care for household contacts, despite their high risk of infection, in cholera response strategies. In 2018, hygiene kit distribution and health promotion was recommended by Médecins Sans Frontières for admitted patients and accompanying household members on admission to a cholera treatment unit in the Democratic Republic of Congo.

METHODS

To investigate the effectiveness of the intervention and risk factors for cholera infection, we conducted a prospective cohort study and followed household contacts for 7 days after patient admission. Clinical surveillance among household contacts was based on self-reported symptoms of cholera and diarrhoea, and environmental surveillance through the collection and analysis of food and water samples.

RESULTS

From 94 eligible households, 469 household contacts were enrolled and 444 completed follow-up. Multivariate analysis suggested evidence of a dose-response relationship with increased kit use associated with decreased relative risk of suspected cholera: household contacts in the high kit-use group had a 66% lower incidence of suspected cholera (adjusted risk ratio (aRR) 0.34, 95% CI 0.11 to 1.03, p=0.055), the mid-use group had a 53% lower incidence (aRR 0.47, 95% CI 0.17 to 1.29, p=1.44) and low-use group had 22% lower incidence (aRR 0.78, 95% CI 0.24 to 2.53, p=0.684), compared with household contacts without a kit. Drinking water contamination was significantly reduced among households in receipt of a kit. There was no significant effect on self-reported diarrhoea or food contamination.

CONCLUSION

The integration of a hygiene kit intervention to case-households may be effective in reducing cholera transmission among household contacts and environmental contamination within the household. Further work is required to evaluate whether other proactive localised distribution among patients and case-households or to households surrounding cholera cases can be used in future cholera response programmes in emergency contexts.

Impact of a demand-side integrated WASH and nutrition community-based care group intervention on behavioural change: a randomised controlled trial in western Kenya

INTRODUCTION

Growth shortfalls and diarrhoeal diseases remain a major cause of morbidity and mortality in low-income settings. Due to the multifaceted causes of undernutrition and the identified limitations of siloed nutrition programmes, improving the delivery of integrated water, sanitation, hygiene (WASH) and nutrition programming could improve child health.

METHODS

We conducted a cluster randomised trial in western Kenya to assess the impact on household behaviours of a novel, theory-informed and integrated WASH and nutrition intervention delivered through care groups as compared with the standard care group approach. We developed an intervention targeting practices relating to food hygiene, mealtime and feeding, and compound cleanliness, each using various behavioural change techniques to influence the uptake of targeted behaviours. Prespecified behavioural outcomes were verified through direct observation, 24 hours recall, and self-reported picture-based methods.

RESULTS

Compared with control households, a greater proportion of intervention households had a hygienic food preparation area (Risk double difference (RDD) 0.81, 95% CI 0.68 to 0.96), had stored food hygienically (RDD 0.76, 95% CI 0.58 to 1.00), had a functional handwashing station (RDD 0.64, 95% CI 0.56 to 0.74), provided a safe space for their child to play (RDD 0.73, 95% CI 0.56 to 0.96), and who fed their children thickened porridge (RDD 0.56, 95% CI 0.51 to 0.63) at endline. The proportion of children 6-24 months in intervention households consuming a sufficient diversity of foods (RDD 0.81, 95% CI 0.64 to 1.04) was higher than in control households; however, there was a non-significant increase in the percentage of pregnant and lactating women receiving an adequate diversity of foods in their diets (RDD 0.86, 95% CI 0.70 to 1.05) among intervention compared with control households at endline.

CONCLUSION

Our integrated WASH and nutrition intervention resulted in important changes in behaviours. This theory-informed intervention could be added to existing care group programmes to considerable advantage.

Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study

BACKGROUND

Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples.

METHODS

In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR.

FINDINGS

Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R² 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR.

INTERPRETATION

The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load.

FUNDING

Wellcome Trust Our Planet, Our Health programme.

Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.

Risk factors for child food contamination in low-income neighbourhoods of Maputo, Mozambique: An exploratory, cross-sectional study

In low‐ and middle‐income countries, food may be a critical transmission route for pathogens causing childhood diarrhoea, but basic food hygiene is often overlooked in public health strategies. Characterising child food contamination and its risk factors could help prioritise interventions to reduce foodborne diarrhoeal disease, especially in low‐income urban areas where the diarrhoeal disease burden is often high. This cross‐sectional study comprised a caregiver questionnaire coupled with food sampling, and food preparation observations, among the study population of an ongoing sanitation trial in Maputo. The aim was to determine the prevalence of child food contamination and associated risk factors. The prevalence of Enterococcus spp., as an indicator of faecal contamination, was estimated in food samples. Risk factor analyses were performed through zero‐inflated negative binomial regression on colony counts. A modified hazard analysis and critical control point approach was used to determine critical control points (CCPs) that might effectively reduce risk. Fifty‐eight linked caregiver questionnaires and food samples were collected, and 59 food preparation observations were conducted. The prevalence of enterococci in child foods exceeding 10 colony forming units per gram was 53% (95% confidence interval [40%, 67%]). Risk factors for child food contamination were identified, including type of food, food preparation practices, and hygiene behaviours. CCPs included cooking/reheating of food and food storage and handling. This exploratory study highlights the need for more research into diarrhoeagenic pathogens and foodborne risks for children living in these challenging urban environments.

Designing a Food Hygiene Intervention in Low-Income, Peri-Urban Context of Kisumu, Kenya: Application of the Trials of Improved Practices Methodology

Food contamination during weaning and complementary feeding can result in high diarrheal incidence among infants. Caregiver practices are important determinants of exposure to foodborne pathogens, and can therefore play a role in reduction in infant food contamination. Through a qualitative approach, we used the Trials of Improved Practices methodology to design a food hygiene intervention in a low-income settlement of Kisumu city in Kenya. These settlements in Kisumu city host a large portion of the city’s population and are faced with a high diarrheal disease burden. Caregivers were selected if they had a child aged 6–9 months, and together, we codesigned a combination of hardware and messaging components targeting handwashing with soap, hygienic feeding, reheating, and hygienic storage of infant food. Caregivers received up to six engagement visits with the research team. The visits were aimed at improving the designed hardware and messaging components. Results showed that feeding items were easily adopted by caregivers, whereas reheating of food was less observed. Households reportedly improved their food storage and handwashing practices. As a result, the hardware components were further refined and tested among the caregivers. Messaging components spurred the aspirations that caregivers had for their children and acted as reminders of practicing good food hygiene. The outcomes of the codesign process provided valuable insights on the knowledge of caregivers, a delivery approach for implementing the intervention, and further informed a subsequent trial that adopted the designed intervention to target early childhood exposure to enteric pathogens through contaminated food.

Infant Food Hygiene and Childcare Practices in Context: Findings from an Urban Informal Settlement in Kenya

Complementary food hygiene is important to reduce infant exposures to enteric pathogens; however, interventions to improve food hygiene in low- and middle-income countries often ignore the larger context in which childcare occurs. In this study, we explore on observational and qualitative information regarding childcare in an informal community in Kenya. Our findings demonstrate that behaviors associated with food contamination, such as hand feeding and storing food for extended periods, are determined largely by the larger social and economic realities of primary caretakers. Data also show how caregiving within an informal settlement is highly dynamic and involves multiple individuals and locations throughout the day. Findings from this study will help inform the development and implementation of food hygiene interventions in informal urban communities.

The Safe Start trial to assess the effect of an infant hygiene intervention on enteric infections and diarrhoea in low-income informal neighbourhoods of Kisumu, Kenya: a study protocol for a cluster randomized controlled trial

BACKGROUND

Symptomatic and asymptomatic enteric infections in early childhood are associated with negative effects on childhood growth and development, especially in low and middle-income countries, and food may be an important transmission route. Although basic food hygiene practices might reduce exposure to faecal pathogens and resulting infections, there have been few rigorous interventions studies to assess this, and no studies in low income urban settings where risks are plausibly very high. The aim of this study is to evaluate the impact of a novel infant food hygiene intervention on infant enteric infections and diarrhoea in peri-urban settlements of Kisumu, Kenya.

METHODS

This is a cluster randomized control trial with 50 clusters, representing the catchment areas of Community Health Volunteers (CHVs), randomly assigned to intervention or control, and a total of 750 infants recruited on a rolling basis at 22 weeks of age and then followed for 15 weeks. The intervention targeted four key caregiver behaviours related to food hygiene: 1) hand washing with soap before infant food preparation and feeding; 2) bringing all infant food to the boil before feeding, including when reheating or reserving; 3) storing all infant food in sealed containers; and, 4) using only specific utensils for infant feeding which are kept separate and clean.

RESULTS

The primary outcome of interest is the prevalence of one or more of 23 pre-specified enteric infections, determined using quantitative real-time polymerase chain reaction for enteric pathogen gene targets. In addition, infant food samples were collected at 33 weeks, and faecal indicator bacteria (Enterococcus) isolated and enumerated to assess the impact of the intervention on infant food contamination.

CONCLUSION

To our knowledge this is the first randomized controlled trial to assess the effect of an infant food hygiene intervention on enteric infections in a high burden, low income urban setting. Our trial responds to growing evidence that food may be a key pathway for early childhood enteric infection and disease and that basic food hygiene behaviours may be able to mitigate these risks. The Safe Start trial seeks to provide new evidence as to whether a locally appropriate infant food hygiene intervention delivered through the local health extension system can improve the health of young children.

TRIAL REGISTRATION

The trial was registered at clinicaltrial.gov on March 16th 2018 before enrolment of any participants (https://clinicaltrials.gov/ct2/show/NCT03468114).