Mycobacterium abscessus complex (Mabc) includes three clinical relevant subspecies; M.abscessus subsp. abscessus (M.abA), M.abscessus subsp. bolletti (M.abB), M.abscessus subsp. massiliense (M.abM). It is a rapid growing mycobacterium that is distributed ubiquitously in the environment, soil and water. There has been an increase awareness of Mabc due to its emerging pathogenicity nature and drug resistant patterns globally.

Mabc is a pathogen responsible in causing infection to skin, soft-tissue and highly associated with chronic pulmonary disease, especially in those affected by Cystic Fibrosis (CF). Currently, in NSW Mycobacterium abscessus isn’t a notifiable disease, therefore no epidemiology surveillance data is available that could assist in examining temporal trends of infection, drug resistance or potential outbreaks of this pathogen.

The use of Whole Genome Sequencing, can aid with the speciation of Mabc and determine markers for epidemiology clusters, drug resistance to macrolides, amikacin, ciprofloxacin and also assist in determining common markers associated with CF patient.

To date 120 Mabc positive culture isolates that were forwarded to the NSW Mycobacterium Reference Laboratory (MRL) from January 2015- December 2017. They have been whole genome sequenced by Illumina NextSeq500. On average the sequencing data had a coverage depth >100x and were assembled and analysed by recommended bioinformatics pipelines and CLC workbench. Core-genome analysis resulted in 93 M.abA with two dominant clads, 25 M.abM and 2 M.abB species. A cluster showing high genomic relatedness with < 20 Nucleotide Difference (SNPs) was observed. Common reported genotypic mutations in erm(41), rrs and rrl gene which are associated to macrolide and aminoglycoside resistance were detected among these samples and a few were confirmed by phenotypic drug susceptibility results.