Utility of whole genome sequencing for multidrug resistant Mycobacterium tuberculosis isolates in a reference TB laboratory in New Zealand.

New Zealand has a low burden of multi-drug resistant TB (MDR-TB), but with increased mobility within the population, rapid detection and treatment of MDR-TB is a priority from the public health point of view. Mycobacterium Reference Laboratory in LabPLUS, Auckland City Hospital receives referred Mycobacterium tuberculosis complex (MTBC) isolates from all over New Zealand for second-line drug susceptibility testing (DST) and 24-loci MIRU VNTR genotyping. Between 2002 and 2013, 38 multidrug resistant Mycobacterium tuberculosis (MDR-TB) isolates were recorded by culture-based DST. A retrospective study revealed that in 12 of these 38 MDR-TB isolates (28%) there was a discrepancy between the genotypic and the phenotypic results. In order to address this, whole genome sequencing (WGS) was performed on the discrepant MDR-TB isolates. Reported here are the additional information on the drug resistant markers from WGS, which shed light on the discordance between results from the culture-based DST and the molecular diagnostic tests. These results underscore the utility of WGS in a reference mycobacterium laboratory in New Zealand to supplement other molecular tests and to assist in a rapid but accurate diagnosis and appropriate management of MDR-TB.