Reference intervals for stool calprotectin in preterm neonates and their utility for the diagnosis of necrotizing enterocolitis.

OBJECTIVE: Calprotectin is an antimicrobial protein found in stool when released by granulocytes. We sought to create stool calprotectin reference ranges in preterm neonates and to evaluate whether levels exceeding the upper reference interval are diagnostic for necrotizing enterocolitis (NEC). STUDY DESIGN: Stool calprotectin was measured in premature neonates without gastrointestinal pathology to create reference intervals. For comparison, levels from infants undergoing "rule out NEC" evaluations were plotted on these reference intervals. RESULTS: Stool calprotectin reference intervals were created according to gestational age at birth and corrected gestational age. Levels during "rule out NEC" evaluations were more often above the upper reference interval with NEC vs. those without NEC. CONCLUSIONS: Stools from preterm neonates have a higher range of calprotectin than stools from healthy term neonates. In evaluating preterm neonates for NEC with stool calprotectin, a calprotectin upper reference interval that incorporates corrected gestational age best predicts the diagnosis of NEC.

Dynamics of the human gut phageome during antibiotic treatment.

Bacterial viruses contribute to the dynamics of the microbiome communities, as they are involved in the horizontal gene transfer. Previously we studied changes in the gut microbiome of the two healthy individuals over the course of a 6-days antibiotics treatment and subsequent 28 days recovery time (Willmann et al., 2015). Now, from the same samples, the virus-like particles were isolated and sequenced. As the phage sequences are currently poorly represented in reference databases, the reads had to be assembled, annotated and their abundance had to be evaluated via reads mapping. We analyzed and compared patterns of changes in abundance of the phage scaffolds and scaffolds with antibiotics resistant genes, in both phage and whole-genome metagenomic sets. We observed an increase in abundance of scaffolds carrying antibiotic-resistant genes in response to the treatment.

Sequencing of the Hepatitis D Virus RNA WHO International Standard.

BACKGROUND: Well-characterized, stable calibration materials are essential to standardize quantitative viral reporting. The preferred calibration materials are the WHO International Standards and secondary standards derived from them. In 2013, the 1st WHO International Standard for Hepatitis D Virus (HDV) RNA became available. During the course of assay development in our laboratory, differences between the published sequence (GenBank ID: HQ005371) and sequence we generated from the WHO HDV Standard were identified. OBJECTIVES: We sought to sequence the entire genome of the WHO HDV Standard and compare the results to the published sequence. STUDY DESIGN: RNA extracted from the WHO HDV Standard was used to generate five overlapping PCR products, including one covering the entire HDV genome, which were Sanger sequenced using standard dye-terminator chemistry. Total RNA from the WHO HDV Standard was also converted to a cDNA library generating 2.1 million sequencing reads on a NextSeq500 instrument. RESULTS: Sanger sequencing produced 32 overlapping, partial sequences of the HDV genome. RNA-seq resulted in 8100 HDV sequences covering the viral genome an average of 645-fold. Sanger and RNA-seq consensus sequences had 100% agreement and showed 89.0% nucleotide identity with the published WHO HDV Standard sequence. BLAST analysis revealed HQ005369 as the closest match with 99.2% nucleotide identity. CONCLUSIONS: HQ005369 was deposited in GenBank along with HQ005371 and seven others from a study of nine Turkish patients. A sample mix-up or clerical error may have resulted in the incorrect association of identifier and sequence. The correct nucleic acid sequence for standards is critical for test accuracy, optimization, calibration, and troubleshooting.

Elevated fecal calprotectin levels during necrotizing enterocolitis are associated with activated neutrophils extruding neutrophil extracellular traps.

OBJECTIVE: Neonates with necrotizing enterocolitis (NEC) have higher calprotectin levels in stool than do healthy neonates. However, it is not known whether high stool calprotectin at the onset of bowel symptoms identifies neonates who truly have NEC vs other bowel disorders. STUDY DESIGN: Neonates were eligible for this study when an x-ray was ordered to 'rule-out NEC'. Stool calprotectin was quantified at that time and in a follow-up stool. Each episode was later categorized as NEC or not NEC. The location of calprotectin in the bowel was determined by immunohistochemistry. RESULTS: Neonates with NEC had higher initial and follow-up stool calprotectin levels than did neonates without NEC. Calprotectin in bowel from neonates with NEC was within neutrophil extracellular traps (NETs). CONCLUSION: At the onset of signs concerning for NEC, fecal calprotectin is likely to be higher in neonates with NEC. Calprotectin in their stools is exported from neutrophils via NETs.

Absence of echovirus sequences in brain and spinal cord of amyotrophic lateral sclerosis patients.

The role of enteroviruses in pathogenesis of amyotrophic lateral sclerosis (ALS) is controversial. A recent study, based on reverse transcription-polymerase chain reaction (RT-PCR) analysis of spinal cord, reported identification of a novel echovirus in 15 of 17 French subjects with ALS and only 1 of 29 subjects with other neurologic diseases. We established a real-time RT-PCR method based on this novel echovirus sequence and used this method and that previously employed for analysis of the French subjects to determine the prevalence of echoviral sequences in spinal cord and motor cortex of sporadic ALS subjects from the United States. No echoviral sequences were found in 20 spinal cord and 10 motor cortex samples from autopsy-confirmed cases of ALS or 13 spinal cord and 5 motor cortex samples from subjects with no motor neuron disease.