Browsing by Author "Miller, Steve"

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    Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
    (Oxford University Press, 2019-05-17) Zinter, Matt S.; Dvorak, Christopher C.; Mayday, Madeline Y.; Iwanaga, Kensho; Ly, Ngoc P.; McGarry, Meghan E.; Church, Gwynne D.; Faricy, Lauren E.; Rowan, Courtney M.; Hume, Janet R.; Steiner, Marie E.; Crawford, Emily D.; Langelier, Charles; Kalantar, Katrina; Chow, Eric D.; Miller, Steve; Shimano, Kristen; Melton, Alexis; Yanik, Gregory A.; Sapru, Anil; DeRisi, Joseph L.; Pediatrics, School of Medicine
    BACKGROUND: Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed to develop a highly sensitive metagenomic next-generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. METHODS: We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children's hospitals from 2014-2016. Samples underwent mechanical homogenization, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. RESULTS: We identified a rich cross-domain pulmonary microbiome that contained bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001). CONCLUSIONS: An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
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    Rotavirus Strain Trends in United States, 2009-2016: Results from the National Rotavirus Strain Surveillance System (NRSSS)
    (MDPI, 2022-08-15) Mijatovic-Rustempasic, Slavica; Jaimes, Jose; Perkins, Charity; Ward, M. Leanne; Esona, Mathew D.; Gautam, Rashi; Lewis, Jamie; Sturgeon, Michele; Panjwani, Junaid; Bloom, Gail A.; Miller, Steve; Reisdorf, Erik; Riley, Ann Marie; Pence, Morgan A.; Dunn, James; Selvarangan, Rangaraj; Jerris, Robert C.; DeGroat, Dona; Parashar, Umesh D.; Cortese, Margaret M.; Bowen, Michael D.; Pathology and Laboratory Medicine, School of Medicine
    Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009-2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009-2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009-2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012-2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1-3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.