المؤلفون: Kumar, Tanya, Bryant, MacKenzie, Cantrell, Kalen, Song, Se, McDonald, Daniel, Tubb, Helena, Farmer, Sawyer, Lewis, Amanda, Lukacz, Emily, Brubaker, Linda, Knight, Robin

المصدر: Microbiology Spectrum. 12(1)

مصطلحات موضوعية: 16S, microbiome, preservation method, sample collection, sample storage, vaginal microbiome

الوصف: The composition of the human vaginal microbiome has been linked to a variety of medical conditions including yeast infection, bacterial vaginosis, and sexually transmitted infection. The vaginal microbiome is becoming increasingly acknowledged as a key factor in personal health, and it is essential to establish methods to collect and process accurate samples with self-collection techniques to allow large, population-based studies. In this study, we investigate if using AssayAssure Genelock, a nucleic acid preservative, introduces microbial biases in self-collected vaginal samples. To our knowledge, we also contribute some of the first evidence regarding the impacts of multiple swabs taken at one time point. Vaginal samples have relatively low biomass, so the ability to collect multiple swabs from a unique participant at a single time would greatly improve the replicability and data available for future studies. This will hopefully lay the groundwork to gain a more complete and accurate understanding of the vaginal microbiome.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4vn5719vTest

المؤلفون: Brennan, Caitriona, Salido, Rodolfo A, Belda-Ferre, Pedro, Bryant, MacKenzie, Cowart, Charles, Tiu, Maria D, González, Antonio, McDonald, Daniel, Tribelhorn, Caitlin, Zarrinpar, Amir, Knight, Rob

المصدر: mSystems. 8(4)

مصطلحات موضوعية: Biological Sciences, Bioinformatics and Computational Biology, Bioengineering, Human Genome, Genetics, Biotechnology, Generic health relevance, Genomics, Sequence Analysis, DNA, Software, Gene Library, High-Throughput Nucleotide Sequencing, metagenomics, large-scale studies, NGS normalization, automation, multiplexing, quantification, high-throughput sequencing

الوصف: Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although the cost of running next-generation sequencing instruments has dropped substantially over time, the cost of sample preparation methods has lagged behind. To counter this, researchers have adapted library miniaturization protocols and large sample pools to maximize the number of samples that can be prepared by a certain amount of reagents and sequenced in a single run. However, due to high variability of sample quality, over and underrepresentation of samples in a sequencing run has become a major issue in high-throughput sequencing. This leads to misinterpretation of results due to increased noise, and additional time and cost rerunning underrepresented samples. To overcome this problem, we present a normalization method that uses shallow iSeq sequencing to accurately inform pooling volumes based on read distribution. This method is superior to the widely used fluorometry methods, which cannot specifically target adapter-ligated molecules that contribute to sequencing output. Our normalization method not only quantifies adapter-ligated molecules but also allows normalization of feature space; for example, we can normalize to reads of interest such as non-ribosomal reads. As a result, this normalization method improves the efficiency of high-throughput next-generation sequencing by reducing noise and producing higher average reads per sample with more even sequencing depth. IMPORTANCE High-throughput next generation sequencing (NGS) has significantly contributed to the field of genomics; however, further improvements can maximize the potential of this important tool. Uneven sequencing of samples in a multiplexed run is a common issue that leads to unexpected extra costs or low-quality data. To mitigate this problem, we introduce a normalization method based on read counts rather than library concentration. This method allows for an even distribution of features of interest across samples, improving the statistical power of data sets and preventing the financial loss associated with resequencing libraries. This method optimizes NGS, which already has huge importance across many areas of biology.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7jq8z2r0Test

المؤلفون: Pendergraft, Matthew A, Belda-Ferre, Pedro, Petras, Daniel, Morris, Clare K, Mitts, Brock A, Aron, Allegra T, Bryant, MacKenzie, Schwartz, Tara, Ackermann, Gail, Humphrey, Greg, Kaandorp, Ethan, Dorrestein, Pieter C, Knight, Rob, Prather, Kimberly A

المصدر: Environmental science & technology. 57(10)

مصطلحات موضوعية: Humans, Bacteria, RNA, Ribosomal, 16S, Aerosols, Rivers, Seawater, Environmental Monitoring, Sewage, Water Pollution, Aerosolized Particles and Droplets, 16S, Imperial Beach, Scripps Institution of Oceanography, Tijuana, Tijuana River, airborne exposure, coastal, mass spectrometry, pathogen, sea spray aerosol, water pollution, Life Below Water, Scripps Institution of, Environmental Sciences

الوصف: Roughly half of the human population lives near the coast, and coastal water pollution (CWP) is widespread. Coastal waters along Tijuana, Mexico, and Imperial Beach (IB), USA, are frequently polluted by millions of gallons of untreated sewage and stormwater runoff. Entering coastal waters causes over 100 million global annual illnesses, but CWP has the potential to reach many more people on land via transfer in sea spray aerosol (SSA). Using 16S rRNA gene amplicon sequencing, we found sewage-associated bacteria in the polluted Tijuana River flowing into coastal waters and returning to land in marine aerosol. Tentative chemical identification from non-targeted tandem mass spectrometry identified anthropogenic compounds as chemical indicators of aerosolized CWP, but they were ubiquitous and present at highest concentrations in continental aerosol. Bacteria were better tracers of airborne CWP, and 40 tracer bacteria comprised up to 76% of the bacteria community in IB air. These findings confirm that CWP transfers in SSA and exposes many people along the coast. Climate change may exacerbate CWP with more extreme storms, and our findings call for minimizing CWP and investigating the health effects of airborne exposure.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7g36f980Test

المؤلفون: Kumar, Tanya, Bryant, MacKenzie, Cantrell, Kalen, Song, Jin, McDonald, Daniel, Tubb, Helena M, Farmer, Sawyer, Lukacz, Emily S, Brubaker, Linda, Knight, Rob

المصدر: mSystems. 8(1)

مصطلحات موضوعية: Microbiology, Biological Sciences, Genetics, Urologic Diseases, Clinical Research, Adult, Female, Humans, United States, RNA, Ribosomal, 16S, Reproducibility of Results, Quality of Life, Microbiota, Urine Specimen Collection, Urinary Tract Infections, Urinary Incontinence, 16S, microbiome, sample storage, urobiome, urogenital microbiome

الوصف: Replicability is a well-established challenge in microbiome research with a variety of contributing factors at all stages, from sample collection to code execution. Here, we focus on voided urine sample storage conditions for urogenital microbiome analysis. Using urine samples collected from 10 adult females, we investigated the microbiome preservation efficacy of AssayAssure Genelock (Genelock), compared with no preservative, under different temperature conditions. We varied temperature over 48 h in order to examine the impact of conditions samples may experience with home voided urine collection and shipping to a central biorepository. The following common lab and shipping conditions were investigated: -20°C, ambient temperature, 4°C, freeze-thaw cycle, and heat cycle. At 48 h, all samples were stored at -80°C until processing. After generating 16S rRNA gene amplicon sequencing data using the highly sensitive KatharoSeq protocol, we observed individual variation in both alpha and beta diversity metrics below interhuman differences, corroborating reports of individual microbiome variability in other specimen types. While there was no significant difference in beta diversity when comparing Genelock versus no preservative, we did observe a higher concordance with Genelock samples shipped at colder temperatures (-20°C and 4°C) when compared with the samples shipped at -20°C without preservative. Our results indicate that Genelock does not introduce a significant amount of microbial bias when used on a range of temperatures and is most effective at colder temperatures. IMPORTANCE The urogenital microbiome is an understudied yet important human microbiome niche. Research has been stimulated by the relatively recent discovery that urine is not sterile; urinary tract microbes have been linked to health problems, including urinary infections, incontinence, and cancer. The quality of life and economic impact of UTIs and urgency incontinence alone are enormous, with $3.5 billion and $82.6 billion, respectively, spent in the United States. annually. Given the low biomass of urine, novelty of the field, and limited reproducibility evidence, it is critical to study urine sample storage conditions to optimize scientific rigor. Efficient and reliable preservation methods inform methods for home self-sample collection and shipping, increasing the potential use in larger-scale studies. Here, we examined both buffer and temperature variation effects on 16S rRNA gene amplicon sequencing results from urogenital samples, providing data on the consequences of common storage methods on urogenital microbiome results.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/4m60d4xkTest

المؤلفون: Gauglitz, Julia M, West, Kiana A, Bittremieux, Wout, Williams, Candace L, Weldon, Kelly C, Panitchpakdi, Morgan, Di Ottavio, Francesca, Aceves, Christine M, Brown, Elizabeth, Sikora, Nicole C, Jarmusch, Alan K, Martino, Cameron, Tripathi, Anupriya, Meehan, Michael J, Dorrestein, Kathleen, Shaffer, Justin P, Coras, Roxana, Vargas, Fernando, Goldasich, Lindsay DeRight, Schwartz, Tara, Bryant, MacKenzie, Humphrey, Gregory, Johnson, Abigail J, Spengler, Katharina, Belda-Ferre, Pedro, Diaz, Edgar, McDonald, Daniel, Zhu, Qiyun, Elijah, Emmanuel O, Wang, Mingxun, Marotz, Clarisse, Sprecher, Kate E, Vargas-Robles, Daniela, Withrow, Dana, Ackermann, Gail, Herrera, Lourdes, Bradford, Barry J, Marques, Lucas Maciel Mauriz, Amaral, Juliano Geraldo, Silva, Rodrigo Moreira, Veras, Flavio Protasio, Cunha, Thiago Mattar, Oliveira, Rene Donizeti Ribeiro, Louzada-Junior, Paulo, Mills, Robert H, Piotrowski, Paulina K, Servetas, Stephanie L, Da Silva, Sandra M, Jones, Christina M, Lin, Nancy J, Lippa, Katrice A, Jackson, Scott A, Daouk, Rima Kaddurah, Galasko, Douglas, Dulai, Parambir S, Kalashnikova, Tatyana I, Wittenberg, Curt, Terkeltaub, Robert, Doty, Megan M, Kim, Jae H, Rhee, Kyung E, Beauchamp-Walters, Julia, Wright, Kenneth P, Dominguez-Bello, Maria Gloria, Manary, Mark, Oliveira, Michelli F, Boland, Brigid S, Lopes, Norberto Peporine, Guma, Monica, Swafford, Austin D, Dutton, Rachel J, Knight, Rob, Dorrestein, Pieter C

المصدر: Nature Biotechnology. 40(12)

مصطلحات موضوعية: Medical Biochemistry and Metabolomics, Analytical Chemistry, Biomedical and Clinical Sciences, Chemical Sciences, Neurodegenerative, Neurosciences, Nutrition, Multiple Sclerosis, Brain Disorders, Humans, Tandem Mass Spectrometry, Metadata, Metabolomics

الوصف: Human untargeted metabolomics studies annotate only ~10% of molecular features. We introduce reference-data-driven analysis to match metabolomics tandem mass spectrometry (MS/MS) data against metadata-annotated source data as a pseudo-MS/MS reference library. Applying this approach to food source data, we show that it increases MS/MS spectral usage 5.1-fold over conventional structural MS/MS library matches and allows empirical assessment of dietary patterns from untargeted data.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/79t6410zTest

المؤلفون: Shaffer, Justin P, Nothias, Louis-Félix, Thompson, Luke R, Sanders, Jon G, Salido, Rodolfo A, Couvillion, Sneha P, Brejnrod, Asker D, Lejzerowicz, Franck, Haiminen, Niina, Huang, Shi, Lutz, Holly L, Zhu, Qiyun, Martino, Cameron, Morton, James T, Karthikeyan, Smruthi, Nothias-Esposito, Mélissa, Dührkop, Kai, Böcker, Sebastian, Kim, Hyun Woo, Aksenov, Alexander A, Bittremieux, Wout, Minich, Jeremiah J, Marotz, Clarisse, Bryant, MacKenzie M, Sanders, Karenina, Schwartz, Tara, Humphrey, Greg, Vásquez-Baeza, Yoshiki, Tripathi, Anupriya, Parida, Laxmi, Carrieri, Anna Paola, Beck, Kristen L, Das, Promi, González, Antonio, McDonald, Daniel, Ladau, Joshua, Karst, Søren M, Albertsen, Mads, Ackermann, Gail, DeReus, Jeff, Thomas, Torsten, Petras, Daniel, Shade, Ashley, Stegen, James, Song, Se Jin, Metz, Thomas O, Swafford, Austin D, Dorrestein, Pieter C, Jansson, Janet K, Gilbert, Jack A, Knight, Rob

المصدر: Nature Microbiology. 7(12)

مصطلحات موضوعية: Microbiology, Biological Sciences, Microbiome, Life Below Water, Animals, Microbiota, Metagenome, Metagenomics, Earth, Planet, Soil, Earth Microbiome Project 500 (EMP500) Consortium, Medical Microbiology

الوصف: Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.

الوصول الحر: https://escholarship.org/uc/item/16b2x6fgTest

المؤلفون: Shaffer, Justin P, Carpenter, Carolina S, Martino, Cameron, Salido, Rodolfo A, Minich, Jeremiah J, Bryant, MacKenzie, Sanders, Karenina, Schwartz, Tara, Humphrey, Gregory, Swafford, Austin D, Knight, Rob

المصدر: BioTechniques. 73(1)

مصطلحات موضوعية: Microbiology, Biological Sciences, Genetics, Clinical Research, Human Genome, Infection, Bacteria, High-Throughput Nucleotide Sequencing, Humans, Metagenomics, Microbiota, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Earth Microbiome Project, high-throughput sequencing, Katharoseq, Macherey-Nagel, MagAttract PowerSoil, mock community, mycobiome, rRNA, whole genome sequencing, Technology, Bioinformatics, Biological sciences

الوصف: Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/54r6s3bjTest

المؤلفون: Cantú, Victor J, Salido, Rodolfo A, Huang, Shi, Rahman, Gibraan, Tsai, Rebecca, Valentine, Holly, Magallanes, Celestine G, Aigner, Stefan, Baer, Nathan A, Barber, Tom, Belda-Ferre, Pedro, Betty, Maryann, Bryant, MacKenzie, Maya, Martín Casas, Castro-Martínez, Anelizze, Chacón, Marisol, Cheung, Willi, Crescini, Evelyn S, De Hoff, Peter, Eisner, Emily, Farmer, Sawyer, Hakim, Abbas, Kohn, Laura, Lastrella, Alma L, Lawrence, Elijah S, Morgan, Sydney C, Ngo, Toan T, Nouri, Alhakam, Plascencia, Ashley, Ruiz, Christopher A, Sathe, Shashank, Seaver, Phoebe, Shwartz, Tara, Smoot, Elizabeth W, Ostrander, R Tyler, Valles, Thomas, Yeo, Gene W, Laurent, Louise C, Fielding-Miller, Rebecca, Knight, Rob

المصدر: mSystems. 7(3)

مصطلحات موضوعية: Vaccine Related, Clinical Research, Lung, Prevention, Pneumonia & Influenza, Biodefense, Pneumonia, Infectious Diseases, Emerging Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Humans, SARS-CoV-2, COVID-19, Housing, RNA, Ribosomal, 16S, Respiratory Aerosols and Droplets, RT-qPCR, Rothia, built-environment, environmental monitoring, isolation, quarantine, surface sampling, swab

الوصف: Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions and to test whether our past observations linking SARS-CoV-2 abundance to Rothia sp. in hospitals also hold in a residential setting, we performed a detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences (to assess the bacterial community at each location), and to the Cq value of the contemporaneous clinical test. Our results showed that the highest SARS-CoV-2 load in this setting is on touched surfaces, such as light switches and faucets, but a detectable signal was present in many untouched surfaces (e.g., floors) that may be more relevant in settings, such as schools where mask-wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g., touching a light switch) or indirectly (e.g., by droplets or aerosols settling). We found the highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g., in schools, where students did not touch the light switches and also wore masks such that they had no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/7gz851k8Test

المؤلفون: Mills, Robert H, Dulai, Parambir S, Vázquez-Baeza, Yoshiki, Sauceda, Consuelo, Daniel, Noëmie, Gerner, Romana R, Batachari, Lakshmi E, Malfavon, Mario, Zhu, Qiyun, Weldon, Kelly, Humphrey, Greg, Carrillo-Terrazas, Marvic, Goldasich, Lindsay DeRight, Bryant, MacKenzie, Raffatellu, Manuela, Quinn, Robert A, Gewirtz, Andrew T, Chassaing, Benoit, Chu, Hiutung, Sandborn, William J, Dorrestein, Pieter C, Knight, Rob, Gonzalez, David J

المصدر: Nature Microbiology. 7(2)

مصطلحات موضوعية: Microbiology, Biological Sciences, Digestive Diseases, Autoimmune Disease, Biotechnology, Inflammatory Bowel Disease, 2.1 Biological and endogenous factors, Aetiology, Oral and gastrointestinal, Adult, Animals, Bacterial Proteins, Bacteroides, Cohort Studies, Colitis, Ulcerative, Feces, Female, Gastrointestinal Microbiome, Humans, Longitudinal Studies, Male, Metagenome, Metagenomics, Mice, Middle Aged, Peptide Hydrolases, Proteomics, Severity of Illness Index, Medical Microbiology

الوصف: Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/881291j7Test

المؤلفون: Cantú, Victor J, Salido, Rodolfo A, Huang, Shi, Rahman, Gibraan, Tsai, Rebecca, Valentine, Holly, Magallanes, Celestine G, Aigner, Stefan, Baer, Nathan A, Barber, Tom, Belda-Ferre, Pedro, Betty, Maryann, Bryant, MacKenzie, Maya, Martin Casas, Castro-Martínez, Anelizze, Chacón, Marisol, Cheung, Willi, Crescini, Evelyn S, De Hoff, Peter, Eisner, Emily, Farmer, Sawyer, Hakim, Abbas, Kohn, Laura, Lastrella, Alma L, Lawrence, Elijah S, Morgan, Sydney C, Ngo, Toan T, Nouri, Alhakam, Ostrander, R Tyler, Plascencia, Ashley, Ruiz, Christopher A, Sathe, Shashank, Seaver, Phoebe, Shwartz, Tara, Smoot, Elizabeth W, Valles, Thomas, Yeo, Gene W, Laurent, Louise C, Fielding-Miller, Rebecca, Knight, Rob

مصطلحات موضوعية: Vaccine Related, Prevention, Emerging Infectious Diseases, Pneumonia & Influenza, Lung, Infectious Diseases, Pneumonia, Biodefense, Clinical Research, 2.2 Factors relating to the physical environment, Aetiology, Infection, Good Health and Well Being

الوصف: UNLABELLED: Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association. IMPORTANCE: Surface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.

الوصول الحر: https://escholarship.org/uc/item/4cd313m0Test