The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.

MOTIVATION: Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data. RESULTS: The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity. AVAILABILITY AND IMPLEMENTATION: All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Klebsiella pneumoniae and Klebsiella oxytoca meningitis in infants. Epidemiological and clinical features.

BACKGROUND: The incidence of meningitis caused by Klebsiella pneumoniae (Kp) and Klebsiella oxytoca (Ko) in high-income countries is unknown, and no series have been published to date. METHODS: We conducted a nationwide multicenter observational study in France between 2006 and 2016. All children from the French national registry for paediatric bacterial meningitis under the age of 1 year and hospitalized for Kp or Ko meningitis were included. Virulence factors of four Klebsiella spp. strains were explored by whole genome sequencing. RESULTS: Of 1859 cases of meningitis in children under the age of 1 year, 13 cases (0.7%) of Klebsiella spp. meningitis (nine for Kp meningitis and four for Ko meningitis) were registered in the French national registry. Three of the patients died and 50% of the survivors had developmental delays. CONCLUSIONS: Prematurity, low birth weight, and congenital anomalies of the urinary tract appear to be risk factors for Klebsiella spp. meningitis as well as virulence factors of the strain.

[Bronchopulmonary dysplasia: outcome and treatment of severe forms]. / Dysplasie bronchopulmonaire: devenir et traitement des formes sévères.

BACKGROUND: The outcome of severe forms of bronchopulmonary dysplasia (BPD) leading to a prolonged dependence on mechanical ventilation (MV) and/or oxygen therapy (O2) is not evaluated, and factors of guidance to treatment are not established. POPULATION AND METHODS: The medical records of 49 infants, born between 1982 and 1990, with BPD who required MV and or O2 after 12 months of life were retrospectively reviewed. Three groups of infants were defined: group I: 26 infants on MV since birth; group II: seven infants weaned from MV after the first month of life then put back on MV belatedly; group III: 16 infants on spontaneous ventilation (SV) under O2. RESULTS: At 12 months of age, the 49 infants showed sleep hypoxemia, failure to thrive and 28% of them pulmonary hypertension. Comparison between MV and O2 infants indicated that subjects on MV had pulmonary dynamic compliance (Cl dyn) lower than 50% (p = 0.01), ventilatory work including respiratory frequency in rest > 40 cycles/min; 70% of them had asynchronous thoracic and abdominal muscles during sleep (p < 0.01 for all comparisons). Seventy percent of patients had bronchospasms (p = 0.02). The 49 infants had a favourable outcome, allowing weaning from MV or O2 between the ages of 2 and 4 years. CONCLUSIONS: These findings suggest that major respiratory failure in prematurely born infants can be overcome with prolonged respiratory and nutritional supports during the post-natal period of lung development; Cl dyn < 50% is a cursor for prolonged MV and weaning from MV should be excluded as long as increased ventilatory work persists.

[Severe neonatal respiratory distress with linear inspiratory pressure-volume curve]. / Détresses respiratoires graves néonatales à courbe pression-volume inspiratoire linéaire.

Twenty-four newborns with severe respiratory distress, treated by mechanical ventilation, are investigated by inspiratory pressure-volume curve. The curves are obtained by slow continuous inflation technique. Two shapes are described: concave curve, ten newborns (group I), linear curve, fourteen newborns (group II). The gestational age is over 36 weeks in both groups. Determination of respiratory mechanics is indicated when mean AaDO2 is higher than 500 torr in both groups, and when there is a hypercapnia (PaCO2 = 53 +/- 11 torr, with p less than 0.05) in group II. Mechanical ventilation is conducted with individually adjusted PEEP in group I, and without PEEP in group II. Twelve hours after; mean AaDO2 in group I (260 +/- 101 torr) and in group II (420 +/- 188 torr) are significantly different (p less than 0.05). The variance analysis in group II shows that PaCO2 and pH are normalized (p less than 0.001). All the newborns in group I recovered. Three newborns in group II died. Group I can be assimilated to hyaline membrane disease in full-term neonates. Practically, the cases of neonatal respiratory distress in which PEEP is not indicated can be identified by the functional characteristics of group II.

Miliary tuberculosis with acute respiratory failure and histiocytic hemophagocytosis. Successful treatment with extracorporeal lung support and epipodophyllotoxin VP 16-213.

A 14-year-old girl with high fever, dyspnea and bilateral miliary nodules on chest X-ray, developed a rapidly progressive respiratory failure associated with histiocytic hemophagocytosis. Histologic examination of bone marrow biopsy revealed tuberculous granulomas with caseating necrosis. We report a pediatric case in which treatment with extracorporeal lung support and epipodophyllotoxin VP 16-213 was successful.