Identification of unique molecular heterogeneity of human CD79, the signaling component of the human B cell antigen receptor (BCR), and synergistic potentiation of the CD79-targeted therapy of B cell tumors by co-targeting of CD79a and CD79b.

We identified unique molecular heterogeneity of CD79 of human B cell antigen receptor (BCR) that may open a new approach to the ongoing CD79b-targeted therapy of B cell tumors. The primary purpose of the present study is to gain new information valuable for the enhanced CD79-targeted therapy. The molecular heterogeneity of CD79 was identified by sequential immunoprecipitation of BCR by use of anti-CD79b monoclonal antibody (mAb) SN8 and anti-CD79a mAb SN8b. SN8 is the antibody component of polatuzumab vedotin, an anti-CD79b antibody drug conjugate, that has been widely used for therapy of diffuse large B-cell lymphoma (DLBCL). The sequential immunoprecipitation shows that anti-CD79b mAb will be able to react only with a subgroup of CD79 molecules while anti-CD79a mAb will react with another subgroup of CD79 molecules; CD79 is a disulfide-linked heterodimer of CD79a and CD79b. Therapeutic study of SCID mice bearing human B-cell tumor shows synergistic potentiation by co-targeting CD79b and CD79a. Furthermore, simultaneous targeting of PD-1 strongly potentiates CD79a/CD79b-targeted therapy of B cell tumors. Flow cytometry analyses of CD79a/CD79b on malignant B cells of patients may provide a method for selection of the candidate patients for the CD79a/CD79b dual targeting therapy.

Quantitative detection of RAS and KKS peptides in COVID-19 patient serum by stable isotope dimethyl labeling LC-MS.

Angiotensin and kinin metabolic pathways are reported to be altered by many diseases, including COVID-19. Monitoring levels of these peptide metabolites is important for understanding mechanisms of disease processes. In this paper, we report dimethyl labeling of amines in peptides by addition of formaldehyde to samples and deutero-formaldehyde to internal standards to generate nearly identical isotopic standards with 4 m/z units larger per amine group than the corresponding analyte. We apply this approach to rapid, multiplexed, absolute LC-MS/MS quantitation of renin angiotensin system (RAS) and kallikrein-kinin system (KKS) peptides in human blood serum. Limits of detection (LODs) were obtained in the low pg mL-1 range with 3 orders of magnitude dynamic ranges, appropriate for determinations of normal and elevated levels of the target peptides in blood serum and plasma. Accuracy is within ±15% at concentrations above the limit of quantitation, as validated by spike-recovery in serum samples. Applicability was demonstrated by measuring RAS and KKS peptides in serum from COVID-19 patients, but is extendable to any class of peptides or other small molecules bearing reactive -NH2 groups.

Endoglin inhibitor TRC105 with or without bevacizumab for bevacizumab-refractory glioblastoma (ENDOT): a multicenter phase II trial.

BACKGROUND: Glioblastoma (GBM), the most lethal primary brain tumor, has limited treatment options upon recurrence after chemoradiation and bevacizumab. TRC105 (carotuximab), a chimeric anti-endoglin (CD105) antibody, inhibits angiogenesis and potentiates activity of VEGF inhibitor bevacizumab in preclinical models. This study sought to assess safety, pharmacokinetics, and efficacy of TRC105 for bevacizumab-refractory GBM. METHODS: We conducted a pre-registered (NCT01564914), multicenter, open-label phase II clinical trial (ENDOT). We administered 10 mg/kg TRC105 monotherapy (first cohort) in adults with GBM and radiographic progression following radiation, temozolomide and bevacizumab therapy. Primary outcome was median time-to-progression (TTP), amended after first cohort's enrollment to median overall survival (mOS). Secondary outcomes were objective response rate, safety and tolerability, and progression-free survival (PFS). RESULTS: 6 patients were enrolled in TRC105 monotherapy cohort. Median TTP and PFS of 5 evaluable patients receiving monotherapy was 1.4 months, in whom plasma VEGF-A levels were elevated post-therapy. Lack of response led to protocol amendment, and second cohort's addition of bevacizumab+TRC105 with primary endpoint of mOS. 16 patients were enrolled in bevacizumab+TRC105 cohort. mOS of 15 evaluable patients was 5.7 (95%CI: 4.2-9.8) months. All 22 patients had measurable disease at baseline. Median PFS of 14 evaluable patients receiving bevacizumab+TRC105 was 1.8 months (95%CI 1.2-2.1). Serum TRC105 was measurable above target concentration of 25 ug/mL in all evaluable patients. Study medications were well-tolerated in both cohorts. Combined administration did not potentiate known toxicities of either medication, with cerebral hemorrhage not observed. CONCLUSIONS: Single-agent TRC105 lacks activity in bevacizumab-refractory GBM, possibly secondary to upregulated VEGF-A expression. Meaningful mOS in bevacizumab+TRC105 cohort warrants further trials to investigate efficacy of combination therapy.

Glioblastoma is an aggressive and lethal brain tumor, with patients typically expected to survive for 14 to 16 months after diagnosis. Nearly all patients experience tumor recurrence once conventional treatment strategies fail, after which a drug called bevacizumab is used. However, subsequent treatment options are extremely limited. We performed a clinical trial in which we investigated how safe and effective a new drug called TRC105 (carotuximab) is in patients who no longer respond to chemotherapy, radiotherapy or bevacizumab. We tested TRC105 both with and without bevacizumab, since TRC105 might enhance the activity of bevacizumab. We found that patients survived for an average of 5.7 months when given TRC105 and bevacizumab in combination. These findings suggest that further clinical trials are needed to confirm whether or not this combination therapy is a useful approach in patients with glioblastoma recurrence.

Pain treatment after total hip arthroplasty: Detailed statistical analysis plan for the RECIPE randomised clinical trial.

BACKGROUND: The RECIPE trial systematically investigates the effects of different combinations of paracetamol, ibuprofen and dexamethasone for pain treatment after total hip arthroplasty. To preserve transparency, minimise risk of bias and to prevent data-driven analysis, we present this detailed statistical analysis plan. METHODS: The RECIPE trial is a randomised, blinded, parallel four-group multicenter clinical trial for patients undergoing planned primary total hip arthroplasty. Interventions are initiated preoperatively and continued for 24 h postoperatively. Primary outcome is total opioid consumption 0-24 h after end of surgery. Primary analysis will be performed in the modified intention to treat population of all patients undergoing total hip arthroplasty, and all analyses will be stratified for site. We will perform pairwise comparisons between each of the four groups. The primary outcome will be analysed using the van Elteren test and we will present Hodges-Lehmann median differences and confidence intervals. Binary outcomes will be analysed using logistic regression. To preserve a family-wise error rate of <0.05, we will use a Bonferroni-adjusted alfa of 0.05/6 = 0.0083 for all six pairwise comparisons between groups when analysing the primary outcome. We will systematically assess the underlying statistical assumptions for each analysis. Data will be analysed by two blinded independent statisticians, and we will write abstracts covering all possible combinations of conclusions, before breaking the blind. DISCUSSION: The RECIPE trial will provide important information on benefit and harm of combinations of the most frequently used non-opioid analgesics for pain after primary hip arthroplasty.

Robotic eTEP versus IPOM evaluation: the REVEAL multicenter randomized clinical trial.

BACKGROUND: For small to medium-sized ventral hernias, robotic intraperitoneal onlay mesh (rIPOM) and enhanced-view totally extraperitoneal (eTEP) repair have emerged as acceptable approaches that each takes advantage of robotic instrumentation. We hypothesized that avoiding mesh fixation in a robotic eTEP repair offers an advantage in early postoperative pain compared to rIPOM. METHODS: This is a multi-center, randomized clinical trial for patients with midline ventral hernias ≤ 7 cm, who were randomized to rIPOM or robotic eTEP. The primary outcome was pain (0-10) on the first postoperative day. Secondary outcomes included same-day discharge, length of stay, opioid consumption, quality of life, surgeon workload, and cost. RESULTS: Between November 2019 and November 2021, 100 patients were randomized (49 rIPOM, 51 eTEP) among 5 surgeons. Pain on the first postoperative day [median (IQR): 5 (4-6) vs. 5 (3.5-7), p = 0.66] was similar for rIPOM and eTEP, respectively, a difference maintained following adjustments for surgeon, operative time, baseline pain, and patient co-morbidities (difference 0.28, 95% CI - 0.63 to 1.19, p = 0.56). No differences in pain on the day of surgery, 7, and 30 days after surgery were identified. Same-day discharge, length of stay, opioid consumption, and 30-day quality of life were also comparable, though rIPOM required less surgeon workload (p < 0.001), shorter operative time [107 (86-139) vs. 165 (129-212) min, p < 0.001], and resulted in fewer surgical site occurrences (0 vs. 8, p = 0.004). The total direct costs for rIPOM and eTEP were comparable [$8282 (6979-11835) vs. $8680 (7550-10282), p = 0.52] as the cost savings for eTEP attributable to mesh use [$442 (434-485) vs. $69 (62-76), p = < 0.0001] were offset by increased expenses for operative time [$669 (579-861) vs. $1075 (787-1367), p < 0.0001] and use of more robotic equipment [$760 (615-933) vs. $946 (798-1203), p = 0.001]. CONCLUSION: The avoidance of fixation in a robotic eTEP repair did not reveal a benefit in postoperative pain to offset the shorter operative time and surgeon workload offered by rIPOM.

A randomized-controlled trial of a digital, small incentive-based intervention for working adults with short sleep.

STUDY OBJECTIVES: We evaluated the efficacy of a digitally delivered, small and scalable incentive-based intervention program on sleep and wellbeing in short-sleeping, working adults. METHODS: A 22-week, parallel-group, randomized-controlled trial was conducted on 21-40 y participants gifted with FitbitTM devices to measure sleep for ≥2 years, as part of a broader healthy lifestyle study. About 225 short sleepers (141 males; average time-in-bed, TIB < 7h) were randomly assigned in a 2:1 ratio to Goal-Setting or Control groups. The Goal-Setting group received health vouchers (~USD 0.24) for meeting each sleep goal (i.e. increasing weeknight TIB by 30 min/sleeping before midnight).The study spanned three phases: (1) 2-week Baseline, (2) 10-week Intervention, and (3) 10-week Follow-Up. Wellbeing questionnaires were administered on Weeks 1-2, 11-12, and 21-22. RESULTS: Baseline weeknight TIB (mean ±â€…SD) was 387 ±â€…43 min (Goal-Setting) and 399 ±â€…44 min (Control), while bedtime was 00:53 ±â€…01:13 (Goal-Setting), and 00:38 ±â€…00:56 (Control). No difference in sleep outcomes was observed at study endpoints, but exploratory week-by-week analysis showed that on Weeks 3-5, TIB in the Goal-Setting group increased (9-18 min; ps < 0.05) while on Week 5, bedtimes shifted earlier (15 min; p < 0.01) compared to Baseline. Morning sleepiness was reduced in the Goal-Setting group (mean[SEM] = -3.17(1.53); p = 0.04) compared to Baseline, although between-group differences were not significant (p = 0.62). Main barriers to sleeping longer were work hours (35%), followed by leisure activities (23%) and family commitments (22%). CONCLUSION: Our program resulted in encouraging subjective sleep improvements and short-term sleep extension, but sustained transformation of sleep will probably require structural measures to overcome significant obstacles to sleep. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04878380 (hiSG Sleep Health Study (hiSG-SHS); https://clinicaltrials.gov/ct2/show/NCT04878380).

Metabolite and thymocyte development defects in ADA-SCID mice receiving enzyme replacement therapy.

Deficiency of adenosine deaminase (ADA, EC3.5.4.4), a housekeeping enzyme intrinsic to the purine salvage pathway, leads to severe combined immunodeficiency (SCID) both in humans and mice. Lack of ADA results in the intracellular accumulation of toxic metabolites which have effects on T cell development and function. While untreated ADA-SCID is a fatal disorder, there are different therapeutic options available to restore ADA activity and reconstitute a functioning immune system, including enzyme replacement therapy (ERT). Administration of ERT in the form of pegylated bovine ADA (PEG-ADA) has proved a life-saving though non-curative treatment for ADA-SCID patients. However, in many patients treated with PEG-ADA, there is suboptimal immune recovery with low T and B cell numbers. Here, we show reduced thymus cellularity in ADA-SCID mice despite weekly PEG-ADA treatment. This was associated with lack of effective adenosine (Ado) detoxification in the thymus. We also show that thymocyte development in ADA-deficient thymi is arrested at the DN3-to-DN4 stage transition with thymocytes undergoing dATP-induced apoptosis rather than defective TCRß rearrangement or ß-selection. Our studies demonstrate at a detailed level that exogenous once-a-week enzyme replacement does not fully correct intra-thymic metabolic or immunological abnormalities associated with ADA deficiency.

Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit.

A recent surge in human mastadenovirus (HAdV) cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. We compared sequences from 37 patients collected over a 20-month period with sequences from GenBank and our own database of HAdVs. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships, paired with the epidemiological data from routine infection prevention and control (IPC) records and hospital activity data. During this time period, two formal outbreaks had been declared by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single-nucleotide polymorphisms. One of the formal outbreaks was confirmed, and the other was not. Of the five HAdV-associated deaths, three were unlinked and the remaining two considered the source of transmission. Mixed infection was frequent (10%), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harboring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into clinical practice to influence IPC policy contemporaneously.

Relative contribution of rice and fish consumption to bioaccessibility-corrected health risks for urban residents in eastern China.

There are global concerns about dietary exposure to metal(loid)s in foods. However, little is known about the relative contribution of rice versus fish to multiple metal(loid) exposure for the general population, especially in Asia where rice and fish are major food sources. We compared relative contributions of rice and fish consumption to multi-metal(loid) exposure on the city-scale (Nanjing) and province-scale in China. The effects of ingestion rate, metal(loid) level, and bioaccessibility were examined to calculate modeled risk from Cu, Zn, total As (TAs), inorganic As (iAs), Se, Cd, Pb, and methylmercury (MeHg). Metal(loid) levels in rice and fish samples collected from Nanjing City were generally low, except iAs. Metal(loid) bioaccessibilities in fish were higher than those in rice, except Se. Calculated carcinogenic risks induced by iAs intake (indicated by increased lifetime cancer risk, ILCR) were above the acceptable level (1 0 -4) in Nanjing City (median: 3 × 10-4 for female and 4 × 10-4 for male) and nine provinces (1.4 × 10-4 to 5.9 × 10-4) in China. Rice consumption accounted for 85.0% to 99.8% of carcinogenic risk. The non-carcinogenic hazard quotients (HQ) for single metals and hazard index (HI) for multi-metal exposure were < 1 in all cases, indicating of their slight non-carcinogen health effects associated. In Guangdong and Jiangsu provinces, results showed that rice and fish intake contributed similarly to the HI (i.e., 42.6% vs 57.4% in Guangdong and 54.6% vs 45.4% in Jiangsu). Sensitivity analysis indicated that carcinogenic risk was most sensitive to rice ingestion rate and rice iAs levels, while non-carcinogenic hazard (i.e., HQ and HI) was most sensitive to ingestion rate of fish and rice, and Cu concentration in rice. Our results suggest that rice is more important than fish for human dietary metal(loid) exposure risk in China, and carcinogenic risk from iAs exposure in rice requires particular attention.

Understanding the Value of the Wellness Visit: A Descriptive Study.

INTRODUCTION: Clinical preventive services can reduce mortality and morbidity, but Americans receive only half of the recommended care. Although wellness visits protect time for clinicians to review needs and discuss care with patients, studies have not shown that having a wellness visit improves health outcomes. This study seeks to understand the types of discussions and volume of care delivered during wellness visits. METHODS: Using a sample of 1,008 patients scheduled for a wellness visit from 22 primary care clinicians across 3 states from 2018 to 2019, electronic health records were reviewed, and a subset of visits was audio recorded. The discussion and delivery of clinical preventive services, as recommended by the U.S. Preventive Services Task Force, were measured, and new diagnoses were identified from the clinical preventive services. Analyses were completed in 2020. RESULTS: Even though patients were up to date with 80% of the recommended clinical preventive services 3 months after the visit, only 0.5% of patients were up to date with all the recommended clinical preventive services. On average, 6.9 clinical preventive service discussions occurred during each wellness visit on the basis of electronic health records review, and 7.7 clinical preventive services discussions occurred on the basis of audio recordings. An average of 0.4 new diagnoses was identified, including cancer diagnoses, cardiovascular risks, and infections. CONCLUSIONS: Wellness visits are an important time for patients and clinicians to discuss prevention strategies and to deliver recommended clinical preventive services, leading to the identification of previously unrecognized diagnoses. This will improve patients' health. Policies and incentives that promote wellness visits are important, and efforts are needed to deliver them to those most in need.

CRAHCN-O: A Consistent Reduced Atmospheric Hybrid Chemical Network Oxygen Extension for Hydrogen Cyanide and Formaldehyde Chemistry in CO2-, N2-, H2O-, CH4-, and H2-Dominated Atmospheres.

Hydrogen cyanide (HCN) and formaldehyde (H2CO) are key precursors to biomolecules such as nucleobases and amino acids in planetary atmospheres. However, many reactions which produce and destroy these species in atmospheres containing CO2 and H2O are still missing from the literature. We use a quantum chemistry approach to find these missing reactions and calculate their rate coefficients using canonical variational transition state theory and Rice-Ramsperger-Kassel-Marcus/master equation theory at the BHandHLYP/aug-cc-pVDZ level of theory. We calculate the rate coefficients for 126 total reactions and validate our calculations by comparing with experimental data in the 39% of available cases. Our calculated rate coefficients are most frequently within a factor of 2 of experimental values and generally always within an order of magnitude of these values. We discover 45 previously unknown reactions and identify 6 from this list that are most likely to dominate H2CO and HCN production and destruction in planetary atmospheres. We highlight 1O + CH3 → H2CO + H as a new key source and H2CO + 1O → HCO + OH as a new key sink, for H2CO in upper planetary atmospheres. In this effort, we develop an oxygen extension to our consistent reduced atmospheric hybrid chemical network (CRAHCN-O), building off our previously developed network for HCN production in N2-, CH4-, and H2-dominated atmospheres (CRAHCN). This extension can be used to simulate both HCN and H2CO production in atmospheres dominated by any of CO2, N2, H2O, CH4, and H2.

Systematic review of outcomes and complications in nonimplant-based mastopexy surgery.

BACKGROUND: Mastopexy is one of the most performed cosmetic surgery procedures in the U.S. Numerous studies on mastopexy techniques have been published in the past decades, including case reports, retrospective reviews, and prospective studies. However, to date, no study has investigated the overall complications or satisfaction rates associated with the wide spectrum of techniques. OBJECTIVES: This review aims to assess the outcomes of the various mastopexy techniques, without the use of implants, thus focusing on associated complications, and to provide a simplified classification system. METHODS: This systematic review was performed in accordance with the PRISMA guidelines. PubMed database was queried in search of clinical studies describing nonprosthetic mastopexy techniques, which reported the technique, indication, and outcomes. RESULTS: Thirty-four studies, published from 1980 through 2016, were included and represented 1888 treated patients. Four main surgical technique categories were identified: dermal reshape, glandular reshape, glandular reshape associated with perforator flaps, and glandular reshape with mesh support. Despite varying techniques, mastopexy was generally found to be a reliable esthetic procedure with unsatisfactory breast shape, thus accounting for only 1.3% of the patients. The overall complication rate was 10.4%. The most represented complications were scar-related (3%, including hypertrophic or unesthetic appearance) and nipple-areola-related problems (2.9%; including distortion, asymmetry, and reduction in sensation). CONCLUSIONS: Mastopexy techniques achieve high patient satisfaction and can be tailored according to patient needs and clinical presentation. Complication rates and morbidity are relatively low. However, a significant number of issues related to scars, asymmetry, and potential ptosis recurrence should be highlighted in the information provided to patients.

An Open Label Phase Ib Dose Escalation Study of TRC105 (Anti-Endoglin Antibody) with Axitinib in Patients with Metastatic Renal Cell Carcinoma.

BACKGROUND: TRC105 is an IgG1 endoglin monoclonal antibody that potentiates VEGF inhibitors in preclinical models. We assessed safety, pharmacokinetics, and antitumor activity of TRC105 in combination with axitinib in patients with metastatic renal cell carcinoma (mRCC). SUBJECTS, MATERIALS, AND METHODS: Heavily pretreated mRCC patients were treated with TRC105 weekly (8 mg/kg and then 10 mg/kg) in combination with axitinib (initially at 5 mg b.i.d. and then escalated per patient tolerance to a maximum of 10 mg b.i.d.) until disease progression or unacceptable toxicity using a standard 3 + 3 phase I design. RESULTS: Eighteen patients (median number of prior therapies = 3) were treated. TRC105 dose escalation proceeded to 10 mg/kg weekly without dose-limiting toxicity. Adverse event characteristics of each drug were not increased in frequency or severity when the two drugs were administered concurrently. TRC105 and axitinib demonstrated preliminary evidence of activity, including partial responses (PR) by RECIST in 29% of patients, and median progression-free survival (11.3 months). None of the patients with PR had PR to prior first-line treatment. Lower baseline levels of osteopontin and higher baseline levels of TGF-ß receptor 3 correlated with overall response rate. CONCLUSION: TRC105 at 8 and 10 mg/kg weekly was well tolerated in combination with axitinib, with encouraging evidence of activity in patients with mRCC. A multicenter, randomized phase II trial of TRC105 and axitinib has recently completed enrollment (NCT01806064). IMPLICATIONS FOR PRACTICE: TRC105 is a monoclonal antibody to endoglin (CD105), a receptor densely expressed on proliferating endothelial cells and also on renal cancer stem cells that is implicated as a mediator of resistance to inhibitors of the VEGF pathway. In this Phase I trial, TRC105 combined safely with axitinib at the recommended single agent doses of each drug in patients with renal cell carcinoma. The combination demonstrated durable activity in a VEGF inhibitor-refractory population and modulated several angiogenic biomarkers. A randomized Phase II trial testing TRC105 in combination with axitinib in clear cell renal cell carcinoma has completed accrual.

Neuroprotection against stroke and encephalopathy after cardiac surgery.

Cerebral ischemia in the perioperative period is a major risk factor for stroke, encephalopathy, and cognitive decline after cardiothoracic surgery. After coronary artery bypass grafting, both stroke and encephalopathy can result in poor patient outcomes and increased mortality. Neuroprotection aims to lessen the severity and occurrence of further injury mediated by stroke and encephalopathy and to aid the recovery of conditions already present. Several pharmacological and non-pharmacological methods of neuroprotection have been investigated in experimental studies and in animal models, and, although some have shown effectiveness in protection of the central nervous system, for most, clinical research is lacking or did not show the expected results. This review summarizes the value and need for neuroprotection in the context of cardiothoracic surgery and examines the use and effectiveness of several agents and methods with an emphasis on clinical trials and clinically relevant neuroprotectants.

Clinical T Cell Receptor Repertoire Deep Sequencing and Analysis: An Application to Monitor Immune Reconstitution Following Cord Blood Transplantation.

Spectratyping assays are well recognized as the clinical gold standard for assessing the T cell receptor (TCR) repertoire in haematopoietic stem cell transplant (HSCT) recipients. These assays use length distributions of the hyper variable complementarity-determining region 3 (CDR3) to characterize a patient's T cell immune reconstitution post-transplant. However, whilst useful, TCR spectratyping is notably limited by its resolution, with the technique unable to provide data on the individual clonotypes present in a sample. High-resolution clonotype data are necessary to provide quantitative clinical TCR assessments and to better understand clonotype dynamics during clinically relevant events such as viral infections or GvHD. In this study we developed and applied a CDR3 Next Generation Sequencing (NGS) methodology to assess the TCR repertoire in cord blood transplant (CBT) recipients. Using this, we obtained comprehensive TCR data from 16 CBT patients and 5 control cord samples at Great Ormond Street Hospital (GOSH). These were analyzed to provide a quantitative measurement of the TCR repertoire and its constituents in patients post-CBT. We were able to both recreate and quantify inferences typically drawn from spectratyping data. Additionally, we demonstrate that an NGS approach to TCR assessment can provide novel insights into the recovery of the immune system in these patients. We show that NGS can be used to accurately quantify TCR repertoire diversity and to provide valuable inference on clonotypes detected in a sample. We serially assessed the progress of T cell immune reconstitution demonstrating that there is dramatic variation in TCR diversity immediately following transplantation and that the dynamics of T cell immune reconstitution is perturbed by the presence of GvHD. These findings provide a proof of concept for the adoption of NGS TCR sequencing in clinical practice.

Use of Whole-Genome Sequencing of Adenovirus in Immunocompromised Pediatric Patients to Identify Nosocomial Transmission and Mixed-Genotype Infection.

Background: Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission among patients in a pediatric tertiary hospital. Methods: We developed a target-enriched adenovirus WGS technique for clinical samples and retrospectively sequenced 107 adenovirus-positive residual diagnostic samples, including viremias (>5 × 104 copies/mL), from 37 patients collected January 2011-March 2016. Whole-genome sequencing was used to determine genotype and for phylogenetic analysis. Results: Adenovirus sequences were recovered from 105 of 107 samples. Full genome sequences were recovered from all 20 nonspecies C samples and from 36 of 85 species C viruses, with partial genome sequences recovered from the rest. Whole-genome phylogenetic analysis suggested linkage of 3 genotype A31 cases and uncovered an unsuspected epidemiological link to an A31 infection first detected on the same ward 4 years earlier. In 9 samples from 1 patient who died, we identified a mixed genotype adenovirus infection. Conclusions: Adenovirus WGS from clinical samples is possible and useful for genotyping and molecular epidemiology. Whole-genome sequencing identified likely nosocomial transmission with greater resolution than conventional genotyping and distinguished between adenovirus disease due to single or multiple genotypes.

The association between community-associated Staphylococcus aureus colonization and disease: a meta-analysis.

BACKGROUND: Colonization with Staphylococcus aureus is a well-defined risk factor for disease in hospitals, which can range from minor skin infections to severe, systemic diseases. However, the generalizability of this finding has not been thoroughly investigated outside of the hospital environment. We aimed to assess the role of S. aureus colonization as a risk factor for disease in the community. METHODS: We performed a meta-analysis of observational studies and searched PubMed for articles published between December 1979 and May 23, 2016. We included cohort, cross-sectional, and case-control studies that reported quantitative estimates of both S. aureus colonization and disease statuses of all study subjects. We excluded studies on recently hospitalized subjects, long-term care facilities, surgery patients, dialysis patients, hospital staff, S. aureus outbreaks, and livestock-associated infections. Our meta-analysis was performed using random-effects analysis to obtain pooled odds ratios (ORs) to compare the odds of S. aureus disease with respect to S. aureus colonization status. RESULTS: We identified 3477 citations, of which 12 articles on 6998 subjects met the eligibility criteria. Overall, subjects colonized with S. aureus were more likely to progress to disease than those who were non-colonized: (OR 1.87, 95% CI 1.21-2.88, n = 7 studies). We observed a larger effect with methicillin-resistant S. aureus colonization (7.06, 4.60-10.84, n = 7 studies). However, the methicillin-sensitive S. aureus colonization was not associated with greater odds of disease (1.20, 0.69-2.06, n = 4 studies). Heterogeneity was present across studies in all of the subgroups: S. aureus (I2 = 95.0%, χ2 = 120.3, p < 0.001), MRSA (I2 = 92.8%, χ2 = 82.8, p = p < 0.001), and MSSA (I2 = 86.3%, χ2 = 21.8, p < 0.001). CONCLUSIONS: While the majority of papers individually support the assumption that colonization is a risk factor for S. aureus disease in the general population, there is marked heterogeneity between studies and further investigation is needed to identify the major sources of this variance. There is a shortage of literature addressing this topic in the community setting and a need for further research on colonization as a focus for disease prevention.