Faculty Bibliography

Cefiderocol is a novel cephalosporin antibiotic with activity against multidrug-resistant gram-negative bacteria and limited pediatric experience. This case series describes 3 immunocompromised children receiving blood transfusion who developed benign red or purple urine with administration of cefiderocol. Interaction with iron from blood products is a possible mechanism. It is important to recognize this phenomenon and distinguish it from hematuria to avoid unnecessary diagnostic testing.

OBJECTIVES:To identify factors associated with the development of fracture-related infection (FRI) in patients who have undergone operative fixation of their fracture. DESIGN:Retrospective study. SETTING:Academic medical center. PATIENTS/PARTICIPANTS:Patients with peripheral extremity long-bone fractures and shoulder and pelvic girdle fractures who underwent operative repair. This included patients who had undergone fixation inside and outside of our institution. INTERVENTION:Chi-square, Fisher exact testing, analysis of variance (ANOVA), and t tests were used for analysis of data, as appropriate. Binomial logistic regression analysis was performed to determine risk factors of FRI. MAIN OUTCOME MEASUREMENTS:Demographics, fracture location, injury mechanism, open wound status, and wound complication type. RESULTS:One hundred ninety-three patients comprised the FRI cohort. Of those with confirmed signs of FRI, 36 (18.7%) had wound breakdown to bone or implant, 120 (62.1%) had a sinus track, and 170 patients (88.1%) had the confirmed presence of microorganisms in deep tissue samples obtained during operative intervention. Factors associated with development of an FRI were as follows: higher BMI; being of Black and Hispanic race; higher American Society of Anesthesiologists class; history of tobacco, alcohol, and drug use; and fractures of the lower extremity (foot, tibia, and femur/pelvis). The results of binary logistic regression demonstrated that treatment at an urban level I trauma center and drug use positively predicted the development of FRI. CONCLUSION:Our results demonstrate that higher BMI; being of Black or Hispanic race; higher American Society of Anesthesiologists; history of tobacco, alcohol, and drug use; and fractures of the foot, tibia, and femur/pelvis are all factors associated with development of FRI. LEVEL OF EVIDENCE:Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins, produced by numerous Gram-positive pathogens. CDCs depend on host membrane cholesterol for pore formation; some CDCs also require surface-associated human CD59 (hCD59) for binding, conferring specificity for human cells. We purified a recombinant version of a putative CDC encoded in the genome of Streptococcus oralis subsp. tigurinus, tigurilysin (TGY), and used CRISPR/Cas9 to construct hCD59 knockout (KO) HeLa and JEG-3 cell lines. Cell viability assays with TGY on wild-type and hCD59 KO cells showed that TGY is a hCD59-dependent CDC. Two variants of TGY exist among S. oralis subsp. tigurinus genomes, only one of which is functional. We discovered that a single amino acid change between these two TGY variants determines its activity. Flow cytometry and oligomerization Western blots revealed that the single amino acid difference between the two TGY isoforms disrupts host cell binding and oligomerization. Furthermore, experiments with hCD59 KO cells and cholesterol-depleted cells demonstrated that TGY is fully dependent on both hCD59 and cholesterol for activity, unlike other known hCD59-dependent CDCs. Using full-length CDCs and toxin constructs differing only in the binding domain, we determined that having hCD59 dependence leads to increased lysis efficiency, conferring a potential advantage to organisms producing hCD59-dependent CDCs.

The receptor tyrosine kinase RET plays a critical role in the fate specification of enteric neural crest-derived cells (ENCDCs) during enteric nervous system (ENS) development. RET loss of function (LoF) is associated with Hirschsprung disease (HSCR), which is marked by aganglionosis of the gastrointestinal (GI) tract. Although the major phenotypic consequences and the underlying transcriptional changes from Ret LoF in the developing ENS have been described, cell type- and state-specific effects are unknown. We performed single-cell RNA sequencing on an enriched population of ENCDCs from the developing GI tract of Ret null heterozygous and homozygous mice at embryonic day (E)12.5 and E14.5. We demonstrate four significant findings: 1) Ret-expressing ENCDCs are a heterogeneous population comprising ENS progenitors as well as glial- and neuronal-committed cells; 2) neurons committed to a predominantly inhibitory motor neuron developmental trajectory are not produced under Ret LoF, leaving behind a mostly excitatory motor neuron developmental program; 3) expression patterns of HSCR-associated and Ret gene regulatory network genes are impacted by Ret LoF; and 4) Ret deficiency leads to precocious differentiation and reduction in the number of proliferating ENS precursors. Our results support a model in which Ret contributes to multiple distinct cellular phenotypes during development of the ENS, including the specification of inhibitory neuron subtypes, cell cycle dynamics of ENS progenitors, and the developmental timing of neuronal and glial commitment.

OBJECTIVE:To estimate the effects of providing access to an alcohol intervention based on a smartphone. DESIGN:Randomised controlled trial.. SETTING:Four higher education institutions in Switzerland. PARTICIPANTS:1770 students (≥18 years) who screened positive for unhealthy alcohol use (ie, a score on the alcohol use disorders identification test-consumption (AUDIT-C) of ≥4 for men and ≥3 for women) were randomly assigned by 1:1 allocation ratio in blocks of 10. INTERVENTION:Providing access to a brief, smartphone based alcohol intervention. OUTCOME MEASURES:six months), and baseline outcome values as fixed effects. RESULTS:Between 26 April 26 2021 and 30 May 2022, 1770 participants (intervention group (n=884); control group (n=886)) were included. Mean age was 22.4 years (standard deviation 3.07); 958 (54.1%) were women; and 1169 (66.0%) were undergraduate students, 533 (30.1%) were studying for a master's degree, 43 (2.4%) were studying for a doctorate, and 25 (1.4%) were students of other higher education programme. The baseline mean number of standard drinks per week was 8.59 (standard deviation 8.18); the baseline number of heavy drinking days was 3.53 (4.02). Of 1770 participants, follow-up rates were 1706 (96.4%) at three months, 1697 (95.9%) at six months, and 1660 (93.8%) at 12 months. Of 884 students randomly assigned to the intervention group, 738 (83.5%) downloaded the smartphone application. The intervention had a significant overall effect on the number of standard drinks per week (incidence rate ratio 0.90 (95% confidence interval 0.85 to 0.96)), heavy drinking days (0.89 (0.83 to 0.96)), and the maximum number of drinks consumed on one occasion (0.96 (0.93 to 1.00), P=0.029), indicating significantly lower drinking outcomes in the intervention group than in the control group during the follow-up period. The intervention did not affect alcohol related consequences or academic performance. CONCLUSIONS:Providing access to the smartphone application throughout the 12 month follow-up was effective at limiting the average drinking volume of university students who had self-reported unhealthy alcohol use at baseline. TRIAL REGISTRATION:ISRCTN 10007691.

The COVID-19 pandemic and resulting public health directives led to many changes in families' social and material environments. Prior research suggests that these changes are likely to impact composition of the gut microbiome, particularly during early childhood when the gut microbiome is developing most rapidly. Importantly, disruption to the gut microbiome during this sensitive period can have potentially long-lasting impacts on health and development. In the current study, we compare gut microbiome composition among a socioeconomically and racially diverse group of 12-month old infants living in New York City who provided stool samples before the pandemic (N = 34) to a group who provided samples during the first 9-months of the pandemic (March-December 2020; N = 20). We found that infants sampled during the pandemic had lower alpha diversity of the microbiome, lower abundance of Pasteurellaceae and Haemophilus, and significantly different beta diversity based on unweighted Unifrac distance than infants sampled before the pandemic. Exploratory analyses suggest that gut microbiome changes due to the pandemic occurred relatively quickly after the start of the pandemic and were sustained. Our results provide evidence that pandemic-related environmental disruptions had an impact on community-level taxonomic diversity of the developing gut microbiome, as well as abundance of specific members of the gut bacterial community.

Our knowledge of non-linear genetic effects on complex traits remains limited, in part, due to the modest power to detect such effects. While kernel-based tests offer a versatile approach to test for non-linear relationships between sets of genetic variants and traits, current approaches cannot be applied to Biobank-scale datasets containing hundreds of thousands of individuals. We propose, FastKAST, a kernel-based approach that can test for non-linear effects of a set of variants on a quantitative trait. FastKAST provides calibrated hypothesis tests while enabling analysis of Biobank-scale datasets with hundreds of thousands of unrelated individuals from a homogeneous population. We apply FastKAST to 53 quantitative traits measured across ≈ 300 K unrelated white British individuals in the UK Biobank to detect sets of variants with non-linear effects at genome-wide significance.

VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a pleiotropic, severe autoinflammatory disease caused by somatic mutations in the ubiquitin-like modifier activating enzyme 1 (UBA1) gene. To elucidate VEXAS pathophysiology, we performed transcriptome sequencing of single bone marrow mononuclear cells and hematopoietic stem and progenitor cells (HSPCs) from VEXAS patients. HSPCs are biased toward myeloid (granulocytic) differentiation, and against lymphoid differentiation in VEXAS. Activation of multiple inflammatory pathways (interferons and tumor necrosis factor alpha) occurs ontogenically early in primitive hematopoietic cells and particularly in the myeloid lineage in VEXAS, and inflammation is prominent in UBA1-mutated cells. Dysregulation in protein degradation likely leads to higher stress response in VEXAS HSPCs, which positively correlates with inflammation. TCR usage is restricted and there are increased cytotoxicity and IFN-γ signaling in T cells. In VEXAS syndrome, both aberrant inflammation and myeloid predominance appear intrinsic to hematopoietic stem cells mutated in UBA1.

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

IMPORTANCE:Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections (LRTIs) and infant hospitalization worldwide. OBJECTIVE:To evaluate the characteristics and outcomes of RSV-related critical illness in US infants during peak 2022 RSV transmission. DESIGN, SETTING, AND PARTICIPANTS:This cross-sectional study used a public health prospective surveillance registry in 39 pediatric hospitals across 27 US states. Participants were infants admitted for 24 or more hours between October 17 and December 16, 2022, to a unit providing intensive care due to laboratory-confirmed RSV infection. EXPOSURE:Respiratory syncytial virus. MAIN OUTCOMES AND MEASURES:Data were captured on demographics, clinical characteristics, signs and symptoms, laboratory values, severity measures, and clinical outcomes, including receipt of noninvasive respiratory support, invasive mechanical ventilation, vasopressors or extracorporeal membrane oxygenation, and death. Mixed-effects multivariable log-binomial regression models were used to assess associations between intubation status and demographic factors, gestational age, and underlying conditions, including hospital as a random effect to account for between-site heterogeneity. RESULTS:The first 15 to 20 consecutive eligible infants from each site were included for a target sample size of 600. Among the 600 infants, the median (IQR) age was 2.6 (1.4-6.0) months; 361 (60.2%) were male, 169 (28.9%) were born prematurely, and 487 (81.2%) had no underlying medical conditions. Primary reasons for admission included LRTI (594 infants [99.0%]) and apnea or bradycardia (77 infants [12.8%]). Overall, 143 infants (23.8%) received invasive mechanical ventilation (median [IQR], 6.0 [4.0-10.0] days). The highest level of respiratory support for nonintubated infants was high-flow nasal cannula (243 infants [40.5%]), followed by bilevel positive airway pressure (150 infants [25.0%]) and continuous positive airway pressure (52 infants [8.7%]). Infants younger than 3 months, those born prematurely (gestational age <37 weeks), or those publicly insured were at higher risk for intubation. Four infants (0.7%) received extracorporeal membrane oxygenation, and 2 died. The median (IQR) length of hospitalization for survivors was 5 (4-10) days. CONCLUSIONS AND RELEVANCE:In this cross-sectional study, most US infants who required intensive care for RSV LRTIs were young, healthy, and born at term. These findings highlight the need for RSV preventive interventions targeting all infants to reduce the burden of severe RSV illness.