7 results on '"Janelle R. Thompson"'
Search Results
2. Gut Ruminococcaceae Levels Correlate with Risk of Antibiotic-Associated Diarrhea
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Franciscus Chandra, Jean Xy Sim, Liang Cui, Janelle R. Thompson, Xiaoqiong Gu, Chen Hongjie, Jenny G. Low, An-Ni Zhang, Federica Armas, Shijie Zhao, Zhanyi Lee, Yvonne Fz Chan, Eng Eong Ooi, Ega Danu Chang, Wei Lin Lee, Yii Ean Teh, Eric J. Alm, and Shirin Kalimuddin
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History ,medicine.medical_specialty ,Polymers and Plastics ,biology ,business.industry ,medicine.drug_class ,Antibiotics ,Faecalibacterium prausnitzii ,biology.organism_classification ,Industrial and Manufacturing Engineering ,Gut microbiome ,Diarrhea ,Internal medicine ,medicine ,Microbiome ,Business and International Management ,medicine.symptom ,Antibiotic-associated diarrhea ,Adverse effect ,business ,Ruminococcaceae - Abstract
Antibiotic-associated diarrhea (AAD) affects a significant proportion of patients receiving antibiotics. We sought to understand if differences in the gut microbiome would influence the development of AAD. We administered a 3-day course of amoxicillin-clavulanate to 30 healthy adult volunteers, and analyzed their stool microbiome, using 16S rRNA gene sequencing, at baseline and up to 4-weeks post-antibiotic administration. Lower levels of gut Ruminococcaceae were significantly and consistently observed from baseline till Day 7 in participants who developed AAD. Overall, participants who developed AAD experienced a greater decrease in microbial diversity. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii . Our findings suggest that a lack of gut Ruminococcaceae influences development of AAD. Quantification of F. prausnitzii in stool prior to antibiotic administration may help identify patients at risk of AAD, and aid clinicians in devising individualised treatment regimens to minimise such adverse effects.
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- 2021
3. Metrics to relate COVID-19 wastewater data to clinical testing dynamics
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William P. Hanage, Steven F Rhode, Timothy B. Erickson, Katya Moniz, Xiaoqiong Gu, Kyle A. McElroy, Federica Armas, Janelle R. Thompson, Claire Duvallet, Jianbo Zhang, Amy Xiao, Maxim Imakaev, Eric J. Alm, Mariana Matus, Hongjie Chen, Peter R. Chai, Wei Lin Lee, Brian J. Arnold, Franciscus Chandra, Newsha Ghaeli, Fuqing Wu, Mary Bushman, Noriko Endo, Asian School of the Environment, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore, and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
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medicine.medical_specialty ,Wastewater-Based Epidemiological Monitoring ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Wastewater-based epidemiology ,Context (language use) ,Wastewater Surveillance ,Wastewater ,Article ,Environmental health ,Pandemic ,Epidemiology ,medicine ,Humans ,Temporal dynamics ,Pandemics ,Waste Management and Disposal ,Water Science and Technology ,Civil and Structural Engineering ,SARS-CoV-2 ,Public health ,Ecological Modeling ,COVID-19 ,Pollution ,Environmental engineering [Engineering] ,Benchmarking ,Environmental science ,RNA, Viral ,Wastewater-Based Epidemiology ,Sewage treatment ,Wastewater surveillance - Abstract
Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance has been applied at various scales to monitor population-level COVID-19 dynamics, there is a need for quantitative metrics to interpret wastewater data in the context of public health trends. 24-hour composite wastewater samples were collected from March 2020 through May 2021 from a Massachusetts wastewater treatment plant and SARS-CoV-2 RNA concentrations were measured using RT-qPCR. The relationship between wastewater copy numbers of SARS-CoV-2 gene fragments and COVID-19 clinical cases and deaths varies over time. We demonstrate the utility of three new metrics to monitor changes in COVID-19 epidemiology: (1) the ratio between wastewater copy numbers of SARS-CoV-2 gene fragments and clinical cases (WC ratio), (2) the time lag between wastewater and clinical reporting, and (3) a transfer function between the wastewater and clinical case curves. The WC ratio increases after key events, providing insight into the balance between disease spread and public health response. Time lag and transfer function analysis showed that wastewater data preceded clinically reported cases in the first wave of the pandemic but did not serve as a leading indicator in the second wave, likely due to increased testing capacity, which allows for more timely case detection and reporting. These three metrics could help further integrate wastewater surveillance into the public health response to the COVID-19 pandemic and future pandemics., Graphical abstract Image, graphical abstract
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- 2022
4. SARS-CoV-2 RNA concentrations in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
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Mariana Matus, Peter R. Chai, Newsha Ghaeli, Timothy B. Erickson, Richard Bonneau, Amy Xiao, Xiaoqiong Gu, Mauricio Santillana, Katya Moniz, Steven F Rhode, Katelyn Foppe, Shijie Zhao, William P. Hanage, Kyle A. McElroy, Janelle R. Thompson, Fuqing Wu, Wei Lin Lee, Joshua A. Tucker, Mary Bushman, Katherine H. Huang, Noriko Endo, Federica Armas, Jonathan Nagler, Eric J. Alm, Jianbo Zhang, Megan A. Brown, Claire Duvallet, and Stefan Wuertz
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Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,viruses ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Wastewater ,Article ,Humans ,Environmental Chemistry ,Medicine ,Symptom onset ,Viral shedding ,Waste Management and Disposal ,SARS-CoV-2 ,business.industry ,COVID-19 ,Pollution ,Virus Shedding ,Clinical diagnosis ,Immunology ,Longitudinal ,RNA, Viral ,Foreshadow ,business ,Convolution model ,Viral load ,Disease transmission ,Wastewater surveillance - Abstract
Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we quantify the SARS-CoV-2 concentration and track its dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4–10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral load as a convolution of back-dated new clinical cases with the average population-level viral shedding function. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. This finding suggests that SARS-CoV-2 concentrations in wastewater may be primarily driven by viral shedding early in infection. This work shows that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and infer early viral shedding dynamics for newly infected individuals, which are difficult to capture in clinical investigations., Graphical abstract Unlabelled Image
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- 2022
5. Geospatial distribution of viromes in tropical freshwater ecosystems
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Karina Yew-Hoong Gin, Nazanin Saeidi, Qi Xiang Martin Tay, Shu Harn Te, Janelle R. Thompson, Xiaoqiong Gu, Ariel Kushmaro, and Shin Giek Goh
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0301 basic medicine ,Geospatial distribution ,Environmental Engineering ,food.ingredient ,Fresh Water ,Freshwater ecosystem ,Article ,03 medical and health sciences ,food ,Caudovirales ,Abundance (ecology) ,Mimiviridae ,Human virome ,Waste Management and Disposal ,Relative species abundance ,Water Science and Technology ,Civil and Structural Engineering ,Dicistroviridae ,Singapore ,Spatial Analysis ,Diversity ,biology ,Virome ,Ecology ,Ecological Modeling ,Freshwater ecosystems ,Human-related viruses ,biology.organism_classification ,Pollution ,030104 developmental biology ,Cyclovirus ,Viruses ,Land use ,Environmental Monitoring - Abstract
This study seeks to understand the general distribution of virome abundance and diversity in tropical freshwater ecosystems in Singapore and the geospatial distribution of the virome under different landuse patterns. Correlations between diversity, environmental parameters and land use patterns were analyzed and significant correlations were highlighted. Overall, the majority (65.5%) of the annotated virome belonged to bacteriophages. The percentage of Caudovirales was higher in reservoirs whereas the percentages of Dicistroviridae, Microviridae and Circoviridae were higher in tributaries. Reservoirs showed a higher Shannon-index virome diversity compared to upstream tributaries. Land use (urbanized, agriculture and parkland areas) influenced the characteristics of the virome distribution pattern. Dicistroviridae and Microviridae were enriched in urbanized tributaries while Mimiviridae, Phycodnaviridae, Siphoviridae and Podoviridae were enriched in parkland reservoirs. Several sequences closely related to the emerging zoonotic virus, cyclovirus, and the human-related virus (human picobirnavirus), were also detected. In addition, the relative abundance of PMMoV (pepper mild mottle virus) sequences was significantly correlated with RT-qPCR measurements (0.588, Graphical abstract Image 1, Highlights • Land use is the main driver of the viral community structure in surface waters. • 66 viral families were detected and 66% of the annotated virome was bacteriophages. • Reservoirs showed a higher Shannon diversity (10.4) than upstream tributaries (8.4). • Sequences closely related to human picobirnavirus and cyclovirus were detected. • The relative abundance of PMMoV sequences was correlated with RT-qPCR measurements.
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- 2018
6. Wastewater surveillance of SARS-CoV-2 across 40 U.S. states from February to June 2020
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Mariana Matus, Timothy B. Erickson, Janelle R. Thompson, Eric J. Alm, Katya Moniz, Jianbo Zhang, Newsha Ghaeli, Peter R. Chai, Mary Bushman, William P. Hanage, Fuqing Wu, Noriko Endo, Amy Xiao, Wei Lin Lee, Steven F Rhode, Federica Armas, Katherine H. Huang, Xiaoqiong Gu, Katelyn Foppe, Claire Duvallet, Stefan Wuertz, and Kyle A. McElroy
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Disease surveillance ,education.field_of_study ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,SARS-CoV-2 ,Ecological Modeling ,Incidence (epidemiology) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Population ,Detection rate ,Outbreak ,Pollution ,Article ,United States ,Geography ,Wastewater ,Environmental health ,Spatiotemporal dynamics ,Sewage treatment ,education ,Waste Management and Disposal ,Wastewater surveillance ,Water Science and Technology ,Civil and Structural Engineering - Abstract
Wastewater-based disease surveillance is a promising approach for monitoring community outbreaks. Here we describe a nationwide campaign to monitor SARS-CoV-2 in the wastewater of 159 counties in 40 U.S. states, covering 13% of the U.S. population from February 18 to June 2, 2020. Out of 1,751 total samples analyzed, 846 samples were positive for SARS-CoV-2 RNA, with overall viral concentrations declining from April to May. Wastewater viral titers were consistent with, and appeared to precede, clinical COVID-19 surveillance indicators, including daily new cases. Wastewater surveillance had a high detection rate (>80%) of SARS-CoV-2 when the daily incidence exceeded 13 per 100,000 people. Detection rates were positively associated with wastewater treatment plant catchment size. To our knowledge, this work represents the largest-scale wastewater-based SARS-CoV-2 monitoring campaign to date, encompassing a wide diversity of wastewater treatment facilities and geographic locations. Our findings demonstrate that a national wastewater-based approach to disease surveillance may be feasible and effective., Graphical Abstract Image, graphical abstract
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- 2021
7. Making waves: Wastewater surveillance of SARS-CoV-2 for population-based health management
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Lee Ching Ng, Monamie Bhadra Haines, Yarlagadda V. Nancharaiah, Janelle R. Thompson, Wei Lin Lee, Stefan Wuertz, Xiaoqiong Gu, Verónica Beatriz Rajal, Rosina Girones, Eric J. Alm, Asian School of the Environment, School of Civil and Environmental Engineering, Singapore Centre for Environmental Life Sciences and Engineering, and CREATE
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medicine.medical_specialty ,Environmental Engineering ,DATA PRIVACY ,Pneumonia, Viral ,0208 environmental biotechnology ,Population ,Otras Ingeniería del Medio Ambiente ,INGENIERÍAS Y TECNOLOGÍAS ,Wastewater Surveillance ,02 engineering and technology ,Disease ,Wastewater ,010501 environmental sciences ,FECAL-ORAL TRANSMISSION ,01 natural sciences ,Article ,Fecal-oral transmission ,Betacoronavirus ,Environmental health ,Sewerage ,medicine ,Humans ,Ingeniería del Medio Ambiente ,education ,Pandemics ,Waste Management and Disposal ,health care economics and organizations ,0105 earth and related environmental sciences ,Water Science and Technology ,Civil and Structural Engineering ,HEALTH MANAGEMENT ,education.field_of_study ,Disease surveillance ,Health management system ,SARS-CoV-2 ,Ecological Modeling ,Public health ,COVID-19 ,Pollution ,Environmental engineering [Engineering] ,020801 environmental engineering ,Ecological Modelling ,Health management ,Sample collection ,Business ,Coronavirus Infections ,Data privacy ,Wastewater surveillance - Abstract
Highlights • Wastewater surveillance cheaper and less invasive than massive testing of individuals. • Useful early alert of viral circulation to prevent outbreaks and inform policy decisions. • Success of surveillance requires public legitimacy and trust of such measures., Worldwide, clinical data remain the gold standard for disease surveillance and tracking. However, such data are limited due to factors such as reporting bias and inability to track asymptomatic disease carriers. Disease agents are excreted in the urine and feces of infected individuals regardless of disease symptom severity. Wastewater surveillance – that is, monitoring disease via human effluent – represents a valuable complement to clinical approaches. Because wastewater is relatively inexpensive and easy to collect and can be monitored at different levels of population aggregation as needed, wastewater surveillance can offer a real-time, cost-effective view of a community's health that is independent of biases associated with case-reporting. For SARS-CoV-2 and other disease-causing agents we envision an aggregate wastewater-monitoring system at the level of a wastewater treatment plant and exploratory or confirmatory monitoring of the sewerage system at the neighborhood scale to identify or confirm clusters of infection or assess impact of control measures where transmission has been established. Implementation will require constructing a framework with collaborating government agencies, public or private utilities, and civil society organizations for appropriate use of data collected from wastewater, identification of an appropriate scale of sample collection and aggregation to balance privacy concerns and risk of stigmatization with public health preservation, and consideration of the social implications of wastewater surveillance.
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- 2020
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