18 results on '"Janelle R. Thompson"'
Search Results
2. Persistence of Dengue (Serotypes 2 and 3), Zika, Yellow Fever, and Murine Hepatitis Virus RNA in Untreated Wastewater
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Hongjie Chen, Wei Lin Lee, Mats Leifels, Stefan Wuertz, Eric J. Alm, Franciscus Chandra, Federica Armas, Janelle R. Thompson, Xiaoqiong Gu, School of Chemical and Biomedical Engineering, Asian School of the Environment, Campus for Research Excellence and Technological Enterprise (CREATE), and Singapore Centre for Environmental Life Sciences and Engineering (SCELSE)
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Serotype ,Murine hepatitis ,Ecology ,Health, Toxicology and Mutagenesis ,Yellow fever ,RNA ,Untreated wastewater ,Freeze-Thaw ,Biology ,medicine.disease ,Pollution ,Virology ,Virus ,Environmental engineering [Engineering] ,Persistence (computer science) ,Dengue fever ,Cyclesclimate-Change ,medicine ,Environmental Chemistry ,Waste Management and Disposal ,Water Science and Technology - Abstract
Arboviruses are viral pathogens transmitted by blood-borne vectors that impose a great social and economic burden globally. Most clinical surveillance of arbovirus outbreaks underestimates the true prevalence as a large proportion of cases exhibit no or only mild clinical symptoms (i.e., are subclinical). Reports of urinary shedding of several arboviruses such as Dengue (DENV), yellow fever (YFV), and Zika (ZIKV) viruses suggest the possibility of utilizing wastewater surveillance to assess the prevalence of arboviral outbreaks. To determine the feasibility of wastewater surveillance, we investigated the decay of representative arboviruses (including DENV-2, DENV-3, YFV, and ZIKV) along with murine hepatitis virus (MHV) as a surrogate for human coronavirus within a wastewater matrix at 6, 25, or 37 °C using RT-qPCR. DENV-2, DENV-3, YFV, ZIKV, and MHV experienced a one log10reduction within 3.95-6.21 days at 25 °C and within 2.60-5.12 days at 37 °C, while incubation at 6 °C did not indicate substantial decay within 21 days. Our work suggests that these arboviruses or their RNA could persist sufficiently in wastewater over a range of temperatures, supporting the potential for wastewater-based surveillance of arboviral outbreaks. Ministry of Education (MOE) National Research Foundation (NRF) Singapore-MIT Alliance for Research and Technology (SMART) This research was supported by the National Research Foundation, Prime Minister’s Office, Singapore, under its Campus for Research Excellence and Technological Enterprise (CREATE) program, through Intra-CREATE Thematic Grant (Cities) Grant NRF2019-THE001-0003 to J.T. and E.J.A., the Singapore-MIT Alliance for Research and Technology (SMART) Antimicrobial Resistance Interdisciplinary Research Group (AMR IRG), and funding from the Singapore Ministry of Education and National Research Foundation through an RCE award to the Singapore Centre for Environmental Life Sciences Engineering (SCELSE).
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- 2021
3. Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis
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C. Thompson, Carlos Alberto Nunes Cosenza, Fabiano L. Thompson, Janelle R. Thompson, Jean Swings, Mónica Medina, Kevin Penn, L A C Tonon, G D Garcia, Adriana M. Fróes, and Arthur W. Silva-Lima
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0301 basic medicine ,Ecology ,biology ,030106 microbiology ,Pantoea ,Soil Science ,medicine.disease ,biology.organism_classification ,Microbiology ,Transcriptome ,Intracellular signal transduction ,03 medical and health sciences ,030104 developmental biology ,Microbial ecology ,Gammaproteobacteria ,medicine ,Dysbiosis ,Ecology, Evolution, Behavior and Systematics ,Bacteria ,Symbiotic bacteria - Abstract
Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.
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- 2020
4. Low Gut Ruminococcaceae Levels are Associated with Occurrence of Antibiotic-associated Diarrhea
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Shijie Zhao, Hongjie Chen, Wei Lin Lee, Zhanyi Lee, Federica Armas, Shirin Kalimuddin, Eric J. Alm, Yvonne Fz Chan, Ega Danu Chang, Xiaoqiong Gu, Janelle R. Thompson, Liang Cui, Eng Eong Ooi, Jenny G. Low, An-Ni Zhang, Franciscus Chandra, Yii Ean Teh, and Jean Xy Sim
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medicine.medical_specialty ,biology ,medicine.drug_class ,business.industry ,Antibiotics ,Faecalibacterium prausnitzii ,biology.organism_classification ,Discontinuation ,Diarrhea ,Internal medicine ,medicine ,Microbiome ,medicine.symptom ,Antibiotic-associated diarrhea ,business ,Adverse effect ,Ruminococcaceae - Abstract
Patients receiving antibiotics often suffer from antibiotic-associated diarrhea (AAD). AAD is of clinical significance as it can result in premature antibiotic discontinuation and suboptimal treatment of infection. The drivers of AAD however, remain poorly understood. We sought to understand if differences in the gut microbiome, both at baseline and during antibiotic administration, would influence the development of AAD. We administered a 3-day course of oral amoxicillin-clavulanate to 30 healthy adult volunteers, and performed a detailed interrogation of their stool microbiome at baseline and up to 4-weeks post antibiotic administration, using 16S rRNA gene sequencing. Lower levels of Ruminococcaceae were significantly and consistently observed from baseline till Day 7 in participants who developed AAD. The probability of AAD could be predicted based on qPCR-derived levels of Faecalibacterium prausnitzii, the most dominant species within the Ruminococcaceae family. Overall, participants who developed AAD experienced a greater decrease in microbial diversity during antibiotic dosing. Our findings suggest that a lack of gut Ruminococcaceae at baseline influences development of AAD. In addition, 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
5. Minimizing Errors in RT-PCR Detection and Quantification of SARS-CoV-2 RNA for Wastewater Surveillance
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Tarja Pitkänen, Rosalie Subburg, Albert Bosch, Coleen C. Naughton, Kyle Bibby, Kerry A. Hamilton, Marta Rusiñol, Joan B. Rose, Wendy Smith, Andrew S. Whiteley, Charles N. Haas, Irene Xagoraraki, Valerie J. Harwood, Heather M. Murphy, Giuseppina La Rosa, Qian Zhang, Michael J. Sadowsky, Sandra L. McLellan, Asja Korajkic, Brandon Reyneke, Kevin V. Thomas, Sílvia Bofill-Mas, Susan Petterson, Daniel Gerrity, Hapuarachchige Chanditha Hapuarachchi, Verónica Beatriz Rajal, Rehnuma Haque, Suzanne Metcalfe, Simon Toze, Paul M. Bertsch, Yin Xiang Setoh, Rachel T. Noble, Daisuke Sano, Andreas H. Farnleitner, Nishita D'Souza, John F. Griffith, Phong K. Thai, Wesaal Khan, Warish Ahmed, Brian R. McMinn, Stefan Wuertz, Josh Tynan, Aaron Bivins, Linda L. Blackall, Orin C. Shanks, Fernando A. Roman, João Brandão, Amity G. Zimmer-Faust, Mark Ciesielski, Samendra P. Sherchan, Raul Gonzalez, Judith Chui Ching Wong, Stuart L. Simpson, Erin K. Lipp, Janelle R. Thompson, Erica Donner, Jochen F. Mueller, Laura Sala-Comorera, Blythe A. Layton, Joshua A. Steele, Gertjan Medema, Greg Jackson, Phil M. Choi, Erin M. Symonds, Wim G. Meijer, Stuart J. Khan, Masaaki Kitajima, Sudhi Payyappat, Kwanrawee Sirikanchana, Pradip Gyawali, Ahmed, Warish, Simpson, Stuart L, Bertsch, Paul M, Bibby, Kyle, Donner, Erica, Shanks, Orin C, Bosch, Albert, Brandão, Joao, La Rosa, Giuseppina, McLellan, Sandra L., Noble, Rachel T., Bosch, Albert [0000-0002-8111-9059], Brandão, Joao [0000-0001-7553-227X], La Rosa, Giuseppina [0000-0002-2657-100X], McLellan, Sandra L. [0000-0003-3283-1151], and Noble, Rachel T. [0000-0001-9071-8312]
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False negative ,Epidemiology ,0211 other engineering and technologies ,02 engineering and technology ,Review ,Wastewater ,010501 environmental sciences ,01 natural sciences ,Aigües residuals ,Pandemic ,Digital polymerase chain reaction ,Prospective Studies ,False positive ,Waste Management and Disposal ,0303 health sciences ,Surveillance ,Warning system ,Sewage ,Reverse Transcriptase Polymerase Chain Reaction ,false negative ,Pollution ,6. Clean water ,3. Good health ,Real-time polymerase chain reaction ,RNA, Viral ,False-negative ,Wastewater-Based Epidemiological Monitoring ,false positive ,medicine.medical_specialty ,Environmental Engineering ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,RT-PCR ,03 medical and health sciences ,False-positive ,medicine ,Humans ,Environmental Chemistry ,Intensive care medicine ,Epidemiologia ,Pandemics ,Retrospective Studies ,030304 developmental biology ,0105 earth and related environmental sciences ,021110 strategic, defence & security studies ,business.industry ,SARS-CoV-2 ,other ,RNA ,Reproducibility of Results ,Data interpretation ,COVID-19 ,Virology ,Environmental science ,business ,Quality assurance - Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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- 2021
6. 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
7. 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
8. SARS-CoV-2 Titers in Wastewater Are Higher than Expected from Clinically Confirmed Cases
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Claire Duvallet, Katya Moniz, Alex D. Washburne, Mariana Matus, Jianbo Zhang, Newsha Ghaeli, Timothy B. Erickson, Kathryn M. Kauffman, Fuqing Wu, Wei Lin Lee, Noriko Endo, Peter R. Chai, William P. Hanage, Mathilde Poyet, Eric J. Alm, Xiaoqiong Gu, Amy Xiao, Federica Armas, and Janelle R. Thompson
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0301 basic medicine ,medicine.medical_specialty ,Physiology ,030106 microbiology ,Population ,lcsh:QR1-502 ,Sewage ,Disease ,010501 environmental sciences ,01 natural sciences ,Biochemistry ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Environmental health ,Modelling and Simulation ,Case fatality rate ,Pandemic ,Epidemiology ,Genetics ,Medicine ,education ,viral titers ,wastewater ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,education.field_of_study ,business.industry ,SARS-CoV-2 ,Outbreak ,COVID-19 prevalence ,QR1-502 ,Computer Science Applications ,Wastewater ,Modeling and Simulation ,PMMoV ,business - Abstract
Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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- 2020
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9. SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases
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Newsha Ghaeli, Megan A. Brown, Mariana Matus, Claire Duvallet, Janelle R. Thompson, Stefan Wuertz, Jianbo Zhang, Federica Armas, Fuqing Wu, Richard Bonneau, Amy Xiao, Kyle A. McElroy, William P. Hanage, Mauricio Santillana, Steven F Rhode, Joshua A. Tucker, Katelyn Foppe, Jonathan Nagler, Xiaoqiong Gu, Katherine H. Huang, Eric J. Alm, Mary Bushman, Katya Moniz, Noriko Endo, Shijie Zhao, Wei Lin Lee, Peter R. Chai, and Timothy B. Erickson
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Coronavirus disease 2019 (COVID-19) ,business.industry ,Applied and Environmental Science ,SARS-CoV-2 ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,COVID-19 prevalence ,Editor's Pick ,Article ,Titer ,Wastewater ,Clinical diagnosis ,Immunology ,PMMoV ,Medicine ,Symptom onset ,Viral shedding ,business ,viral titers ,Disease transmission ,wastewater ,Research Article - Abstract
Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence., Wastewater surveillance represents a complementary approach to clinical surveillance to measure the presence and prevalence of emerging infectious diseases like the novel coronavirus SARS-CoV-2. This innovative data source can improve the precision of epidemiological modeling to understand the penetrance of SARS-CoV-2 in specific vulnerable communities. Here, we tested wastewater collected at a major urban treatment facility in Massachusetts and detected SARS-CoV-2 RNA from the N gene at significant titers (57 to 303 copies per ml of sewage) in the period from 18 to 25 March 2020 using RT-qPCR. We validated detection of SARS-CoV-2 by Sanger sequencing the PCR product from the S gene. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of 25 March. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks. IMPORTANCE Wastewater-based surveillance is a promising approach for proactive outbreak monitoring. SARS-CoV-2 is shed in stool early in the clinical course and infects a large asymptomatic population, making it an ideal target for wastewater-based monitoring. In this study, we develop a laboratory protocol to quantify viral titers in raw sewage via qPCR analysis and validate results with sequencing analysis. Our results suggest that the number of positive cases estimated from wastewater viral titers is orders of magnitude greater than the number of confirmed clinical cases and therefore may significantly impact efforts to understand the case fatality rate and progression of disease. These data may help inform decisions surrounding the advancement or scale-back of social distancing and quarantine efforts based on dynamic wastewater catchment-level estimations of prevalence.
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- 2020
10. SARS-CoV-2 titers in wastewater are higher than expected from clinically confirmed cases
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Amy Xiao, Newsha Ghaeli, Peter R. Chai, Kathryn M. Kauffman, Wei Lin Lee, Claire Duvallet, Eric J. Alm, Katya Moniz, Mariana Matus, Jianbo Zhang, Xiaoqiong Gu, Timothy B. Erickson, William P. Hanage, Janelle R. Thompson, Fuqing Wu, and Noriko Endo
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Titer ,Wastewater ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Pandemic ,Pcr cloning ,Outbreak ,Medicine ,business ,Virology - Abstract
Wastewater surveillance may represent a complementary approach to measure the presence and even prevalence of infectious diseases when the capacity for clinical testing is limited. Moreover, aggregate, population-wide data can help inform modeling efforts. We tested wastewater collected at a major urban treatment facility in Massachusetts and found the presence of SARS-CoV-2 at high titers in the period from March 18 - 25 using RT-qPCR. We then confirmed the identity of the PCR product by direct DNA sequencing. Viral titers observed were significantly higher than expected based on clinically confirmed cases in Massachusetts as of March 25. The reason for the discrepancy is not yet clear, and until further experiments are complete, these data do not necessarily indicate that clinical estimates are incorrect. Our approach is scalable and may be useful in modeling the SARS-CoV-2 pandemic and future outbreaks.
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- 2020
11. 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
12. 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
13. Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters
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Charmaine Ng, Martin Tay, Boonfei Tan, Thai-Hoang Le, Laurence Haller, Hongjie Chen, Tse H. Koh, Timothy M. S. Barkham, Janelle R. Thompson, and Karina Y.-H. Gin
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0301 basic medicine ,Microbiology (medical) ,Klebsiella ,tributary ,Klebsiella pneumoniae ,030106 microbiology ,lcsh:QR1-502 ,antibiotic resistant genes ,beta-lactamase resistant genes ,010501 environmental sciences ,beta lactamase resistant genes ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,Antibiotic resistance ,medicine ,hospital ,Original Research ,0105 earth and related environmental sciences ,biology ,Correction ,Enterobacter ,biology.organism_classification ,medicine.disease ,Citrobacter freundii ,Resistome ,water body ,municipal ,Klebsiella pneumonia ,Enterobacter cloacae ,comparative metagenomics ,wastewaters - Abstract
The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., blaKPC, blaCTX-M, blaSHV, blaTEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of blaKPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin–antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the blaKPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (blaTEM-1) were recovered in wastewater samples which may aid the transfer of AMR.
- Published
- 2017
14. Insights from the draft genome of the subsection V (Stigonematales) cyanobacterium Hapalosiphon sp. Strain MRB220 associated with 2-MIB production
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BoonFei Tan, Chek Yin Boo, Karina Yew-Hoong Gin, Janelle R. Thompson, Shu Harn Te, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, Singapore-MIT Alliance in Research and Technology (SMART), Tan, Boon Fei, and Thompson, Janelle Renee
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0301 basic medicine ,Cyanobacteria ,Geosmin synthase ,030106 microbiology ,Secondary metabolite ,Genome ,Hapalosiphon ,03 medical and health sciences ,Stigonematales ,Botany ,Genetics ,medicine ,Extended Genome Report ,Gene ,Whole genome sequencing ,biology ,Strain (biology) ,2-MIB ,16S ribosomal RNA ,biology.organism_classification ,030104 developmental biology ,Subsection V cyanobacterium ,Fischerella ,medicine.drug ,Filamentous heterocysts - Abstract
A non-axenic unialgal culture containing a Subsection V (Stigonematales) cyanobacterium, Hapalosiphon strain MRB 220, was obtained from a benthic freshwater algal mat through multiple transfers following growth in sterile media. Physiological characterization demonstrated the culture was capable of nitrogen-fixation and production of the off flavor compound 2-methylisoborneol (2-MIB). Total DNA isolated from this culture was sequenced using Illumina HiSeq and de novo assembled into contigs. The genome of MRB 220 was separated from co-occurring heterotrophic bacteria using sequence homology and compositional approaches, and its purity was confirmed based on best BLAST hit classification and principle component analysis of the tetranucleotide frequencies of fragmented contigs. The genome of ~7.4 Mbp contains 6,345 protein coding genes with 4,320 of these having functional prediction including predicted pathways for biosynthesis of the secondary metabolite welwitindolinone. Analyses of 16S rRNA gene and whole genome sequence average nucleotide identity indicated close relatedness of MRB 220 to the genera Hapalosiphon and Fischerella within the order Stigonematales. Microscopic examination showed that MRB 220 formed heterocystous branched filaments, thereby supporting identification of strain MRB 220 as a morphospecies of Hapalosiphon. Availability of the draft genome of Hapalosiphon strain MRB 220 enables future work to elucidate the pathway and dynamics for biosynthesis of 2-MIB and other secondary metabolites and understand the ecology and physiology of Stigonematales cyanobacteria in tropical freshwaters., Singapore. National Research Foundation (under its Environmental & Water Technologies Strategic Research Programme and administered by the Environment & Water Industry Programme Office (EWI) of the PUB (Grant number: 1102-IRIS-14-02)), Singapore. National Research Foundation (Singapore MIT Alliance for Research and Technology’s (SMART) Center for Environmental Sensing and Modeling (CENSAM) research program)
- Published
- 2015
15. Vibrio campbellii hmgA-mediated pyomelanization impairs quorum sensing, virulence, and cellular fitness
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Anahita Mostaghim, Baochuan Lin, Pimonsri Mittraparp-arthorn, Gary J. Vora, Evan R. Glaser, Zheng Wang, Janelle R. Thompson, Varaporn Vuddhakul, and Robert A. Rubin
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Microbiology (medical) ,Mutant ,tyrosine catabolism ,Wild type ,HMGA ,lcsh:QR1-502 ,Virulence ,quorum sensing ,Biology ,biology.organism_classification ,medicine.disease_cause ,Microbiology ,bioluminescence ,lcsh:Microbiology ,melanin ,Quorum sensing ,Regulon ,Vibrio cholerae ,medicine ,Original Research Article ,Vibrio campbellii ,Vibrio - Abstract
Melanization due to the inactivation of the homogentisate-1,2-dioxygenase gene (hmgA) has been demonstrated to increase stress resistance, persistence, and virulence in some bacterial species but such pigmented mutants have not been observed in pathogenic members of the Vibrio Harveyi clade. In this study, we used Vibrio campbellii ATCC BAA-1116 as model organism to understand how melanization affected cellular phenotype, metabolism, and virulence. An in-frame deletion of the hmgA gene resulted in the overproduction of a pigment in cell culture supernatants and cellular membranes that was identified as pyomelanin. Unlike previous demonstrations in Vibrio cholerae, Burkholderia cepacia, and Pseudomonas aeruginosa, the pigmented V. campbellii mutant did not show increased UV resistance and was found to be ~2.7 times less virulent than the wild type strain in Penaeus monodon shrimp virulence assays. However, the extracted pyomelanin pigment did confer a higher resistance to oxidative stress when incubated with wild type cells. Microarray-based transcriptomic analyses revealed that the hmgA gene deletion and subsequent pyomelanin production negatively effected the expression of 129 genes primarily involved in energy production, amino acid, and lipid metabolism, and protein translation and turnover. This transcriptional response was mediated in part by an impairment of the quorum sensing regulon as transcripts of the quorum sensing high cell density master regulator LuxR and other operonic members of this regulon were significantly less abundant in the hmgA mutant. Taken together, the results suggest that the pyomelanization of V. campbellii sufficiently impairs the metabolic activities of this organism and renders it less fit and virulent than its isogenic wild type strain.
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- 2013
- Full Text
- View/download PDF
16. Correction: Sigma E Regulators Control Hemolytic Activity and Virulence in a Shrimp Pathogenic Vibrio harveyi
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Janelle R. Thompson, Pimonsri Rattanama, John J. Mekalanos, Kanchana Srinitiwarawong, Varaporn Vuddhakul, and Natthawan Kongkerd
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Genetics ,Multidisciplinary ,Science ,Medicine ,Virulence ,Correction ,Biology ,Bioinformatics ,Control (linguistics) ,Pathogenic vibrio - Abstract
The accession numbers were not provided in the manuscript text. Genome regions containing open reading frames for genes and proteins identified in this study have been deposited at NCBI with accessions {"type":"entrez-nucleotide-range","attrs":{"text":"JQ677126-JQ677134","start_term":"JQ677126","end_term":"JQ677134","start_term_id":"388329424","end_term_id":"388329466"}}JQ677126-JQ677134.
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- 2012
17. Sigma E Regulators Control Hemolytic Activity and Virulence in a Shrimp Pathogenic Vibrio harveyi
- Author
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Kanchana Srinitiwarawong, Varaporn Vuddhakul, Pimonsri Rattanama, Natthawan Kongkerd, John J. Mekalanos, Janelle R. Thompson, Massachusetts Institute of Technology. Department of Civil and Environmental Engineering, and Thompson, Janelle Renee
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Proteomics ,Operon ,Aquaculture ,Virulence factor ,Hemolysin Proteins ,Sigma factor ,Genetics ,Genome ,Multidisciplinary ,Virulence ,biology ,Escherichia coli Proteins ,Serine Endopeptidases ,Agriculture ,Hemolysin ,Medicine ,Research Article ,Science ,Immunology ,Molecular Sequence Data ,Porins ,Mutagenesis (molecular biology technique) ,Sigma Factor ,Microbiology ,Binding, Competitive ,Hemolysis ,Molecular Genetics ,Open Reading Frames ,Bacterial Proteins ,Penaeidae ,Genetic Mutation ,Virology ,Animals ,Biology ,Vibrio ,Sheep ,Base Sequence ,Immunity ,Computational Biology ,biology.organism_classification ,Mutagenesis ,Mutation ,DNA Transposable Elements ,bacteria ,Transposon mutagenesis - Abstract
Members of the genus Vibrio are important marine and aquaculture pathogens. Hemolytic activity has been identified as a virulence factor in many pathogenic vibrios including V. cholerae, V. parahaemolyticus, V. alginolyticus, V. harveyi and V. vulnificus. We have used transposon mutagenesis to identify genes involved in the hemolytic activity of shrimp-pathogenic V. harveyi strain PSU3316. Out of 1,764 mutants screened, five mutants showed reduced hemolytic activity on sheep blood agar and exhibited virulence attenuation in shrimp (Litopenaeus vannamei). Mutants were identified by comparing transposon junction sequences to a draft of assembly of the PSU3316 genome. Surprisingly none of the disrupted open reading frames or gene neighborhoods contained genes annotated as hemolysins. The gene encoding RseB, a negative regulator of the sigma factor (σE), was interrupted in 2 out of 5 transposon mutants, in addition, the transcription factor CytR, a threonine synthetase, and an efflux-associated cytoplasmic protein were also identified. Knockout mutations introduced into the rpoE operon at the rseB gene exhibited low hemolytic activity in sheep blood agar, and were 3-to 7-fold attenuated for colonization in shrimp. Comparison of whole cell extracted proteins in the rseB mutant (PSU4030) to the wild-type by 2-D gel electrophoresis revealed 6 differentially expressed proteins, including two down-regulated porins (OmpC-like and OmpN) and an upregulated protease (DegQ) which have been associated with σE in other organisms. Our study is the first report linking hemolytic activity to the σE regulators in pathogenic Vibrio species and suggests expression of this virulence-linked phenotype is governed by multiple regulatory pathways within the V. harveyi., Thailand Research Fund (Royal Golden Jubilee Ph.D. program (Grant No. HD/0153/2547)), Harvard University, Massachusetts Institute of Technology
- Published
- 2012
18. Sigma E regulators control hemolytic activity and virulence in a shrimp pathogenic Vibrio harveyi.
- Author
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Pimonsri Rattanama, Janelle R Thompson, Natthawan Kongkerd, Kanchana Srinitiwarawong, Varaporn Vuddhakul, and John J Mekalanos
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Medicine ,Science - Abstract
Members of the genus Vibrio are important marine and aquaculture pathogens. Hemolytic activity has been identified as a virulence factor in many pathogenic vibrios including V. cholerae, V. parahaemolyticus, V. alginolyticus, V. harveyi and V. vulnificus. We have used transposon mutagenesis to identify genes involved in the hemolytic activity of shrimp-pathogenic V. harveyi strain PSU3316. Out of 1,764 mutants screened, five mutants showed reduced hemolytic activity on sheep blood agar and exhibited virulence attenuation in shrimp (Litopenaeus vannamei). Mutants were identified by comparing transposon junction sequences to a draft of assembly of the PSU3316 genome. Surprisingly none of the disrupted open reading frames or gene neighborhoods contained genes annotated as hemolysins. The gene encoding RseB, a negative regulator of the sigma factor (σ(E)), was interrupted in 2 out of 5 transposon mutants, in addition, the transcription factor CytR, a threonine synthetase, and an efflux-associated cytoplasmic protein were also identified. Knockout mutations introduced into the rpoE operon at the rseB gene exhibited low hemolytic activity in sheep blood agar, and were 3-to 7-fold attenuated for colonization in shrimp. Comparison of whole cell extracted proteins in the rseB mutant (PSU4030) to the wild-type by 2-D gel electrophoresis revealed 6 differentially expressed proteins, including two down-regulated porins (OmpC-like and OmpN) and an upregulated protease (DegQ) which have been associated with σ(E) in other organisms. Our study is the first report linking hemolytic activity to the σ(E) regulators in pathogenic Vibrio species and suggests expression of this virulence-linked phenotype is governed by multiple regulatory pathways within the V. harveyi.
- Published
- 2012
- Full Text
- View/download PDF
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