Whole genome sequencing of samples suspected to be Mycobacterium chimaera from clinical samples and from water samples originating from Heating-Cooling Units in medical centers in Israel.

Non-tuberculous mycobacteria (NTM) are opportunistic pathogens that cause illness primarily in the elderly, in the immunocompromised or in patients with underlying lung disease. Mycobacterium chimaera is a NTM species belonging to the M. avium Complex (MAC) group of species. Since 2013, a global outbreak of M. chimaera infection related to heater-cooler units (HCU) used in cardio-thoracic surgery has been identified. This outbreak was caused by a single strain of M. chimaera. In order to estimate the prevalence of this outbreak strain in Israel, we sampled M. chimaera from several HCU machines in Israel, as well as from patients, sequenced their genomes and compared them to the outbreak strain. The presence of mixed mycobacteria species in the samples complicated the analysis of obtained sequences. By applying a metagenomic binning strategy, we were able to obtain genomes of single strains from the mixed samples, and characterized them. M. chimaera strains were compared to each other and to previously reported genomes from other countries. The strain causing the outbreak related to the HCU machines was identified in several such machines in Israel but not in any of the clinical samples.