Genome sequence of a Coxiella burnetti strain isolated directly from a native heart valve of a patient with severe infective endocarditis

A 48-year-old man from Sfax in Tunisia presented with progressive dyspnea and leg swelling lasting more than one month. He was admitted to a local hospital for chest pain. Physical examination revealed signs of acute heart failure with bilateral inspiratory crackles on pulmonary auscultation, elevated jugular venous pressure, peripheral edema and painful hepatomegaly. Cardiac auscultation revealed a diastolic murmur at the aortic region. Laboratory findings showed a white blood cell count of 13 G/L, a hemoglobin of 84 g/l, platelets of 79000/mm3, a C-reactive protein of 75.6 mg/L, liver enzyme alteration with an ASAT at 25 U/L and ALAT at 171 U/L, and a altered kidney function with a creatinine at 350 µmol/L. Transesophagal echocardiography showed severe aortic regurgitation and the presence of vegetations on the aortic valve. The left ventricle (LV) was enlarged with mild systolic dysfunction (LV ejection fraction 50%). Serial blood cultures remained negative. The patient was treated empirically with intravenous amoxicillin-clavulanate and gentamicin. He developed hemodynamic instability, needing cardiac surgery with the insertion of a biological prosthesis. Surgery was complicated by post-operative bleeding. The patient developed disseminated intravascular coagulation (DIC) and died on day one post-surgery. Extended microbiological investigations were all negative except a serology for C. burnetti, which came positive ( IgG phase 1 antibodies, 1> 12’800). Culture of the valve remained sterile. Quantitative PCR (qPCR) analysis of the valvular sample was strongly positive (355'395'350 copies/ml) for C. burnetti. Whole genome sequencing of the strain was performed directly on the valvular sample, to test whether direct sequencing is feasible for such highly positive and to provide genomic data on a Tunisian strain.