Envisioning Academic Global Oncologists: Proposed Competencies for Global Oncology Training From ASCO.

Recognizing the rising incidence, prevalence, and mortality of cancer in low- and middle-resource settings, as well as the increasingly international profile of its membership, ASCO has committed to expanding its engagement at a global level. In 2017, the ASCO Academic Global Oncology Task Force sought to define the potential role for ASCO in supporting global oncology as an academic field. A set of recommendations to advance the status of global oncology as an academic discipline were created through a consensus-based process involving participation by a diverse group of global oncology and global health practitioners; these recommendations were then published. The recommendations included developing a set of global oncology competencies for trainees and faculty interested in a career in academic global oncology. Here, we describe the global oncology competencies developed by this task force. These competencies consist of knowledge and skills needed in general global health as well as cancer-specific care and research, including understanding global cancer health disparities, defining unique resources and needs in low- and middle-resource settings, and promoting international collaboration. Although the competencies were originally developed for US training programs, they are intended to be widely applicable globally. By formalizing the training of oncologists and supporting career pathways in the field of global oncology, we can make progress in achieving global equity in cancer care and control.

Expanding the human gut microbiome atlas of Africa.

Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ~84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens. Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.

Analysis and culturing of the prototypic crAssphage reveals a phage-plasmid lifestyle.

The prototypic crAssphage (Carjivirus communis) is one of the most abundant, prevalent, and persistent gut bacteriophages, yet it remains uncultured and its lifestyle uncharacterized. For the last decade, crAssphage has escaped plaque-dependent culturing efforts, leading us to investigate alternative lifestyles that might explain its widespread success. Through genomic analyses and culturing, we find that crAssphage uses a phage-plasmid lifestyle to persist extrachromosomally. Plasmid-related genes are more highly expressed than those implicated in phage maintenance. Leveraging this finding, we use a plaque-free culturing approach to measure crAssphage replication in culture with Phocaeicola vulgatus, Phocaeicola dorei, and Bacteroides stercoris, revealing a broad host range. We demonstrate that crAssphage persists with its hosts in culture without causing major cell lysis events or integrating into host chromosomes. The ability to switch between phage and plasmid lifestyles within a wide range of hosts contributes to the prolific nature of crAssphage in the human gut microbiome.

Advancing Wearable Biosensors for Congenital Heart Disease: Patient and Clinician Perspectives: A Science Advisory From the American Heart Association.

Wearable biosensors (wearables) enable continual, noninvasive physiologic and behavioral monitoring at home for those with pediatric or congenital heart disease. Wearables allow patients to access their personal data and monitor their health. Despite substantial technologic advances in recent years, issues with hardware design, data analysis, and integration into the clinical workflow prevent wearables from reaching their potential in high-risk congenital heart disease populations. This science advisory reviews the use of wearables in patients with congenital heart disease, how to improve these technologies for clinicians and patients, and ethical and regulatory considerations. Challenges related to the use of wearables are common to every clinical setting, but specific topics for consideration in congenital heart disease are highlighted.

Telehealth use during the early COVID-19 public health emergency and subsequent health care costs and utilization.

Telehealth utilization increased during the COVID-19 pandemic, yet few studies have documented associations of telehealth use with subsequent medical costs and health care utilization. We examined associations of telehealth use during the early COVID-19 public health emergency (March-June 2020) with subsequent total medical costs and health care utilization among people with heart disease (HD). We created a longitudinal cohort of individuals with HD using MarketScan Commercial Claims data (2018-2022). We used difference-in-differences methodology adjusting for patients' characteristics, comorbidities, COVID-19 infection status, and number of in-person visits. We found that using telehealth during the stay-at-home order period was associated with a reduction in total medical costs (by -$1814 per person), number of emergency department visits (by -88.6 per 1000 persons), and number of inpatient admissions (by -32.4 per 1000 persons). Telehealth use increased per-person per-year pharmacy prescription claims (by 0.514) and average number of days' drug supply (by 0.773 days). These associated benefits of telehealth use can inform decision makers, insurance companies, and health care professionals, especially in the context of disrupted health care access.

Racial and Ethnic Differences in Hypertension-Related Telehealth and In-Person Outpatient Visits Before and During the COVID-19 Pandemic Among Medicaid Beneficiaries.

Background: Little is known about the trends and costs of hypertension management through telehealth among individuals enrolled in Medicaid. Methods: Using MarketScan® Medicaid database, we examined outpatient visits among people with hypertension aged 18-64 years. We presented the numbers of hypertension-related telehealth and in-person outpatient visits per 100 individuals and the proportion of hypertension-related telehealth outpatient visits to total outpatient visits by month, overall, and by race and ethnicity. For the cost analysis, we presented total and patient out-of-pocket (OOP) costs per visit for telehealth and in-person visits in 2021. Results: Of the 229,562 individuals, 114,445 (49.9%) were non-Hispanic White, 80,692 (35.2%) were non-Hispanic Black, 3,924 (1.71%) were Hispanic. From February to April 2020, the number of hypertension-related telehealth outpatient visits per 100 persons increased from 0.01 to 6.13, the number of hypertension-related in-person visits decreased from 61.88 to 52.63, and the proportion of hypertension-related telehealth outpatient visits increased from 0.01% to 10.44%. During that same time, the proportion increased from 0.02% to 13.9% for non-Hispanic White adults, from 0.00% to 7.58% for non-Hispanic Black adults, and from 0.12% to 19.82% for Hispanic adults. The average total and patient OOP costs per visit in 2021 were $83.82 (95% confidence interval [CI], 82.66-85.05) and $0.55 (95% CI, 0.42-0.68) for telehealth and $264.48 (95% CI, 258.87-269.51) and $0.72 (95% CI, 0.65-0.79) for in-person visits, respectively. Conclusions: Hypertension management via telehealth increased among Medicaid recipients regardless of race and ethnicity, during the COVID-19 pandemic. These findings may inform telehealth policymakers and health care practitioners.

Viroid-like colonists of human microbiomes.

Here, we describe the "Obelisks," a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. "Obelisks" share several properties: (i) apparently circular RNA ~1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the "Oblins". We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in ~7% of analysed stool metatranscriptomes (29/440) and in ~50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme. Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.

Transcatheter Pulmonary Valve Replacement With Balloon-Expandable Valves: Utilization and Procedural Outcomes From the IMPACT Registry.

BACKGROUND: Transcatheter pulmonary valve replacement (TPVR) has expanded and evolved since its initial commercial approval in the United States in 2010. OBJECTIVES: This study sought to characterize real-world practice, including patient selection, procedural outcomes, complications, and off-label usage. METHODS: Characteristics and outcomes for patients undergoing balloon-expandable TPVR were collected from the American College of Cardiology National Cardiovascular Data Registry IMPACT (Improving Pediatric and Adult Congenital Treatment) Registry. RESULTS: Between April 2016 and March 2021, 4,513 TPVR procedures were performed in patients with a median age of 19 years, 57% with a Melody (Medtronic Inc) and 43% with a SAPIEN (Edwards Lifesciences) valve. Most implanting centers performed <10 cases annually. One-third of transcatheter pulmonary valve implants were into homograft conduits, one-third were into bioprosthetic valves (BPVs), 25% were in native or patched right ventricular outflow tracts (RVOTs), and 6% were into Contegra (Medtronic Inc) conduits. Over the course of the study period, SAPIEN valve use grew from ∼25% to 60%, in large part because of implants in patients with a native/patched RVOT. Acute success was achieved in 95% of patients (95.7% in homografts, 96.2% in BPVs, 94.2% in native RVOTs, and 95.4% in Contegra conduits). Major adverse events occurred in 2.4% of procedures, more commonly in patients with a homograft (2.9%) or native RVOT (3.4%) than a prior BPV (1.4%; P = 0.004). CONCLUSIONS: This study describes novel population data on the use and procedural outcomes of TPVR with balloon-expandable valves. Over time, there has been increasing use of TPVR to treat regurgitant native RVOT anatomy, with the SAPIEN valve more commonly used for this application.

Quantifying bias introduced by sample collection in relative and absolute microbiome measurements.

To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.

Acute Steroid-Refractory Gastrointestinal Graft-Versus-Host Disease Is Not Associated With Significant Differences in Gut Taxonomic Composition Compared to Steroid-Sensitive Gastrointestinal Graft-Versus-Host Disease Immediately Before Onset of Disease.

Taxonomic composition of the gut microbiota at the time of neutrophil engraftment is associated with the development of acute gastrointestinal graft-versus-host disease (GI GVHD) in patients undergoing allogeneic hematopoietic stem cell transplantation. However, less is known about the relationship between the gut microbiota and development of steroid-refractory GI GVHD immediately before the onset of disease. Markers of steroid-refractory GI GVHD are needed to identify patients who may benefit from the early initiation of non-corticosteroid-based GVHD treatment. Our aim was to identify differences in taxonomic composition in stool samples from patients without GVHD, with steroid-responsive GVHD and with steroid-refractory GI GVHD to identify predictive microbiome biomarkers of steroid-refractory GI GVHD. We conducted a retrospective case-control, single institution study, performing shotgun metagenomic sequencing on stool samples from patients with (n = 36) and without GVHD (n = 34) matched for time since transplantation. We compared the taxonomic composition of the gut microbiome in those with steroid-sensitive GI GVHD (n = 17) and steroid-refractory GI GVHD (n = 19) to each other and to those without GVHD. We also performed associations between steroid-refractory GI GVHD, gut taxonomic composition, and fecal calprotectin, a marker of GI GVHD to develop composite fecal markers of steroid-refractory GVHD before the onset of GI disease. We found that fecal samples within 30 days of GVHD onset from patients with and without GVHD or with and without steroid-refractory GI GVHD did not differ significantly in Shannon diversity (alpha-diversity) or in overall taxonomic composition (beta-diversity). Although those patients without GVHD had higher relative abundance of Clostridium spp., those with and without steroid-refractory GI GVHD did not significantly differ in taxonomic composition between one another. In our study, fecal calprotectin before disease onset was significantly higher in patients with GVHD compared to those without GVHD and higher in patients with steroid-refractory GI GVHD compared to steroid-sensitive GI GVHD. No taxa were significantly associated with higher levels of calprotectin.

Phage-inclusive profiling of human gut microbiomes with Phanta.

Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.

Rural and Urban Differences in Hypertension Management Through Telehealth Before and During the COVID-19 Pandemic Among Commercially Insured Patients.

BACKGROUND: The COVID-19 pandemic prompted a rapid increase in telehealth use. However, limited evidence exists on how rural and urban residents used telehealth and in-person outpatient services to manage hypertension during the pandemic. METHODS: This longitudinal study analyzed 701,410 US adults (18-64 years) in the MarketScan Commercial Claims Database, who were continuously enrolled from January 2017 through March 2022. We documented monthly numbers of hypertension-related telehealth and in-person outpatient visits (per 100 individuals), and the proportion of telehealth visits among all hypertension-related outpatient visits, from January 2019 through March 2022. We used Welch's two-tail t-test to differentiate monthly estimates by rural-urban status and month-to-month changes. RESULTS: From February through April 2020, the monthly number of hypertension-related telehealth visits per 100 individuals increased from 0.01 to 6.05 (P < 0.001) for urban residents and from 0.01 to 4.56 (P < 0.001) for rural residents. Hypertension-related in-person visits decreased from 20.12 to 8.30 (P < 0.001) for urban residents and from 20.48 to 10.15 (P < 0.001) for rural residents. The proportion of hypertension-related telehealth visits increased from 0.04% to 42.15% (P < 0.001) for urban residents and from 0.06% to 30.98% (P < 0.001) for rural residents. From March 2020 to March 2022, the monthly average of the proportions of hypertension-related telehealth visits was higher for urban residents than for rural residents (10.19% vs. 6.96%; P < 0.001). CONCLUSIONS: Data show that rural residents were less likely to use telehealth for hypertension management. Understanding trends in hypertension-related telehealth utilization can highlight disparities in the sustained use of telehealth to advance accessible health care.

Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition.

The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.

Identification of over ten thousand candidate structured RNAs in viruses and phages.

Structured RNAs play crucial roles in viruses, exerting influence over both viral and host gene expression. However, the extensive diversity of structured RNAs and their ability to act in cis or trans positions pose challenges for predicting and assigning their functions. While comparative genomics approaches have successfully predicted candidate structured RNAs in microbes on a large scale, similar efforts for viruses have been lacking. In this study, we screened over 5 million DNA and RNA viral sequences, resulting in the prediction of 10,006 novel candidate structured RNAs. These predictions are widely distributed across taxonomy and ecosystem. We found transcriptional evidence for 206 of these candidate structured RNAs in the human fecal microbiome. These candidate RNAs exhibited evidence of nucleotide covariation, indicative of selective pressure maintaining the predicted secondary structures. Our analysis revealed a diverse repertoire of candidate structured RNAs, encompassing a substantial number of putative tRNAs or tRNA-like structures, Rho-independent transcription terminators, and potentially cis-regulatory structures consistently positioned upstream of genes. In summary, our findings shed light on the extensive diversity of structured RNAs in viruses, offering a valuable resource for further investigations into their functional roles and implications in viral gene expression and pave the way for a deeper understanding of the intricate interplay between viruses and their hosts at the molecular level.

Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology.

The most prevalent microbial eukaryote in the human gut is Blastocystis, an obligate commensal protist also common in many other vertebrates. Blastocystis is descended from free-living stramenopile ancestors; how it has adapted to thrive within humans and a wide range of hosts is unclear. Here, we cultivated six Blastocystis strains spanning the diversity of the genus and generated highly contiguous, annotated genomes with long-read DNA-seq, Hi-C, and RNA-seq. Comparative genomics between these strains and two closely related stramenopiles with different lifestyles, the lizard gut symbiont Proteromonas lacertae and the free-living marine flagellate Cafeteria burkhardae, reveal the evolutionary history of the Blastocystis genus. We find substantial gene content variability between Blastocystis strains. Blastocystis isolated from an herbivorous tortoise has many plant carbohydrate metabolizing enzymes, some horizontally acquired from bacteria, likely reflecting fermentation within the host gut. In contrast, human-isolated Blastocystis have gained many heat shock proteins, and we find numerous subtype-specific expansions of host-interfacing genes, including cell adhesion and cell surface glycan genes. In addition, we observe that human-isolated Blastocystis have substantial changes in gene structure, including shortened introns and intergenic regions, as well as genes lacking canonical termination codons. Finally, our data indicate that the common ancestor of Blastocystis lost nearly all ancestral genes for heterokont flagella morphology, including cilia proteins, microtubule motor proteins, and ion channel proteins. Together, these findings underscore the huge functional variability within the Blastocystis genus and provide candidate genes for the adaptations these lineages have undergone to thrive in the gut microbiomes of diverse vertebrates.

Collaborative Intelligence to catalyze the digital transformation of healthcare.

Collaborative intelligence reflects the promise and limits of leveraging artificial intelligence (AI) technologies in clinical care. It involves the use of advanced analytics and computing power with an understanding that humans bear responsibility for the accuracy, completeness and any inherent bias found in the training data. Clinicians benefit from using this technology to address increased complexity and information overload, support continuous care and optimized resource allocation, and to enact efforts to eradicate disparities in health care access and quality. This requires active clinician engagement with the technology, a general understanding of how the machine produced its insight, the limitations of the algorithms, and the need to screen datasets for bias. Importantly, by interacting, the clinician and the analytics will create trust based on the clinician's critical thinking skills leveraged to discern value of machine outputs within clinical context. Utilization of collaborative intelligence should be staged with the level of understanding and evidence. It is particularly well suited to low-complexity non-urgent care and to identifying individuals at rising risk within a population. Clinician involvement in algorithm development and the amassing of evidence to support safety and efficacy will propel adoption. Utilization of collaborative intelligence represents the natural progression of health care innovation, and if thoughtfully constructed and equitably deployed, holds the promise to decrease clinician burden and improve access to care.

Human gut metagenomic mining reveals an untapped source of peptide antibiotics.

Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.

The Tomato Brown Rugose Fruit Virus Movement Protein Gene Is a Novel Microbial Source Tracking Marker.

Microbial source tracking (MST) identifies sources of fecal contamination in the environment using host-associated fecal markers. While there are numerous bacterial MST markers that can be used herein, there are few such viral markers. Here, we designed and tested novel viral MST markers based on tomato brown rugose fruit virus (ToBRFV) genomes. We assembled eight nearly complete genomes of ToBRFV from wastewater and stool samples from the San Francisco Bay Area in the United States. Next, we developed two novel probe-based reverse transcription-PCR (RT-PCR) assays based on conserved regions of the ToBRFV genome and tested the markers' sensitivities and specificities using human and non-human animal stool as well as wastewater. The ToBRFV markers are sensitive and specific; in human stool and wastewater, they are more prevalent and abundant than a commonly used viral marker, the pepper mild mottle virus (PMMoV) coat protein (CP) gene. We used the assays to detect fecal contamination in urban stormwater samples and found that the ToBRFV markers matched cross-assembly phage (crAssphage), an established viral MST marker, in prevalence across samples. Taken together, these results indicate that ToBRFV is a promising viral human-associated MST marker. IMPORTANCE Human exposure to fecal contamination in the environment can cause transmission of infectious diseases. Microbial source tracking (MST) can identify sources of fecal contamination so that contamination can be remediated and human exposures can be reduced. MST requires the use of host-associated MST markers. Here, we designed and tested novel MST markers from genomes of tomato brown rugose fruit virus (ToBRFV). The markers are sensitive and specific to human stool and highly abundant in human stool and wastewater samples.

Phage diversity in cell-free DNA identifies bacterial pathogens in human sepsis cases.

Bacteriophages, viruses that infect bacteria, have great specificity for their bacterial hosts at the strain and species level. However, the relationship between the phageome and associated bacterial population dynamics is unclear. Here we generated a computational pipeline to identify sequences associated with bacteriophages and their bacterial hosts in cell-free DNA from plasma samples. Analysis of two independent cohorts, including a Stanford Cohort of 61 septic patients and 10 controls and the SeqStudy cohort of 224 septic patients and 167 controls, reveals a circulating phageome in the plasma of all sampled individuals. Moreover, infection is associated with overrepresentation of pathogen-specific phages, allowing for identification of bacterial pathogens. We find that information on phage diversity enables identification of the bacteria that produced these phages, including pathovariant strains of Escherichia coli. Phage sequences can likewise be used to distinguish between closely related bacterial species such as Staphylococcus aureus, a frequent pathogen, and coagulase-negative Staphylococcus, a frequent contaminant. Phage cell-free DNA may have utility in studying bacterial infections.