TY - JOUR T1 - CoxBase: an online platform for epidemiological surveillance, visualization, analysis and typing of <em>Coxiella burnetii</em> genomic sequence JF - bioRxiv DO - 10.1101/2020.11.29.402362 SP - 2020.11.29.402362 AU - Akinyemi. M. Fasemore AU - Andrea Helbich AU - Mathias. C. Walter AU - Thomas Dandekar AU - Gilles Vergnaud AU - Konrad U. Förstner AU - Dimitrios Frangoulidis Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/11/30/2020.11.29.402362.abstract N2 - Q (query) fever is an infectious zoonotic disease, caused by the Gram-negative bacteria Coxiella burnetii, that sometimes is transmitted to humans from small ruminants like sheep, goat and cattle. Although the disease has been studied since decades, it still represents a threat due to sporadic outbreaks across farms in Europe. The reason for this has been linked to the interaction of several dynamic factors including reservoir type and vector diversity. One important control measure we have identified is a central platform for Coxiella typing data management. This is particularly important in the case of an outbreak where the nature of the pathogen and type would need to be rapidly identified and compared to existing isolates as well as further documented and made available for researcher to aid future investigations. The existing platforms are focused on MLVA (multiple locus VNTR analysis) genotyping. We have designed and implemented an online, open, web-based platform called CoxBase (https://coxbase.q-gaps.de), that is capable of in silico genotyping of completely or minimally assembled Coxiella sequences using five different typing methods, included with a database that holds genotyping information of more than 400 Coxiella isolates with their metadata such as host type, source and year of isolation together with further metadata information. Also, it includes a query and submission interface for interrogating existing isolates and depositing new isolates. Attractive visualization features include maps showing the geographical source of the isolates and plots that can be used to summarize isolates metadata on a country level. We tested our in silico typing method on 50 Coxiella genomes downloaded from the RefSeq database and we could type almost all the genomes except for cases where the sequences are poorly assembled. We identified new spacer sequences using our MST in silico typing methods, and could categorize adaA gene phenotypes for all 50 genomes as well as their plasmid types.Competing Interest StatementThe authors have declared no competing interest. ER -