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1. SARS-CoV-2 RNA Is Readily Detectable at Least 8 Months after Shedding in an Isolation Facility

Author

Coil, David A, Pechacek, Randi, Kaze, Mo, Zuniga-Montanez, Rogelio, Guerrero, Roque G, Eisen, Jonathan A, Shapiro, Karen, and Bischel, Heather N

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Infectious Diseases, Lung, Pneumonia & Influenza, Genetics, Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being, Humans, COVID-19, SARS-CoV-2, RNA, Viral, Wastewater, Pandemics, RNA, relic RNA, genome sequencing, surface samples, virus, Immunology, Microbiology
Abstract

Environmental monitoring of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for research and public health purposes has grown exponentially throughout the coronavirus disease 2019 (COVID-19) pandemic. Monitoring wastewater for SARS-CoV-2 provides early warning signals of virus spread and information on trends in infections at a community scale. Indoor environmental monitoring (e.g., swabbing of surfaces and air filters) to identify potential outbreaks is less common, and the evidence for its utility is mixed. A significant challenge with surface and air filter monitoring in this context is the concern of "relic RNA," noninfectious RNA found in the environment that is not from recently deposited virus. Here, we report detection of SARS-CoV-2 RNA on surfaces in an isolation unit (a university dorm room) for up to 8 months after a COVID-19-positive individual vacated the space. Comparison of sequencing results from the same location over two time points indicated the presence of the entire viral genome, and sequence similarity confirmed a single source of the virus. Our findings highlight the need to develop approaches that account for relic RNA in environmental monitoring. IMPORTANCE Environmental monitoring of SARS-CoV-2 is rapidly becoming a key tool in infectious disease research and public health surveillance. Such monitoring offers a complementary and sometimes novel perspective on population-level incidence dynamics relative to that of clinical studies by potentially allowing earlier, broader, more affordable, less biased, and less invasive identification. Environmental monitoring can assist public health officials and others when deploying resources to areas of need and provides information on changes in the pandemic over time. Environmental surveillance of the genetic material of infectious agents (RNA and DNA) in wastewater became widely applied during the COVID-19 pandemic. There has been less research on other types of environmental samples, such as surfaces, which could be used to indicate that someone in a particular space was shedding virus. One challenge with surface surveillance is that the noninfectious genetic material from a pathogen (e.g., RNA from SARS-CoV-2) may be detected in the environment long after an infected individual has left the space. This study aimed to determine how long SARS-CoV-2 RNA could be detected in a room after a COVID-positive person had been housed there.

Published
2022

2. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Author

Zuniga-Montanez, Rogelio, Coil, David A, Eisen, Jonathan A, Pechacek, Randi, Guerrero, Roque G, Kim, Minji, Shapiro, Karen, and Bischel, Heather N

Subjects
Humans, RNA, Viral, Dust, Environmental Monitoring, Schools, COVID-19, SARS-CoV-2, Emerging Infectious Diseases, Clinical Trials and Supportive Activities, Prevention, Biodefense, Vaccine Related, Infectious Diseases, Clinical Research, Infection, General Science & Technology
Abstract

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units (n = 2,341 swabs). Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07-38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing through Healthy Davis Together (HDT). HDT also offered on-site clinical testing in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to contain relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. High-Ct positive results from environmental swabs detected in the absence of known active infections supports this conclusion. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions.

Published
2022

3. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Author

Zuniga-Montanez, Rogelio, Coil, David A, Eisen, Jonathan A, Pechacek, Randi, Guerrero, Roque G, Kim, Minji, Shapiro, Karen, and Bischel, Heather N

Subjects
Infectious Diseases, Emerging Infectious Diseases, Prevention, Clinical Trials and Supportive Activities, Biodefense, Vaccine Related, Clinical Research, Infection, Good Health and Well Being
Abstract

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units. Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07–38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing. On-site clinical testing was offered in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to reflect relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. The high-Ct positive results from environmental swabs further suggest the absence of active infections. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions.

Published
2021

7. Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance

Author

Munk, Patrick, Brinch, Christian, Møller, Frederik Duus, Petersen, Thomas N., Hendriksen, Rene S., Seyfarth, Anne Mette, Kjeldgaard, Jette S., Svendsen, Christina Aaby, van Bunnik, Bram, Berglund, Fanny, Bego, Artan, Power, Pablo, Rees, Catherine, Lambrinidis, Dionisia, Neilson, Elizabeth Heather Jakobsen, Gibb, Karen, Coventry, Kris, Collignon, Peter, Cassar, Susan, Allerberger, Franz, Begum, Anowara, Hossain, Zenat Zebin, Worrell, Carlon, Vandenberg, Olivier, Pieters, Ilse, Victorien, Dougnon Tamègnon, Gutierrez, Angela Daniela Salazar, Soria, Freddy, Grujić, Vesna Rudić, Mazalica, Nataša, Rahube, Teddie O., Tagliati, Carlos Alberto, Rodrigues, Dalia, Oliveira, Guilherme, de Souza, Larissa Camila Ribeiro, Ivanov, Ivan, Juste, Bonkoungou Isidore, Oumar, Traoré, Sopheak, Thet, Vuthy, Yith, Ngandijo, Antoinette, Nzouankeu, Ariane, Olivier, Ziem A. Abah Jacques, Yost, Christopher K., Kumar, Pratik, Brar, Satinder Kaur, Tabo, Djim-Adjim, Adell, Aiko D., Paredes-Osses, Esteban, Martinez, Maria Cristina, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Lau, Lok Ting, Chung, Teresa, Jiao, Xiaoyang, Yu, Yongjie, JiaYong, Zhao, Morales, Johan F. Bernal, Valencia, Maria Fernanda, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Deogratias, Zozo Nyarukweba, Elsborg, Bodil, Hansen, Lisbeth Truelstrup, Jensen, Pernille Erland, Abouelnaga, Mohamed, Salem, Mohamed Fathy, Koolmeister, Marliin, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Le Guyader, Soizick, Schaeffer, Julien, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Schubert, Sara, Hesse, Sina, Berendonk, Thomas U., Saba, Courage Kosi Setsoafia, Mohammed, Jibril, Feglo, Patrick Kwame, Banu, Regina Ama, Kotzamanidis, Charalampos, Lytras, Efthymios, Lickes, Sergio A., Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Ballal, Mamatha, Bangera, Sohan Rodney, Fani, Fereshteh, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Diaconu, Elena Lavinia, Corno, Gianluca, Di Cesare, Andrea, Alba, Patricia, Hisatsune, Junzo, Yu, Liansheng, Kuroda, Makoto, Sugai, Motoyuki, Kayama, Shizuo, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Jamil, Kazi, Fakhraldeen, Saja Adel, Alaati, Tareq, Bērziņš, Aivars, Avsejenko, Jeļena, Kokina, Kristina, Streikisa, Madara, Bartkevics, Vadims, Matar, Ghassan M., Daoud, Ziad, Pereckienė, Asta, Butrimaite-Ambrozeviciene, Ceslova, Penny, Christian, Bastaraud, Alexandra, Rasolofoarison, Tiavina, Collard, Jean-Marc, Samison, Luc Hervé, Andrianarivelo, Mala Rakoto, Banda, Daniel Lawadi, Amin, Arshana, Rajandas, Heraa, Parimannan, Sivachandran, Spiteri, David, Haber, Malcolm Vella, Santchurn, Sunita J., Vujacic, Aleksandar, Djurovic, Dijana, Bouchrif, Brahim, Karraouan, Bouchra, Vubil, Delfino Carlos, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, Jeunen, Gert-Jan, Gemmell, Neil, Chambers, Stephen T., Mendoza, Fania Perez, Huete-Pιrez, Jorge, Vilchez, Samuel, Ahmed, Akeem Olayiwola, Adisa, Ibrahim Raufu, Odetokun, Ismail Ayoade, Fashae, Kayode, Sørgaard, Anne-Marie, Wester, Astrid Louise, Ryrfors, Pia, Holmstad, Rune, Mohsin, Mashkoor, Hasan, Rumina, Shakoor, Sadia, Gustafson, Natalie Weiler, Schill, Claudia Huber, Rojas, Maria Luz Zamudio, Velasquez, Jorge Echevarria, Magtibay, Bonifacio B., Catangcatang, Kris, Sibulo, Ruby, Yauce, Felipe Campos, Wasyl, Dariusz, Manaia, Celia, Rocha, Jaqueline, Martins, Jose, Álvaro, Pedro, Di Yoong Wen, Doris, Shin, Hanseob, Hur, Hor-Gil, Yoon, Sukhwan, Bosevska, Golubinka, Kochubovski, Mihail, Cojocaru, Radu, Burduniuc, Olga, Hong, Pei-Ying, Perry, Meghan Rose, Gassama, Amy, Radosavljevic, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Pastuchová, Katarína, Truska, Peter, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Song, Min Joon, Quintela-Baluja, Marcos, Lopez, Mariano Gomez, Cerdà-Cuéllar, Marta, Perera, R.R.D.P., Bandara, N.K.B.K.R.G.W., Premasiri, H.I., Pathirage, Sujatha, Charlemagne, Kareem, Rutgersson, Carolin, Norrgren, Leif, Örn, Stefan, Boss, Renate, Van der Heijden, Tanja, Hong, Yu-Ping, Kumburu, Happiness Houka, Mdegela, Robinson Hammerthon, Hounmanou, Yaovi Mahuton Gildas, Chonsin, Kaknokrat, Suthienkul, Orasa, Thamlikitkul, Visanu, de Roda Husman, Ana Maria, Bidjada, Bawimodom, Njanpop-Lafourcade, Berthe-Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Kurekci, Cemil, Ejobi, Francis, Kalule, John Bosco, Thomsen, Jens, Obaidi, Ouidiane, Jassim, Laila Mohamed, Moore, Andrew, Leonard, Anne, Graham, David W., Bunce, Joshua T., Zhang, Lihong, Gaze, William H., Lefor, Brett, Capone, Drew, Sozzi, Emanuele, Brown, Joe, Meschke, John Scott, Sobsey, Mark D., Davis, Michael, Beck, Nicola Koren, Sukapanpatharam, Pardi, Truong, Phuong, Lilienthal, Ronald, Kang, Sanghoon, Wittum, Thomas E., Rigamonti, Natalia, Baklayan, Patricia, Van, Chinh Dang, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Larsson, D. G. Joakim, Koopmans, Marion, Woolhouse, Mark, Aarestrup, Frank M., Virology, Producció Animal, and Sanitat Animal

Subjects
genomic analysis, sewage, antimicrobial resistance, Multidisciplinary, Sewage, Drug Resistance, Bacterial, Metagenome, General Physics and Astronomy, Drug Resistance, Bacterial/genetics, Genomics, General Chemistry, General Biochemistry, Genetics and Molecular Biology, Anti-Bacterial Agents/pharmacology, Anti-Bacterial Agents
Abstract

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention. Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Published
2022

11. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author

Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, Aarestrup, Frank M., Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, University of Helsinki, Food Hygiene and Environmental Health, Producció Animal, Sanitat Animal, Tilraunastöð í meinafræði að Keldum (HÍ), Institute for Experimental Pathology, Keldur (UI), Heilbrigðisvísindasvið (HÍ), School of Health Sciences (UI), Háskóli Íslands, University of Iceland, Food Hygiene and Environmental Health, Helsinki One Health (HOH), Zoonotic Antimicrobial Resistance, and Virology

Subjects
0301 basic medicine, Water microbiology, global surveillance, Sanitation, Kwantitatieve Veterinaire Epidemiologie, Drug Resistance, General Physics and Astronomy, Sewage, 02 engineering and technology, Drug resistance, Antimicrobial resistance, 413 Veterinary science, BU Veterinary Drugs, Abundance (ecology), Drug Resistance, Multiple, Bacterial, Genamengi, AMR, lcsh:Science, resistome, Ónæmisfræði, Multidisciplinary, Population Health, 021001 nanoscience & nanotechnology, 3. Good health, Europe, machine learning, Geography, Epidemiological Monitoring, 0210 nano-technology, Asia, Science, Microbial Consortia, Oceania, Article, General Biochemistry, Genetics and Molecular Biology, BU Dierbehandelingsmiddelen, 03 medical and health sciences, Antibiotic resistance, SDG 3 - Good Health and Well-being, Environmental health, Erfðafræði, Life Science, Humans, ddc:610, wastewater, Ecological epidemiology, Bacteria, business.industry, Quantitative Veterinary Epidemiology, prediction, General Chemistry, South America, Resistome, 030104 developmental biology, Genes, Socioeconomic Factors, 416 Food Science, Genes, Bacterial, Metagenomics, ENVIRONMENTAL SURVEILLANCE, Africa, North America, Metagenome, UPDATE, lcsh:Q, business, 610 Medizin und Gesundheit
Abstract

Publisher's version (útgefin grein), Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR., We are grateful to Hanne Nørgaard Nielsen, Christina Aaby Svendsen, Jacob Dyring Jensen, Birthe S. Rosenqvist Lund, Kate Vina Vibefeldt, Inge Marianne Hansen, Gunhild Larsen, Hanne Mordhorst, and Carsten Bidstrup for technical assistance. We also thank Jeffrey Edward Skiby for internal review. This study has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 643476 (COMPARE), the World Health Organization, The Villum Foundation (VKR023052), and The Novo Nordisk Foundation (NNF16OC0021856: Global Surveillance of Antimicrobial Resistance).

Published
2019

13. Additional data for preprint: 'Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing'

Author

Arumugam, Krithika, Williams, Rohan, Haryono, Mindia, Bessarab, Irina, Liu, Xianghui, Zuniga-Montanez, Rogelio, Roy, Samarapita, Wuertz, Stefan, Huson, Daniel, Lauro, Federico, Law, Ying Yu, and Drautz-Moses, Daniela

Subjects
metagenomics, long read sequencing, Nanopore, activated sludge, enrichment culture
Abstract

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities. Using long read (MinION) obtained from an ensemble of activated sludge enrichment bioreactors, we 1) describe new methods for validating long read assembled genomes using their counterpart short read metagenome assembled genomes; 2) assess the influence of different correction procedures ongenome quality and predicted gene qualityand 3) contribute 21 new closed or complete genomes of community members, including several species known to play key functional roles in wastewater bioprocesses, including from microbes known to exhibit the polyphosphate-and glycogen-accumulating organism phenotypes, and filamentous bacteria associated the formation and stability of activated sludge flocs. Our findings further establish the feasibility of long read metagenome-assembled genome recovery, and demonstrate the utility of parallel sampling of moderately complex enrichments communities for recovery of genomes of key functional species from activated sludge bioprocesses. This submission provides additional data and intermediate results not provided in the raw data submission to NCBI Short Read Archive (SRA). The provided dataare as follows (see tree file for more detailed breakdown) in 387 directories and3723 files: 1. LRAC.tar.gz: the Canu assembled sequencein FASTA format for each of the four datasets (PAO*). Includes Canu cmd specification in files names canu.e* 2. SRAC.tar.gz: the short read assemblies (FASTA) and binning results (contig membership of each provided within an .RData file) for each of the four datasets (PAO*). 3. srac2lrac.tar.gz: summary results and data for the concordance statistic analysis for each of the four datasets (PAO*). The BLASTN analysis was run as specified in blastn.sh file, and the tabularoutput is provided insrac_spades2corrlrac_canu.out. The output from the concordance statistic analysis is provided in the .RData files called blastn3-6_canu.RData andblastn3-6_canu_fil.RData. Seehttps://github.com/rbhwilliams/srac2lrac for a fully workedexample. 4. LRGenomes.tar.gz: FASTA sequence, Prokka and CheckM annotations for each of the 21 recovered genomes from each correction procedure (uncorrected, MEGAN-FS, Medaka, Racon and multiple [4 rounds of Racon and 1 of Medaka]). 5.LRGenomesCoverage.tar.gz: for MEGAN-FS versions of the 21 genomes, the perbase coverage data for both long read (LR) and short read (SR) data. 6.LRAccumulibacterGenomes.tar.gz: two refined genomes (.fasta)from Candidatus Accumulibacter and detailed notes on procedures applied (.txt). 7. tree: text file with contents of the above files in a tree-like format. &nbsp

Published
2020
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14. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P.G., IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Singapore Centre for Environmental Life Sciences and Engineering, Nanyang Technological University Food Technology Centre (NAFTEC), Producció Animal, Sanitat Animal, Virology, University of Helsinki, Food Hygiene and Environmental Health, Helsinki One Health (HOH), Zoonotic Antimicrobial Resistance, IRAS OH Epidemiology Microbial Agents, and dIRAS RA-I&I I&I

Subjects
0301 basic medicine, lcsh:Medicine, Sewage, Pilot Projects, POLIOVIRUS, Disease, CORONAVIRUS, Disease Outbreaks, BU Veterinary Drugs, 0302 clinical medicine, Vegetables, lcsh:Science, metagenomic sequencing, sewage, viral pathogens, virome, virus, 11832 Microbiology and virology, Public health, Multidisciplinary, Virome, ENTEROVIRUSES, 3142 Public health care science, environmental and occupational health, Environmental engineering [Engineering], Geography, Public Health, Environmental Monitoring, VIRUSES, High density, Early detection, Food Contamination, CLASSIFICATION, BU Dierbehandelingsmiddelen, Article, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Environmental health, Humans, Life Science, Human virome, Author Correction, business.industry, lcsh:R, Outbreak, SEASONALITY, Cross-Sectional Studies, 030104 developmental biology, Megacity, Metagenomics, PATTERNS, Metagenome, lcsh:Q, business, 030217 neurology & neurosurgery
Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020

15. Setting a baseline for global urban virome surveillance in sewage

Author

IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P.G., IRAS OH Epidemiology Microbial Agents, dIRAS RA-I&I I&I, Nieuwenhuijse, David F., Oude Munnink, Bas B., Phan, My V.T., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenovic, Jasna, Jergović, Matijana, Karpíšková, Renáta, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Villacis, Jose Eduardo, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O’Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Bērziņš, Aivars, Avsejenko, Jeļena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G.M., Zuidema, Tina, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama†, Amy, Radosavljevic, Vladimir, Tay, Moon Y.F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavačová, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Larsson, D. G.Joakim, Norrgren, Leif, Örn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van Dang, Chinh, Tran, Doan Minh Nguyen, Do Phuc, Nguyen, Kwenda, Geoffrey, Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, and Koopmans, Marion P.G.

Published
2020

16. Setting a baseline for global urban virome surveillance in sewage

Author

Nieuwenhuijse, David, Munnink, Bas B. Oude, Phan, My V. T., Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim-adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Li, Baisheng, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenović, Jasna, Jergović, Matijana, Karpiskova, Renata, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Eduardo Villacis, Jose, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafa, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O'Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng'eno, Eric, Raka, Lul, Berzins, Aivars, Avsejenko, Jelena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G. M., Zuidema, Tina, Jeunen, Gert-Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Zamudio Rojas, Maria Luz, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljević, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavacova, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerda-Cuellar, Marta, Pathirage, Sujatha, Larsson, D. G. Joakim, Norrgren, Leif, Orn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe-Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Chinh, Van Dang, Doan Minh Nguyen, Tran, Nguyen, Do Phuc, Kwenda, Geofrey, Nieuwenhuijse, David, Munnink, Bas B. Oude, Phan, My V. T., Munk, Patrick, Venkatakrishnan, Shweta, Aarestrup, Frank M., Cotten, Matthew, Koopmans, Marion P., Hendriksen, Rene S., Bego, Artan, Rees, Catherine, Neilson, Elizabeth Heather, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Sopheak, Thet, Vuthy, Yith, Yost, Christopher K., Tabo, Djim-adjim, Cuadros-Orellana, Sara, Ke, Changwen, Zheng, Huanying, Li, Baisheng, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Hrenović, Jasna, Jergović, Matijana, Karpiskova, Renata, Elsborg, Bodil, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Eduardo Villacis, Jose, Sanneh, Bakary, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafa, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, O'Connor, Louise, Cormican, Martin, Moran-Gilad, Jacob, Battisti, Antonio, Alba, Patricia, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng'eno, Eric, Raka, Lul, Berzins, Aivars, Avsejenko, Jelena, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Schmitt, Heike, van Passel, Mark, van de Schans, Milou G. M., Zuidema, Tina, Jeunen, Gert-Jan, Gemmell, Neil, Fashae, Kayode, Wester, Astrid Louise, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Zamudio Rojas, Maria Luz, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljević, Vladimir, Tay, Moon Y. F., Zuniga-Montanez, Rogelio, Wuertz, Stefan, Gavacova, Dagmar, Trkov, Marija, Keddy, Karen, Esterhuyse, Kerneels, Cerda-Cuellar, Marta, Pathirage, Sujatha, Larsson, D. G. Joakim, Norrgren, Leif, Orn, Stefan, Van der Heijden, Tanja, Kumburu, Happiness Houka, de RodaHusman, Ana Maria, Njanpop-Lafourcade, Berthe-Marie, Bidjada, Pawou, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Chinh, Van Dang, Doan Minh Nguyen, Tran, Nguyen, Do Phuc, and Kwenda, Geofrey

Abstract

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective.

Published
2020

17. Global warming readiness: Feasibility of enhanced biological phosphorus removal from wastewater at 35°C

Author

Qiu, Guanglei, primary, Law, Yingyu, additional, Zuniga-Montanez, Rogelio, additional, Lu, Yang, additional, Roy, Samarpita, additional, Thi, Sara Swa, additional, Hoon, Huiyi, additional, Nguyen, Thi Quynh Ngoc, additional, Eganathan, Kaliyamoorthy, additional, Liu, Xianghui, additional, Nielsen, Per H., additional, Williams, Rohan B.H., additional, and Wuertz, Stefan, additional

Published
2021
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19. Analysis procedures for assessing recovery of high quality, complete, closed genomes from Nanopore long read metagenome sequencing

Author

Arumugam, Krithika, primary, Bessarab, Irina, additional, Haryono, Mindia A. S., additional, Liu, Xianghui, additional, Zuniga-Montanez, Rogelio E., additional, Roy, Samarpita, additional, Qiu, Guanglei, additional, Drautz-Moses, Daniela I., additional, Law, Ying Yu, additional, Wuertz, Stefan, additional, Lauro, Federico M., additional, Huson, Daniel H., additional, and Williams, Rohan B. H., additional

Published
2020
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20. Metabolic Traits of Candidatus Accumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal

Author

Qiu, Guanglei, primary, Liu, Xianghui, additional, Saw, Nay Min Min Thaw, additional, Law, Yingyu, additional, Zuniga-Montanez, Rogelio, additional, Thi, Sara Swa, additional, Ngoc Nguyen, Thi Quynh, additional, Nielsen, Per H., additional, Williams, Rohan B.H., additional, and Wuertz, Stefan, additional

Published
2019
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21. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Author

Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, Aarestrup, Frank M., Sub RIVM, dIRAS RA-I&I RA, One Health Microbieel, dIRAS RA-I&I I&I, Hendriksen, Rene S., Munk, Patrick, Njage, Patrick, van Bunnik, Bram, McNally, Luke, Lukjancenko, Oksana, Röder, Timo, Nieuwenhuijse, David, Pedersen, Susanne Karlsmose, Kjeldgaard, Jette, Kaas, Rolf S., Clausen, Philip Thomas Lanken Conradsen, Vogt, Josef Korbinian, Leekitcharoenphon, Pimlapas, van de Schans, Milou G.M., Zuidema, Tina, de Roda Husman, Ana Maria, Rasmussen, Simon, Petersen, Bent, Bego, Artan, Rees, Catherine, Cassar, Susan, Coventry, Kris, Collignon, Peter, Allerberger, Franz, Rahube, Teddie O., Oliveira, Guilherme, Ivanov, Ivan, Vuthy, Yith, Sopheak, Thet, Yost, Christopher K., Ke, Changwen, Zheng, Huanying, Baisheng, Li, Jiao, Xiaoyang, Donado-Godoy, Pilar, Coulibaly, Kalpy Julien, Jergović, Matijana, Hrenovic, Jasna, Karpíšková, Renáta, Villacis, Jose Eduardo, Legesse, Mengistu, Eguale, Tadesse, Heikinheimo, Annamari, Malania, Lile, Nitsche, Andreas, Brinkmann, Annika, Saba, Courage Kosi Setsoafia, Kocsis, Bela, Solymosi, Norbert, Thorsteinsdottir, Thorunn R., Hatha, Abdulla Mohamed, Alebouyeh, Masoud, Morris, Dearbhaile, Cormican, Martin, O’Connor, Louise, Moran-Gilad, Jacob, Alba, Patricia, Battisti, Antonio, Shakenova, Zeinegul, Kiiyukia, Ciira, Ng’eno, Eric, Raka, Lul, Avsejenko, Jeļena, Bērziņš, Aivars, Bartkevics, Vadims, Penny, Christian, Rajandas, Heraa, Parimannan, Sivachandran, Haber, Malcolm Vella, Pal, Pushkar, Jeunen, Gert Jan, Gemmell, Neil, Fashae, Kayode, Holmstad, Rune, Hasan, Rumina, Shakoor, Sadia, Rojas, Maria Luz Zamudio, Wasyl, Dariusz, Bosevska, Golubinka, Kochubovski, Mihail, Radu, Cojocaru, Gassama, Amy, Radosavljevic, Vladimir, Wuertz, Stefan, Zuniga-Montanez, Rogelio, Tay, Moon Y.F., Gavačová, Dagmar, Pastuchova, Katarina, Truska, Peter, Trkov, Marija, Esterhuyse, Kerneels, Keddy, Karen, Cerdà-Cuéllar, Marta, Pathirage, Sujatha, Norrgren, Leif, Örn, Stefan, Larsson, D. G.Joakim, Heijden, Tanja Van der, Kumburu, Happiness Houka, Sanneh, Bakary, Bidjada, Pawou, Njanpop-Lafourcade, Berthe Marie, Nikiema-Pessinaba, Somtinda Christelle, Levent, Belkis, Meschke, John Scott, Beck, Nicola Koren, Van, Chinh Dang, Tran, Doan Minh Nguyen, Kwenda, Geoffrey, Tabo, Djim adjim, Wester, Astrid Louise, Cuadros-Orellana, Sara, Amid, Clara, Cochrane, Guy, Sicheritz-Ponten, Thomas, Schmitt, Heike, Alvarez, Jorge Raul Matheu, Aidara-Kane, Awa, Pamp, Sünje J., Lund, Ole, Hald, Tine, Woolhouse, Mark, Koopmans, Marion P., Vigre, Håkan, Petersen, Thomas Nordahl, and Aarestrup, Frank M.

Published
2019

23. Metabolic Traits of CandidatusAccumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal

Author

Qiu, Guanglei, Liu, Xianghui, Saw, Nay Min Min Thaw, Law, Yingyu, Zuniga-Montanez, Rogelio, Thi, Sara Swa, Ngoc Nguyen, Thi Quynh, Nielsen, Per H., Williams, Rohan B.H., and Wuertz, Stefan

Abstract

Despite recent evidence from full-scale plants suggesting that CandidatusAccumulibacter may be capable of using amino acids, this metabolic trait has never been confirmed in a bioreactor experiment. Here we show that an enriched culture of Ca. Accumulibacter clade IIF strain SCELSE-1 could metabolize 11 of 20 α-amino acids, with aspartate, glutamate, asparagine, and glutamine resulting in the highest phosphorus removal. The anaerobic uptake of aspartate and glutamate was achieved through a glutamate/aspartate-proton symporter fully powered by the proton motive force (PMF). Under anaerobic conditions aspartate was deaminized and routed into core carbon metabolic pathways to form polyhydroxyalkanoates (PHA). The lack of genes encoding NADH dependent isocitrate dehydrogenase in the Ca. Accumulibacter genome resulted in a kinetic barrier for glutamate to be channelled to the TCA cycle. Glutamate was stored as glutamate polymer. When amino acids (aspartate or glutamate) and acetate were supplied together, Ca. Accumulibacter took up both carbon sources simultaneously, with the uptake rate of each carbon source largely preserved. Overall energy savings (up to 17%) were achieved under mixed carbon scenarios, due to the ability of Ca. Accumulibacter to rearrange its anaerobic carbon metabolism based on the reducing power, PMF and ATP balance.

Published
2020
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24. Metabolic Traits of Candidatus Accumulibacter clade IIF Strain SCELSE-1 Using Amino Acids As Carbon Sources for Enhanced Biological Phosphorus Removal.

Author

Qiu G, Liu X, Saw NMMT, Law Y, Zuniga-Montanez R, Thi SS, Ngoc Nguyen TQ, Nielsen PH, Williams RBH, and Wuertz S

Subjects
Amino Acids, Anaerobiosis, Bioreactors, Carbon, Phosphorus
Abstract

Despite recent evidence from full-scale plants suggesting that Candidatus Accumulibacter may be capable of using amino acids, this metabolic trait has never been confirmed in a bioreactor experiment. Here we show that an enriched culture of Ca . Accumulibacter clade IIF strain SCELSE-1 could metabolize 11 of 20 α-amino acids, with aspartate, glutamate, asparagine, and glutamine resulting in the highest phosphorus removal. The anaerobic uptake of aspartate and glutamate was achieved through a glutamate/aspartate-proton symporter fully powered by the proton motive force (PMF). Under anaerobic conditions aspartate was deaminized and routed into core carbon metabolic pathways to form polyhydroxyalkanoates (PHA). The lack of genes encoding NADH dependent isocitrate dehydrogenase in the Ca . Accumulibacter genome resulted in a kinetic barrier for glutamate to be channelled to the TCA cycle. Glutamate was stored as glutamate polymer. When amino acids (aspartate or glutamate) and acetate were supplied together, Ca . Accumulibacter took up both carbon sources simultaneously, with the uptake rate of each carbon source largely preserved. Overall energy savings (up to 17%) were achieved under mixed carbon scenarios, due to the ability of Ca . Accumulibacter to rearrange its anaerobic carbon metabolism based on the reducing power, PMF and ATP balance.

Published
2020
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