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Delineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing

M Diricks(1,2,3) M Merker(1,2) N Wetzstein(4) T A Kohl(1,2,3) S Niemann(1,2,3) F P Maurer(1,3,5)

1:Research Center Borstel; 2:German Center for Infection Research (DZIF); 3:National and WHO Supranational Reference Laboratory for Mycobacteria (Borstel); 4:University Hospital Frankfurt; 5:University Medical Center Hamburg-Eppendorf

Mycobacterium abscessus (Mab) is a rapidly growing, multidrug-resistant nontuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate prospective molecular surveillance, we sought to establish a novel harmonized core genome multilocus sequence typing (cgMLST) scheme and thresholds for genetic distances to delineate global clonal complexes, transmission events, and within-patient diversity. We developed a cgMLST scheme based on 97 diverse Mab genomes and used it to analyse the global population structure of 1,797 publicly available genomes including strains of seven recently described dominant circulating clones. To calibrate genetic distance thresholds, we analysed 342 sequential isolates from chronically infected cystic fibrosis (CF) patients, and from three Mab outbreaks. CgMLST results were compared with 7-loci MLST, and core genome single nucleotide polymorphism (cgSNP) typing. The cgMLST scheme comprises 2,904 loci and can be used to genotype all three Mab subspecies (massiliense, bolletii, and abscessus). Most global clonal complexes previously classified using cgSNP were confirmed by our cgMLST approach, and also correlated well with traditional MLST sequence types. 1620 out of 1637 (99%) pairwise comparisons between epidemiologically linked isolates, i.e. isolates from the same patient, isolates belonging to same extra-pulmonary outbreak or isolates from CF patients with suggested nosocomial transmission were below 25 alleles and 90% below 10 alleles. These distance thresholds can be used to guide further epidemiological investigations. Overall, the scheme facilitates prospective Mab surveillance and will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.

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