Challenges in Forecasting Antimicrobial Resistance.

Antimicrobial resistance is a major threat to human health. Since the 2000s, computational tools for predicting infectious diseases have been greatly advanced; however, efforts to develop real-time forecasting models for antimicrobial-resistant organisms (AMROs) have been absent. In this perspective, we discuss the utility of AMRO forecasting at different scales, highlight the challenges in this field, and suggest future research priorities. We also discuss challenges in scientific understanding, access to high-quality data, model calibration, and implementation and evaluation of forecasting models. We further highlight the need to initiate research on AMRO forecasting using currently available data and resources to galvanize the research community and address initial practical questions.

Risk-aware temporal cascade reconstruction to detect asymptomatic cases.

This paper studies the problem of detecting asymptomatic cases in a temporal contact network in which multiple outbreaks have occurred. We show that the key to detecting asymptomatic cases well is taking into account both individual risk and the likelihood of disease-flow along edges. We consider both aspects by formulating the asymptomatic case detection problem as a directed prize-collecting Steiner tree (Directed PCST) problem. We present an approximation-preserving reduction from this problem to the directed Steiner tree problem and obtain scalable algorithms for the Directed PCST problem on instances with more than 1.5M edges obtained from both synthetic and fine-grained hospital data. On synthetic data, we demonstrate that our detection methods significantly outperform various baselines (with a gain of 3.6 × ). We apply our method to the infectious disease prediction task by using an additional feature set that captures exposure to detected asymptomatic cases and show that our method outperforms all baselines. We further use our method to detect infection sources ("patient zero") of outbreaks that outperform baselines. We also demonstrate that the solutions returned by our approach are clinically meaningful by presenting case studies.

Fast and near-optimal monitoring for healthcare acquired infection outbreaks.

According to the Centers for Disease Control and Prevention (CDC), one in twenty five hospital patients are infected with at least one healthcare acquired infection (HAI) on any given day. Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads extensively. Here, we develop an efficient data and model driven method to detect outbreaks with high accuracy. We leverage mechanistic modeling of C. difficile infection, a major HAI disease, to simulate its spread in a hospital wing and design efficient near-optimal algorithms to select people and locations to monitor using an optimization formulation. Results show that our strategy detects up to 95% of "future" C. difficile outbreaks. We design our method by incorporating specific hospital practices (like swabbing for infections) as well. As a result, our method outperforms state-of-the-art algorithms for outbreak detection. Finally, a qualitative study of our result shows that the people and locations we select to monitor as sensors are intuitive and meaningful.

Hospitalizations among family members increase the risk of MRSA infection in a household.

OBJECTIVE: Estimate the risk for household transmission of Methicillin-Resistant Staphylococcus aureus (MRSA) following exposure to infected family members or family members recently discharged from a hospital. DESIGN: Analysis of monthly MRSA incidence from longitudinal insurance claims using the Merative MarketScan Commercial and Medicare (2001-2021) databases. SETTING: Visits to inpatient, emergency department, and outpatient settings. PATIENTS: Households with ≥2 family members enrolled in the same insurance plan for the entire month. METHODS: We estimated a monthly incidence model, where enrollees were binned into monthly enrollment strata defined by demographic, patient, and exposure characteristics. Monthly incidence within each stratum was computed, and a regression analysis was used to estimate the incidence rate ratio (IRR) associated with household exposures of interest while accounting for potential confounding factors. RESULTS: A total of 157,944,708 enrollees were included and 424,512 cases of MRSA were identified. Across all included enrollees, exposure to a family member with MRSA in the prior 30 days was associated with significantly increased risk of infection (IRR: 71.03 [95% CI, 67.73-74.50]). After removing enrollees who were hospitalized or exposed to a family member with MRSA, exposure to a family member who was recently discharged from the hospital was associated with increased risk of infection (IRR: 1.44 [95% CI, 1.39-1.49]) and the risk of infection increased with the duration of the family member's hospital stay (P value < .001). CONCLUSIONS: Exposure to a recently hospitalized and discharged family member increased the risk of MRSA infection in a household even when the hospitalized family member was not diagnosed with MRSA.

Gas emissions as influenced by home composting system configuration.

Home composting systems (HC) are known to facilitate municipal solid waste management, but little is known about their environmental impact including their greenhouse gas emissions (GGE). The present research focused on selecting HC configuration producing the least CH(4) and N(2)O. Thus, 4 HC types were used to compost food and yard waste for 150 days and monitored for CO(2), CH(4) and N(2)O as of day 15: the wood and plastic bins (WB and PB), the mixed and unmixed ground pile (GPM and GP). Using the same waste recipe, all HC were filled at once (batch fed) to maximize gaseous emissions. Weekly as of day 15, CO(2), N(2)O and CH(4) emissions were measured during 2-h sessions using a closed chamber inserted into the compost surface. Monitored compost characteristics indicated little differences over time except for moisture content. From day 15 to 150, CH(4) emissions were not measurable. Generation of N(2)O occurred between day 20 and 120 with PB producing the least because of top and bottom slots providing continuous convective aeration, as compared to the WB with slats over its full height and the naturally aerated mixed and unmixed ground piles. Total N(2)O emissions of 56 kg CO(2)-eq (tonne wet waste treated)(-1) for PB, 75 for GP, 97 for WB and 99 for GPM represented average value for centralized composting facilities. Present and past scientific works suggest the need for more research to establish the combined effect of management and HC configuration on gaseous emissions, with close CH(4) measurements from day 0 to 15.

Performance of five Montreal West Island home composters.

Even if home composting can eliminate municipal organic waste collection, handling and treatment costs, its compost quality requires investigation outside the laboratory. A study was thus conducted to evaluate the influence of the following management practices on the compost quality produced by five backyards home composters in Montreal West Island from June to October 2010: the type and backyard location of the home composter (HC), and the rate and type of organic waste (OW) fed into the home composter. The parameters monitored were compost temperature and final characteristics including trace elements and pathogens. For all HC compost, maximum but not necessarily thermophilic temperatures were highly probable within one week of adding more than 10 kg of OW composed of equal volumes of food waste (FW) and yard trimmings (YT). Top and bottom HC perforations enhanced convective aeration but concentrated OW decomposition within the bottom layer. Fed an equal volume of FW and YT, the final HC compost had a dry and organic matter content exceeding 30%, and 50%, respectively, and a total nitrogen, phosphorous and potassium level of 2, 1 and 3% on a dry matter basis, representing a good quality soil amendment. Clean OW feeding resulted in compost respecting Canadian and European regulations for Escherichia coli and Salmonella, irrespective of the temperature regime. For trace elements, regulatory limits may be exceeded when the home composter is fed ashes and soil. Homeowners must also be careful when applying pesticides to their lawns and gardens and then feeding the residues to the home composter.

Home and community composting for on-site treatment of urban organic waste: perspective for Europe and Canada.

As a result of urbanization and economic prosperity, which has accelerated the generation of municipal solid waste (MSW) along with its organic fraction, the management of MSW is a challenge faced by urban centres worldwide, including the European Union (EU) and Canada. Within a concept of waste recovery, the source separation and on-site treatment of urban organic waste (UOW) can resolve some of the major economic issues faced by urban centres along with the environmental and social issues associated with landfilling. In this context and in a comparison with the traditional landfilling practice, this paper examines on-site UOW composting strategies using a combination of centralized composting facilities, community composting centres and home composting. This study consisted of a feasibility and economic study based on available data and waste management costs. The results indicate that on-site treatment of UOW using practices such as home and community composting can lower management costs by 50, 37 and 34% for the rich European countries (annual GDP over US$25,000), the poorer European countries (annual GDP under US$25 000), and Canada, respectively. Furthermore, on-site composting can reduce greenhouse gas emissions by 40% for Europe and Canada, despite gas capture practices on landfill sites. However, the performance of home composters and the quality of the compost products are issues to be further addressed for the successful implementation of UOW on-site composting.

Effectiveness of three bulking agents for food waste composting.

Rather than landfilling, composting the organic fraction of municipal solid wastes recycles the waste as a safe and nutrient enriched soil amendment, reduces emissions of greenhouse gases and generates less leachate. The objective of this project was to investigate the composting effectiveness of three bulking agents, namely chopped wheat (Triticum) straw, chopped mature hay consisting of 80% timothy (milium) and 20% clover (triphullum) and pine (pinus) wood shavings. These bulking agents were each mixed in duplicates at three different ratios with food waste (FW) and composted for 10 days using prototype in-vessel composters to observe their temperature and pH trends. Then, each mixture was matured in vertical barrels for 56 days to measure their mass loss and final nutrient content and to visually evaluate their level of decomposition. Chopped wheat straw (CWS) and chopped hay (CH) were the only two formulas that reached thermophilic temperatures during the 10 days of active composting when mixed with FW at a wet mass ratio of 8.9 and 8.6:1 (FW:CWS and FW:CH), respectively. After 56 days of maturation, these two formulas were well decomposed with no or very few recognizable substrate particles, and offered a final TN exceeding the original. Wood shavings (WS) produced the least decomposed compost at maturation, with wood particles still visible in the final product, and with a TN lower than the initial. Nevertheless, all bulking agents produced compost with an organic matter, TN, TP and TK content suitable for use as soil amendment.

Characterization of food waste and bulking agents for composting.

The characterization of food waste (FW) and locally available bulking agents (BA) are a prerequisite to optimizing compost recipes. This study measured the variation in FW characteristics (pH, dry matter (DM), carbon (C), wet bulk density and Total Kjeldahl Nitrogen (TKN)) produced by a restaurant and a community kitchen in downtown Montreal, Canada from May to August 2004. The project also measured the mass of FW produced by another restaurant and a group of 20-48 households, from June to August 2004. Locally available BA (hay, straw, pine wood shavings, cardboard, left over cattle feed and wheat residue pellets) were also characterized to formulate composting recipes based on the FW characteristics observed during a period representative of winter and summer conditions. Residential and restaurant FW characteristics varied significantly over the summer months, although the mass produced remained constant at 0.61 and 0.56 kg capita(-1)day(-1), respectively. In addition, the number of customers served by the restaurant increased by nearly 50% from June to August. The BA with the highest moisture adsorption capacity was found to be the wheat residue pellets, followed by chopped straw. Wheat residue pellets, chopped hay and left over cattle feed all presented a balanced C/N ratio. Wheat residue pellets and wheat straw, chopped hay and cardboard demonstrated neutral pH values. Based on the variable FW characteristics and monthly production rates, the formulation of recipes indicates that compost facilities must be flexible enough to handle seasonal variations of as much as 50% by volume.

Predicted growth of world urban food waste and methane production.

Landfill gas emissions are one of the largest anthropogenic sources of methane especially because of food waste (FW). To prevent these emissions growing with world population, future FW best management practices need to be evaluated. The objective of this paper was therefore to predict FW production for 2025 if present management practices are maintained, and then, to compare the impact of scenario 1: encouraging people to stay in rural areas and composting 75% of their FW, and; of scenario 2, where in addition to scenario 1, composting or anaerobically digesting 75% of urban FW (UFW). A relationship was established between per capita gross domestic product (GDP) and the population percentage living in urban areas (%UP), as well as production of municipal solid waste (MSW) and UFW. With estimated GDP and population growth per country, %UP and production of MSW and UFW could be predicted for 2025. A relatively accurate (R(2) > 0.85) correlation was found between GDP and %UP, and between GDP and mass of MSW and FW produced. On a global scale, MSW and UFW productions were predicted to increase by 51 and 44%, respectively, from 2005 to 2025. During the same period, and because of its expected economic development, Asia was predicted to experience the largest increase in UFW production, of 278 to 416 Gkg. If present MSW management trends are maintained, landfilled UFW was predicted to increase world CH4 emissions from 34 to 48 Gkg and the landfill share of global anthropogenic emissions from 8 to 10%. In comparison with maintaining present FW management practices, scenario 1 can lower UFW production by 30% and maintain the landfill share of the global anthropogenic emissions at 8%. With scenario 2, the landfill share of global anthropogenic emissions could be further reduced from 8 to 6% and leachate production could be reduced by 40%.