The Bacterial and Viral Complexity of Postinfectious Hydrocephalus in Uganda

Postinfectious hydrocephalus (PIH), often following neonatal sepsis, is the most common cause of pediatric hydrocephalus world-wide, yet the microbial pathogens remain uncharacterized. Characterization of the microbial agents causing PIH would lead to an emphasis shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention. We examined blood and CSF from 100 consecutive cases of PIH and control cases of non-postinfectious hydrocephalus (NPIH) in infants in Uganda. Genomic testing was undertaken for bacterial, fungal, and parasitic DNA, DNA and RNA sequencing for viral identification, and extensive bacterial culture recovery. We uncovered a major contribution to PIH from Paenibacillus, upon a background of frequent cytomegalovirus (CMV) infection. CMV was only found in CSF in PIH cases. A facultatively anaerobic isolate was recovered. Assembly of the genome revealed a strain of P. thiaminolyticus. In mice, this isolate designated strain Mbale, was lethal in contrast with the benign reference strain. These findings point to the value of an unbiased pan-microbial approach to characterize PIH in settings where the organisms remain unknown, and enables a pathway towards more optimal treatment and prevention of the proximate neonatal infections. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Supported by NIH Director Pioneer Award 1DP1HD086071 and NIH Director Transformative Award 1R01AI145057. JEE was supported by National Center for Advancing Translational Sciences KL2 TR002015. MYG was supported by the NIH Intramural Research Program at the National Library of Medicine. ADW received salary support by an in-kind contribution from the University of Liverpool. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was conducted at the CURE Children's Hospital of Uganda (CCHU), a freestanding pediatric neurosurgical hospital in eastern Uganda that serves as a countrywide referral center for patients with hydrocephalus. Infants were eligible for participation in the trial if they were 3 months of age or younger, met criteria for postinfectious or non-postinfectious hydrocephalus (PIH and NPIH respectively), and had a mother who was at least 18 years of age. The study was designed as a waste-fluid study at surgery with verbal consent. Ethics oversight was provided by the CCHU Institutional Review Board, the Mbarara University of Science and Technology Research Ethics Committee, and with oversight of the Ugandan National Council on Science and Technology. The study was approved by the Penn State University Institutional Review Board, and a Materials Transfer Agreement was in place between CCHU and Penn State University. A US Centers for Disease Control permit for the importation of infectious materials covered the transfer of specimens from CCHU to Penn State. An Institutional Biosafety Committee provided oversight of specimen handling at Penn State. A Materials Transfer Agreement between Penn State and Columbia University covered the transport of materials between these research sites. All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The assembled genome of Paenibacillus thiaminolyticus Mbale was deposited in GenBank with Accession [CP041404][1]. Sequencing data for bacterial 16S DNA, in silico host-depleted mRNA, and VirCapSeq data, along with sample metadata are available at the NCBI archive under project ID PRJNA605220. All custom code utilized in this study will be made available to investigators upon request. All data associated with this study are in the paper or supplementary materials. [1]: /lookup/external-ref?link_type=GEN&access_num=CP041404&atom=%2Fmedrxiv%2Fearly%2F2020%2F08%2F04%2F2020.08.03.20167544.atom