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Microbial maturation disrupted by early life dysbiosis has been linked with increased asthma risk and severity, however the immunological mechanisms underpinning this connection are poorly understood. We sought to understand how delaying microbial maturation drives worsened asthma outcomes later in life and its long-term durability. Drinking water was supplemented with antibiotics on postnatal days 10-20. To assess the immediate and long-term effects of delaying microbial maturation on experimental asthma, we initiated house dust mite exposure when bacterial diversity was either at a minimum or had recovered. Airway hyperresponsiveness, histology, pulmonary leukocyte recruitment, flow cytometric analysis of cytokine producing lymphocytes, and assessment of serum IgG1 and IgE levels were performed. RT-PCR was used to measure IL-13-induced gene expression in sequentially sorted mesenchymal, epithelial, endothelial and leukocyte cell populations from the lung. Delayed microbial maturation increased allergen driven airway hyperresponsiveness and Th17 frequency compared to allergen exposed control mice, even when allergen exposure began after bacterial diversity recovered. Blockade of IL-17A reversed the airway hyperresponsiveness phenotype. Additionally, allergen exposure in animals that experienced delayed microbial maturation showed signs of synergistic signaling between IL-13 and IL-17A in the pulmonary mesenchymal compartment. Delaying microbial maturation in neonates promotes the development of more severe asthma by increasing Th17 frequency, even if allergen exposure is initiated weeks after microbial diversity is normalized. Additionally, IL-17A-aggravated asthma is associated with increased expression of IL-13-induced genes in mesenchymal, but not epithelial cells.

Background Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD. Methods A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn’s disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs. Results In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC. Conclusions Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.

Intestinal permeability may correlate with adverse outcomes during hematopoietic stem cell transplantation (HSCT), but longitudinal quantification with traditional oral mannitol and lactulose is not feasible in HSCT recipients due to mucositis and diarrhea. A modified lactulose:rhamnose (LR) assay is validated in children with environmental enteritis. Our study objective was to quantify peri-HSCT intestinal permeability changes using the modified LR assay. The LR assay was administered pretransplant, Day+7 and +30 to 80 pediatric and young adult allogeneic HSCT patients. Lactulose and rhamnose were detected by urine mass spectrometry and expressed as an L:R ratio. Metagenomic shotgun sequencing of stool for microbiome analyses and ELISA analyses of plasma lipopolysaccharide binding protein (LBP), ST2, REG3α, claudin1, occludin, and intestinal alkaline phosphatase were performed at the same timepoints. L:R ratios were increased at Day+7 but returned to baseline at Day+30 in most patients (p=0.014). Conditioning regimen intensity did not affect the trajectory of L:R (p=0.39). Baseline L:R ratios did not vary by diagnosis. L:R correlated with LBP levels (r2= 0.208, p=0.0014). High L:R ratios were associated with lower microbiome diversity (p=0.035), loss of anaerobic organisms (p=0.020) and higher plasma LBP (p=0.0014). No adverse gastrointestinal effects occurred due to LR. Intestinal permeability as measured by L:R ratios after allogeneic HSCT correlates with intestinal dysbiosis and elevated plasma LBP. The lactulose/rhamnose assay is well-tolerated and may identify transplant recipients more likely to experience adverse outcomes.

Intestinal epithelial cells (IECs) constitute a critical first line of defense against microbes. While IECs are known to respond to various microbial signals, the precise upstream cues regulating diverse IEC responses are not clear. Here, we discover a dual role for IEC-intrinsic interleukin-1 receptor (IL-1R) signaling in regulating intestinal homeostasis and inflammation. Absence of IL-1R in epithelial cells abrogates a homeostatic antimicrobial program including production of antimicrobial peptides (AMPs). Mice deficient for IEC-intrinsic IL-1R are unable to clear Citrobacter rodentium (C. rodentium) but are protected from DSS-induced colitis. Mechanistically, IL-1R signaling enhances IL-22R–induced signal transducer and activator of transcription 3 (STAT3) phosphorylation in IECs leading to elevated production of AMPs. IL-1R signaling in IECs also directly induces expression of chemokines as well as genes involved in the production of reactive oxygen species. Our findings establish a protective role for IEC-intrinsic IL-1R signaling in combating infections but a detrimental role during colitis induced by epithelial damage.

The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single-cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.

Objectives We report the clinical, radiological, laboratory, and neuropathological findings in support of the first diagnosis of lethal, small-vessel cerebral vasculitis triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a pediatric patient. Patient description A previously healthy, 8-year-old Hispanic female presented with subacute onset left-sided weakness two weeks after a mild febrile illness. SARS-CoV-2 nasopharyngeal swab was positive. Magnetic resonance imaging (MRI) revealed an enhancing right frontal lobe lesion with significant vasogenic edema. Two brain biopsies of the lesion showed perivascular and intraluminal lymphohistiocytic inflammatory infiltrate consistent with vasculitis. Despite extensive treatment with immunomodulatory therapies targeting primary angiitis of the central nervous system, she experienced neurologic decline and died 93 days after presentation. SARS-CoV-2 testing revealed positive serum IgG and positive cerebrospinal fluid IgM. Comprehensive infectious, rheumatologic, hematologic/oncologic, and genetic evaluation did not identify an alternative etiology. Post-mortem brain autopsy remained consistent with vasculitis. Discussion This is the first pediatric presentation to suggest SARS-CoV-2 can lead to a fatal, post-infectious, inflammatory small-vessel cerebral vasculitis. Our case is unique in including supportive cerebrospinal fluid and post-mortem tissue analysis. While most children recover well from neurologic complications of SARS-CoV-2, we emphasize the potential mortality in a child with no risk factors for severe disease.

Metagenomic next-generation sequencing (mNGS) has the theoretical capacity to detect any microbe present in a host. mNGS also has the potential to infer a pathogen’s phenotypic characteristics, including the ability to colonize humans, cause disease, and resist treatment. Concurrent host nucleic acid sequencing can assess the infected individual’s physiological state, including characterization and appropriateness of the immune response. When the pathogen cannot be identified, host RNA sequencing may help infer the organism’s nature. While the full promise of mNGS remains far from realization, the potential ability to identify all microbes in a complex clinical sample, assess each organism’s virulence and antibiotic susceptibility traits, and simultaneously characterize the host’s response to infection provide opportunities for mNGS to supplant existing technologies and become the primary method of infectious diseases diagnostics.

Mucosal tissues are constitutively colonized by a wide assortment of host-adapted microbes. This includes the polymorphic fungus Candida albicans which is a primary target of human adaptive responses. Immunogenicity is replicated after intestinal colonization in preclinical models with a surprising array of protective benefits for most hosts, but harmful consequences for a few. The interaction between fungus and host is complex, and traditionally, the masking of antigenic fungal ligands has been viewed as a tactic for fungal immune evasion during invasive infection. However, we propose that dynamic expression of cell wall moieties, host cell lysins, and other antigenic C. albicans determinants is necessary during the more ubiquitous context of intestinal colonization to prime immunogenicity and optimize mammalian host symbiosis.

Despite evidence-based guidelines, antibiotics prescribed for uncomplicated skin and soft tissue infections can involve inappropriate microbial coverage. Our aim was to evaluate the appropriateness of antibiotic prescribing practices for mild nonpurulent cellulitis in a pediatric tertiary academic medical center over a 1-year period.Eligible patients treated in the emergency department or urgent care settings for mild nonpurulent cellulitis from January 2017 to December 2017 were identified by an International Classification of Diseases, Tenth Revision, code for cellulitis. The primary outcome was appropriateness of prescribed antibiotics as delineated by adherence with the Infectious Diseases Society of America guidelines. Secondary outcomes include reutilization rate as defined by revisit to the emergency department/urgent cares within 14 days of the initial encounter.A total of 967 encounters were evaluated with 60.0% overall having guideline-adherent care. Common reasons for nonadherence included inappropriate coverage of MRSA with clindamycin (n = 217, 56.1%) and single-agent coverage with sulfamethoxazole-trimethoprim (n = 129, 33.3%). There were 29 revisits within 14 days of initial patient encounters or a reutilization rate of 3.0%, which was not significantly associated with the Infectious Diseases Society of America adherence.Our data show antibiotic prescription for nonpurulent cellulitis as a potential area of standardization and optimization of care at our center.

Background: Vedolizumab for inflammatory bowel disease (IBD) is often intensified based on distinct pharmacokinetics in children. Prior adult-specific population pharmacokinetic models have identified limited covariates of drug clearance. Aims: To establish a population pharmacokinetic model for children and young adults to identify novel covariates of drug clearance to better account for paediatric-specific inter-patient variability in vedolizumab pharmacokinetics; a key secondary exploratory aim was to identify microbial signatures of pharmacokinetic outcomes in a subset of patients. Methods: The study included data from 463 observed vedolizumab concentrations (59 peaks and 404 troughs) from 74 patients with IBD (52 with Crohn's disease and 22 with ulcerative colitis or unclassified IBD, median age 16 years). Pharmacokinetic analysis was conducted with non-linear mixed effects modelling. For the evaluation of the exposure–response relationship, clinical outcomes were evaluated by trough levels, clearance and vedolizumab exposure. Whole-genome metagenomic sequencing was conducted at baseline and week 2. Results: A two-compartment population pharmacokinetic model was identified with a clear correlation between CL and weight, erythrocyte sedimentation rate, and hypoalbuminemia. Trough concentrations before infusion 3 (37 μg/ml) and before infusion 4 (20 μg/ml) best predicted steroid-free clinical remission at infusion 4. Using faecal metagenomics, we identified an early (baseline and week 2) abundance of butyrate-producing species and pathways that were associated with an infusion 4 trough concentration >20 μg/ml. Conclusions: This novel paediatric vedolizumab pharmacokinetic model could inform precision dosing. While additional studies are needed, an abundance of faecal butyrate producers is associated with early response to vedolizumab, suggesting that microbial analysis may be beneficial to biological selection.

The coevolution of mammalian hosts and their beneficial commensal microbes has led to development of symbiotic host–microbiota relationships1. Epigenetic machinery permits mammalian cells to integrate environmental signals2; however, how these pathways are fine-tuned by diverse cues from commensal bacteria is not well understood. Here we reveal a highly selective pathway through which microbiota-derived inositol phosphate regulates histone deacetylase 3 (HDAC3) activity in the intestine. Despite the abundant presence of HDAC inhibitors such as butyrate in the intestine, we found that HDAC3 activity was sharply increased in intestinal epithelial cells of microbiota-replete mice compared with germ-free mice. This divergence was reconciled by the finding that commensal bacteria, including Escherichia coli, stimulated HDAC activity through metabolism of phytate and production of inositol-1,4,5-trisphosphate (InsP3). Both intestinal exposure to InsP3 and phytate ingestion promoted recovery following intestinal damage. Of note, InsP3 also induced growth of intestinal organoids derived from human tissue, stimulated HDAC3-dependent proliferation and countered butyrate inhibition of colonic growth. Collectively, these results show that InsP3 is a microbiota-derived metabolite that activates a mammalian histone deacetylase to promote epithelial repair. Thus, HDAC3 represents a convergent epigenetic sensor of distinct metabolites that calibrates host responses to diverse microbial signals. Phytate metabolism and production of inositol trisphosphate by commensal bacteria activates epithelial histone deacetylase 3 and promotes intestinal repair.

Background Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes. Results Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate-producing genera, including Clostridium and Blautia, were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short-chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at 3 weeks after birth. Conclusions Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants.

Exposure to nephrotoxic medications is a common risk factor for acute kidney injury (AKI) in pediatric stem cell transplantation (SCT). We hypothesized that reducing nephrotoxic antimicrobial exposure for SCT patients would be associated with lower nephrotoxin-associated AKI (NTMx-AKI) rates and no increase in infection treatment failures. We conducted a prospective cohort analysis of all inpatient SCT patients at Cincinnati Children's Hospital Medical Center between January 2014 and December 2017. In January 2016, first line fever coverage was changed from piperacillin-tazobactam to cefepime, acknowledging that the change resulted in a loss of enterococcal coverage, and the duration of antimicrobial exposures was limited, specifically including vancomycin. We collected data using prospective NTMx-AKI and antimicrobial utilization monitoring platforms within the electronic health record. AKI days and severity were extracted for patients exposed to 3+ nephrotoxins, 3+ days of IV aminoglycosides, or 3+ days of IV vancomycin. AKI was identified using KDIGO serum creatinine criteria. We assessed rates of nephrotoxin exposure and NTMx-AKI in all SCT inpatients for 2 years pre- and post-intervention. Data were grouped and analyzed by calendar month, normalized to a denominator of 1000 patient-days. Statistical process control methods were used to monitor adherence to the intervention and identify changes in mean rate of nephrotoxin exposure and NTMx-AKI. Infection rates, alternate antimicrobial usage rates, and the fraction of repeat positive cultures were used to identify treatment failures. PTZ usage decreased from 196 to 33 days/1000 patient days, cefepime usage increased from 62 to 290 days/1000 patient days, and vancomycin usage decreased from 62 to 41 days/1000 patient days. High nephrotoxin exposure decreased by 33% (143 to 96 days/1000 patient days), and NTMx-AKI decreased by 74% (24 to 6 days/1000 patient days). Rates of all KDIGO stages of NTMx-AKI decreased ≥50% after the intervention. Stage 3, the most severe, decreased by >80%. The fraction of repeat positive cultures remained stable between the two eras at .1 (standard deviation 0.21) and .07 (standard deviation 0.17), respectively. There were no increases in infection rates, alternate antimicrobial usage rates, or treatment failures. Reduction of nephrotoxic antimicrobial exposure can decrease the amount and severity of NTMx-AKI in SCT patients without an increase in treatment failures.

Klebsiella pneumoniae sequence type (ST) 307 is an emerging global antimicrobial drug–resistant clone. We used whole-genome sequencing and PCR to characterize K. pneumoniae ST307 with oxacillinase (OXA) 181 carbapenemase across several private hospitals in South Africa during 2014–2016. The South Africa ST307 belonged to a different clade (clade VI) with unique genomic characteristics when compared with global ST307 (clades I–V). Bayesian evolution analysis showed that clade VI emerged around March 2013 in Gauteng Province, South Africa, and then evolved during 2014 into 2 distinct lineages. K. pneumoniae ST307 clade VI with OXA-181 disseminated over a 15-month period within 42 hospitals in 23 cities across 6 northeastern provinces, affecting 350 patients. The rapid expansion of ST307 was most likely due to intrahospital, interhospital, intercity, and interprovince movements of patients. This study highlights the importance of molecular surveillance for tracking emerging antimicrobial clones.

Human studies have shown loss of diversity of the gut microbiome following hematopoietic stem cell transplantation (HSCT) in association with significant gut injury caused by the preparative regimen. Prolonged antibiotic use worsens loss of microbiome diversity and increases risk of complications such as graft-versus-host disease (GVHD). Our data support the hypothesis that loss of intestinal commensals that produce short-chain fatty acids (SCFAs) may increase dysbiosis. Here, we report an extensive longitudinal examination of changes in the luminal SCFAs in children undergoing allogeneic HSCT, and the relationship of those changes to the microbiota and antibiotic exposure. We found significant and progressive alterations in butyrate, and in additional SCFAs in stool in the first 14 days after transplant, a finding not observed in published mouse studies. SCFA levels were lower in children receiving antibiotics with activity against anaerobic organisms. Moreover, day 14 post-HSCT butyrate and propionate levels are lower in children who went on to develop GVHD, although our disease population was small. These data provide insight into the mechanism of prior observations that loss of diversity and increased antibiotic use are associated with GVHD following HSCT. Our findings offer potential modifiable targets to reduce risk of GVHD and improve survival after HSCT.

OBJECTIVE Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs. METHODS Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA. RESULTS Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome. CONCLUSION This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs. LEVEL OF EVIDENCE 2c Laryngoscope, 129:317-323, 2019.

Summary Interactions between the microbiota and mammalian host are essential for defense against infection, but the microbial-derived cues that mediate this relationship remain unclear. Here, we find that intestinal epithelial cell (IEC)-associated commensal bacteria, segmented filamentous bacteria (SFB), promote early protection against the pathogen Citrobacter rodentium, independent of CD4+ T cells. SFB induced histone modifications in IECs at sites enriched for retinoic acid receptor motifs, suggesting that SFB may enhance defense through retinoic acid (RA). Consistent with this, inhibiting RA signaling suppressed SFB-induced protection. Intestinal RA levels were elevated in SFB mice, despite the inhibition of mammalian RA production, indicating that SFB directly modulate RA. Interestingly, RA was produced by intestinal bacteria, and the loss of bacterial-intrinsic aldehyde dehydrogenase activity decreased the RA levels and increased infection. These data reveal RA as an unexpected microbiota-derived metabolite that primes innate defense and suggests that pre- and probiotic approaches to elevate RA could prevent or combat infections.

Background Nephrotoxic medication exposure and associated acute kidney injury (AKI) occur commonly in hospitalized children. At Cincinnati Children's Hospital Medical Center, there is an initiative to increase awareness of nephrotoxic medication exposure and decrease rates of associated AKI. The oncology service utilized these data in a quality improvement project to drive reductions in AKI rates. Methods Three interventions were implemented targeted at decreasing the incidence of nephrotoxic exposure, as well as protecting against the conversion of exposures to AKI episodes. Cefepime replaced piperacillin-tazobactam for febrile neutropenia, vancomycin stewardship limited empiric courses to 72 hours, and nephroprotection for intravenous contrast administration was standardized for defined high-risk patients. Results The study cohort comprised 42 520 noncritically ill patient days admitted to the oncology service at Cincinnati Children's Hospital Medical Center. A total of 273 unique patients were exposed to combination nephrotoxic medications, leading to 111 AKI episodes. The rate of nephrotoxic medication exposure within the oncology service decreased by 49% from 16.08 to 8.17 per 1000 patient days. Episodes of AKI associated with nephrotoxic medication exposure decreased by 45% from 3.48 to 1.92 per 1000 patient days. Conclusion Interventions to decrease AKI took a three-pronged approach. Collectively, this approach was proven successful with significant reductions in both rates of nephrotoxic medication exposure and associated AKI among hospitalized oncology patients.

Background Lyme disease is the most common tick-borne illness in the USA, Canada, and Europe. Clinical manifestations vary greatly, with localized skin findings functioning as early signs of the disease, followed by disseminated disease. The rarest dermatologic presentation of Lyme is a borrelial lymphocytoma, occurring distinctly in Europe and caused typically by Borrelia afzelii. Case presentation We report a case of a Caucasian 5-year-old European-American boy with slowly progressing, painless edema and erythema of his right pinna. Travel history revealed significant exposure to ticks during a recent trip to Eastern Europe. Laboratory testing for Borrelia burgdorferi demonstrated mixed positivity. He was treated with a 21-day course of amoxicillin, with complete resolution of symptoms and no sign of secondary Lyme disease. Conclusions Borrelial lymphocytoma is a rare manifestation of Lyme disease in North America, although not uncommon in Europe. Diagnosis is made by the presence of a painless erythematous swelling typically found on the ear lobe, nipples, or testes. Laboratory tests are available but with low sensitivity, therefore, a high index of suspicion is necessary for a clinical diagnosis to be made. Treatment for isolated borrelial lymphocytoma is doxycycline 4 mg/kg up to 100 mg twice daily, whereas for children less than 8 years of age amoxicillin 50 mg/kg divided three times daily, for 3–4 weeks, is preferred.

Severe Clostridiodes difficile infection (CDI) is life-threatening and responds poorly to treatment. Obesity is associated with development of severe CDI. Therefore, to define the mechanisms that exacerbate disease severity, we examined CDI pathogenesis in high-fat diet (HFD)-fed obese mice. Compared to control mice, HFD-fed mice failed to clear C. difficile bacteria which resulted in protracted diarrhea, weight loss and colonic damage. After infection, HFD-induced obese mice had an intestinal bile acid (BA) pool that was dominated by primary BAs which are known promoters of C. difficile spore germination, and lacked secondary BAs that inhibit C. difficile growth. Concurrently, synthesis of primary BAs from liver was significantly increased in C. difficile-infected HFD-fed mice. A key pathway that regulates hepatic BA synthesis is via feedback inhibition from intestinal Farnesoid X receptors (FXRs). Our data reveal that the proportion of FXR agonist BAs to FXR antagonist BAs in the intestinal lumen was significantly reduced in HFD-fed mice after CDI. Treatment of HFD-fed mice with an FXR agonist Obeticholic acid, resulted in decreased primary BA synthesis, fewer C. difficile bacteria and better CDI outcomes. Thus, OCA treatment holds promise as a therapy for severe CDI.

Antibiotic-resistant superbug bacteria represent a global health problem with no imminent solutions. Here we demonstrate that the combination (termed AB569) of acidified nitrite (A-NO 2 − ) and Na 2 -EDTA (disodium ethylenediaminetetraacetic acid) inhibited all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing the model organism Pseudomonas aeruginosa in biofilms and in a murine chronic lung infection model. AB569 was not toxic to human cell lines at bactericidal concentrations using a basic viability assay. RNA-Seq analyses upon treatment of P. aeruginosa with AB569 revealed a catastrophic loss of the ability to support core pathways encompassing DNA, RNA, protein, ATP biosynthesis, and iron metabolism. Electrochemical analyses elucidated that AB569 produced more stable SNO proteins, potentially explaining one mechanism of bacterial killing. Our data implicate that AB569 is a safe and effective means to kill pathogenic bacteria, suggesting that simple strategies could be applied with highly advantageous therapeutic/toxicity index ratios to pathogens associated with a myriad of periepithelial infections and related disease scenarios.

Ongoing biomarker development programs have been designed to identify serologic or imaging signatures of clinico-pathologic entities, assuming distinct biological boundaries between them. Identified putative biomarkers have exhibited large variability and inconsistency between cohorts, and remain inadequate for selecting suitable recipients for potential disease-modifying interventions. We launched the Cincinnati Cohort Biomarker Program (CCBP) as a population-based, phenotype-agnostic longitudinal study. While patients affected by a wide range of neurodegenerative disorders will be deeply phenotyped using clinical, imaging, and mobile health technologies, analyses will not be anchored on phenotypic clusters but on bioassays of to-be-repurposed medications as well as on genomics, transcriptomics, proteomics, metabolomics, epigenomics, microbiomics, and pharmacogenomics analyses blinded to phenotypic data. Unique features of this cohort study include (1) a reverse biology-to-phenotype direction of biomarker development in which clinical, imaging, and mobile health technologies are subordinate to biological signals of interest; (2) hypothesis free, causally- and data driven-based analyses; (3) inclusive recruitment of patients with neurodegenerative disorders beyond clinical criteria-meeting patients with Parkinson's and Alzheimer's diseases, and (4) a large number of longitudinally followed participants. The parallel development of serum bioassays will be aimed at linking biologically suitable subjects to already available drugs with repurposing potential in future proof-of-concept adaptive clinical trials. Although many challenges are anticipated, including the unclear pathogenic relevance of identifiable biological signals and the possibility that some signals of importance may not yet be measurable with current technologies, this cohort study abandons the anchoring role of clinico-pathologic criteria in favor of biomarker-driven disease subtyping to facilitate future biosubtype-specific disease-modifying therapeutic efforts.

Background Clostridioides difficile infection and colonization are common in pediatric Crohn’s disease (CD). Our aims were to test the relationship between C. difficile positivity and bowel resection surgery and to characterize microbial shifts associated with C. difficile carriage and surgery. Methods A retrospective single-center study of 75 pediatric CD patients tested for association between C. difficile carriage and bowel resection surgery. A prospective single-center study of 70 CD patients utilized C. difficile testing and shotgun metagenomic sequencing of fecal samples to define microbiota variation stratified by C. difficile carriage or history of surgery. Results The rate of bowel resection surgery increased from 21% in those without C. difficile to 67% in those with (P = 0.003). From a Kaplan-Meier survival model, the hazard ratio for time to first surgery was 4.4 (95% CI, 1.2–16.2; P = 0.00) in patients with positive C. difficile testing in the first year after diagnosis. Multivariable logistic regression analysis confirmed this association (odds ratio 16.2; 95% CI, 2.2–120; P = 0.006). Larger differences in microbial abundance and metabolic pathways were observed in patients with prior surgery than in those with C. difficile carriage. Depletion of Alistipes and Ruminococcus species and reduction in methionine biosynthesis were noted in patients with both C. difficile carriage and past surgery. Conclusions A positive C. difficile test during the first year after diagnosis is associated with decreased time to first bowel resection surgery in pediatric Crohn’s disease. Depletion of beneficial commensals and methionine biosynthesis in patients with C. difficile carriage may contribute to increased risk for surgery.

Clostridium difficile is the leading cause of nosocomial infections in the United States. Clinical disease outcomes after C. difficile infection (CDI) are dependent on intensity of host inflammatory responses. Specifically, peak peripheral white blood cell (WBC) count >20 × 109 l−1 is an indicator of adverse outcomes in CDI patients, and is associated with higher 30-day mortality. We show that homozygosity for a common single nucleotide polymorphism (Q to R mutation in leptin receptor that is present in up to 50% of people), significantly increases the risk of having peak peripheral WBC count >20 × 109 l−1 (odds ratio=5.41; P=0.0023) in CDI patients. In a murine model of CDI, we demonstrate that mice homozygous for the same single nucleotide polymorphism (RR mice) have more blood and tissue leukocytes (specifically neutrophils), exaggerated tissue inflammation, and higher mortality as compared with control mice, despite similar pathogen burden. Further, we show that neutrophilia in RR mice is mediated by gut microbiota-directed expression of CXC chemokine receptor 2 (CXCR2), which promotes the release of neutrophils from bone marrow reservoir. Overall these studies provide novel mechanistic insights into the role of human genetic polymorphisms and gut microbiota in regulating the fundamental biological process of CDI-induced neutrophilia.

Elevated stool fibrinogen has recently been shown to predict disease course in ulcerative colitis (UC), suggesting that fibrin(ogen) in the colitis microenvironment promotes UC pathogenesis. This conclusion is consistent with previous studies from our laboratory showing that fibrin(ogen)/leukocyte interactions mediated by the integrin receptor α Mβ 2 promote experimental colitis and colitis-associated cancer, but the mechanisms are not well defined. To delineate the mechanism coupling fibrinogen to colitis pathogenesis, we induced colitis in Fib WT and mice carrying a mutant fibrinogen lacking the α Mβ 2 binding motif (Fibg 390-396A) with Dextran Sulfate Sodium (DSS). We performed flow cytometric, protein analyses of colons and fecal microbiome and metabolomics analyses after DSS exposure. Five days after DSS challenge, a timepoint prior to significant epithelial damage, we observed significantly diminished infiltration of natural killer cells, T cells, dendritic cells, macrophages and neutrophils in colons harvested from DSS-challenged Fibg 390-396A mice relative to Fib WT mice. We also observed significantly diminished proinflammatory cytokine production by NK cells, macrophages and dendritic cells isolated from DSS-challenged Fibg 390-396A colons. It is well-established that the microbiome composition is a major determinant of colitis in humans and mice. One mechanism by which microbiome contents alter the course of colitis is by the elaboration of certain fecal metabolites. NMR-based fecal metabolomics analyses demonstrated no significant changes in short-chain fatty acids (acetate, propionate, and butyrate) and various amino acids (valine, proline, alanine) however we found significantly less uracil in fecal from Fibg 390-296A relative to Fib WT mice following DSS exposure. Uracil is a key ligand for Duox2 (dual NADPH oxidase), a gut epithelial specific enzyme, that drives reactive oxygen species production by gut epithelial in response to dysbiosis. Notably, Duox2 is the highest induced gene in inflammatory bowel disease (IBD) and has been identified as a risk gene. Our molecular analyses showed no difference in colonic Duox2 expression between genotypes at baseline, but Duox2 expression significantly increased in Fib WT relative to Fibg 390-296A after just 5 days of DSS exposure. Further western blot analyses revealed that Duox2 expression only in the colonic epithelial cells and not in the lamina propria cells. To determine if fibrinogen cause dysbiosis in DSS-induced colitis model, we performed shotgun sequencing on fecal samples from Fib WT and Fibg 390-396A mice at baseline and after 7 days of DSS challenge. Interesting shotgun sequencing analyses revealed major fibrin genotype dependent significant differences in the microbiomes of Fib WT and Fibg 390-396A mice at baseline as well as following DSS challenge. Our studies are the first to show that fibrin(ogen) is a major determinant of the gut-microbiome in the context of experimental colitis. Altogether, these studies demonstrate that fibrin(ogen) in the colitis microenvironment promotes the infiltration and activation of multiple leukocyte subsets that drive colitis pathogenesis. These results also suggest that fibrin(ogen) promotes colitis-associated dysbiosis and Duox2 expression, leading to ROS production that contributes to colitis pathogenesis and possibley tumorigenesis. Overall, these studies suggest that fibrin(ogen)-α Mβ 2 interactions represent an attractive therapeutic target for IBD without incurring the potential bleeding risks associated with anticoagulants or other modalities targeting fibrin deposition. Disclosures No relevant conflicts of interest to declare.

Objectives Inflammatory bowel diseases (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient reported outcome measures (PROs) are increasingly utilized in clinical care and research. Our study aim was to determine if fecal microbial shifts were associated with PROs in children and young adults with IBD. Methods A longitudinal prospective single center study of 93 patients tested for association between fecal microbial shifts, mucosal inflammation as measured by fecal calprotectin, and self-reported symptoms including diarrhea, rectal bleeding, and abdominal pain. For CD, abdominal pain and diarrhea determined disease activity or overall PRO. For UC, diarrhea and rectal bleeding were used. Fecal calprotectin and shotgun metagenomic sequencing were performed on all samples. Demographic and clinical characteristics (Table 1) were incorporated into a negative binomial mixed-effects model in “R” to identify differentially abundant species by PRO and fecal calprotectin. Metabolic pathways were mapped using the HUMAnN2 pipeline and compared to overall PRO, individual symptoms and fecal calprotectin level. Results In 70 CD patients with 244 stool samples, there was no association between symptoms and fecal calprotectin. In 23 UC patients with 76 stool samples, increased fecal calprotectin was associated with rectal bleeding (OR 4.93 [1.18, 20.64], p=0.03). Examination of differentially abundant species in those with self-reported active UC showed increased Klebsiella species and reduced Bacteroides. Conversely, UC patients with fecal calprotectin < 100 µg/gm had reduction in Klebsiella and increase in Bifidobacteria and Bacteroides (Figure 1). Analysis of differentially abundant species in those with abdominal pain in CD showed increase in Haemophilus and reduction in Bacteroides. No microbial shifts were identified in CD patients in association with overall PRO, diarrhea, nor with fecal calprotectin < 250 µg/gm. Metabolic pathway analysis showed no differences in those with CD. In UC patients, increases in sulfoglycolysis and ornithine biosynthesis were associated with overall PROs. Conclusions Fecal microbial shifts including decreased commensals such as Bacteroides correlate with UC patient symptoms. Increased fecal calprotectin level was associated with rectal bleeding in these patients, but not diarrhea. In CD, there was no association with fecal calprotectin and symptoms, and microbial shifts were detected in association with abdominal pain. Similarly, metabolic pathways differed relative to patient-reported symptoms in UC, but not in CD. Data suggests that microbial shifts may directly contribute to symptoms in children and young adults with IBD.

Nonalcoholic fatty liver disease (NAFLD), a common prelude to cirrhosis and hepatocellular carcinoma, is the most common chronic liver disease worldwide. Defining the molecular mechanisms underlying the pathogenesis of NAFLD has been hampered by a lack of animal models that closely recapitulate the severe end of the disease spectrum in humans, including bridging hepatic fibrosis. Here we demonstrate that a novel experimental model employing thermoneutral housing, as opposed to standard housing, resulted in lower stress-driven production of corticosterone, augmented mouse proinflammatory immune responses and markedly exacerbated high-fat diet (HFD)-induced NAFLD pathogenesis. Disease exacerbation at thermoneutrality was conserved across multiple mouse strains and was associated with augmented intestinal permeability, an altered microbiome and activation of inflammatory pathways that are associated with the disease in humans. Depletion of Gram-negative microbiota, hematopoietic cell deletion of Toll-like receptor 4 (TLR4) and inactivation of the IL-17 axis resulted in altered immune responsiveness and protection from thermoneutral-housing-driven NAFLD amplification. Finally, female mice, typically resistant to HFD-induced obesity and NAFLD, develop full disease characteristics at thermoneutrality. Thus, thermoneutral housing provides a sex-independent model of exacerbated NAFLD in mice and represents a novel approach for interrogation of the cellular and molecular mechanisms underlying disease pathogenesis.

Background Methicillin-resistant Staphylococcus aureus (MRSA) colonization predisposes Neonatal Intensive Care Unit (NICU) infants to subsequent infection. Reservoirs for acquisition remain poorly understood, limiting infection prevention efforts to prevent transmission. Methods Infants with known MRSA nasal colonization based on hospital surveillance and controls with negative MRSA screening cultures, and their parents, were enrolled in a prospective cohort study. Weekly cultures were collected from infants (4 sites), parents (3 sites), and NICU environmental surfaces (5 sites). Factors associated with MRSA colonization and infection were identified using generalized linear mixed modeling. Whole-genome sequencing (WGS) and pairwise comparisons were performed across entire genomes on 1041 S. aureus isolates using kSNP3. Isolates differing by less than 80 single nucleotide polymorphisms were considered highly related; highly related strains from different sources suggested transmission. Results Samples were collected 1–28 (median 7) times from 29 MRSA-colonized infants, 29 controls, 49 mothers, and 21 fathers. Over the study period MRSA colonization was detected in 10 (34%) infants who were not known to be MRSA-colonized based on hospital nasal surveillance cultures. Parent MRSA colonization (OR=11.0; 95% CI: 2.2, 55.0) and environmental MRSA contamination (OR=5.0; 95% CI: 1.6, 15.3) were associated with infant MRSA colonization. Specifically, 87% of infants with an MRSA-colonized parent were MRSA-colonized. MRSA infections occurred in 6 (21%) MRSA-colonized infants and 0 controls (P = 0.05). Infant rectal colonization (OR=15.0; 95% CI 1.6, 140.5) and persistent MRSA colonization (i.e., 3 or more consecutive positive MRSA cultures) (OR=8.4; 95% CI 1.3, 52.5) were associated with MRSA infection. Thirty clusters of highly related isolates were detected, including 12 clusters with highly related isolates from multiple study families (2–6 [median 3] unique families per cluster; Figures 1 and 2). Conclusion Our findings suggest MRSA transmission between infants, their parents, and the environment as well as transmission between patients. Future infection prevention efforts should consider parent and environmental reservoirs, as well as the role of extranasal sites of colonization. Disclosures All authors: No reported disclosures.