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Cancer care providers at Queen Elizabeth Central Hospital in Malawi identified a need for educational materials for their low-literacy patients. Global Oncology, a nonprofit focused on improving cancer care, research, and education in resource-limited settings, partnered with THE MEME to develop cancer patient educational materials (PEMs). The goal of the project was to create clinically relevant and culturally appropriate low-literacy PEMs to improve clinical care, support services, and patient adherence in resource-limited settings. The team also aimed to develop a product strategy and business model for long-term sustainability. The article introduces the challenge from a global health perspective and the ways design can have a significant impact. It presents the collaborative process of developing the “Cancer and You” booklet for multiple cultural contexts and focuses on the results of a pilot study in Haiti evaluating the efficacy of the design in simplifying complex medical information, facilitating patient education, and improving communication.

Allogeneic hematopoietic stem cell transplantation (HSCT) is curative for many patients with severe benign and malignant hematologic disorders. The success of allogeneic HSCT is limited by the development of transplant-related complications such as acute graft-versus-host disease (GvHD). Early pre-clinical studies suggested that intestinal microflora contribute to the pathogenesis of acute GvHD, and that growth suppression or eradication of intestinal bacteria prevented the development of acute GvHD even in MHC-mismatched transplants. These observations led to the practice of gut decontamination (GD) with oral non-absorbable antibiotics in patients undergoing allogeneic HSCT as a method of acute GvHD prophylaxis. Microbiome studies in the modern sequencing era are beginning to challenge the benefit of this practice. In this review, we provide a historical perspective on the practice of GD and highlight findings from the limited number of clinical trials evaluating the use of GD for acute GvHD prevention in allogeneic HSCT patients. In addition, we examine the role of the gut microbiota in allogeneic HSCT in the context of recent studies linking the microflora to regulation of intestinal immune homeostasis. We discuss the implications of these findings for future strategies to reduce acute GvHD risk by selective manipulation of the microbiota.

Pulmonary valve replacement (PVR) is the most common adult congenital cardiac operation performed. Valve degeneration leading to prosthetic stenosis and/or regurgitation is a long-term risk in this population and may be associated with paravalvular leak (PVL). Complications involving the proximal pulmonary artery, including dissection, are less clearly defined. Herein, we report the case of a 30-year-old patient with a history of multiple pulmonary valve interventions secondary to congenital pulmonic stenosis, who developed dehiscence of a bioprosthetic PVR associated with significant paravalvular leak (PVL) and further complicated by a focal dissection of the proximal pulmonary artery.

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer and the second most common acute leukemia in adults. Despite best existing therapy, older children and elderly ALL patients have poor prognoses. Thus, there is a need to identify alternative therapeutics for these patients. There has been controversy about the function of the gut microbiota in cancer, with some reports showing that it supports tumor growth and others showing tumor growth inhibition. Recently, Dr. Melvyn Greaves proposed that ALL development may have a microbial trigger; however, gut microbiota studies in ALL are scarce. Little is known about the role of the gut microbiota in ALL progression and in reshaping cancer cell-intrinsic pathways that are as important as immune responses in the outcome of ALL. Recently, we found that gut microbiota depletion in immunocompromised mice reduces ALL growth by inducing apoptosis and inhibiting proliferation. We show that in immunocompromised microbiome-depleted mice, the rate of ALL tumor growth is reduced compared to microbiome-competent mice. Molecularly, we found that microbiome ablation results in changes in cancer cell-intrinsic pathways of apoptosis and proliferation in these tumors. To further understand how the gut microbiota affects these cancer cell-intrinsic pathways, we have performed RNA sequencing on tumors from microbiome-competent and microbiome-depleted mice accompanied by 16s rRNA sequencing from stool samples and mass spectrometry of blood serum to identify metabolites secreted by the gut microbiota that reach the tumor site, affecting cancer cell growth. Our goal is to define bacterial species and metabolites involved in ALL progression and to mechanistically determine how these bacterial species and metabolites regulate ALL growth via regulation of cancer cell-intrinsic pathways. These data suggest that the gut microbiota may regulate ALL progression in an immune-independent manner via transcriptional changes of cancer cell-autonomous pathways. We envision that the gut microbiota can be reshaped in ALL patients who are elderly, chemo-refractive, and/or immunocompromised to alter cancer cell-intrinsic pathways to treat ALL. The clinical impact of these findings is significant given that ALL patients who are immunocompromised could still benefit from therapeutics aiming at modulating the gut microbiota. Citation Format: Wadie Mahauad-Fernandez, Soumaya Zlitni, Ami Bhatt, Dean Felsher. The gastrointestinal microbiota controls cancer cell intrinsic mechanisms to promote the progression of acute lymphoblastic leukemia [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B21.

Specialized adult congenital heart disease (ACHD) care decreases mortality for this growing patient population. Telemedicine has emerged as a strategy to increase access to subspecialty care. We describe the successful implementation of synchronous videoconferencing virtual visits to increase ACHD

CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation.

Summary Mobile genetic elements (MGEs) contribute to bacterial adaptation and evolution; however, high-throughput, unbiased MGE detection remains challenging. We describe MGEfinder, a bioinformatic toolbox that identifies integrative MGEs and their insertion sites by using short-read sequencing data. MGEfinder identifies the genomic site of each MGE insertion and infers the identity of the inserted sequence. We apply MGEfinder to 12,374 sequenced isolates of 9 prevalent bacterial pathogens, including Mycobacterium tuberculosis, Staphylococcus aureus, and Escherichia coli, and identify thousands of MGEs, including candidate insertion sequences, conjugative transposons, and prophage elements. The MGE repertoire and insertion rates vary across species, and integration sites often cluster near genes related to antibiotic resistance, virulence, and pathogenicity. MGE insertions likely contribute to antibiotic resistance in laboratory experiments and clinical isolates. Additionally, we identified thousands of mobility genes, a subset of which have unknown function opening avenues for exploration. Future application of MGEfinder to commensal bacteria will further illuminate bacterial adaptation and evolution.

Author(s): Sberro, Hila; Greenfield, Nicholas; Pavlopoulos, Georgios; Kyrpides, Nikos; Bhatt, Ami | Abstract: Abstract Small proteins likely abound in prokaryotes, and may mediate much of the communication that occurs between organisms within a microbiome and their host. Unfortunately, small proteins are traditionally overlooked in biology, in part due to the computational and experimental difficulties in detecting them. To systematically identify novel small proteins, we carried out a large comparative genomics study on 1,773 HMP human-associated metagenomes from four different body sites (mouth, gut, skin and vagina). We describe more than four thousand 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, emphasizing the incompleteness of knowledge in this space. Our analysis exposes putative novel ‘housekeeping’ small protein families, including a potential novel ribosomally associated protein, as well as ‘mammalian-specific’ or ‘human-specific’ protein families. By analyzing the genomic neighborhood of small genes, we pinpoint a subset of families that are potentially associated with defense against bacteriophage. Finally, we identify families that may be subject to horizontal transfer and are thus potentially involved in adaptation of bacteria to the changing human environment. Our study suggest that small proteins are highly abundant and that those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.

We present the first method for efficient recovery of complete, closed genomes directly from microbiomes using nanopore long-read sequencing and assembly. We apply our approach to three healthy human gut communities and compare results to short read and read cloud approaches. We obtain nine finished genomes including the first reported closed genome of Prevotella copri, an organism with highly repetitive genome structure prevalent in non-western human gut microbiomes.

The healthy human fecal microbiota is too diverse to comprehensively study with the current throughput of proteomic methods. Shotgun sequencing technologies allow for much more comprehensive profiling. Here, we develop and apply MetaRibo-Seq, a method for simultaneous ribosome profiling of multiple taxa within a complex bacterial community. This approach captures taxonomic diversity in fecal samples. As expected, the detected ribosome-bound transcripts are relatively enriched within coding regions and significantly correlate to detectable protein abundances. In a low diversity fecal sample, we show that MetaRibo-Seq is more strongly correlated than metatranscriptomic data to protein abundance. This significant correlation of metatranscriptomics and MetaRibo-Seq with protein levels is maintained, though with decreased strength as taxonomic diversity increases. Finally, we identify genes that are consistently regulated at the translational level across bacterial taxa within fecal communities. In conclusion, MetaRibo-Seq enables comprehensive translational profiling in complex bacterial communities for the first time.

The prevalence, co-morbidities, and healthcare utilization in adolescents with congenital heart defects (CHDs) is not well understood. Adolescents (11 to 19 years old) with a healthcare encounter between January 1, 2008 (January 1, 2009 for MA) and December 31, 2010 with a CHD diagnosis code were identified from multiple administrative data sources compiled at 3 US sites: Emory University, Atlanta, Georgia (EU); Massachusetts Department of Public Health (MA); and New York State Department of Health (NY). The estimated prevalence for any CHD was 4.77 (EU), 17.29 (MA), and 4.22 (NY) and for severe CHDs was 1.34 (EU), 3.04 (MA), and 0.88 (NY) per 1,000 adolescents. Private or commercial insurance was the most common insurance type for EU and NY, and Medicaid for MA. Inpatient encounters were more frequent in severe CHDs. Cardiac co-morbidities included rhythm and conduction disorders at 20% (EU), 46% (MA), and 9% (NY) as well as heart failure at 3% (EU), 15% (MA), and 2% (NY). Leading noncardiac co-morbidities were respiratory/pulmonary (22% EU, 34% MA, 16% NY), infectious disease (17% EU, 22% MA, 20% NY), non-CHD birth defects (12% EU, 23% MA, 14% NY), gastrointestinal (10% EU, 28% MA, 13% NY), musculoskeletal (10% EU, 32% MA, 11% NY), and mental health (9% EU, 30% MA, 11% NY). In conclusion, this study used a novel approach of uniform CHD definition and variable selection across administrative data sources in 3 sites for the first population-based CHD surveillance of adolescents in the United States. High resource utilization and co-morbidities illustrate ongoing significant burden of disease in this vulnerable population.

Low intestinal microbial diversity, often leading to domination of the intestine by a single organism, is associated with poor outcomes following hematopoietic cell transplantation (HCT). Understanding how certain organisms achieve domination in the intestine is limited by current metagenomic sequencing technologies, which are typically unable to reconstruct complete genome drafts without bacterial isolation and culture. Recently, we developed a metagenomic read cloud sequencing approach that provides significantly improved genome drafts for individual organisms compared to conventional short-read sequencing methods. Here, we apply read cloud sequencing to four longitudinal stool samples collected from an HCT patient before and after heavy antibiotic exposure. During this time period, the patient experienced Escherichia coli gut domination and an E. coli bloodstream infection. We find that read clouds enable the placement of multiple copies of antibiotic resistance genes both within and across genomes, and the presence of resistance genes correlates with the timing of antibiotics administered to the patient. Comparative genomic analysis reveals that the E. coli bloodstream infection likely originated from the gut. The pre-transplant E. coli genome harbors 46 known resistance genes, whereas all other organisms from the pre-transplant time point contain 5 or fewer resistance genes, supporting a model in which the E. coli outgrowth was a result of selection by heavy antibiotic exposure. This case study highlights the application of metagenomic read cloud sequencing in a clinical context to elucidate the genomic underpinnings of microbiome dynamics under extreme selective pressures.

Purpura fulminans (PF) is a rare life-threatening complication of bacterial sepsis that is characterized by a highly thrombotic subtype of disseminated intravascular coagulation (DIC) and mortality of up to 80%.[1][1] Patients with PF develop a severe deficiency in protein C (PC), a serine protease

CrAss-like phages are double-stranded DNA viruses that are prevalent in human gut microbiomes. Here, we analyze gut metagenomic data from mother-infant pairs and patients undergoing fecal microbiota transplantation to evaluate the patterns of acquisition, transmission and strain diversity of crAss-like phages. We find that crAss-like phages are rarely detected at birth but are increasingly prevalent in the infant microbiome after one month of life. We observe nearly identical genomes in 50% of cases where the same crAss-like clade is detected in both the mother and the infant, suggesting vertical transmission. In cases of putative transmission of prototypical crAssphage (p-crAssphage), we find that a subset of strains present in the mother are detected in the infant, and that strain diversity in infants increases with time. Putative tail fiber proteins are enriched for nonsynonymous strain variation compared to other genes, suggesting a potential evolutionary benefit to maintaining strain diversity in specific genes. Finally, we show that p-crAssphage can be acquired through fecal microbiota transplantation., CrAss-like phages are bacterial viruses often found in the human gut. Here, Siranosian et al. analyze gut metagenomic data to evaluate the patterns of acquisition, transmission and strain diversity of these phages in mother-infant pairs and in patients undergoing fecal microbiota transplantation.

Probiotics and other bacteriotherapies are actively being explored and applied as symptom- and disease-modifying agents. In a recent issue of Cell, two papers contribute to our understanding of how live bacterial therapies variably affect individuals and the short- and longer-term impact of these therapies on colonization and host response.

Summary The intestinal microbiota provides colonization resistance against pathogens, limiting pathogen expansion and transmission. These microbiota-mediated mechanisms were previously identified by observing loss of colonization resistance after antibiotic treatment or dietary changes, which severely disrupt microbiota communities. We identify a microbiota-mediated mechanism of colonization resistance against Salmonella enterica serovar Typhimurium (S. Typhimurium) by comparing high-complexity commensal communities with different levels of colonization resistance. Using inbred mouse strains with different infection dynamics and S. Typhimurium intestinal burdens, we demonstrate that Bacteroides species mediate colonization resistance against S. Typhimurium by producing the short-chain fatty acid propionate. Propionate directly inhibits pathogen growth in vitro by disrupting intracellular pH homeostasis, and chemically increasing intestinal propionate levels protects mice from S. Typhimurium. In addition, administering susceptible mice Bacteroides, but not a propionate-production mutant, confers resistance to S. Typhimurium. This work provides mechanistic understanding into the role of individualized microbial communities in host-to-host variability of pathogen transmission.

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) bla(OXA-48 like), 20.8% (5/24) bla(KPC), 20.8% (5/24) bla(NDM), 20.8% (5/24) bla(SME), 8.3% (2/24) bla(IMP), and 4.2% (1/24) bla(VIM). Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing bla(KPC) were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, and imipenem–relebactam; bla(OXA-48 like)–positive isolates were 100% susceptible to ceftazidime–avibactam; and metallo β-lactamase–positive isolates were nearly all nonsusceptible to above antibiotics. Carbapenemase gene-negative CRE were 100% (38/38), 92.1% (35/38), 89.5% (34/38), and 31.6% (12/38) susceptible to ceftazidime–avibactam, meropenem–vaborbactam, imipenem–relebactam, and ceftolozane–tazobactam, respectively. None of the CRE strains were identical by whole genome sequencing. At this health system, CRE were mediated by diverse mechanisms with predictable susceptibility to newer β-lactamase inhibitors.

A comprehensive evaluation of every patient with a bloodstream infection includes an attempt to identify the infectious source. Pathogens can originate from various places, such as the gut microbiota, skin and the external environment. Identifying the definitive origin of an infection would enable precise interventions focused on management of the source1,2. Unfortunately, hospital infection control practices are often informed by assumptions about the source of various specific pathogens; if these assumptions are incorrect, they lead to interventions that do not decrease pathogen exposure3. Here, we develop and apply a streamlined bioinformatic tool, named StrainSifter, to match bloodstream pathogens precisely to a candidate source. We then leverage this approach to interrogate the gut microbiota as a potential reservoir of bloodstream pathogens in a cohort of hematopoietic cell transplantation recipients. We find that patients with Escherichia coli and Klebsiella pneumoniae bloodstream infections have concomitant gut colonization with these organisms, suggesting that the gut may be a source of these infections. We also find cases where typically nonenteric pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiota, thereby challenging the existing informal dogma of these infections originating from environmental or skin sources. Thus, we present an approach to distinguish the source of various bloodstream infections, which may facilitate more accurate tracking and prevention of hospital-acquired infections.

The Annual Advances in Genome Biology and Technology (AGBT) General Meeting was held in Orlando, Florida, USA, on the 12–15 February 2018. Professors Ami S. Bhatt and Christina Curtis from Stanford University, USA, report advances and applications in the field that were discussed at the meeting.

Bloodstream infection is the most common infectious complication in hematopoietic cell transplantation recipients. Culture-based sequencing approaches have been previously applied to interrogate the intestine as a reservoir of these bloodstream pathogens. To evaluate the genomic concordance of bloodstream pathogens and bacterial strains within the intestinal microbiome using whole genome sequencing (WGS), we developed StrainSifter, a bioinformatic pipeline to compare nucleotide variation between bacterial isolate strains and stool metagenomes. We applied StrainSifter to bloodstream isolates and stool metagenome samples from a cohort of 30 hematopoietic stem cell transplant recipients with bloodstream infections at a single academic center. StrainSifter is designed to 1) identify single nucleotide variants (SNVs) between isolate and metagenomic short reads aligned to assembled draft genomes using stringent alignment, coverage, and variant frequency criteria, and 2) output both phylogenetic trees and SNV counts for clinical and epidemiologic strain comparison. Using StrainSifter, we identified enteric BSI isolates - including Enterococcus faecium, Klebsiella pneumoniae, Escherichia coli, and Streptococcus mitis - that were highly concordant with those in the gut microbiota. We also identified highly concordant strains of Staphylococcus epidermidis and Pseudomonas aeruginosa between the bloodstream and gut microbiome, an unexpected finding for typically non-enteric organisms. In contrast to previous studies demonstrating intestinal domination by pathogenic bacteria preceding BSI, we found significant heterogeneity in relative pathogen abundance prior to infection. These findings demonstrate not only the utility of StrainSifter in strain matching between isolate and metagenomic sequencing data, but also provide a more precise and comprehensive investigation of the intestine as a reservoir of diverse pathogens capable of causing bloodstream infections in hematopoietic stem cell transplant patients.

Carbapenem-resistant Enterobacteriaceae (CRE) are emerging as a major health threat in North America. The mechanism of resistance to carbapenems has therapeutic and public health implications. We comprehensively characterized the underlying mechanisms of carbapenem resistance in CRE isolates recovered between 2013 and 2016 at a health system in Northern California. Genotypic methods were used to detect carbapenemases and plasmid-encoded cephalosporinases, and mass spectrometry was used to quantify relative porin levels for OmpC and OmpF and their analogs. MICs for imipenem-relebactam, meropenem-vaborbactam, ceftazidime-avibactam, and ceftolozane-tazobactam were measured. Whole genome sequencing was used for strain typing. A carbapenemase gene encoding blaOXA-48 like, blaNDM, blaKPC, blaSME, blaIMP, and blaVIM was detected in 38.7% (24/62) of CRE isolates. Porin levels was down at least 2-fold in 91.9% (57/62) of isolates. Including carbapenemase genes and porin loss, the mechanism of resistance was identified in 95.2% (59/62) of CRE isolates. Of the carbapenemase gene-positive isolates, blaKPC -positive isolates were 100% susceptible to ceftazidime-avibactam, meropenem-vaborbactam, and imipenem-relebactam; blaOXA-48 like-positive isolates were 100% susceptible to ceftazidime-avibactam; and blaSME-positive isolates were 100% susceptible to meropenem-vaborbactam and ceftolozane-tazobactam. 100% (38/38), 92.1% (35/38), 89.5% (34/38), and 31.6% (12/38) of carbapenemase gene-negative CRE isolates were susceptible to ceftazidime-avibactam, meropenem-vaborbactam, imipenem-relebactam, and ceftolozane-tazobactam, respectively. None of the CRE strains were genetically identical. In conclusion, at this health system in Silicon Valley, carbapenemase-producing CRE occurred sporadically and were mediated by diverse mechanisms. Nucleic acid testing for blaOXA-48 like, blaNDM, blaKPC, blaIMP, and blaVIM was sufficient to distinguish between carbapenemase-producing and non-producing CRE and accurately predicted susceptibility to ceftazidime-avibactam, meropenem-vaborbactam and imipenem-relebactam.

Although shotgun metagenomic sequencing of microbiome samples enables partial reconstruction of strain-level community structure, obtaining high-quality microbial genome drafts without isolation and culture remains difficult. Here, we present an application of read clouds, short-read sequences tagged with long-range information, to microbiome samples. We present Athena, a de novo assembler that uses read clouds to improve metagenomic assemblies. We applied this approach to sequence stool samples from two healthy individuals and compared it with existing short-read and synthetic long-read metagenomic sequencing techniques. Read-cloud metagenomic sequencing and Athena assembly produced the most comprehensive individual genome drafts with high contiguity (200-kb N50, fewer than ten contigs), even for bacteria with relatively low (20×) raw short-read-sequence coverage. We also sequenced a complex marine-sediment sample and generated 24 intermediate-quality genome drafts (70% complete,10% contaminated), nine of which were complete (90% complete,5% contaminated). Our approach allows for culture-free generation of high-quality microbial genome drafts by using a single shotgun experiment.

Our understanding of natural microbial communities is shaped by the careful investigation of a relatively small number of isolated and cultured organisms, and by analysis of genomic sequences obtained by culture-free metagenomic sequencing approaches. Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire. Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture. Recent molecular techniques that partition long DNA fragments and then barcode short fragments derived from them produce “read clouds”, which are short-read sequences containing long-range information. Here, we present a novel application of a read cloud technique to microbiome samples, as well as Athena, a de novo assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to sequence human stool samples from two healthy individuals, and compare it to existing short read and synthetic long read metagenomic sequencing approaches. We find that read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts. These genome drafts are also highly contiguous (>200kb N50

Differences in microbial genomes can result in vastly different phenotypes and functions. Consequently, it is critical to understand the genome variations that differentiate microbial strains. Here, we discuss recent exciting advances that enable structural variant measurement, their associated phenotypes and the horizon for future discovery.

Invariant natural killer T (iNKT) cells can potently inhibit graft-versus-host-disease (GVHD) in animal models through the production of Interleukin-4. Once considered a homogeneous population, it is now well established that murine iNKT cells differentiate during thymic development into three distinct sublineages, distinguished based on the expression of transcription factors and effector molecules: Th1-like iNKT (iNKT1) cells, Th2-like iNKT (iNKT2) cells, and Th17-like iNKT (iNKT17) cells. In this study, we investigated the immune regulatory potential of iNKT1, iNKT2 and iNKT17 cell subsets. In order to identify surface molecules whose expression would allow us to isolate viable iNKT1, iNKT2 and iNKT17 cells, we performed single cell RNA sequencing analysis on murine thymic iNKT cells isolated from FVB/N mice by flow cytometry based on PBS-57-CD1d-Tetramer staining. The results of this analysis together with previous knowledge allowed us to develop a sorting strategy to isolate iNKT1 (ICOS- PD1- CD27+ CD24-), iNKT2 (ICOS+ PD1+ CD27+ CD4+ CD24-), iNKT17 (ICOS+ PD1+ CD4- CD27- CD24-) cells, whose purity was confirmed by intra-nuclear staining for the transcription factors PLZF and RORgT. To assess the immune regulatory potential of the three iNKT sublineages, we employed a murine major histocompatibility complex (MHC)–mismatched bone marrow transplantation model. Lethally irradiated BALB/c (H-2Kd) mice were injected intravenously with T cell depleted-bone marrow (TCD-BM) cells and conventional CD4 and CD8 T cells (Tcon, 10e6 cells/mouse) from FVB/N (H-2kq) mice. Additionally, 5 × 10e4 sorted iNKT1, iNKT2 or iNKT17 cells from FVB/N donors were injected the same day. A significant survival benefit was observed when iNKT2 (p=0.0166) and iNKT17 (p=0.033) cells were adoptively transferred compared to mice that only received TCD-BM and Tcon, whereas there was no survival benefit in the group that received iNKT1 cells. In addition, body weight was improved in mice that received iNKT2 (day +41: p=0.009, day +49: p=0.005 and day +59: p= 0.005) or iNKT17 (day +59: p= 0.006) compared to mice that received iNKT1 cells. Clinical GVHD scores were also improved in mice that received iNKT2 (day +41: p= 0.012, day +51: p= 0.005) or iNKT17 (day +28: p=0.05, day +51: p=0.007) compared to mice that received iNKT1 cells. Interestingly, we found that even 1 × 10e4 iNKT2 (p= 0.008) and iNKT17 (p= 0.04) significantly suppressed GVHD. In summary, we demonstrate here that only iNKT2 and iNKT17 cells mitigated GVHD, whereas iNKT1 had no detectable immune regulatory potential. To our knowledge, this is the first study to show functional differences between iNKT sublineages, indicating that iNKT1, iNKT2 and iNKT17 cells have diverse functions and providing new biological insights that will be useful for developing iNKT cell-based cell therapies.

Ami S. Bhatt F.W.H. and A.S.B. contributed equally to this work. Corresponding author: Ami S. Bhatt, MD, PhD, Departments of Medicine and Genetics, Center for Innovation in Global Health, Stanford University, 269 Campus Dr, Stanford, CA 94305; e-mail: asbhatt@stanford.edu Despite living in a connected world, many research projects are developed with a so-called “convenience bias,” resulting in partnerships based on existing professional networks and collaborations. In addition, community-based cancer control programs are often implemented independently to address specific urgent and existing needs. Consequently, these projects and programs do not benefit as much as they could from best practices and protocols developed through other long-term engagements. As the global burden of cancer increases, cancer researchers and program managers are likely to benefit from a more complete understanding of ongoing work in cancer control. The limited availability of tools for collaboration and sharing of best practices have resulted in a call to action for the scientific community to partner on the development of a platform that provides knowledge of existing resources and expertise.

Humans are now understood to be in complex symbiosis with a diverse ecosystem of microbial organisms, including bacteria, viruses, and fungi. Efforts to characterize the role of these microorganisms, commonly referred as the microbiota, in human health have sought to answer the fundamental questions of what organisms are present, how are they functioning to interact with human cells, and by what mechanism are these interactions occurring. In this review, we describe recent efforts to describe the microbiota in healthy and diseased individuals, summarize the role of various molecular technologies (ranging from 16S ribosomal RNA to shotgun metagenomic sequencing) in enumerating the community structure of the microbiota, and explore known interactions between the microbiota and humans, with a focus on the microbiota’s role in hematopoiesis and hematologic diseases.

Rising rates of infections resulting from antibiotic-resistant bacteria (ARB) have led to a worldwide public health crisis calling for a significant improvement in antimicrobial stewardship in all healthcare settings [1]. The burden of antibiotic resistance is high for immunocompromised patients or those who have prolonged exposure to a healthcare setting; particularly vulnerable populations include those who undergo allogeneic hematopoietic stem cell transplantation (allo-HCT) [2]. Immunocompromised patients have higher rates of morbidity and mortality as a result of ARBs [3–6] and colitis resulting from Clostridium difficile (CDI) [7]. This finding is corroborated by the report by Bilinski et al. [8] in this issue of Biology of Blood and Marrow Transplantation in which intestinal colonization of allo-HCT patients with ARBs was associated with higher mortality. In their retrospective analysis, patients were screened for ARBs, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus spp., and extended-spectrum beta-lactamase-producing or carbapenamase-producing Enterobacteriaceae, before HCT by rectal swab and culture methods. Within the cohort of 107 allo-HCT patients, gut colonization by ARBs on admission was not only associated with decreased overall survival compared with noncolonized patients (34% versus 74%, respectively, at 24 months, P < .001) but also with an increased incidence of systemic infection, acute graft-versus-host disease (GVHD), and nonrelapse mortality. In a multivariate analysis the only significant predictor for overall survival was gut colonization by ARBs (hazard ratio, 3.53; 95% confidence interval, 1.71 to 7.28). Positive blood cultures were observed more often in colonized patients, and these patients were also more likely to die from infection. Although details of these infectious deaths are not presented, it would be interesting to know which specific systemic infections were found and whether CDI contributed to the increase in mortality, as has been found previously [7]. Assuming that in-hospital use of broad-spectrum antibiotics is a major driver of ARB colonization, the report by Bilinksi et al. supports a growing body of evidence that promotes antimicrobial stewardship practices even—and perhaps especially—in those who are immunocompromised.

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.

BackgroundOrganizations that issue guidance on breast cancer recommend the use of immunohistochemistry (IHC) for providing appropriate and precise care. However, little focus has been directed to the identification of maximum allowable turnaround times for IHC, which is necessary given the diversity of hospital settings in the world. Much less effort has been committed to the development of digital tools that allow hospital administrators to monitor service utilization histories of their patients.MethodsIn this retrospective cohort study, we reviewed electronic and paper medical records of all suspected breast cancer patients treated at one secondary-care hospital of the Mexican Institute of Social Security (IMSS), located in western Mexico. We then followed three years of medical history of those patients with IHC testing.ResultsIn 2014, there were 402 breast cancer patients, of which 30 were tested for some IHC biomarker (ER, PR, HER2). The subtyping allowed doctors to adjust (56.7 %) or confirm (43.3 %) the initial therapeutic regimen. The average turnaround time was 56 days. Opportune IHC testing was found to be beneficial when it was available before or during the first rounds of chemotherapy.ConclusionsThe use of data mining tools applied to health record data revealed that there is an association between timely immunohistochemistry and improved outcomes in breast cancer patients. Based on this finding, inclusion of turnaround time in clinical guidelines is recommended. As much of the health data in the country becomes digitized, our visualization tools allow a digital dashboard of the hospital service utilization histories.

In this issue of Cell Host & Microbe, Caballero et al. (2017) define a precise, limited consortium of commensal bacteria that restores resistance to colonization by clinically vexing vancomycin-resistant Enterococcus species.

In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products. This decision was due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC-containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the intestinal microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction of either infant or maternal intestinal microbiotas following 10 months of exposure after birth. However, broadly antibiotic-resistant species from the phylum Proteobacteria were enriched in stool samples from mothers in TC households only after the introduction of triclosan-containing toothpaste. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, these results suggest detected taxonomic differences are associated with potential harmful effects on host physiology, highlighting the need for consumer safety testing of self-care products not subject to the ban on the human microbiome and health outcomes.

Introduction: Cognitive errors are commonly made by patients during medical visits, traditionally thought to be due to gaps in communication and a complicated subject matter; use of diagrams and post-visit summaries has had a modest effect in improving in patient understanding and recall. We hypothesize that those cognitive errors can also be understood by using the behavioral economics framework of “System 1” mindset, in which patients are reliant on intuition and vulnerable to heuristics, as opposed to “System 2” mindset, which is reflective, slow and detailed-oriented, and that patient-reported outcome measures (PROMs) can shift patients to a “System 2” mindset. Methods: In this pilot, patients from a tertiary center adult congenital heart disease clinic were given Frederick’s Cognitive Reflection Test (CRT; score of 0 to 3, with low scores associated with System 1 mindset) prior to a routine clinical visit. They were randomly assigned to complete the PROMIS and Kansas City Cardiomyopathy Questionnaire either before or after the CRT. The primary endpoint was the mean CRT score in all patients; the secondary endpoint was a comparison of the effect of PROMs. Kruskal-Wallis test was used to compare ordinal variables. Results: Patients (N=47) had a mean age of 48, 93% were native English speakers and all had completed high school (93% at least started college). The median CRT score was 0 (IQR 0-1; 74% had a score of 0), and the mean score was 0.45 (SD 0.85), which is lower than any previously published results in control populations (mean scores 0.57 to 2.18 in 35 studies with 3428 respondents). CRT scores were numerically but not statistically higher in the group who completed the PROMs first (32% vs 20% had a score >0, mean 0.5 vs. 0.4, p=0.46). Patients randomized to PROMs first reported more often that they remembered to ask the physician the questions they had (94.7% vs. 86.7%) and were less nervous during the visit (15.8% vs. 46.7%). Conclusions: The finding that patients are in an intuitive state of mind prior to routine clinic visits, reliant on heuristics and vulnerable to biases, offers an important new framework in which to devise interventions to improve patient participation in their medical visits, recall of information, and decision-making. PROM are a promising candidate for intervention that will be further studied.

Background Bronchiolitis obliterans syndrome (BOS) is a clinical manifestation of chronic allograft rejection following lung transplantation. We examined the quantitative measurements of the proximal airway and vessels and pathologic correlations in subjects with BOS. Methods Patients who received a lung transplant at the Brigham and Women's Hospital between December 1st 2002 and December 31st 2010 were included in this study. We characterized the quantitative CT measures of proximal airways and vessels and pathological changes. Results 94 (46.1%) of the 204 subjects were included in the study. There was a significant increase in the airway vessel ratio in subjects who developed progressive BOS compared to controls and non-progressors. There was a significant increase in airway lumen area and decrease in vessel cross sectional area in patients with BOS compared to controls. Patients with BOS had a significant increase in proximal airway fibrosis compared to controls. Conclusions BOS is characterized by central airway dilation and vascular remodeling the degree of which is correlated to decrements in lung function. Our data suggests that progressive BOS is a pathologic process that affects both the central and distal airways. This article is protected by copyright. All rights reserved.

The microbiota is known to influence the generation of hematopoietic progenitors, although the pathways underlying this process are still poorly understood. NOD1 and NOD2 are intracellular sensors for both Gram-positive and Gram-negative bacteria, but their role in steady-state hematopoiesis has never been characterized. We observed that stimulation with NOD1 or NOD2 ligand had no effect on the survival/proliferation of hematopoietic precursors. Nonetheless, NOD1, but not NOD2, ligand induced expression of multiple hematopoietic cytokines (interleukin-7 [IL-7], Flt3L, stem cell factor [SCF], ThPO, and IL-6) from bone marrow mesenchymal stromal cells (MSCs) in vitro. Moreover, in vivo administration of NOD1 ligand to germ-free mice restored the numbers of hematopoietic stem cells and precursors in bone marrow as well as serum concentrations of IL-7, Flt3L, SCF, and ThPO to the levels displayed by specific pathogen-free control animals. Based on these findings, we propose that NOD1 signaling in MSCs serves as an important pathway underlying the requirement for microbiota in the maintenance of steady-state hematopoiesis. This function is distinct from that triggered by lipopolysaccharide in both its broad effects on multiple progenitors and specific targeting of MSCs as cytokine producing intermediates.

Immunocompromised individuals are at high risk of developing Clostridium difficile-associated disease (CDAD). Fecal microbiota transplantation (FMT) is a highly effective therapy for refractory or recurrent CDAD and, despite safety concerns, has recently been offered to immunocompromised patients. We investigated the genomics of bacterial composition following FMT in immunocompromised patients over a 1-year period. Metagenomic, strain and gene-level bacterial dynamics were characterized in two CDAD-affected hematopoietic stem cell (HCT) recipients following FMT. We found alterations in gene content, including loss of virulence and antibiotic resistance genes. These alterations were accompanied by long-term bacterial divergence at the species and strain levels. Our findings suggest limited durability of the specific bacterial consortium introduced with FMT and indicate that alterations of the functional potential of the microbiome are more complex than can be inferred by taxonomic information alone. Our observation that FMT alone cannot induce long-term donor-like alterations of the microbiota of HCT recipients suggests that FMT cannot indefinitely supersede environmental and/or host factors in shaping bacterial composition.

During medical visits, the stakes are high for many patients, who are put in a position to make, or to begin to make, important health-related decisions. But in such visits, patients often make cognitive errors. Traditionally, those errors are thought to result from poor communication with physicians; complicated subject matter; and patient anxiety. To date, measures to improve patient understanding and recall have had only modest effects. This paper argues that an understanding of those cognitive errors can be improved by reference to a behavioral science framework, which distinguishes between a “System 1” mindset, in which patients are reliant on intuition and vulnerable to biases and imperfectly reliable heuristics, and a “System 2” mindset, which is reflective, slow, deliberative, and detailed-oriented. To support that argument, we present the results of a randomized-assignment experiment that shows that patients perform very poorly on the Cognitive Reflection Test and thus are overwhelmingly in a System 1 state prior to a physician visit. Assigning patients the task of completing patient-reported outcomes measures immediately prior to the visit had a small numerical, but not statistically significant, shift towards a reflective frame of mind. We describe hypotheses to explain poor performance by patients, which may be due to anxiety, a bandwidth tax, or a scarcity effect, and outline further direction for study. Understanding the behavioral sources of errors on the part of patients in their interactions with physicians and in their decision-making is necessary to implement measures improve shared decision-making, patient experience, and (perhaps above all) clinical outcomes.

Objective To characterize the microbiome of the temporal artery in patients with giant cell arteritis (GCA), and to apply an unbiased and comprehensive shotgun sequencing-based approach to determine whether there is an enrichment of candidate pathogens in the affected tissue. Methods Temporal artery biopsy specimens were collected from patients at a single institution over a period of 4 years, and unbiased DNA sequencing was performed on 17 formalin-fixed, paraffin-embedded specimens. Twelve of the 17 patients fulfilled the clinical and histopathologic criteria for GCA, and the other 5 patients served as controls. Using PathSeq software, human DNA sequences were computationally subtracted, and the remaining non-human DNA sequences were taxonomically classified using a comprehensive microbial sequence database. The relative abundance of microbes was inferred based on read counts assigned to each organism. Comparison of the microbial diversity between GCA cases and controls was carried out using hierarchical clustering and linear discriminant analysis of effect size. Results Propionibacterium acnes and Escherichia coli were the most abundant microorganisms in 16 of the 17 samples, and Moraxella catarrhalis was the most abundant organism in 1 control sample. Pathogens previously described to be correlated with GCA were not differentially abundant in cases compared to controls. There was not a significant burden of likely pathogenic viruses. Conclusion DNA sequencing of temporal artery biopsy specimens from GCA cases, in comparison with non-GCA controls, showed no evidence of previously identified candidate GCA pathogens. A single pathogen was not clearly and consistently associated with GCA in this case series.

Graft-versus-host disease (GVHD) remains the major source of morbidity and transplant-related mortality after allogeneic hematopoietic cell transplant (alloHCT). Since the mid-1980s, the standard prophylaxis for GVHD has been a calcineurin inhibitor plus methotrexate (MTX). Subsequent clinical trials designed to intensify GVHD prophylaxis have shown an increased risk of relapse, thus negating survival benefit. The ideal GVHD prophylaxis regimen is therefore associated with a high graft-versus-host disease-free, relapse-free survival (GRFS), a composite endpoint that reflects survival without morbidity. A recent 3-arm randomized phase II study conducted through the Blood and Marrow Transplant Clinical Trials Network (BMT CTN 1203) showed a benefit in GRFS using post-transplant cyclophosphamide, tacrolimus, and mycophenolate mofetil (PTCy/Tac/MMF) with a hazard ratio of 0.72 (90% confidence interval 0.54 - 0.94, p-0.044) compared to contemporary non-randomized CIBMTR Tac/MTX controls. Based upon these results, the BMT CTN has launched 1703, a multicenter randomized phase III study of standard Tac/MTX vs PTCy/Tac/MMF in the setting of reduced intensity conditioning, matched peripheral blood stem cell transplantation (RIC PBSCT). The primary endpoint of 1703 is GRFS at 1 year, and several secondary endpoints, including patient-reported outcomes, will be analyzed. A series of recent, predominantly single-center studies have shown an association with the composition of intestinal microbiota and the development of acute GVHD, which suggests that this may be a potential modifiable biomarker of disease. The generalizability of findings from these studies is yet unknown, and no large multi-center studies on the intestinal microbiota of HCT patients has yet been carried out. Patients enrolled in 1703 will be eligible to co-enroll in BMT CTN 1801, the Mi-Immune study, detailing microbiota and immune reconstitution in this cohort. The primary endpoint of 1801 is 1-year non-relapse mortality by tertiles of stool microbial diversity at engraftment. Secondary objectives, including effect of GVHD prophylaxis on diversity, oligodomination and risk of bloodstream infection, volume of antimicrobial exposure, and T-cell receptor diversity, will be analyzed. The combined studies of BMT CTN 1703/1801 will define the standard of care for GVHD prophylaxis in the RIC PBSCT setting and vastly expand our knowledge on the impact of intestinal microbiota in critical outcomes after alloHCT. This clinical trial is registered at ClinicalTrials.gov NCT03959241. Figure Disclosures Holtan: Incyte: Consultancy; Bristol-Myers Squibb: Consultancy; Janssen: Consultancy; CSL Behring: Consultancy. Bhatt:ArcBio: Other: Scientific Advisory Board; January.ai: Other: Scientific Advisory Board; Caribou Bioscience: Other: Scientific Advisory Board; Kaleido Biosciences: Consultancy, Other: Paid Consultant; Janssen Human Microbiome Institute: Consultancy, Other: Paid Consultant; Illumina: Honoraria; 10x Genomics: Other: Research collaboration without funding support; Illumina: Other: Research collaboration without funding support; Agilent: Research Funding; Global Oncology, Inc: Other: Nonprofit Board. Perales:Bellicum: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bristol-Meyers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees; MolMed: Membership on an entity's Board of Directors or advisory committees; NexImmune: Membership on an entity's Board of Directors or advisory committees; Abbvie: Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees; Omeros: Honoraria, Membership on an entity's Board of Directors or advisory committees; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Merck: Consultancy, Honoraria; Medigene: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees; Kyte/Gilead: Research Funding; Miltenyi: Research Funding; Incyte: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Nektar Therapeutics: Honoraria, Membership on an entity's Board of Directors or advisory committees. Kean:HiFiBio: Consultancy; BlueBirdBio: Research Funding; Gilead: Research Funding; Regeneron: Research Funding; EMDSerono: Consultancy; FortySeven: Consultancy; Magenta: Research Funding; Kymab: Consultancy; Jazz: Research Funding; Bristol Meyers Squibb: Patents & Royalties, Research Funding. Hamadani:Medimmune: Consultancy, Research Funding; Takeda: Research Funding; Pharmacyclics: Consultancy; Janssen: Consultancy; Merck: Research Funding; Celgene: Consultancy; Otsuka: Research Funding; ADC Therapeutics: Consultancy, Research Funding; Sanofi Genzyme: Research Funding, Speakers Bureau. Bolaños-Meade:Incyte Corporation: Other: DSMB fees.

Introduction: Early preclinical studies demonstrating that eradication of intestinal bacteria could prevent the development of acute graft-versus-host disease (aGVHD) after allogeneic hematopoietic stem cell transplantation (HSCT) led many adult and pediatric HSCT programs to practice "gut decontamination" (GD) with non-absorbable oral antibiotics for aGVHD prophylaxis. However, there is insufficient data supporting a clear benefit for GD in HSCT patients. Recent adult HSCT studies show that GVHD-related mortality is associated with decreased bacterial diversity in the gut microbiome, suggesting that certain bacterial species are protective against aGVHD. GD may decrease microbiome diversity and lead to worse post-HSCT outcomes. Methods: We conducted a randomized phase 2 study to examine the impact of GD on intestinal microbiome composition in pediatric allogeneic HSCT patients. 20 patients were enrolled and randomized to receive (GD) or not receive (no GD) oral vancomycin-polymyxin per our institutional standard from day -5 through engraftment. Stool samples were collected pre-transplant, weekly until neutrophil engraftment, monthly through day +100, then at 6 months and 1-year post-HSCT. Our primary endpoint is bacterial diversity, quantified by Shannon diversity index, at 2 weeks post-HSCT. Change in diversity is defined as the delta of diversity before transplantation compared to the minimum diversity seen in a single patient in a one-week window (around 14 days post-transplantation). This change in diversity was then averaged (mean) across each treatment arm. The stool microbiome was characterized using shotgun metagenomic sequencing (Nextera Tagmentation and Illumina HiSeq4000 Sequencing) for 10 patients to date, with median count of 1.4x107 reads per sample (range 1.3x106 to 3.3x107). Following quality control (FastQC, Trim Galore, Super Deduper), reads are assigned taxonomic designations using Kraken2 and GenBank (Oct. 2018) database. Secondary endpoints include the frequency of diarrhea (defined as >3 bowel movements per day in the first 7 days post-HSCT), incidence of aGVHD and bacteremia during the first 100 days post-transplant, immune reconstitution, survival, and malignant disease relapse at 2 years after study entry. Comparisons by treatment group were performed with Fisher's exact test (binary) or Wilcoxon rank-sum test (continuous). Results: Baseline patient characteristics were similar between the two arms (Table 1). At present,5 patients (25%) have completed 2 years of follow up, 4 of 15 patients with malignant disease (27%) have had relapse (3 GD, 1 No GD), and 2 patients (10%) in the No GD arm have died (1 malignant relapse, 1 refractory chronic GVHD). Microbiome analysis in the first 10 patients (4 GD, 6 No GD) demonstrates that the average change in Shannon diversity score at 2 weeks is 1.7 (SD 0.86) in GD and 0.65 (SD 0.61) in No GD (Table 2). Diarrhea occurred in 4/10 patients in GD vs 4/10 patients in no GD (p≥0.99).1/10 patients in GD and 3/10 in No GD developed aGVHD grade II or above(p=0.58). Bacteremia within the first 100 days post-HSCT occurred in 1/10 patient in GD, whereas 5/10 patients in No GD had 8 different bacteremia events (p=0.14) (Table 3). Conclusions: This is the first randomized study of gut decontamination in pediatric patients undergoing HSCT with long-term prospective post-transplant stool sample collection and immune monitoring. Though the small sample size is currently not powered to detect differences in clinical outcomes between the 2 study arms, the descriptive microbiome and immune reconstitution data will inform larger studies. There is no statistical difference in the diarrhea, aGVHD, or bacteremia incidence between the two groups but it is interesting that there was 1 vs 8 bacteremia events in GD vs No GD. Microbiota diversity results from our pilot study with 10 patients indicate a trend toward lower diversity at 2 weeks post-transplant in the GD arm. Microbiome analysis of the remaining samples from the remaining 10 patients is underway as well as longitudinal analysis of samples from all patients. Describing the changes to the microbiota composition over time in two groups will provide insight to practice of GD, potential targets for aGVHD, and will provide preliminary data to understand which microbes and microbial gene-pathways may influence immune reconstitution. Disclosures London: United Therapeutics: Consultancy; ArQule, Inc: Consultancy. Ritz:Draper Labs: Consultancy; Kite Pharma: Research Funding; Avrobio: Consultancy; LifeVault Bio: Consultancy; Merck: Research Funding; TScan Therapeutics: Consultancy; Talaris Therapeutics: Consultancy; Celgene: Consultancy; Aleta Biotherapeutics: Consultancy; Equillium: Research Funding. Bhatt:ArcBio: Other: Scientific Advisory Board; January.ai: Other: Scientific Advisory Board; Caribou Bioscience: Other: Scientific Advisory Board; Kaleido Biosciences: Consultancy, Other: Paid Consultant; Janssen Human Microbiome Institute: Consultancy, Other: Paid Consultant; Illumina: Honoraria; 10x Genomics: Other: Research collaboration without funding support; Illumina: Other: Research collaboration without funding support; Agilent: Research Funding; Global Oncology, Inc: Other: Nonprofit Board.

Transcatheter pulmonary valve replacement (TPVR) was approved in 2015. Real world practice, including patient selection, outcomes and complications, in patients who may not meet the trial instructions for use, is not well known. Demographics, procedural characteristics and outcomes were collected

Alternative graft sources (umbilical cord blood [UCB], matched unrelated donors [MUD], or mismatched unrelated donors [MMUD]) enable patients without a matched sibling donor to receive potentially curative hematopoietic cell transplantation (HCT). Retrospective studies demonstrate comparable outcomes among different graft sources. However, the risk and types of infections have not been compared among graft sources. Such information may influence the choice of a particular graft source. We compared the incidence of bacterial, viral, and fungal infections in 1781 adults with acute leukemia who received alternative donor HCT (UCB, n= 568; MUD, n = 930; MMUD, n = 283) between 2008 and 2011. The incidences of bacterial infection at 1 year were 72%, 59%, and 65% (P

Ebstein’s anomaly is a congenital malformation of the tricuspid valve and the right heart with a spectrum of clinical and morphologic presentations. Minor anomalies of the tricuspid valve may not be recognized until adulthood whereas major anomalies leading to heart failure and cyanosis require surgical intervention earlier in life. Echocardiography is the imaging modality of choice for both diagnosis and management of patients with Ebstein’s anomaly. Surgical correction includes tricuspid valve repair or replacement and associated findings such as interatrial communications and arrhythmias should be addressed at the time of surgery. Pre-pregnancy evaluation should be considered in all Ebstein’s anomaly patients and for those who are cyanotic, surgical correction must be considered due to the maternal and fetal ramifications of cyanosis in pregnancy. Most acyanotic Ebstein’s anomaly patients are able to tolerate pregnancy with manageable or no complications. Those patients with mild anomalies and no right heart dilation can participate in sports whereas those with severe anomalies are discouraged from competitive sports. Physical activity as tolerated is important in all patients with adult congenital heart disease. Adult congenital heart specialists should evaluate patients prior to cardiac or noncardiac surgery. Longitudinal clinical follow-up in all Ebstein’s anomaly patients (both repaired and unrepaired) is warranted to follow for signs and symptoms of heart failure, arrhythmias, cyanosis, and other associated findings. This should be ideally performed in collaboration with an adult congenital heart center of excellence.

After allogeneic hematopoietic stem cell transplantation (allo-HSCT), intestinal bacteria modulate risks of infection and graft-versus-host disease (GVHD). Neutropenic fever is common and treated with a choice of clinically equivalent antibiotics that target obligately anaerobic bacteria (anaerobes) to varying degrees. We retrospectively examined 857 allo-HSCT recipients and found that treatment of neutropenic fever with imipenem-cilastatin and piperacillin-tazobactam was associated with increased GVHD-related mortality at 5 years (21.5% in imipenem-cilastatin-treated patients vs. 13.1% in untreated patients, p=0.025, and 19.8% in piperacillin-tazobactam-treated patients vs. 11.9% in untreated patients, p=0.007). However, two other antibiotics also used to treat neutropenic fever, aztreonam and cefepime, were not associated with GVHD-related mortality (p=0.78 and p=0.98, respectively). Analysis of stool microbiota composition showed that piperacillin-tazobactam administration was associated with increased compositional perturbation. Studies in mouse models demonstrated similar effects of these antibiotics, as well as aggravated GVHD mortality with imipenem-cilastatin or piperacillin-tazobactm compared to aztreonam (p

Hematopoietic stem cell transplantation (HSCT) is a potentially life-saving therapy that often comes at the cost of complications such as graft-versus-host disease and post-transplant infections. With improved technology to under-stand the ecosystem of microorganisms (viruses, bacteria, fungi, and microeukaryotes) that make up the gut microbiota, there is increasing evidence of the microbiota’s contribution to the development of post-transplant complications. Antibiotics have traditionally been the mainstay of microbiota-altering therapies available to physicians. Recently, interest is increasing in the use of prebiotics and probiotics to support the development and sustainability of a healthier microbiota. In this review, we will describe the evidence for the use of prebiotics and probiotics in combating microbiota dysbiosis and explore the ways in which they may be used in future research to potentially improve clinical outcomes and decrease rates of graft-versus-host disease (GVHD) and post-transplant infection.

Background The aorta in patients with bicuspid aortic valve (BAV) is larger and grows more rapidly than in patients with tricommissural aortic valve. Young patients with BAV can have significant aortic dilation that places them at risk for morbidity and mortality. Objective The aims of this study were to determine the rate of growth of the aorta in young patients with BAV and to identify predictors of significant dilation and rapid aortic growth. Methods 333 patients were randomly selected from an inception cohort of 1192 patients with BAV identified between 1986 and 1999. Results Median age at the most recent study was 13.5 (0–30) years, 74% were male. Moderate/severe (Z>4) aortic root and ascending aortic dilation was present in 14/333 (5%) and 53/333 (16%) of patients, respectively. In longitudinal follow-up, only a minimal change in aortic Z-score was noted. Predictors of moderate/severe aortic root dilation included moderate/severe aortic regurgitation, absence of moderate/severe aortic stenosis and fusion of the right and left coronary leaflets. Predictors of moderate/severe ascending aortic dilation included moderate/severe aortic regurgitation and absence of aortic coarctation. Conclusion Moderate/severe dilation of the ascending aorta is common in young patients with BAV, but moderate/severe dilation of the aortic root is less common. The Z-scores for both remained relatively constant over time even in patients with significant dilation, implying that young children with moderate/severe aortic dilation may be at the highest risk for dilation-related complications as adults.

Recipients of hematopoietic stem cell transplantion (HCT) are at high risk for bloodstream infections (BSI); culture-based and marker gene sequencing approaches have been previously applied to interrogate the intestine as a reservoir of these pathogens. Identifying the source of bloodstream infections can impact infection control and prevention practices such as removing central venous catheters and placing patients in isolation. To evaluate the genomic concordance of bloodstream pathogens and bacterial strains within the intestinal microbiome, we developed StrainSifter (Figure 1), a streamlined bioinformatic pipeline using whole genome shotgun sequencing to compare nucleotide variation between bacterial isolate strains and metagenomes. We applied StrainSifter to bloodstream isolates and stool metagenome samples from a cohort of 30 HCT recipients with bloodstream infections at a single academic center. StrainSifter is designed to 1) identify single nucleotide variants (SNVs) between isolate and metagenomic short reads aligned to assembled draft genomes using stringent alignment, coverage, and variant frequency criteria, and 2) output both phylogenetic trees and SNV counts for clinical and epidemiologic strain typing and comparison. Using StrainSifter, we identified enteric BSI isolates - including Enterococcus faecium, Klebsiella pneumoniae, Escherichia coli, and Streptococcus mitis - that were identical or nearly identical with those in the gut microbiota. We also identified highly concordant strains of Staphylococcus epidermidis and Pseudomonas aeruginosa between the bloodstream and gut microbiome, an unexpected finding for typically non-enteric organisms. Although intestinal domination by pathogenic bacteria preceded BSI with E. faecium and E. coli as previous studies have demonstrated, we found significant heterogeneity in the relative abundance of pathogens prior to infection for other bacteria. These findings demonstrate the utility of StrainSifter in strain matching between isolate and metagenomic sequencing data, and provide a more precise and comprehensive investigation of the intestine as a potential reservoir of diverse pathogens capable of causing bloodstream infections in HCT recipients. These findings may have implications for the tracking and prevention of BSI previously classified as central-line associated bloodstream infections. Disclosures No relevant conflicts of interest to declare.

Invariant natural killer T (iNKT) cells are an interesting subpopulation of T cells that can potently inhibit graft-versus-host-disease (GVHD) through the production of Interleukin 4 (IL-4), while also carrying anti-tumor potential (Leveson-Gower et al. Blood. 2011;117:3220-9; Schneidawind et al. Blood. 2014;124:3320-8). Murine iNKT cells differentiate during thymic development into three distinct sublineages, named according to the classification of conventional T cells: Th1-like iNKT (iNKT1) cells, Th2-like iNKT (iNKT2) cells, and Th-17 like iNKT (iNKT17) cells (Brennan et al. Nat Rev Immunol. 2013; 13:101-1). In this study we investigated the immune regulatory and anti-tumor potential of iNKT1, iNKT2 and iNKT17 cell subsets. Thymic iNKT1 cells, iNKT2 cells and iNKT17 cells were isolated from 8-10 week-old FVB/NJ mice by flow cytometry based on PBS-57-CD1d-Tetramer and a combination of cell surface molecules (iNKT1: ICOS- PD1- CD27+ CD24-; iNKT2: ICOS+ PD1+ CD27+ CD4+ CD24-; iNKT17: ICOS+ PD1+ CD4- CD27- CD24-) and purity was confirmed by intra-nuclear staining for the transcription factors PLZF and RORγT. RNA sequencing analysis determined that iNKT1 cells were the main subset expressing proinflammatory and cytotoxic genes, such as Interferon gamma (IFN-γ), Fas Ligand (FasL), Perforin, and Granzyme B (Gzmb), whereas IL-4 was expressed by iNKT2 cells and, at a lesser extent, by iNKT17 cells. To assess the immuno-regulatory potential of the three iNKT sublineages, we employed a murine major histocompatibility complex (MHC)-mismatched bone marrow transplantation model. BALB/c (H-2Kd) recipients were lethally irradiated with 8.8 Gy; on the same day, 4 x 106 TCD-BM cells and 1 x 106 conventional CD4 and CD8 T cells (Tcon) from FVB/NJ (H-2kq) mice were injected intravenously. Additionally, 5 x 104 purified iNKT1, iNKT2 or iNKT17 cell subsets from FVB donors were injected. A significant survival benefit was observed when iNKT2 (p=0.017) and iNKT17 (p=0.033) cells were adoptively transferred compared to mice that only received TCD-BM and Tcon, whereas there was no survival benefit in the group that received iNKT1 cells. In addition, body weight was improved in mice that received iNKT2 (day +41: p=0.009, day +49: p=0.005 and day +59: p= 0.005) or iNKT17 (day +59: p= 0.006) compared to mice that received iNKT1 cells. Clinical GVHD scores were also improved in mice that received iNKT2 (day +41: p= 0.012, day +51: p= 0.005) or iNKT17 (day +28: p=0.05, day +51: p=0.007) compared to mice that received iNKT1 cells. Interestingly, we found that even 1 x104 iNKT2 (p= 0.008) and iNKT17 (p= 0.04) significantly suppressed GVHD. As iNKT1, iNKT2 and iNKT17 have a very different gene expression profile, we tested the ability of the sublineages to kill a B-cell lymphoma cell line transduced to express high levels of CD1d (A20-CD1d) in vitro and found that iNKT1 cells killed A20-CD1d cells significantly better than iNKT2 (p=0.006) or iNKT17 (p=0.0001) cells. These findings are in line with the sequencing data mentioned above, showing that iNKT1 cells express a more inflammatory phenotype. In summary, we demonstrate here that only iNKT2 and iNKT17 cells protect from GVHD, whereas iNKT1 cells have cytotoxic function. To our knowledge, this is the first study to show functional differences between the iNKT sublineages, suggesting that iNKT1, iNKT2 and iNKT17 cells have diverse functions. Therefore, these data provide new biological insights, which will be useful for developing iNKT cell-based cell therapy. Disclosures Chang: Spring Discovery: Membership on an entity's Board of Directors or advisory committees; Epinomics and Accent Therapeutics: Equity Ownership, Membership on an entity's Board of Directors or advisory committees.