Nursing home wastewater surveillance for early warning of SARS-CoV-2-positive occupants-Insights from a pilot project at 8 facilities.

BACKGROUND: Wastewater surveillance for SARS-CoV-2 has been used widely in the United States for indication of community incidence during the COVID-19 pandemic, but less is known about the feasibility of its use on a building level in nursing homes to provide early warning and prevent transmission. METHODS: A pilot study was conducted at 8 Department of Veterans Affairs nursing homes across the United States to examine operational feasibility. Wastewater from the participating facilities was sampled daily during the week for 6 months (January 11, 2021-July 2, 2021) and analyzed for SARS-CoV-2 genetic material. Wastewater results were compared to new SARS-CoV-2 infections in nursing home residents and employees to determine if wastewater surveillance could provide early warning of a COVID-19-positive occupant. RESULTS: All 8 nursing homes had wastewater samples positive for SARS-CoV-2 and COVID-19-positive occupants. The sensitivity of wastewater surveillance for early warning of COVID-19-positive residents was 60% (3/5) and for COVID-19-positive employees was 46% (13/28). CONCLUSIONS: Wastewater surveillance may provide additional information for reinforcing infection control practices and lead to preventing transmission in a setting with high-risk residents. The low sensitivity for early warning in this real-world pilot highlights limitations and insights for applicability in buildings.

Efficacy of a filtered far-UVC handheld disinfection device in reducing the microbial bioburden of hospital surfaces.

BACKGROUND: The filtered far-UV-C (FFUV) handheld disinfection device is a small portable device that emits far UV-C at 222 nm. The objective of this study was to evaluate the device's ability to kill microbial pathogens on hospital surfaces and compare it to manual disinfection using germicidal sodium hypochlorite wipes. METHODS: A total of 344 observations (4 observations from 86 objects' surfaces) were sampled with 2 paired samples per surface: a pre- and a post-sodium hypochlorite and FFUV sample. The results were analyzed via a Bayesian multilevel negative binomial regression model. RESULTS: The estimated mean colony counts for the sodium hypochlorite control and treatment groups were 20.5 (95% uncertainty interval: 11.7-36.0) and 0.1 (0.0-0.2) colony forming units (CFUs), respectively. The FFUV control and treatment groups had mean colony counts of 22.2 (12.5-40.1) and 4.1 (2.3-7.2) CFUs. The sodium hypochlorite group and the FFUV group had an estimated 99.4% (99.0%-99.7%) and 81.4% (76.2%-85.7%) reduction in colony counts, respectively. CONCLUSIONS: The FFUV handheld device effectively reduced the microbial bioburden on surfaces in the health care setting. The major benefit of FFUV is likely seen when manual disinfection is not possible or when supplementing cleaners or disinfectants with the low-level disinfection properties.

miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism.

Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis-H. schachtii interactions.

Establishment and maintenance of DNA methylation in nematode feeding sites.

A growing body of evidence indicates that epigenetic mechanisms, particularly DNA methylation, play key regulatory roles in plant-nematode interactions. Nevertheless, the transcriptional activity of key genes mediating DNA methylation and active demethylation in the nematode feeding sites remains largely unknown. Here, we profiled the promoter activity of 12 genes involved in maintenance and de novo establishment of DNA methylation and active demethylation in the syncytia and galls induced respectively by the cyst nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita in Arabidopsis roots. The promoter activity assays revealed that expression of the CG-context methyltransferases is restricted to feeding site formation and development stages. Chromomethylase1 (CMT1), CMT2, and CMT3 and Domains Rearranged Methyltransferase2 (DRM2) and DRM3, which mediate non-CG methylation, showed similar and distinct expression patterns in the syncytia and galls at various time points. Notably, the promoters of various DNA demethylases were more active in galls as compared with the syncytia, particularly during the early stage of infection. Mutants impaired in CG or CHH methylation similarly enhanced plant susceptibility to H. schachtii and M. incognita, whereas mutants impaired in CHG methylation reduced plant susceptibility only to M. incognita. Interestingly, hypermethylated mutants defective in active DNA demethylation exhibited contrasting responses to infection by H. schachtii and M. incognita, a finding most likely associated with differential regulation of defense-related genes in these mutants upon nematode infection. Our results point to methylation-dependent mechanisms regulating plant responses to infection by cyst and root-knot nematodes.

Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones.

DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using ß-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development.

Phytopathogen-induced changes to plant methylomes.

DNA methylation is a dynamic and reversible type of epigenetic mark that contributes to cellular physiology by affecting transcription activity, transposon mobility and genome stability. When plants are infected with pathogens, plant DNA methylation patterns can change, indicating an epigenetic interplay between plant host and pathogen. In most cases methylation can change susceptibility. While DNA hypomethylation appears to be a common phenomenon during the susceptible interaction, the levels and patterns of hypomethylation in transposable elements and genic regions may mediate distinct responses against various plant pathogens. The effect of DNA methylation on the plant immune response and other cellular activities and molecular functions is established by localized differential DNA methylation via cis-regulatory mechanisms as well as through trans-acting mechanisms. Understanding the epigenetic differences that control the phenotypic variations between susceptible and resistant interactions should facilitate the identification of new sources of resistance mediated by epigenetic mechanisms, which can be exploited to endow pathogen resistance to crops.

Transcriptional activity of transposable elements may contribute to gene expression changes in the syncytium formed by cyst nematode in arabidopsis roots.

Transposable elements (TEs) are mobile genetic materials that constitute a large fraction of plant genomes. Recent experimental evidences indicate that TEs can play key regulatory roles in controlling the expression of adjacent genes during plant development and stress responses. Nevertheless, information about the transcriptional activity of TEs and their impact on proximal genes during plant-nematode interaction remains largely unknown. Here, we identify of differentially expressed TEs and report their possible influence on the expression of nearby genes during the susceptible interaction between the beet cyst nematode Heterodera schachtii and Arabidopsis thaliana. Analysis of our RNA-seq data of H. schachtii-infected roots, and the corresponding non-infected controls, resulted in the identification of 99 and 93 differentially expressed TEs at 5 and 10 d post infection, respectively. More than 2-thirds of these TEs were activated, suggesting that H. schachtii infection induces TE activation to a much greater degree than repression. Remarkably, the majority of these TEs were located within 2 kb of protein-coding genes, many of these genes were previously found to change expression in the H. schachtii-induced feeding sites. Taken together, our analysis provides novel insight into a possible role of actively transcribed TEs in the regulation of gene transcription in the nematode feeding sites during H. schachtii parasitism of Arabidopsis.