Metagenomic analysis during capecitabine therapy reveals microbial chemoprotective mechanisms and predicts drug toxicity in colorectal cancer patients.

Purpose: Unpredictable chemotherapy side effects are a major barrier to successful treatment. Cell culture and mouse experiments indicate that the gut microbiota is influenced by and influences anti-cancer drugs. However, metagenomic data from patients paired to careful side effect monitoring remains limited. Herein, we focus on the oral fluoropyrimidine capecitabine (CAP). We investigate CAP-microbiome interactions through metagenomic sequencing of longitudinal stool sampling from a cohort of advanced colorectal cancer (CRC) patients. Methods: We established a prospective cohort study including 56 patients with advanced CRC treated with CAP monotherapy across 4 centers in the Netherlands. Stool samples and clinical questionnaires were collected at baseline, during cycle 3, and post-treatment. Metagenomic sequencing to assess microbial community structure and gene abundance was paired with transposon mutagenesis, targeted gene deletion, and media supplementation experiments. An independent US cohort was used for model validation. Results: CAP treatment significantly altered gut microbial composition and pathway abundance, enriching for menaquinol (vitamin K2) biosynthesis genes. Transposon library screens, targeted gene deletions, and media supplementation confirmed that menaquinol biosynthesis protects Escherichia coli from drug toxicity. Microbial menaquinol biosynthesis genes were associated with decreased peripheral sensory neuropathy. Machine learning models trained in this cohort predicted hand-foot syndrome and dose reductions in an independent cohort. Conclusion: These results suggest treatment-associated increases in microbial vitamin biosynthesis serve a chemoprotective role for bacterial and host cells, with implications for toxicities outside the gastrointestinal tract. We provide a proof-of-concept for the use of microbiome profiling and machine learning to predict drug toxicities across independent cohorts. These observations provide a foundation for future human intervention studies, more in-depth mechanistic dissection in preclinical models, and extension to other cancer treatments.

Human Impacts on Great Lakes Walleye Sander vitreus Structure, Diversity and Local Adaptation.

Artificial propagation and wild release may influence the genetic integrity of wild populations. This practice has been prevalent in fisheries for centuries and is often termed 'stocking'. In the Laurentian Great Lakes (Great Lakes here-on), walleye populations faced declines from the 1950s to the 1970s, prompting extensive stocking efforts for restoration. By the mid-2010s, walleye populations showed signs of recovery, but the genetic legacy of stocking on population structure at the genomic level remains unclear. Using a dataset of 45,600 genome-aligned SNP loci genotyped in 1075 walleye individuals, we investigated the genetic impacts of over 50 years of stocking across the Great Lakes. Population structure was associated with both natural geographic barriers and stocking from non-native sources. Admixture between Lake Erie walleye and walleye from the re-populated Tittabawassee River indicate that stocking may have re-distributed putatively adaptive alleles around the Great Lakes. Genome scans identified FST outliers and evidence of selective sweeps, indicating local adaptation of spawning populations is likely. Notably, one genomic region showed strong differentiation between Muskegon River and walleye from the Tittabawassee River, which was re-populated by Muskegon strain walleye, suggesting admixture and selection both impact the observed genetic diversity. Overall, our study underscores how artificial propagation and translocations can significantly alter the evolutionary trajectory of populations. The findings highlight the complex interplay between stocking practices and population genetic diversity, emphasising the need for careful management strategies to preserve the genetic integrity of wild populations amidst conservation efforts.

SARS-CoV-2 Variants May Affect Saliva RT-PCR Assay Sensitivity.

BACKGROUND: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants demonstrate predilection for different regions of the respiratory tract. While saliva-based reverse transcription-polymerase chain reaction (RT-PCR) testing is a convenient, cost-effective alternative to nasopharyngeal swabs (NPS), few studies to date have investigated whether saliva sensitivity differs across variants of concern. METHODS: SARS-CoV-2 RT-PCR was performed on paired NPS and saliva specimens collected from individuals with acute coronavirus disease 2019 (COVID-19) symptoms or exposure to a COVID-19 household contact. Viral genome sequencing of NPS specimens and Los Angeles County surveillance data were used to determine the variant of infection. Saliva sensitivity was calculated using NPS-positive RT-PCR as the reference standard. Factors contributing to the likelihood of saliva SARS-CoV-2 RT-PCR positivity were evaluated with univariate and multivariable analyses. RESULTS: Between June 2020 and December 2022, 548 saliva samples paired with SARS-CoV-2 positive NPS samples were tested by RT-PCR. Overall, saliva sensitivity for SARS-CoV-2 detection was 61.7% (95% CI, 57.6%-65.7%). Sensitivity was highest with Delta infection (79.6%) compared to pre-Delta (58.5%) and Omicron (61.5%) (P = 0.003 and 0.01, respectively). Saliva sensitivity was higher in symptomatic individuals across all variants compared to asymptomatic cases [pre-Delta 80.6% vs 48.3% (P < 0.001), Delta 100% vs 72.5% (P = 0.03), Omicron 78.7% vs 51.2% (P < 0.001)]. Infection with Delta, symptoms, and high NPS viral load were independently associated with 2.99-, 3.45-, and 4.0-fold higher odds of SARS-CoV-2 detection by saliva-based RT-PCR (P = 0.004, <0.001, and <0.001), respectively. CONCLUSIONS: As new variants emerge, evaluating saliva-based testing approaches may be crucial to ensure effective virus detection.

Genotype Characterization and MiRNA Expression Profiling in Usher Syndrome Cell Lines.

Usher syndrome (USH) is an inherited disorder characterized by sensorineural hearing loss (SNHL), retinitis pigmentosa (RP)-related vision loss, and vestibular dysfunction. USH presents itself as three distinct clinical types, 1, 2, and 3, with no biomarker for early detection. This study aimed to explore whether microRNA (miRNA) expression in USH cell lines is dysregulated compared to the miRNA expression pattern in a cell line derived from a healthy human subject. Lymphocytes from USH patients and healthy individuals were isolated and transformed into stable cell lines using Epstein-Barr virus (EBV). DNA from these cell lines was sequenced using a targeted panel to identify gene variants associated with USH types 1, 2, and 3. Microarray analysis was performed on RNA from both USH and control cell lines using NanoString miRNA microarray technology. Dysregulated miRNAs identified by the microarray were validated using droplet digital PCR technology. DNA sequencing revealed that two USH patients had USH type 1 with gene variants in USH1B (MYO7A) and USH1D (CDH23), while the other two patients were classified as USH type 2 (USH2A) and USH type 3 (CLRN-1), respectively. The NanoString miRNA microarray detected 92 differentially expressed miRNAs in USH cell lines compared to controls. Significantly altered miRNAs exhibited at least a twofold increase or decrease with a p value below 0.05. Among these miRNAs, 20 were specific to USH1, 14 to USH2, and 5 to USH3. Three miRNAs that are known as miRNA-183 family which are crucial for inner ear and retina development, have been significantly downregulated as compared to control cells. Subsequently, droplet digital PCR assays confirmed the dysregulation of the 12 most prominent miRNAs in USH cell lines. This study identifies several miRNA signatures in USH cell lines which may have potential utility in Usher syndrome identification.

Shifts in receptors during submergence of an encephalitic arbovirus.

Western equine encephalitis virus (WEEV) is an arthropod-borne virus (arbovirus) that frequently caused major outbreaks of encephalitis in humans and horses in the early twentieth century, but the frequency of outbreaks has since decreased markedly, and strains of this alphavirus isolated in the past two decades are less virulent in mammals than strains isolated in the 1930s and 1940s1-3. The basis for this phenotypic change in WEEV strains and coincident decrease in epizootic activity (known as viral submergence3) is unclear, as is the possibility of re-emergence of highly virulent strains. Here we identify protocadherin 10 (PCDH10) as a cellular receptor for WEEV. We show that multiple highly virulent ancestral WEEV strains isolated in the 1930s and 1940s, in addition to binding human PCDH10, could also bind very low-density lipoprotein receptor (VLDLR) and apolipoprotein E receptor 2 (ApoER2), which are recognized by another encephalitic alphavirus as receptors4. However, whereas most of the WEEV strains that we examined bind to PCDH10, a contemporary strain has lost the ability to recognize mammalian PCDH10 while retaining the ability to bind avian receptors, suggesting WEEV adaptation to a main reservoir host during enzootic circulation. PCDH10 supports WEEV E2-E1 glycoprotein-mediated infection of primary mouse cortical neurons, and administration of a soluble form of PCDH10 protects mice from lethal WEEV challenge. Our results have implications for the development of medical countermeasures and for risk assessment for re-emerging WEEV strains.

Assessing the prevalence of workplace telepressure on resident and attending physicians: A validated scale.

Background: Physician wellbeing and burnout are significant threats to the healthcare workforce. Mobile electronic medical record access and smartphones allow for efficient communication in healthcare but may lead to workplace telepressure (WPT). Methods: An IRB-approved survey related to five domains of burnout [WPT, smartphone usage, boundary control, and psychologic detachment] was circulated. Internal medicine and general surgery faculty and residents were surveyed between 3/2021 and 6/2021. Survey results were analyzed for internal consistency with a Cronbach alpha coefficient and validation against a known physician burnout scale. Results: The domains were internally valid with a Cronbach alpha of 0.888. Validation against the physician burnout scale was significantly correlated with WPT domains but was overall positively correlated across domains. Surgical trainees reported the highest burnout rate related to every domain. Conclusion: Survey-based WPT burnout scales provide insight into the daily pressures on physicians. Targeted interventions to limit WPT are needed to improve physician wellbeing.

Barriers to Incident Reporting by Physicians: A Survey of Surgical Residents and Attending Physicians.

Objectives Incident reporting is vital to a culture of safety; however, physicians report at an alarmingly low rate. This study aimed to identify barriers to incident reporting among surgeons at a quaternary care center. Methods A survey was created utilizing components of the Agency for Healthcare Research and Quality (AHRQ) validated survey on patient safety culture. This tool was distributed to residents and attending physicians in general surgery and urology at a single academic medical center. Responses were de-identified and recorded for data analysis using REDCap (Research Electronic Data Capture) database tool (Vanderbilt University, Nashville, Tennessee, United States). Results We received 39 survey responses from 116 residents and attending physicians (34% response rate), including nine urologists and 30 general surgeons (24 attendings, 15 residents). Residents and attendings feel the person is being written up and not the issue (67%) and that there is a lack of feedback after changes are implemented (64%), though most believe adequate action is taken to address patient safety concerns (72%). Most do not report near-misses (64%), only significant adverse events (59%). Residents are likely to stay silent when patient safety events involve those in authority (60%). Faculty feel those in authority are open to patient safety concerns (67%), though residents feel neutral (47%) or disagree (33%). Conclusion Underreporting of incidents among physicians remains multifaceted and complex, from fear of retaliation to lack of feedback. Residents tend to feel less comfortable addressing authority figures when concerned about patient safety. While misunderstanding still exists about the applications and utility of incident reporting, a focus on quality over quantity could afford more meaningful progress toward high reliability in healthcare.

loco-pipe: an automated pipeline for population genomics with low-coverage whole-genome sequencing.

Summary: We developed loco-pipe, a Snakemake pipeline that seamlessly streamlines a set of essential population genomic analyses for low-coverage whole genome sequencing (lcWGS) data. loco-pipe is highly automated, easily customizable, massively parallelized, and thus is a valuable tool for both new and experienced users of lcWGS. Availability and implementation: loco-pipe is published under the GPLv3. It is freely available on GitHub (github.com/sudmantlab/loco-pipe) and archived on Zenodo (doi.org/10.5281/zenodo.10425920).

Effects of riparian vegetation restoration and environmental context on ecosystem functioning in tropical streams of southeastern Brazil.

Tropical stream ecosystems are under increasing human pressure, making the development of effective restoration approaches and expanding knowledge in this field urgent. This study evaluated the impact of riparian vegetation restoration and environmental context on stream ecosystem functioning by measuring key ecosystem functions - gross primary production (GPP), ecosystem respiration (ER), and nutrient uptake of ammonium and soluble reactive phosphorus - across ten tropical streams in southeastern Brazil. The streams represented a gradient from clearcut areas (impacted reaches) to relatively pristine conditions (reference reaches), including intermediate stages of vegetation recovery (restored reaches). In the short-term (~15-20 years after restoration), restoration led to reduced GPP akin to reference reaches. Yet, ER did not show the anticipated increase, suggesting a longer timeframe is necessary for restored streams to emulate the functional characteristics of reference reaches. Additionally, the restored reaches did not achieve the nutrient uptake efficiencies observed in both impacted and reference reaches, pointing to a partial recovery of ecosystem function. This study suggests that while riparian vegetation restoration contributes positively to certain aspects of stream function, environmental variables less related to this type of restoration, such as discharge and hydromorphology, significantly influence stream ecosystem functioning, highlighting the importance of considering environmental context in restoration efforts. A more holistic approach, possibly encompassing broader hydromorphological and habitat enhancements, is needed to fully restore ecological processes in these vital ecosystems. These insights are critical for informing future tropical stream restoration projects, advocating the use of ecosystem function metrics as comprehensive indicators of ecological recovery and restoration success.

Lesion characteristics are associated with bowel, bladder, and overall independence following cervical spinal cord injury.

CONTEXT/OBJECTIVE: There is a growing global interest in quantifying spinal cord lesions and spared neural tissue using magnetic resonance imaging (MRI) in individuals with spinal cord injury (SCI). The primary objective of this study was to assess the relationships between spinal cord lesion characteristics assessed on MRI and bowel, bladder, and overall independence following SCI. DESIGN: Retrospective, exploratory study. PARTICIPANTS: 93 individuals with cervical SCI who were enrolled in a local United States Model Systems SCI database from 2010 to 2017. METHODS: Clinical and MRI data were obtained for potential participants, and MRIs of eligible participants were analyzed. Explanatory variables, captured on MRIs, included intramedullary lesion length (IMLL), midsagittal ventral tissue bridge width (VTBW), midsagittal dorsal tissue bridge width (DTBW), and axial damage ratio (ADR). OUTCOME MEASURES: Bowel and bladder management scale of the Functional Independence Measure (FIM) and FIM total motor score. RESULTS: When accounting for all four variables, only ADR was significantly associated with bowel independence (OR = 0.970, 95% CI: 0.942-0.997, P = 0.030), and both ADR and IMLL were strongly associated with bladder independence (OR = 0.967, 95% CI: 0.936-0.999, P = 0.046 and OR = 0.948, 95% CI: 0.919-0.978, P = 0.0007, respectively). 32% of the variation in overall independence scores were explained by all four predictive variables, but only ADR was significantly associated with overall independence after accounting for all other predictive variables (ß = -0.469, 95% CI: -0.719, -0.218, P = 0.0004). CONCLUSIONS: Our results suggest that the MRI-measured extent of spinal cord lesion may be predictive of bowel, bladder, and overall independence following cervical SCI.

Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae.

BACKGROUND: The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. RESULTS: We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. CONCLUSIONS: Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

A replication-deficient gammaherpesvirus vaccine protects mice from lytic disease and reduces latency establishment.

Gammaherpesviruses are oncogenic viruses that establish lifelong infections and are significant causes of morbidity and mortality. Vaccine strategies to limit gammaherpesvirus infection and disease are in development, but there are no FDA-approved vaccines for Epstein-Barr or Kaposi sarcoma herpesvirus. As a new approach to gammaherpesvirus vaccination, we developed and tested a replication-deficient virus (RDV) platform, using murine gammaherpesvirus 68 (MHV68), a well-established mouse model for gammaherpesvirus pathogenesis studies and preclinical therapeutic evaluations. We employed codon-shuffling-based complementation to generate revertant-free RDV lacking expression of the essential replication and transactivator protein encoded by ORF50 to arrest viral gene expression early after de novo infection. Inoculation with RDV-50.stop exposes the host to intact virion particles and leads to limited lytic gene expression in infected cells yet does not produce additional infectious particles. Prime-boost vaccination of mice with RDV-50.stop elicited virus-specific neutralizing antibody and effector T cell responses in the lung and spleen. In contrast to vaccination with heat-inactivated WT MHV68, vaccination with RDV-50.stop resulted in a near complete abolishment of virus replication in the lung 7 days post-challenge and reduction of latency establishment in the spleen 16 days post-challenge with WT MHV68. Ifnar1-/- mice, which lack the type I interferon receptor, exhibit severe disease and high mortality upon infection with WT MHV68. RDV-50.stop vaccination of Ifnar1-/- mice prevented wasting and mortality upon challenge with WT MHV68. These results demonstrate that prime-boost vaccination with a gammaherpesvirus that is unable to undergo lytic replication offers protection against acute replication, impairs the establishment of latency, and prevents severe disease upon the WT virus challenge. Our study also reveals that the ability of a gammaherpesvirus to persist in vivo despite potent pre-existing immunity is an obstacle to obtaining sterilizing immunity.

Resident-as-Teacher: Can It Be Done With an E-Learning Module?

Background Resident-as-teacher initiatives are traditionally specialty-specific and performed in-person, limiting ability to disseminate essential teaching skills to all residents. Objective The aim of this study was to develop, implement, and evaluate a resident-as-teacher interactive e-learning module on growth mindset and coaching. Methods The module was designed and implemented between August 2022 and March 2023. It was distributed to postgraduate year (PGY) 1 residents in all specialties at a large academic institution. Completion rates, Likert ratings, and answers to 2 open-ended questions were used for assessment. Descriptive statistics and 1-way analysis of variance with Sîdák correction for multiple comparisons were performed on Likert ratings. Responses to open-ended questions were evaluated using content analysis. Results The module was completed by all 277 PGY-1 residents (100%), with the evaluation completed by 276 of 277 (99.6%) residents. Mean rating of the module's relevance to the role of resident teacher was 4.06±0.90 (5-point Likert scale), with general surgery residents rating the module less favorably compared to all specialties (3.28±1.06; P<.01; 95% CI 0.26-1.30). Open-ended comments revealed that residents most liked the delivery of relevant teaching strategies and the interactive design of the module. The most common area for suggested improvement was the addition of content such as teaching in challenging situations. Time needed for design, implementation, and evaluation was 80 hours total. Conclusions An e-learning module offers an interactive platform for teaching skills and was found to be an acceptable method of instruction for residents.

Prkd1 regulates the formation and repair of plasma membrane disruptions (PMD) in osteocytes.

We and others have seen that osteocytes sense high-impact osteogenic mechanical loading via transient plasma membrane disruptions (PMDs) which initiate downstream mechanotransduction. However, a PMD must be repaired for the cell to survive this wounding event. Previous work suggested that the protein Prkd1 (also known as PKCµ) may be a critical component of this PMD repair process, but the specific role of Prkd1 in osteocyte mechanobiology had not yet been tested. We treated MLO-Y4 osteocytes with Prkd1 inhibitors (Go6976, kbNB 142-70, staurosporine) and generated an osteocyte-targeted (Dmp1-Cre) Prkd1 conditional knockout (CKO) mouse. PMD repair rate was measured via laser wounding and FM1-43 dye uptake, PMD formation and post-wounding survival were assessed via fluid flow shear stress (50 dyn/cm2), and in vitro osteocyte mechanotransduction was assessed via measurement of calcium signaling. To test the role of osteocyte Prkd1 in vivo, Prkd1 CKO and their wildtype (WT) littermates were subjected to 2 weeks of unilateral axial tibial loading and loading-induced changes in cortical bone mineral density, geometry, and formation were measured. Prkd1 inhibition or genetic deletion slowed osteocyte PMD repair rate and impaired post-wounding cell survival. These effects could largely be rescued by treating osteocytes with the FDA-approved synthetic copolymer Poloxamer 188 (P188), which was previously shown to facilitate membrane resealing and improve efficiency in the repair rate of PMD in skeletal muscle myocytes. In vivo, while both WT and Prkd1 CKO mice demonstrated anabolic responses to tibial loading, the magnitude of loading-induced increases in tibial BMD, cortical thickness, and periosteal mineralizing surface were blunted in Prkd1 CKO as compared to WT mice. Prkd1 CKO mice also tended to show a smaller relative difference in the number of osteocyte PMD in loaded limbs and showed greater lacunar vacancy, suggestive of impaired post-wounding osteocyte survival. While P188 treatment rescued loading-induced increases in BMD in the Prkd1 CKO mice, it surprisingly further suppressed loading-induced increases in cortical bone thickness and cortical bone formation. Taken together, these data suggest that Prkd1 may play a pivotal role in the regulation and repair of the PMD response in osteocytes and support the idea that PMD repair processes can be pharmacologically targeted to modulate downstream responses, but suggest limited utility of PMD repair-promoting P188 in improving bone anabolic responses to loading.

Synthesis of P-Containing Polycyclic Aromatic Hydrocarbons from Alkynyl-phosphonium Salts.

This work presents a straightforward method for synthesizing a series of phosphorus-containing polycyclic aromatic hydrocarbons (P-PAHs) featuring an internal ylidic bond. The method involves anion exchange, alkyne annulation, and deprotonation reactions, enabling the efficient production of cyclic phosphonium salts, which serve as pivotal intermediates in the synthesis of P-PAHs. The alkyne annulation reaction exhibits high regioselectivity, ensuring the successful synthesis of λ5-phosphaphenanthrene isomers. Additionally, the incorporation of electron-withdrawing groups effectively stabilizes the internal ylidic bond of P-PAHs.

Surgical Intraoperative Handoff Initiative: Standardizing Operating Room Communication Using SHRIMPS.

BACKGROUND: Operating room (OR) handoffs are not universally standardized, although standardized sign outs have been proven to provide effective communication in other aspects of healthcare. We hypothesize that creating a standardized handoff will improve communication between OR staff. STUDY DESIGN: A frontline stakeholder approached our quality improvement team with concern regarding inadequate quality surgical technician handoffs during staff changes. An audit tool was created for a pilot cohort of 23 cases to evaluate surgical technician handoffs from May 2022 to November 2022. Handoffs occurred in 82.6% of cases. Elements of handoff varied significantly, with an average of 34.4% completion of critical handoff elements. Audits were reviewed with stakeholders to develop a standardized communication checklist, including domains regarding sponges, sharps, hidden items, replaced items, instruments, implants, medications, procedure overview, and specimens. An acronym of these domains, SHRIMPS, was affixed to each OR wall. RESULTS: In the initial Plan-Do-Study-Act cycle, piloted in urology, general surgery, and neurosurgery, 100% of the 15 observed cases included handoff, averaging 76 seconds per handoff. Additionally, 100% of cases announced a handoff to the surgeon, and all elements were addressed 99.6% of the time. Plan-Do-Study-Act cycle 2 involved implementation to all service lines. Of the 68 cases observed, 100% included handoff, averaging 69.4 seconds per handoff, with 98.2% of elements addressed, though only 97.1% of handoffs were announced. CONCLUSIONS: Little communication standardization exists within the OR, especially regarding intraoperative staff changes. Implementation of a standardized handoff between surgical technicians resulted in substantial improvement in critical communication during staff changes.

Detection of SARS-CoV-2-Specific Secretory IgA and Neutralizing Antibodies in the Nasal Secretions of Exposed Seronegative Individuals.

Mucosal immunity may contribute to clearing SARS-CoV-2 infection prior to systemic infection, thereby allowing hosts to remain seronegative. We describe the meaningful detection of SARS-CoV-2-specific nasal mucosal antibodies in a group of exposed-household individuals that evaded systemic infection. Between June 2020 and February 2023, nasopharyngeal swab (NPS) and acute and convalescent blood were collected from individuals exposed to a SARS-CoV-2-confirmed household member. Nasal secretory IgA (SIgA) antibodies targeting the SARS-CoV-2 spike protein were measured using a modified ELISA. Of the 36 exposed individuals without SARS-CoV-2 detected by the RT-PCR of NPS specimens and seronegative for SARS-CoV-2-specific IgG at enrollment and convalescence, 13 (36.1%) had positive SARS-CoV-2-specific SIgA levels detected in the nasal mucosa at enrollment. These individuals had significantly higher nasal SIgA (median 0.52 AU/mL) compared with never-exposed, never-infected controls (0.001 AU/mL) and infected-family participants (0.0002 AU/mL) during the acute visit, respectively (both p < 0.001). The nasal SARS-CoV-2-specific SIgA decreased rapidly over two weeks in the exposed seronegative individuals compared to a rise in SIgA in infected-family members. The nasal SARS-CoV-2-specific SIgA may have a protective role in preventing systemic infection.

Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity.

Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene sequencing revealed significant shifts in gut microbial community structure during oral fluoropyrimidine treatment across multiple patient cohorts, in mouse small and large intestinal contents, and in patient-derived ex vivo communities. Metagenomic sequencing revealed marked shifts in pyrimidine-related gene abundance during oral fluoropyrimidine treatment, including enrichment of the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). preTA + bacteria depleted 5-FU in gut microbiota grown ex vivo and the mouse distal gut. Germ-free and antibiotic-treated mice experienced increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA + E. coli, or preTA-high CRC patient stool. Finally, preTA abundance was negatively associated with fluoropyrimidine toxicity in patients. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.