Mining human microbiomes reveals an untapped source of peptide antibiotics.

Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential 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. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.

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.

Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.

Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota.

Osmotic diarrhea is a prevalent condition in humans caused by food intolerance, malabsorption, and widespread laxative use. Here, we assess the resilience of the gut ecosystem to osmotic perturbation at multiple length and timescales using mice as model hosts. Osmotic stress caused reproducible extinction of highly abundant taxa and expansion of less prevalent members in human and mouse microbiotas. Quantitative imaging revealed decimation of the mucus barrier during osmotic perturbation, followed by recovery. The immune system exhibited temporary changes in cytokine levels and a lasting IgG response against commensal bacteria. Increased osmolality prevented growth of commensal strains in vitro, revealing one mechanism contributing to extinction. Environmental availability of microbiota members mitigated extinction events, demonstrating how species reintroduction can affect community resilience. Our findings (1) demonstrate that even mild osmotic diarrhea can cause lasting changes to the microbiota and host and (2) lay the foundation for interventions that increase system-wide resilience.

Sequencing-based analysis of microbiomes.

Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level.

Post-Transplantation Cyclophosphamide-Based Graft-versus-Host Disease Prophylaxis.

BACKGROUND: In patients undergoing allogeneic hematopoietic stem-cell transplantation (HSCT), a calcineurin inhibitor plus methotrexate has been a standard prophylaxis against graft-versus-host disease (GVHD). A phase 2 study indicated the potential superiority of a post-transplantation regimen of cyclophosphamide, tacrolimus, and mycophenolate mofetil. METHODS: In a phase 3 trial, we randomly assigned adults with hematologic cancers in a 1:1 ratio to receive cyclophosphamide-tacrolimus-mycophenolate mofetil (experimental prophylaxis) or tacrolimus-methotrexate (standard prophylaxis). The patients underwent HSCT from an HLA-matched related donor or a matched or 7/8 mismatched (i.e., mismatched at only one of the HLA-A, HLA-B, HLA-C, and HLA-DRB1 loci) unrelated donor, after reduced-intensity conditioning. The primary end point was GVHD-free, relapse-free survival at 1 year, assessed in a time-to-event analysis, with events defined as grade III or IV acute GVHD, chronic GVHD warranting systemic immunosuppression, disease relapse or progression, and death from any cause. RESULTS: In a multivariate Cox regression analysis, GVHD-free, relapse-free survival was significantly more common among the 214 patients in the experimental-prophylaxis group than among the 217 patients in the standard-prophylaxis group (hazard ratio for grade III or IV acute GVHD, chronic GVHD, disease relapse or progression, or death, 0.64; 95% confidence interval [CI], 0.49 to 0.83; P = 0.001). At 1 year, the adjusted GVHD-free, relapse-free survival was 52.7% (95% CI, 45.8 to 59.2) with experimental prophylaxis and 34.9% (95% CI, 28.6 to 41.3) with standard prophylaxis. Patients in the experimental-prophylaxis group appeared to have less severe acute or chronic GVHD and a higher incidence of immunosuppression-free survival at 1 year. Overall and disease-free survival, relapse, transplantation-related death, and engraftment did not differ substantially between the groups. CONCLUSIONS: Among patients undergoing allogeneic HLA-matched HSCT with reduced-intensity conditioning, GVHD-free, relapse-free survival at 1 year was significantly more common among those who received cyclophosphamide-tacrolimus-mycophenolate mofetil than among those who received tacrolimus-methotrexate. (Funded by the National Heart, Lung, and Blood Institute and others; BMT CTN 1703 ClinicalTrials.gov number, NCT03959241.).

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.

Chemoproteomic identification of a DPP4 homolog in Bacteroides thetaiotaomicron.

Serine hydrolases have important roles in signaling and human metabolism, yet little is known about their functions in gut commensal bacteria. Using bioinformatics and chemoproteomics, we identify serine hydrolases in the gut commensal Bacteroides thetaiotaomicron that are specific to the Bacteroidetes phylum. Two are predicted homologs of the human dipeptidyl peptidase 4 (hDPP4), a key enzyme that regulates insulin signaling. Our functional studies reveal that BT4193 is a true homolog of hDPP4 that can be inhibited by FDA-approved type 2 diabetes medications targeting hDPP4, while the other is a misannotated proline-specific triaminopeptidase. We demonstrate that BT4193 is important for envelope integrity and that loss of BT4193 reduces B. thetaiotaomicron fitness during in vitro growth within a diverse community. However, neither function is dependent on BT4193 proteolytic activity, suggesting a scaffolding or signaling function for this bacterial protease.

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.

Cancer Demographics and Time-to-Care in Belize.

BACKGROUND: Belize is a middle-income Caribbean country with poorly described cancer epidemiology and no comprehensive cancer care capacity. In 2018, GO, Inc., a US-based NGO, partnered with the Ministry of Health and the national hospital in Belize City to create the first public oncology clinic in the country. Here, we report demographics from the clinic and describe time intervals to care milestones to allow for public health targeting of gaps. PATIENTS AND METHODS: Using paper charts and a mobile health platform, we performed a retrospective chart review at the Karl Heusner Memorial Hospital (KHMH) clinic from 2018 to 2022. RESULTS: During this time period, 465 patients with cancer presented to the clinic. Breast cancer (28%) and cervical cancer (12%) were most common. Most patients (68%) presented with stage 3 or 4 disease and were uninsured (78%) and unemployed (79%). Only 21% of patients ever started curative intent treatment. Median time from patient-reported symptoms to a biopsy or treatment was 130 and 189 days. For the most common cancer, breast, similar times were seen at 140 and 178 days. Time intervals at the clinic: <30 days from initial visit to biopsy (if not previously performed) and <30 days to starting chemotherapy. CONCLUSION: This study reports the first clinic-based cancer statistics for Belize. Many patients have months between symptom onset and treatment. In this setting, the clinic has built infrastructure allowing for minimal delays in care despite an underserved population. This further affirms the need for infrastructure investment and early detection programs to improve outcomes in Belize.

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.

Invariant natural killer T-cell subsets have diverse graft-versus-host-disease-preventing and antitumor effects.

Invariant natural killer T (iNKT) cells are a T-cell subset with potent immunomodulatory properties. Experimental evidence in mice and observational studies in humans indicate that iNKT cells have antitumor potential as well as the ability to suppress acute and chronic graft-versus-host-disease (GVHD). Murine iNKT cells differentiate during thymic development into iNKT1, iNKT2, and iNKT17 sublineages, which differ transcriptomically and epigenomically and have subset-specific developmental requirements. Whether distinct iNKT sublineages also differ in their antitumor effect and their ability to suppress GVHD is currently unknown. In this work, we generated highly purified murine iNKT sublineages, characterized their transcriptomic and epigenomic landscape, and assessed specific functions. We show that iNKT2 and iNKT17, but not iNKT1, cells efficiently suppress T-cell activation in vitro and mitigate murine acute GVHD in vivo. Conversely, we show that iNKT1 cells display the highest antitumor activity against murine B-cell lymphoma cells both in vitro and in vivo. Thus, we report for the first time that iNKT sublineages have distinct and different functions, with iNKT1 cells having the highest antitumor activity and iNKT2 and iNKT17 cells having immune-regulatory properties. These results have important implications for the translation of iNKT cell therapies to the clinic for cancer immunotherapy as well as for the prevention and treatment of GVHD.

Glucagon-like peptide 2 for intestinal stem cell and Paneth cell repair during graft-versus-host disease in mice and humans.

Acute graft-versus-host disease (GVHD) is a life-threatening complication after allogeneic hematopoietic cell transplantation (allo-HCT). Although currently used GVHD treatment regimens target the donor immune system, we explored here an approach that aims at protecting and regenerating Paneth cells (PCs) and intestinal stem cells (ISCs). Glucagon-like-peptide-2 (GLP-2) is an enteroendocrine tissue hormone produced by intestinal L cells. We observed that acute GVHD reduced intestinal GLP-2 levels in mice and patients developing GVHD. Treatment with the GLP-2 agonist, teduglutide, reduced de novo acute GVHD and steroid-refractory GVHD, without compromising graft-versus-leukemia (GVL) effects in multiple mouse models. Mechanistically GLP-2 substitution promoted regeneration of PCs and ISCs, which enhanced production of antimicrobial peptides and caused microbiome changes. GLP-2 expanded intestinal organoids and reduced expression of apoptosis-related genes. Low numbers of L cells in intestinal biopsies and high serum levels of GLP-2 were associated with a higher incidence of nonrelapse mortality in patients undergoing allo-HCT. Our findings indicate that L cells are a target of GVHD and that GLP-2-based treatment of acute GVHD restores intestinal homeostasis via an increase of ISCs and PCs without impairing GVL effects. Teduglutide could become a novel combination partner for immunosuppressive GVHD therapy to be tested in clinical trials.

Cardiovascular Prevention Among Young Adults with Congenital Heart Disease.

PURPOSE OF REVIEW: There are over a million adults living with congenital heart disease (CHD) in the USA. There have been improvements in CHD management which have led to an expansion of the adult congenital heart disease (ACHD) population. There is a high prevalence of atherosclerotic cardiovascular disease (ASCVD) encountered in the aging ACHD population. This review focuses on the most recent literature regarding the primary prevention of ASCVD in young ACHD patients. RECENT FINDINGS: There are unique considerations for ASCVD risk reduction in ACHD patients. ASCVD may be as prevalent in ACHD compared in the general population. However, there may be a perceived shorter life expectancy in ACHD patients; therefore, primary prevention of ASCVD may not be considered important. Preventative strategies for ASCVD are underutilized in ACHD patients. As these patients are followed for a lifetime by cardiologists, we can truly pursue primary prevention in this aging population.

Laparoscopic Surgery Requiring Abdominal Insufflation in Patients With Congenital Heart Disease.

OBJECTIVE: To determine if patients with congenital heart disease are undergoing laparoscopic surgery requiring abdominal insufflation and to compare the outcomes of these procedures with those who underwent an open surgical approach. DESIGN, SETTING, PARTICIPANTS: This was a retrospective study using the National Inpatient Sample from 2006 to 2014. Individuals with congenital heart disease who underwent at least one of six selected surgical procedures (laparoscopic or open) were included in the study. Subgroup analysis was performed on patients with Fontan palliation. MEASUREMENTS AND MAIN RESULTS: The primary outcome was to determine the frequency with which congenital heart disease patients undergo laparoscopic surgery requiring abdominal insufflation compared with open surgery. Secondary outcomes included all-cause in-hospital mortality and in-hospital length of stay. Of the 5,527 patients included, nearly half underwent laparoscopic surgery (46.3%), and 128 (2.3%) had single-ventricle circulation. All-cause mortality was significantly higher for those who underwent open surgery compared with the laparoscopic approach (3.6% v 0.9%; odds ratio [OR], 4.0 [2.6-6.3]; p < 0.0001). Subgroup analysis of patients with Fontal palliation older than five years showed 30 (42%) underwent laparoscopic surgery and there was no mortality difference between the laparoscopic and open approaches (OR, 1.4 [0.2-21.3], p = 0.8). Length of stay was significantly shorter for patients undergoing laparoscopic compared with open surgery (median three days [interquartile range, two-five] v six days [three-13], p < 0.0001). CONCLUSIONS: Individuals with congenital heart disease are being offered laparoscopic surgery that requires abdominal insufflation. All-cause mortality and length of stay were higher for patients who underwent open surgical operations.

Patient evaluation of a virtual visit program for adults with congenital heart disease.

BACKGROUND: Improved longevity for adults with congenital heart disease (ACHD) necessitates regular, longitudinal care for this population. Telemedicine has emerged as a strategy to increase access to subspecialty care. We evaluated patient experience with a virtual visit program in the pre-COVID era to identify patient-centered benefits and limitations. METHODS: We enrolled patients for 30-minute synchronous videoconferencing virtual visits at our institution between October 2013 and March 2019. All patients were Massachusetts residents. Patients were surveyed and their characteristics were abstracted from electronic medical records. RESULTS: A total of 264 virtual visits were conducted among 174 patients with a median age of 40 years. Patients traveled a median of 70 miles for in-person visits. Many visits were to review patient data (47%), and most individuals had moderate complexity CHD (45%). Patients reported very high satisfaction with a median visit rating of 10. Patients mostly preferred virtual visits when considering convenience and cost. No difference in preference to in-person visits was reported when considering sharing private information, confidence that concerns would be addressed, and overall visit quality. In-person visits were still preferred for personal connections and showing a physical problem. CONCLUSION: We find that patients are highly satisfied with virtual visits. ACHD programs should consider blended virtual and in-person care. Long-term regulatory provisions will further improve care through the expansion of telemedicine in the post-COVID era.

Interventional Therapy Versus Medical Therapy for Secundum Atrial Septal Defect: A Systematic Review (Part 2) for the 2018 AHA/ACC Guideline for the Management of Adults With Congenital Heart Disease: A Report of the American College of Cardiology/American Heart Association Task Force on Clinical Practice Guidelines.

Secundum atrial septal defect (ASD) is the most common adult congenital heart defect and can present with wide variation in clinical findings. With the intention of preventing morbidity and mortality associated with late presentation of ASD, consensus guidelines have recommended surgical or percutaneous ASD closure in adults with right heart enlargement, with or without symptoms. The aim of the present analysis was to determine if the protective effect of secundum ASD closure in adults could be qualified by pooling data from published studies. A systematic review and meta-analysis were performed by using EMBASE, MEDLINE (through PubMed), and the Cochrane Library databases to assess the effect of secundum ASD percutaneous or surgical closure in unoperated adults ≥18 years of age. Data were pooled across studies with the DerSimonian-Laird random-effects model or a Bayesian meta-analysis model. Between-study heterogeneity was assessed with Cochran's Q test. Bias assessment was performed with the Newcastle-Ottawa Scale and the Cochrane Risk of Bias Tool, and statistical risk of bias was assessed with Begg and Mazumdar's test and Egger's test. A total of 11 nonrandomized studies met the inclusion criteria, contributing 603 patients. Pooled analysis showed a protective effect of ASD closure on New York Heart Association functional class and on right ventricular systolic pressure, volumes, and dimensions. Two additional studies comprising 652 patients were reviewed separately for mortality outcome and primary outcome of interest because they did not meet the inclusion criteria. Those studies showed that ASD closure was associated with a weak protective effect on adjusted mortality rate but no significant impact on atrial arrhythmias in patients >50 years of age. Across all studies, there was significant heterogeneity between studies for nearly all clinical outcomes. The overall body of evidence was limited to observational cohort studies, the limitations of which make for low-strength evidence. Even within the parameters of the included studies, quality of evidence was further diminished by the lack of well-defined clinical outcomes. In conclusion, pooled data analysis on the impact of secundum ASD closure in adults was notably limited because of the lack of randomized controlled trials in patients with only secundum ASD. The few cohort studies in this population demonstrated improvement in functional status and right ventricular size and function as shown by echocardiogram. However, our findings suggest that at the time of this publication, insufficient data are available to determine the impact of ASD repair on mortality rate in adults.

Assessing and Addressing the Need for Cancer Patient Education in a Resource-Limited Setting in Haiti.

PURPOSE: Misinformation and lack of information about cancer and its treatment pose significant challenges to delivering cancer care in resource-limited settings and may undermine patient engagement in care. We aimed to investigate patients' knowledge and attitudes toward cancer and its treatment and to adapt, implement, and evaluate a low-literacy cancer patient education booklet at the Hôpital Universitaire de Mirebalais (HUM) in rural Haiti. MATERIALS AND METHODS: A low-literacy cancer patient education booklet was adapted into Haitian Creole in collaboration with clinicians at HUM. Patients were recruited for structured interviews (n = 20) and two focus groups (n = 13) designed to explore patients' attitudes toward cancer and its treatment and to assess whether the booklet increased patients' knowledge via an investigator-designed knowledge test. RESULTS: Participants reported a subjective lack of knowledge about cancer and its treatments and described views of cancer as deadly or incurable. Patients of varying education levels valued receiving written materials that set expectations about cancer treatment and expressed a desire to share the booklet with caregivers and others in their community. Participants across all levels of education significantly increased their performance on a knowledge test after counseling using the booklet (p < .001). CONCLUSION: We found that an educational booklet about cancer developed in collaboration with local providers was well received by patients with variable literacy levels and improved their knowledge of cancer and its treatment in a resource-limited setting. Such educational materials have the potential to serve as tools to engage patients with cancer and their families in care. IMPLICATIONS FOR PRACTICE: Misinformation and lack of information pose significant challenges to delivering cancer care in resource-limited settings; however, there are often no culturally and literacy appropriate tools available to aid in patient education. This article shows that written educational materials are well received by patients of variable literacy levels and can be effective tools for increasing patients' knowledge of cancer and its treatment in a limited-resource setting. Furthermore, the authors have made their educational booklet, Cancer and You, freely available online and welcome the opportunity to connect with readers of The Oncologist interested in implementing this educational booklet in clinical care.

Intestinal microbiota domination under extreme selective pressures characterized by metagenomic read cloud sequencing and assembly.

BACKGROUND: Low diversity of the gut microbiome, often progressing to the point of intestinal domination by a single species, has been linked to poor outcomes in patients undergoing hematopoietic cell transplantation (HCT). Our ability to understand how certain organisms attain intestinal domination over others has been restricted in part by current metagenomic sequencing technologies that are typically unable to reconstruct complete genomes for individual organisms present within a sequenced microbial community. We recently developed a metagenomic read cloud sequencing and assembly approach that generates improved draft genomes for individual organisms compared to conventional short-read sequencing and assembly methods. Herein, we applied metagenomic read cloud sequencing to four stool samples collected longitudinally from an HCT patient preceding treatment and over the course of heavy antibiotic exposure. RESULTS: Characterization of microbiome composition by taxonomic classification of reads reveals that that upon antibiotic exposure, the subject's gut microbiome experienced a marked decrease in diversity and became dominated by Escherichia coli. While diversity is restored at the final time point, this occurs without recovery of the original species and strain-level composition. Draft genomes for individual organisms within each sample were generated using both read cloud and conventional assembly. Read clouds were found to improve the completeness and contiguity of genome assemblies compared to conventional assembly. Moreover, read clouds enabled the placement of antibiotic resistance genes present in multiple copies both within a single draft genome and across multiple organisms. The occurrence of resistance genes associates with the timing of antibiotics administered to the patient, and comparative genomic analysis of the various intestinal E. coli strains across time points as well as the bloodstream isolate showed that the subject's E. coli bloodstream infection likely originated from the intestine. The E. coli genome from the initial pre-transplant stool sample harbors 46 known antimicrobial resistance genes, while all other species from the pre-transplant sample each contain at most 5 genes, consistent with a model of heavy antibiotic exposure resulting in selective outgrowth of the highly antibiotic-resistant E. coli. CONCLUSION: This study demonstrates the application and utility of metagenomic read cloud sequencing and assembly to study the underlying strain-level genomic factors influencing gut microbiome dynamics under extreme selective pressures in the clinical context of HCT.