Clinical immunogenetics laboratories performing routine sequencing of human leukocyte antigen (HLA) genes in support of hematopoietic cell transplantation are motivated to upgrade to next-generation sequencing (NGS) technology by its potential for cost savings as well as testing accuracy and flexibility. While NGS machines are available and simple to operate, there are few systems available that provide comprehensive sample preparation and data analysis workflows to complete the process. We report on the development and testing of the Integrated Genotyping System (IGS), which has been designed to specifically address the challenges associated with the adoption of NGS in clinical laboratories. To validate the system for a variety of sample DNA sources, we have tested 336 DNA specimens from whole blood, dried blood spots, buccal swabs, and lymphoblastoid cell lines. HLA class I and class II genotypes were derived from amplicon sequencing of HLA-A, -B, -C for exons 1-7 and HLA-DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, -DRB5 for exons 1-4. Additionally, to demonstrate the extensibility of the IGS to other genetic loci, KIR haplotyping of 93 samples was carried out in parallel with HLA typing using a workflow based on the HLA system. These results are discussed with respect to their applications in the clinical setting and consequent potential for advancing precision medicine.

Inflammatory bowel diseases (IBDs) are chronic intestinal diseases, frequently associated with comorbid psychological and cognitive deficits. These neuropsychiatric effects include anxiety, depression, and memory impairments that can be seen both during active disease and following remission and are more frequently seen in pediatric patients. The mechanism(s) through which these extra-intestinal deficits develop remain unknown and the study of these phenomenon are hampered by a lack of murine pediatric IBD models. Herein we describe microbiota-gut-brain (MGB) axis deficits following induction of colitis in a pediatric setting. Acute colitis was induced by administration of 2% dextran sodium sulfate (DSS) for 5 days starting at weaning (post-natal day [P]21) causing reduced weight gain, colonic shortening, and colonic inflammation by 8 days post-DSS (P29), which were mostly resolved in adult (P56) mice. Despite resolution of acute disease, cognitive deficits (novel object recognition task) and anxiety-like behavior (light/dark box) were identified, in the absence of changes in exploratory behavior (open field test) in P56 mice previously treated with DSS at weaning. Behavioral deficits were found in conjunction with neuroinflammation, decreased neurogenesis, and altered expression of pattern recognition receptor genes in the hippocampus. In addition, persistent alterations in the gut microbiota composition were observed at P56, including reduced butyrate-producing species. Taken together, these results describe for the first time the presence of MGB axis deficits following induction of colitis at weaning, which persist in adulthood.

Background . Diarrheal diseases are a leading cause of death in children under age five worldwide. Repeated early life exposures to diarrheal pathogens can result in co-morbidities including stunted growth and cognitive deficits suggesting an impairment in the microbiota-gut-brain (MGB) axis. Methods . Neonatal C57BL/6 mice were infected with EPEC (strain e2348/69; ΔescV [type 3 secretion system (T3SS) mutant]), or vehicle (LB broth) via orogastric gavage at post-natal day (P7). Behavior (novel object recognition [NOR] task, light/dark [L/D] box, and open field test [OFT]), intestinal physiology (Ussing chambers), and the gut microbiota (16S Illumina sequencing) were assessed in adulthood (6-8 weeks). Results . Neonatal infection of mice with EPEC, but not the T3SS mutant, caused ileal inflammation in neonates and impaired recognition memory (NOR task) in adulthood. Cognitive impairments were coupled with increased neurogenesis (Ki67 and doublecortin immunostaining) and neuroinflammation (increased microglia activation [Iba1]) in adulthood. Intestinal pathophysiology in adult mice was characterized by increased secretory state (short circuit current; Isc) and permeability (conductance; FITC-dextran flux) in the ileum and colon of neonatally EPEC-infected mice, along with increased expression of pro-inflammatory cytokines ( Tnfα, Il12, Il6 ) and pattern recognition receptors ( Nod1/2, Tlr2/4 ). Finally, neonatal EPEC infection caused significant dysbiosis of the gut microbiota, including decreased Firmicutes, in adulthood. Conclusions . Together these findings demonstrate that infection in early life can significantly impair the MGB axis in adulthood.

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Enteropathogenic Escherichia coli (EPEC) is a food‐borne pathogen and causes enteric illnesses in children. EPEC infection is often associated with malnutrition of the host, especially in individuals experiencing severe and prolonged infection, and/or in those who are nutritionally compromised. While EPEC infection impacts nutrient transporter function and expression in intestinal epithelial cells, to date the consequences of EPEC infection on intestinal absorption of ascorbic acid (AA) are not known. Therefore, we investigated this issue using human intestinal epithelial Caco‐2 cells (in vitro) and mouse (in vivo) models. Infecting Caco‐2 cells with EPEC (WT) markedly inhibited AA uptake. EPEC mutants (ΔescN, ΔespA, ΔespB and ΔespD) did not affect AA uptake, whereas ΔespF and ΔespG/G2 mutants significantly inhibited AA uptake in Caco‐2 cells. Further, we observed significantly reduced expression of both hSVCT1 and hSVCT2 protein and mRNA levels upon infection. Similarly, infecting mice with EPEC (WT) significantly inhibited AA uptake and also reduced the expression of both mSVCT1 and mSVCT2 protein and mRNA levels in jejunum and colon. Studies have shown that epigenetic mechanisms (microRNA) play a role in mediating responses to bacterial infection in the intestine. Therefore, we determined miR103a, miR141 and miR200a expression levels, which were recently shown to regulate SVCT1 and SVCT2. Data from in vitro and in vivo models showed that all three microRNAs were up‐regulated significantly upon EPEC infection. In addition, expression of the accessory protein human glyoxalate reductase/hydroxypyruvate reductase (hGRHPR), which regulates the SVCT1 function, was also markedly decreased by EPEC in both models. These findings suggest that in intestinal epithelial cells, EPEC infection markedly inhibits AA uptake via dysregulation of both SVCT1 and SVCT2 expression. Support or Funding Information Supported by NIH grants DK 107474, DK 58057, DK 56057, MH108154, GM088790, and a grant from the DVA