Investigation of two Mycobacterium abscessus outbreaks in Quebec using whole genome sequencing

In recent decades, non-tuberculous mycobacteria (NTM) infections are of emerging public health concern and have contributed towards significant clinical and economic burden globally. One such rapid growing mycobacteria, Mycobacterium abscessus, can cause clonal outbreaks and these bacteria exhibit a highly resistant antimicrobial susceptibility profile. Here we present an investigation of two small outbreaks of M. abscessus; first in a pediatric clinic setting and second in a tattoo parlour from Quebec. Two whole genome sequencing approaches were utilized for genotyping: MAB-MLST, a multi locus sequencing typing scheme containing housekeeping, identification and antimicrobial resistance genes; and SNVPhyl that uses phylogenetics to determine single nucleotide variations between strains. MAB-MLST results showed that the pediatric outbreak strains had two distinct sequence types, demonstrating that one strain did not belong to the outbreak, while all tattoo isolates belonged to the same sequence type. SNVPhyl results were similar to MAB-MLST results and showed that the pediatric outbreak strains tightly clustered together with 0-1 SNVs between isolates, a sharp contrast between unrelated strains used as controls. Similar results were seen for tattoo outbreak cases with 3-11 SNVs between isolates. NTM infections can be difficult to identify and outbreak investigations can be complicated. Thus, WGS tools can be used in public health outbreak investigations as they provide high discriminatory power.