Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes, which play a role in some space-derived health disorders. However, documenting the response of microbiota to spaceflight has been difficult thus far due to mission constraints that lead to limited sampling. Here, we executed a six-month longitudinal study centered on a three-day flight to quantify the high-resolution microbiome response to spaceflight. Via paired metagenomics and metatranscriptomics alongside single immune profiling, we resolved a microbiome "architecture" of spaceflight characterized by time-dependent and taxonomically divergent microbiome alterations across 750 samples and ten body sites. We observed pan-phyletic viral activation and signs of persistent changes that, in the oral microbiome, yielded plaque-associated pathobionts with strong associations to immune cell gene expression. Further, we found enrichments of microbial genes associated with antibiotic production, toxin-antitoxin systems, and stress response enriched universally across the body sites. We also used strain-level tracking to measure the potential propagation of microbial species from the crew members to each other and the environment, identifying microbes that were prone to seed the capsule surface and move between the crew. Finally, we identified associations between microbiome and host immune cell shifts, proposing both a microbiome axis of immune changes during flight as well as the sources of some of those changes. In summary, these datasets and methods reveal connections between crew immunology, the microbiome, and their likely drivers and lay the groundwork for future microbiome studies of spaceflight.

Biopsy of the Parietal Branch of the Superficial Temporal Artery for the Diagnosis of Giant Cell Arteritis

BACKGROUND

Biopsy of the superficial temporal artery (STA) is central to the diagnosis of giant cell arteritis (GCA), but determining the ideal biopsy site along the course of the STA continues to be a challenge. Traditionally, the frontal branch or preauricular region of the STA is biopsied because of their accessibility, but biopsy at these locations can produce visible cosmetic defects and social disruption that can be distressing to patients, as well as increase the likelihood of adverse events such as injury to the facial nerve. The authors describe a surgical technique of biopsy of the parietal branch of the STA to improve the patient's perioperative and postoperative experience.

METHODS

In this retrospective review, 24 patients with clinical suspicion of GCA who underwent biopsy of the parietal branch of the STA were identified. Patients underwent mapping of the branches of the STA with Doppler ultrasound before the procedure. Biopsy of the parietal branch of the STA was conducted using a CO 2 laser.

RESULTS

Twenty-four patients underwent biopsy of the parietal branch of the STA. Two patients were diagnosed on histopathology with GCA. All patients tolerated the procedure well and without complications.

CONCLUSION

Application of preoperative Doppler ultrasound mapping, use of a CO 2 laser for incisions and hemostasis, and selection of the parietal branch allowed for improved cosmetic outcomes, no associated adverse events, and improved overall patient experience. The authors advocate biopsy of the parietal branch of the superficial temporal artery for the diagnosis of GCA in the absence of contraindications.

Collection of Biospecimens from the Inspiration4 Mission Establishes the Standards for the Space Omics and Medical Atlas (SOMA)

The SpaceX Inspiration4 mission provided a unique opportunity to study the impact of spaceflight on the human body. Biospecimen samples were collected from the crew at different stages of the mission, including before (L-92, L-44, L-3 days), during (FD1, FD2, FD3), and after (R+1, R+45, R+82, R+194 days) spaceflight, creating a longitudinal sample set. The collection process included samples such as venous blood, capillary dried blood spot cards, saliva, urine, stool, body swabs, capsule swabs, SpaceX Dragon capsule HEPA filter, and skin biopsies, which were processed to obtain aliquots of serum, plasma, extracellular vesicles, and peripheral blood mononuclear cells. All samples were then processed in clinical and research laboratories for optimal isolation and testing of DNA, RNA, proteins, metabolites, and other biomolecules. This paper describes the complete set of collected biospecimens, their processing steps, and long-term biobanking methods, which enable future molecular assays and testing. As such, this study details a robust framework for obtaining and preserving high-quality human, microbial, and environmental samples for aerospace medicine in the Space Omics and Medical Atlas (SOMA) initiative, which can also aid future experiments in human spaceflight and space biology.

Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments

Pathogenic bacteria and viruses in medical environments can lead to treatment complications and hospital-acquired infections. Current disinfection protocols do not address hard-to-access areas or may be beyond line-of-sight treatment, such as with ultraviolet radiation. The COVID-19 pandemic further underscores the demand for reliable and effective disinfection methods to sterilize a wide array of surfaces and to keep up with the supply of personal protective equipment (PPE). We tested the efficacy of Sani Sport ozone devices to treat hospital equipment and surfaces for killing Escherichia coli, Enterococcus faecalis, Bacillus subtilis, and Deinococcus radiodurans by assessing Colony Forming Units (CFUs) after 30 min, 1 h, and 2 h of ozone treatment. Further gene expression analysis was conducted on live E. coli K12 immediately post treatment to understand the oxidative damage stress response transcriptome profile. Ozone treatment was also used to degrade synthetic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA as assessed by qPCR CT values. We observed significant and rapid killing of medically relevant and environmental bacteria across four surfaces (blankets, catheter, remotes, and syringes) within 30 min, and up to a 99% reduction in viable bacteria at the end of 2 h treatment cycles. RNA-seq analysis of E. coli K12 revealed 447 differentially expressed genes in response to ozone treatment and an enrichment for oxidative stress response and related pathways. RNA degradation of synthetic SARS-CoV-2 RNA was seen an hour into ozone treatment as compared to non-treated controls, and a non-replicative form of the virus was shown to have significant RNA degradation at 30 min. These results show the strong promise of ozone treatment of surfaces for reducing the risk of hospital-acquired infections and as a method for degradation of SARS-CoV-2 RNA.

The Lowly Chalazion

Chalazia are localized cysts of chronic lipogranulomatous inflammation arising from the obstruction of sebaceous glands of the eyelid tarsal plate, including the Meibomian gland (deep chalazion) or Zeis gland (superficial chalazion). This disease entity is differentiated from the hordeolum (stye), an acute purulent localized swelling of the eyelid often associated with an eyelash follicle, Zeis gland, or Moll gland obstruction and infection. Ambiguously, the chalazion, hordeolum, and blepharitis are commonly categorized and described on a continuum in the literature. While it is one of the most common eyelid disorders across all age demographics, the chalazion remains largely understudied and pathophysiological, epidemiological, and therapeutic findings exist fragmented in the literature. We discuss current understandings of the chalazion and provide current best practice guidelines supported by clinical anecdotal evidence.

A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling

While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.

System-wide transcriptome damage and tissue identity loss in COVID-19 patients

The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body-wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.

Sutureless Transconjunctival Insertion of Eyelid Weights: A Novel Technique

PURPOSE

To describe a novel surgical technique for implanting eyelid weights via a sutureless transconjunctival approach. In comparison to the traditional supratarsal crease approach, this technique does not involve any external incisions or suture placement. The procedure can reduce surgical time and complications associated with the traditional external approach.

METHODS

This case series includes 13 patients who underwent eyelid weight placement via the transconjunctival approach for paralytic lagophthalmos secondary to facial nerve paralysis (12 patients had unilateral paralysis and 1 patient had bilateral) with a total of 14 eyelid weights placed. The procedures were performed at an outpatient office-based surgical center. All procedures were performed or supervised by the same surgeon. Patients were followed for an average 6-month postoperative period for postoperative complications.

RESULTS

The sutureless transconjunctival approach to eyelid weight insertion was successful in achieving the desired functional and aesthetic outcomes. Patients undergoing this technique avoided the discomfort of postoperative suture removal. All patients achieved comparable outcomes postoperatively. There were no complications reported across the 13 patients throughout the 6-month postoperative period.

CONCLUSIONS

This case series demonstrates that the transconjunctival approach for metal eyelid weight insertion is practical, relatively easy to perform, and associated with functional outcomes that are comparable to those achieved with the traditional approach, however, without external incision or placement of sutures.

Congenital tooth-bearing tumor of the eyelid leading to lacrimal system obstruction

PURPOSE

We present an unusual case of a congenital lesion presenting with concomitant chronic dacryocystitis. The clinical presentation, examination, management, and histopathology are reviewed.

OBSERVATIONS

A healthy male infant born at 37 weeks gestation presented with an isolated painless 5mm congenital mass of the left medial lower eyelid. Parents also reported episodic epiphora and discharge from the left eye. A surgical excision of the mass revealed an underlying dacryocystitis and the presence of a formed tooth. A dacryocystorhinostomy was performed together with a repair of the soft tissue defect. Histopathology revealed components of disorganized epithelial and mesenchymal tissues including a tooth, skeletal muscle, fat, fibrous tissue, nonkeratinized epithelium, and myelinated nerves. A diagnosis of an odontogenic choristoma of the eyelid was made. Furthermore, a lacrimal sac culture was positive for oxacillin-susceptible Staphylococcus aureus with pathological evidence of chronic dacryocystitis.

CONCLUSIONS AND IMPORTANCE

Odontogenic choristoma is a very rare finding in the periocular region with only a few cases reported in the literature. Awareness of clinical findings from this case may allow for a more accurate clinical diagnosis and understanding of the embryologic mechanisms underpinning eyelid and nasolacrimal development. Timely management of this condition is critical to ensure normal oculofacial development and prevent future complications.

A Rapid, Isothermal, and Point-of-Care System for COVID-19 Diagnostics

The COVID-19 pandemic has had a profound, detrimental effect on economies and societies worldwide. Where the pandemic has been controlled, extremely high rates of diagnostic testing for the SARS-CoV-2 virus have proven critical, enabling isolation of cases and contact tracing. Recently, diagnostic testing has been supplemented with wastewater measures to evaluate the degree to which communities have infections. Whereas much testing has been done through traditional, centralized, clinical, or environmental laboratory methods, point-of-care testing has proven successful in reducing time to result. As the pandemic progresses and becomes more broadly distributed, further decentralization of diagnostic testing will be helpful to mitigate its spread. This will be particularly both challenging and critical in settings with limited resources due to lack of medical infrastructure and expertise as well as requirements to return results quickly. In this article, we validate the tiny isothermal nucleic acid quantification system (TINY) and a novel loop-mediated isothermal amplification (LAMP)-based assay for the point-of-care diagnosis of SARS-CoV-2 infection in humans and also for in-the-field, point-of-collection surveillance of wastewater. The TINY system is portable and designed for use in settings with limited resources. It can be powered by electrical, solar, or thermal energy and is robust against interruptions in services. These applied testing examples demonstrate that this novel detection platform is a simpler procedure than reverse-transcription quantitative polymerase chain reaction, and moreover, this TINY instrument and LAMP assay combination has the potential to effectively provide both point-of-care diagnosis of individuals and point-of-collection environmental surveillance using wastewater.

Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications

As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.