Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis

Akshaya Ramesh; Sara Nakielny; Jennifer Hsu; Mary Kyohere; Oswald Byaruhanga; Charles de Bourcy; Rebecca Egger; Boris Dimitrov; Yun-Fang Juan; Jonathan Sheu; James Wang; Katrina Kalantar; Charles Langelier; Theodore Ruel; Arthur Mpimbaza; Michael R. Wilson; Philip J. Rosenthal; Joseph L. DeRisi

We studied children admitted to Tororo District Hospital, Tororo, Uganda, with febrile 357 illnesses. Potential subjects were identified by clinic staff, who notified study personnel, who 358 subsequently evaluated the children for study eligibility. Inclusion criteria were: 1) age 2-60 359 months; 2) admission to Tororo District Hospital for acute illness; 3) documentation of axillary 360 temperature >38.0°C on admission or within 24 hours of admission; and 4) provision of 361 informed consent from the parent or guardian for study procedures. 362 . CC-BY-ND 4.0 International license is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/385005 doi: bioRxiv preprint Study specimens: 364 NP swabs and blood were collected from each enrolled subject within 24 hours of 365 hospital admission. Approximately 5 ml of blood was collected by phlebotomy, the sample was 366 centrifuged at room temperature, and serum was then stored at -80°C. NP swab samples 367 collected with FLOQSwabs™ swabs (COPAN) were placed into cryovials with Trizol 368 (Invitrogen), and stored at -80°C within ~5 min of collection. For subjects with acute diarrhea (≥ 369 3 loose or watery stools in 24 hours), stool was collected into clean plastic containers and stored 370 at -80°C within ~5 min of collection. Samples were stored at -80°C until shipment on dry ice to 371 UCSF for sequencing. 372