Genomic typing of Mycobacterium abscessus

Abstract

Mycobacterium abscessus is a rapid growing, non-tuberculosis mycobacteria, an opportunistic pathogen that infect lungs of cystic fibrosis patients. The incidence among CF-patients is increasing and the bacterial infection is difficult to treat. Epidemiology is important to understand how the infection spread, although until now, no sufficient methods for genetic strain typing have been available for this species. Previous methods, e.g. PFGE, could type the bacteria into subspecies. In this project, 45 clinical isolates and 3 reference strains were sequenced with Ion Torrent, a next generation sequencing platform. The data was analysed using the software CLC Genomics Workbench. Trimmed reads were mapped to a reference genome, variant calling was performed, and SNP trees were modelled from the data. As a result, the isolates were clustered into three distinct groups for the subspecies Mycobacterium abscessus subsp. abscessus, Mycobacterium abscessus subsp. massiliense and Mycobacterium abscessus subsp. bolletii. Different isolates from the same patient differed only 0-16 SNPs. Smaller clusters could be distinguished were isolates from different individuals could be proposed to belong to the same strain (less than 20 SNPs). Additional bacterial species and contaminated isolates were detected among the samples using de novo assembly, previously missed using other typing methods. BLAST search was performed on the contigs and they were also analysed online, with average nucleotide identity, to identify the strain. It was also possible to detect point mutations in known genes conferring antibiotic resistance with 100% resemblance to GenoType NTM-DR kit currently in use in clinical practice. In conclusion, whole genome sequencing with NGS can be used as a reliable method for subtyping and typing of strains as well as detection of resistance mutations.