Quantitative Microbial Risk Assessment and Molecular Biology: Paths to Integration

Integrating quantitative microbiological risk assessment and disability-adjusted life years to evaluate the effects of urbanization on health risks for river recreationists

Urban rivers provide an excellent opportunity for water recreation. This study probabilistically assessed health risks associated with water recreation in urban rivers in the Bitan Scenic Area, Taiwan, by employing quantitative microbial risk assessment and disability-adjusted life years (DALYs). Moreover, the effects of urbanization on the health risks of river recreation induced by waterborne pathogenic Escherichia coli (E. coli) were investigated. First, data on river E. coli levels were collected in both the Bitan Scenic Area and the upstream river section, and model parameters were obtained through a questionnaire administered to river recreationists. Monte Carlo simulation was then employed to address parameter uncertainty. Finally, DALYs were calculated to quantify the cumulative effects in terms of potential life lost and years lived with disability. The results indicated that the 90 % confidence intervals for the disease burden (DB) were 0.2-74.1 × 10-6, 0.01-94.0 × 10-6, and 0.3-128.9 × 10-6 DALY per person per year (pppy) for canoeing, swimming, and fishing, respectively, in the Bitan Scenic Area. Furthermore, urbanization near the Bitan Scenic Area approximately doubled the DB risks to river recreationists in upstream rural areas. At the 95th percentile, the DB risks exceeded the tolerances recommended by the World Health Organization (1 × 10-6) or U.S. Environmental Protection Agency (1 × 10-4). The findings suggest that the simultaneous implementation of effluent sewer systems and best management practices can reduce health risks to river recreationists by at least half, reducing the DALY levels below 1 × 10-4 or even 1 × 10-5 pppy.

The Wells-Riley model revisited: Randomness, heterogeneity, and transient behaviours

The Wells-Riley model has been widely used to estimate airborne infection risk, typically from a deterministic point of view (i.e., focusing on the average number of infections) or in terms of a per capita probability of infection. Some of its main limitations relate to considering well-mixed air, steady-state concentration of pathogen in the air, a particular amount of time for the indoor interaction, and that all individuals are homogeneous and behave equally. Here, we revisit the Wells-Riley model, providing a mathematical formalism for its stochastic version, where the number of infected individuals follows a Binomial distribution. Then, we extend the Wells-Riley methodology to consider transient behaviours, randomness, and population heterogeneity. In particular, we provide analytical solutions for the number of infections and the per capita probability of infection when: (i) susceptible individuals remain in the room after the infector leaves, (ii) the duration of the indoor interaction is random/unknown, and (iii) infectors have heterogeneous quanta production rates (or the quanta production rate of the infector is random/unknown). We illustrate the applicability of our new formulations through two case studies: infection risk due to an infectious healthcare worker (HCW) visiting a patient, and exposure during lunch for uncertain meal times in different dining settings. Our results highlight that infection risk to a susceptible who remains in the space after the infector leaves can be nonnegligible, and highlight the importance of incorporating uncertainty in the duration of the indoor interaction and the infectivity of the infector when estimating risk.

Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies

The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.

Footprints of total coliforms, faecal coliforms and E. coli in a wastewater treatment plant and the probabilistic assessment and reduction of E. coli infection risks

Wastewater contains various pathogenic microorganisms, and the disease of workers caused by exposure to wastewater at the wastewater treatment plants (WWTPs) is a growing concern. The footprints of total coliforms (TC), faecal coliforms (FC) and Escherichia coli (E. coli) in a conventional activated sludge WWTP during 12 consecutive months were clarified. It was found that TC, FC and E.coli in influent were significantly removed (log 4.71, log 4.43 and log 4.62, respectively) by WWTP with sand filtration playing a key role, and excess sludge was a major potential pathway for them flowing to the environment. Through quantitative microbial risk assessment (QMRA), hand-to-mouth ingestion of untreated wastewater and wastewater in secondary/efficient sedimentation tanks, as well as accidental ingestion of sludge in dewatering workshop presented the highest infection risks of pathogenic E.coli in the WWTP, considerably exceeded the U.S. EPA benchmark (≤1 × 10-4 pppy). PPE application and E.coli concentration reduction in wastewater or sludge were recommended to reduce the infection risks at these stages. Further, partial ozonation and dissolved ozone flotation thickening were investigated able to reduce the infection risks at the stages of secondary and tertiary treatment of wastewater or sludge treatment by 90- 98 %. The findings of this study would assist in selecting appropriate processes for the further sanitation of WWTPs.

Quantitative Microbial Risk Assessment for Quantification of the Effects of Ultraviolet Germicidal Irradiation on COVID-19 Transmission

Quantitative microbial risk assessment (QMRA) is presented as a tool for evaluation of the effectiveness of ultraviolet germicidal irradiation (UVGI) systems for the disinfection of indoor air. The QMRA is developed in the context of UVGI system implementation for control of SARS-CoV-2 infection and comprises submodels to address problem formulation, exposure assessment, and health effects assessment, all of which provide input to a risk characterization submodel. The model simulations indicate that UVGI systems can effectively control the risk of infection associated with SARS-CoV-2 for low to moderate virus emission rates. The risk of disease transmission is strongly influenced by the rate of pathogen emission by an infected individual, the output power of UVGI fixtures and their configuration, the source of UV-C radiation implemented in the UVGI fixtures, and the characteristics of the heating, ventilation, and air conditioning (HVAC) system. The QMRA framework provides a quantitative link between UVGI/HVAC system characteristics and changes in the risk of disease transmission. The framework can be adapted to other airborne pathogens and provides a rational basis for the design, testing, and validation of UVGI systems.

Quantitative Microbial Risk Assessment of Contracting COVID-19 Derived from Measured and Simulated Aerosol Particle Transmission in Aircraft Cabins

BACKGROUND

SARS-CoV-2 can be effectively transmitted between individuals located in close proximity to each other for extended durations. Aircraft provide such conditions. Although high attack rates during flights were reported, little was known about the risk levels of aerosol transmission of SARS-CoV-2 in aircraft cabins.

OBJECTIVES

The major objective was to estimate the risk of contracting COVID-19 from transmission of aerosol particles in aircraft cabins.

METHODS

In two single-aisle and one twin-aisle aircraft, dispersion of generated aerosol particles over a seven-row economy class cabin section was measured under cruise and taxi conditions and simulated with a computational fluid dynamic model under cruise conditions. Using the aerosol particle dispersion data, a quantitative microbial risk assessment was conducted for scenarios with an asymptomatic infectious person expelling aerosol particles by breathing and speaking. Effects of flight conditions were evaluated using generalized additive mixed models.

RESULTS

Aerosol particle concentration decreased with increasing distance from the infectious person, and this decrease varied with direction. On a typical flight with an average shedder, estimated mean risk of contracting COVID-19 ranged from 1.3 × 10 - 3 to 9.0 × 10 - 2 . Risk increased to 7.7 × 10 - 2 with a super shedder (< 3 % of cases) on a long flight. Risks increased with increasing flight duration: 2-23 cruise flights of typical duration and 2-10 flights of longer duration resulted in at least 1 case of COVID-19 due to onboard aerosol transmission by one average shedder, and in the case of one super shedder, at least 1 case in 1-3 flights of typical duration cruise and 1 flight of longer duration.

DISCUSSION

Our findings indicate that the risk of contracting COVID-19 by aerosol transmission in an aircraft cabin is low, but it will not be zero. Testing before boarding may help reduce the chance of a (super)shedder boarding an aircraft and mask use further reduces aerosol transmission in the aircraft cabin. https://doi.org/10.1289/EHP11495.

Producing ratio measures of effect with quantitative microbial risk assessment

Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.

Producing ratio measures of effect with quantitative microbial risk assessment

Estimating the risk of infections or other outcomes incident to pathogen exposure is a primary goal of quantitative microbial risk assessment (QMRA). Such estimates are useful to predict population-level risks, to evaluate exposures based on normative or tolerable risk guidelines, and to interpret the likely public health relevance of microbial measurements in environmental media. To evaluate alternative control measures (interventions), ratio estimates of effect (e.g., odds and risk ratios) are needed that are more broadly interpretable in the health sciences and consistent with convention in epidemiology. In this paper, we propose a general method for estimating widely used ratio measures of effect derived from stochastic QMRA approaches, including the generation of appropriate confidence intervals. Such QMRA-derived ratios can be used as a basis for evaluating interventions via hypothesis testing and for inclusion in systematic reviews and meta-analyses in a form consistent with risk estimation approaches commonly used in epidemiology.

Urban Onsite Sanitation Upgrades and Synanthropic Flies in Maputo, Mozambique: Effects on Enteric Pathogen Infection Risks

Synanthropic filth flies transport enteric pathogens from feces to food, which upon consumption poses an infection risk. We evaluated the effect of an onsite sanitation intervention─including fly control measures─in Maputo, Mozambique, on the risk of infection from consuming fly-contaminated food. After enumerating flies at intervention and control sites, we cultured fecal indicator bacteria, quantified gene copies for 22 enteric pathogens via reverse transcription quantitative polymerase chain reaction (RT-qPCR), and developed quantitative microbial risk assessment (QMRA) models to estimate annual risks of infection attributable to fly-contaminated foods. We found that the intervention reduced fly counts at latrine entrances by 69% (aRR = 0.31, [0.13, 0.75]) but not at food preparation areas (aRR = 0.92, [0.33, 2.6]). Half of (23/46) of individual flies were positive for culturable Escherichia coli, and we detected ≥1 pathogen gene from 45% (79/176) of flies, including enteropathogenic E. coli (37/176), adenovirus (25/176), Giardia spp. (13/176), and Trichuris trichiura (12/176). We detected ≥1 pathogen gene from half the flies caught in control (54%, 30/56) and intervention compounds (50%, 17/34) at baseline, which decreased 12 months post-intervention to 43% (23/53) at control compounds and 27% (9/33) for intervention compounds. These data indicate flies as a potentially important mechanical vector for enteric pathogen transmission in this setting. The intervention may have reduced the risk of fly-mediated enteric infection for some pathogens, but infrequent detection resulted in wide confidence intervals; we observed no apparent difference in infection risk between groups in a pooled estimate of all pathogens assessed (aRR = 0.84, [0.61, 1.2]). The infection risks posed by flies suggest that the design of sanitation systems and service delivery should include fly control measures to prevent enteric pathogen transmission.

CrAssphage as an indicator of human-fecal contamination in water environment and virus reduction in wastewater treatment

Viral indicators of human-fecal contamination in wastewaters and environmental waters have been getting much attention in the past decade. Cross-assembly phage (crAssphage) is the most abundant DNA virus in human feces. Recently, the usefulness of crAssphage as a microbial source tracking and water quality monitoring tool for human-fecal contamination has been highlighted. Here, we conducted a comprehensive review on crAssphage in water, focusing on detection methodology, concentration range in various waters and wastewaters, specificity to human-fecal contamination, and reduction in wastewater treatment systems. This review highlights that crAssphage is globally distributed in wastewaters and various fecal-contaminated water bodies at high concentrations without seasonal fluctuations. CrAssphage is highly specific to human-fecal contamination and is rarely found in animal feces. It also has a good potential as a performance indicator to ensure virus reduction in wastewater treatment systems. Accordingly, crAssphage could be an effective tool for monitoring of human-fecal contamination and potential presence of fecal pathogenic microbes in environmental waters. Bridging the research gaps highlighted in this review would make crAssphage a powerful tool to support the control of water-related health risks.

Quantitative microbial risk assessment of outdoor aerosolized pathogens in cities with poor sanitation

The aeromicrobiological transmission pathway of enteric pathogens in places with unsafe sanitation services is poorly understood. In an attempt to partly fill this knowledge gap, we assessed the potential public health impact of bioaerosols near open waste canals (OWCs) using Quantitative Microbial Risk Assessment (QMRA). We used data acquired in La Paz, Bolivia to characterize the risk of disease that aerosolized enteric pathogens may pose through food, fomites and inhalation (all followed by ingestion). Three reference pathogens were selected to conduct the assessment: enterotoxigenic Escherichia coli (ETEC), Shigella flexneri, and Campylobacter jejuni. Inhalation followed by ingestion had the highest median infection risk per event i.e. 3 × 10^-5 (3 infections for every 100,000 exposures), compared to contaminated food e.g. 5 × 10^-6 and fomites e.g. 2 × 10^-7, all for C. jejuni infections. Our sensitivity analysis showed that bacterial fluxes from the air were the most influential factor on risk. Our results suggest that fecal bacterial aerosols from OWCs present non-negligible risks of infection in La Paz, with median annual infection risks by C. jejuni being 18 (food), and 100 (inhalation) times greater than the EPA's standard for drinking water (1 × 10^-4). We included two of the QMRA models presented here in a novel web application we developed for user-specified application in different contexts.

Elevated Fecal Mitochondrial DNA from Symptomatic Norovirus Infections Suggests Potential Health Relevance of Human Mitochondrial DNA in Fecal Source Tracking

An end goal of fecal source tracking (FST) is to provide information on risk of transmission of waterborne illnesses associated with fecal contamination. Ideally, concentrations of FST markers in ambient waters would reflect exposure risk. Human mtDNA is an FST marker that is exclusively human in origin and may be elevated in feces of individuals experiencing gastrointestinal inflammation. In this study, we examined whether human mtDNA is elevated in fecal samples from individuals with symptomatic norovirus infections using samples from the United States (US), Mozambique, and Bangladesh. We quantified hCYTB484 (human mtDNA) and HF183/BacR287 (human-associated Bacteroides) FST markers using droplet digital polymerase chain reaction. We observed the greatest difference in concentrations of hCYTB484 when comparing samples from individuals with symptomatic norovirus infections versus individuals without norovirus infections or diarrhea symptoms: log₁₀ increase of 1.42 in US samples (3,820% increase, p-value = 0.062), 0.49 in Mozambique (308% increase, p-value = 0.061), and 0.86 in Bangladesh (648% increase, p-value = 0.035). We did not observe any trends in concentrations of HF183/BacR287 in the same samples. These results suggest concentrations of fecal mtDNA may increase during symptomatic norovirus infection and that mtDNA in environmental samples may represent an unambiguously human source-tracking marker that correlates with enteric pathogen exposure risk.

Visualization of the infection risk assessment of SARS-CoV-2 through aerosol and surface transmission in a negative-pressure ward

Since December 2019, coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a great challenge to the world's public health system. Nosocomial infections have occurred frequently in medical institutions worldwide during this pandemic. Thus, there is an urgent need to construct an effective surveillance and early warning system for pathogen exposure and infection to prevent nosocomial infections in negative-pressure wards. In this study, visualization and construction of an infection risk assessment of SARS-CoV-2 through aerosol and surface transmission in a negative-pressure ward were performed to describe the distribution regularity and infection risk of SARS-CoV-2, the critical factors of infection, the air changes per hour (ACHs) and the viral variation that affect infection risk. The SARS-CoV-2 distribution data from this model were verified by field test data from the Wuhan Huoshenshan Hospital ICU ward. ACHs have a great impact on the infection risk from airborne exposure, while they have little effect on the infection risk from surface exposure. The variant strains demonstrated significantly increased viral loads and risks of infection. The level of protection for nurses and surgeons should be increased when treating patients infected with variant strains, and new disinfection methods, electrostatic adsorption and other air purification methods should be used in all human environments. The results of this study may provide a theoretical reference and technical support for reducing the occurrence of nosocomial infections.

Rapid absolute quantification of pathogens and ARGs by nanopore sequencing

Compositional nature of relative abundance data in the current standard microbiome studies limits microbial dynamics interpretations and cross-sample comparisons. Here, we demonstrate the first rapid (1-h sequencing) method coupling Nanopore metagenomic sequencing with cellular spike-in to facilitate the absolute quantification and removal assessment of pathogens and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). Nanopore sequencing-based quantification results for both simple mock community and complex real environmental samples showed a high consistency with those from the widely-used Illumina and culture-based approaches. Implementing such method, we quantified 46 predominant putative pathogenic species, and 361 ARGs in three WWTP sample sets. Though high log removals of dominant pathogens (2.23 logs) and ARGs (1.98 logs) were achieved, complete removal of all pathogens and ARGs were not achieved. Noticeably, Mycobacterium spp., Clostridium_P perfringens, and Borrelia hermsii exhibited low removal, and 13 ARGs even increased in absolute abundance after the treatment. Our proposed approach manifested its profound ability in providing absolute quantitation information guiding wastewater-based epidemiological surveillance and quantitative risk assessment facilitating microbial hazards management.

Estimating the Risk of Acute Gastrointestinal Disease Attributed to E. coli O157:H7 in Irrigation Water and Agricultural Soil: A Quantitative Microbial Risk Assessment

Introduction: The occurrence of E. coli O157:H7 in the agricultural environment poses a serious threat to public health. The primary aim was to estimate the probability of illness caused by E. coli O157:H7 in irrigation water and agricultural soil niches. Methods: The Quantitative Microbial Risk Assessment was used and the risks were characterized using the Monte Carlo simulation with 10,000 iterations. Results: The mean levels of E. coli O157:H7 in the irrigation water and agricultural soil samples was 1.328 × 103 CFU/100 mL (Range: 0.00 to 13.000 × 103 CFU/100 mL) and 2.482 × 103 CFU/g (Range: 0.167 × 103 to 16.333 × 103 CFU/g), respectively. The risk of infection in humans exposed to this water and soil was 100%. In addition, a high risk of acute diarrheal disease was estimated at 25.0 × 10−2 for humans exposed to contaminated water and/or soil. Summary: These results exceeded the WHO diarrheal disease risk standard of 1.0 × 10−3. These findings demonstrated a high probability of acute gastrointestinal disease among humans exposed to E. coli O157:H7 in irrigation water and agricultural soil samples collected from the study sites representing a huge public health threat.

Comparison of the bacterial viability assessments for the disinfected quarantined water along with an effect of total residual oxidants

The water discarded from the quarantine station inspecting aquatic products can be served as an influx channel of invasive microorganisms to our own ecosystem. This study thus compared the viability of three different pathogenic bacteria (Escherichia coli, Vibrio harveyi, and Enterococcus faecalis) in either seawater or freshwater after their disinfection. For that, they were treated by ozonation (2.08 mM of ozone), ultraviolet irradiation (UVC-254), or thermal treatment (90℃) for 10 min, during which their resultant viability was monitored using colorimetric ATP assay, colony counting, and real-time quantitative RT-PCR. From this, ATP measurement and real-time quantitative RT-PCR have proved to be a much stronger correlation built in the fraction of each of their assays versus the colony counting, although they differed in the type of disinfection implemented. Especially, ATP assay was the most sensitively influenced by high levels of total residual oxidants (TRO) undesirably produced during the ozonation of V. harveyi and E. faecalis in seawater, although easily and shortly measured within 1 h, with higher accuracy. Aside from that, the real-time quantitative RT-PCR had a stronger correlation versus either that of seawater ozonation or thermal treatment. It is decided referring to measurement time and convenience in the field that ATP assay can be more reliably used in bacterial cell viability measurement in the quarantine after the ozonation in seawater to specifically allow the bacterial deactivation, not to overwhelmingly produce TRO due to the residual ozone provided.

Detection and Quantification of Enteric Pathogens in Aerosols Near Open Wastewater Canals in Cities with Poor Sanitation

Urban sanitation infrastructure is inadequate in many low-income countries, leading to the presence of highly concentrated, uncontained fecal waste streams in densely populated areas. Combined with mechanisms of aerosolization, airborne transport of enteric microbes and their genetic material is possible in such settings but remains poorly characterized. We detected and quantified enteric pathogen-associated gene targets in aerosol samples near open wastewater canals (OWCs) or impacted (receiving sewage or wastewater) surface waters and control sites in La Paz, Bolivia; Kanpur, India; and Atlanta, USA, via multiplex reverse-transcription qPCR (37 targets) and ddPCR (13 targets). We detected a wide range of enteric targets, some not previously reported in extramural urban aerosols, with more frequent detections of all enteric targets at higher densities in La Paz and Kanpur near OWCs. We report density estimates ranging up to 4.7 × 10² gc per m_air³ across all targets including heat-stable enterotoxigenic Escherichia coli, Campylobacter jejuni, enteroinvasive E. coli/Shigella spp., Salmonella spp., norovirus, and Cryptosporidium spp. Estimated 25, 76, and 0% of samples containing positive pathogen detects were accompanied by culturable E. coli in La Paz, Kanpur, and Atlanta, respectively, suggesting potential for viability of enteric microbes at the point of sampling. Airborne transmission of enteric pathogens merits further investigation in cities with poor sanitation.

Quantitative Microbial Risk Assessment for Contaminated Private Wells in the Fractured Dolomite Aquifer of Kewaunee County, Wisconsin

BACKGROUND

Private wells are an important source of drinking water in Kewaunee County, Wisconsin. Due to the region's fractured dolomite aquifer, these wells are vulnerable to contamination by human and zoonotic gastrointestinal pathogens originating from land-applied cattle manure and private septic systems.

OBJECTIVE

We determined the magnitude of the health burden associated with contamination of private wells in Kewaunee County by feces-borne gastrointestinal pathogens.

METHODS

This study used data from a year-long countywide pathogen occurrence study as inputs into a quantitative microbial risk assessment (QMRA) to predict the total cases of acute gastrointestinal illness (AGI) caused by private well contamination in the county. Microbial source tracking was used to associate predicted cases of illness with bovine, human, or unknown fecal sources.

RESULTS

Results suggest that private well contamination could be responsible for as many as 301 AGI cases per year in Kewaunee County, and that 230 and 12 cases per year were associated with a bovine and human fecal source, respectively. Furthermore, Cryptosporidium parvum was predicted to cause 190 cases per year, the most out of all 8 pathogens included in the QMRA.

DISCUSSION

This study has important implications for land use and water resource management in Kewaunee County and informs the public health impacts of consuming drinking water produced in other similarly vulnerable hydrogeological settings. https://doi.org/10.1289/EHP7815.

Action Levels for SARS-CoV-2 in Air: Preliminary Approach

Quantitative microbial risk assessment has been used to develop criteria for exposure to many microorganisms. In this article, the dose-response curve for Coronavirus 229E is used to develop preliminary risk-based exposure criteria for SARS-CoV-2 via the respiratory portals of entry.

Impact of sampling depth on pathogen detection in pit latrines

Wastewater based epidemiology (WBE) is increasingly used to provide decision makers with actionable data about community health. WBE efforts to date have primarily focused on sewer-transported wastewater in high-income countries, but at least 1.8 billion people in low- and middle-income countries (LMIC) use onsite sanitation systems such as pit latrines and septic tanks. Like wastewater, fecal sludges from such systems offer similar advantages in community pathogen monitoring and other epidemiological applications. To evaluate the distribution of enteric pathogens inside pit latrines-which could inform sampling methods for WBE in LMIC settings unserved by sewers-we collected fecal sludges from the surface, mid-point, and maximum-depth of 33 pit latrines in urban and peri-urban Malawi and analyzed the 99 samples for 20 common enteric pathogens via multiplex quantitative reverse transcription PCR. Using logistic regression adjusted for household population, latrine sharing, the presence of a concrete floor or slab, water source, and anal cleansing materials, we found no significant difference in the odds of detecting the 20 pathogens from the mid-point (adjusted odds ratio, aOR = 1.1; 95% confidence interval = 0.73, 1.6) and surface samples (aOR = 0.80, 95% CI = 0.54, 1.2) compared with those samples taken from the maximum depth. Our results suggest that, for the purposes of routine pathogen monitoring, pit latrine sampling depth does not strongly influence the odds of detecting enteric pathogens by molecular methods. A single sample from the pit latrines' surface, or a composite of surface samples, may be preferred as the most recent material contributed to the pit and may be easiest to collect.

Quantitative Microbial Risk Assessment of Pediatric Infections Attributable to Ingestion of Fecally Contaminated Domestic Soils in Low-Income Urban Maputo, Mozambique

Rigorous studies of water, sanitation, and hygiene interventions in low- and middle-income countries (LMICs) suggest that children are exposed to enteric pathogens via multiple interacting pathways, including soil ingestion. In 30 compounds (household clusters) in low-income urban Maputo, Mozambique, we cultured Escherichia coli and quantified gene targets from soils (E. coli: ybbW, Shigella/enteroinvasive E. coli (EIEC): ipaH, Giardia duodenalis: β-giardin) using droplet digital PCR at three compound locations (latrine entrance, solid waste area, dishwashing area). We found that 88% of samples were positive for culturable E. coli (mean = 3.2 log10 CFUs per gram of dry soil), 100% for molecular E. coli (mean = 5.9 log10 gene copies per gram of dry soil), 44% for ipaH (mean = 2.5 log10), and 41% for β-giardin (mean = 2.1 log10). Performing stochastic quantitative microbial risk assessment using soil ingestion parameters from an LMIC setting for children 12-23 months old, we estimated that the median annual infection risk by G. duodenalis was 7100-fold (71% annual infection risk) and by Shigella/EIEC was 4000-fold (40% annual infection risk) greater than the EPA's standard for drinking water. Compounds in Maputo, and similar settings, require contact and source control strategies to reduce the ingestion of contaminated soil and achieve acceptable levels of risk.

Forty Years of Food Safety Risk Assessment: A History and Analysis

Before the founding of the Society for Risk Analysis (SRA) in 1980, food safety in the United States had long been a concern, but there was a lack of systematic methods to assess food-related risks. In 1906, the U.S. Congress passed, and President Roosevelt signed, the Pure Food and Drug Act and the Meat Inspection Act to regulate food safety at the federal level. This Act followed the publication of multiple reports of food contamination, culminating in Upton Sinclair's novel The Jungle, which highlighted food and worker abuses in the meatpacking industry. Later in the 20th century, important developments in agricultural and food technology greatly increased food production. But chemical exposures from agricultural and other practices resulted in major amendments to federal food laws, including the Delaney Clause, aimed specifically at cancer-causing chemicals. Later in the 20th century, when quantitative risk assessment methods were given greater scientific status in a seminal National Research Council report, food safety risk assessment became more systematized. Additionally, in these last 40 years, food safety research has resulted in increased understanding of a range of health effects from foodborne chemicals, and technological developments have improved U.S. food safety from farm to fork by offering new ways to manage risks. We discuss the history of food safety and the role risk analysis has played in its evolution, starting from over a century ago, but focusing on the last 40 years. While we focus on chemical risk assessment in the U.S., we also discuss microbial risk assessment and international food safety.

Preliminary Evidence of a Molecular Detection Method to Analyze Bacterial DNA as a Quality Indicator in Cosmetics

Cosmetics are a category of widely consumed and distributed products, and their manufacture is always subject to specific guidelines. Quality Control (QC) tests provide information supporting the absence of injurious organisms and regarding the microbiological stability of cosmetics. The microbiological risk analysis is typically performed using the plate count method, which is a time-consuming and operator-dependent approach. Molecular technologies allow a deeper and more sensitive testing than traditional cultures. The demand for rapid and sensitive methods is recently increasing. The aim of our study was to compare different DNA extraction methods in order to detect and quantify bacterial load in cosmetics using a qPCR system. Known numbers of microorganisms were spiked into six different cosmetics to simulate contaminated samples. DNA was extracted with seven extraction kits and then quantified by real-time qPCR. Results revealed differences in terms of cell recovery, DNA yield, and quality. The bead-beating approaches were the most suitable in our molecular workflow and lead to good quality DNA for analysis by qPCR within four hours. Combined with mechanical extraction, qPCR may represent an efficient and easy method for microorganism identification in cosmetics, and can be automated. This approach also is also applicable for the detection of probiotics used as beneficial biological components in cosmetic products. The results of our molecular method provided preliminary evidences for the rapid identification of cells (10–100) and nucleic acids in complex preparations employed for human health, in compliance with regulatory limits. The suggested methodology is easy, fast, and sensitive. Its scalability allows serial microbiological evaluation at every manufacturing step.

Analysis of fecal sludges reveals common enteric pathogens in urban Maputo, Mozambique

Sewage surveillance is increasingly used in public health applications: metabolites, biomarkers, and pathogens are detectable in wastewater and can provide useful information about community health. Work on this topic has been limited to wastewaters in mainly high-income settings, however. In low-income countries, where the burden of enteric infection is high, non-sewered sanitation predominates. In order to assess the utility of fecal sludge surveillance as a tool to identify the most prevalent enteric pathogens circulating among at-risk children, we collected 95 matched child stool and fecal sludge samples from household clusters sharing latrines in urban Maputo, Mozambique. We analyzed samples for 20 common enteric pathogens via multiplex real-time quantitative PCR. Among the 95 stools matched to fecal sludges, we detected the six most prevalent bacterial pathogens (Enteroaggregative E. coli, Shigella/Enteroinvasive E. coli, Enterotoxigenic E. coli, Enteropathogenic E. coli, shiga-toxin producing E. coli, Salmonella) and all three protozoan pathogens (Giardia duodenalis, Cryptosporidium parvum, Entamoeba histolytica) in the same rank order in both matrices. We did not observe the same trend for viral pathogens or soil-transmitted helminths, however. Our results suggest that sampling fecal sludges from onsite sanitation offers potential for localized pathogen surveillance in low-income settings where enteric pathogen prevalence is high.