The first reported case of human infection with Variovorax durovernensis; a novel Variovorax sp. Isolated from the prosthetic aortic graft of a shepherd

Abstract

Background: We describe a case of a 55-year-old shepherd with history of mycotic aneurysm presenting with a chronic aortic endovascular graft infection caused by Nocardia nova and a newly identified Variovorax sp which we named ‘Variovorax durovernensis’. This is the first case of this Variovorax sp. causing human pathology. This organism was identified with whole-genome sequencing as a new species of Variovorax, with ‘Durovernum’ (the Latin name for Canterbury) suggested at our patients request; an ancient town where they work as a shepherd. Case Report: Our patient presented with a ruptured left common iliac mycotic aneurysm with Campylobacter fetus isolated, requiring emergent endovascular stenting. Seven months post-discharge they re-presented with headache, weight loss and back pain. A half-body fluorodeoxyglucose positron emission tomography (FDG-PET) scan showed aorto-bi-iliac graft uptake in the left periureteric region. The infected graft was explanted and revascularisation obtained with autologous harvested veins. Results: Graft samples grew Nocardia nova 3/5 samples on day 5 of incubation and yellow colonies of a gram-negative on 3/5 samples after 7 days. Identification of Variovorax genus was obtained using the Bruker MALDI-TOF Biotyper (Bruker Daltonics, Germany). Variovorax Sp. DNA was sequenced using Genomic DNA (SQK-LSK109 kit) on GridION (Oxford Nanopore Technologies). Sequence data was filtered and polished with genome Minimap2 and Nanopolish v0.8.4. Epi2Me identified a Variovorax sp.; in silico genomic analysis and in vitro phenotypic testing confirmed it as a new species. Conclusion: As diagnostic capabilities improve unusual clinical isolates can be reliably identified. The Bruker MALDI-TOF allowed identification of Variovorax Sp. causing clinical disease in this setting. This new species was defined with whole-genome sequencing allowing identification and recognition in international repositories.This case highlights the importance of an open mind interpreting results from clinical samples as more atypical infections from the environmental microbiome may be isolated.