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.

Comparison of the MGIT TBc immunochromatographic assay with the Accuprobe Gen-Probe TB assay for identification of Mycobacterium tuberculosis complex: results from a low-burden tuberculosis setting.

We compared the BD MPT64 TBc Antigen assay with the Gen-Probe TB assay for identifying Mycobacterium tuberculosis (MTB) from liquid culture vials. The BD TBc Antigen assay was more sensitive than and as specific as the Gen-Probe TB assay, making it a useful alternative for the rapid detection of MTB.

High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study.

We examined the pattern of tuberculosis (TB) transmission (i.e., reactivation versus recent transmission) and the impact of human immunodeficiency virus (HIV) infection in Harare, Zimbabwe. Consecutive adult smear-positive pulmonary TB patients presenting to an urban hospital in Harare were enrolled. A detailed epidemiological questionnaire was completed, and tests for HIV type 1 and CD4 cell counts were performed for each patient. Molecular fingerprinting of the genomic DNA recovered from cultures of sputum was performed by two molecular typing methods: spacer oligonucleotide typing (spoligotyping) and analysis of variable number of tandem DNA repeats (VNTRs). A cluster was defined as isolates from two or more patients that shared the same spoligotype pattern or the same VNTR pattern, or both. DNA suitable for typing was recovered from 224 patients. The prevalence of HIV infection was 79%. Of 187 patient isolates (78.6%) typed by both spoligotyping and analysis of VNTRs, 147 were identified as part of a cluster by both methods. By spoligotyping alone, 84.1% of patient isolates were grouped into 20 clusters. The cluster size was generally <8 patient isolates, although three large clusters comprised 68, 25, and 23 patient isolates. A total of 89.4% of the patient isolates grouped into 12 clusters defined by analysis of VNTRs, with 2 large clusters consisting of 127 and 13 patient isolates, respectively. Thirty-six percent of patient isolates with a shared spoligotype and 17% with a shared VNTR pattern were geographically linked within Harare, but they were not linked on the basis of the patient's home district. In a multivariate analysis, there were no independent predictors of clustering, including HIV infection status. Comparison with the International Spoligotype database (Pasteur Institute, Pointe a Pitre, Guadeloupe) demonstrated that our three largest spoligotype clusters are well recognized and ubiquitous in Africa. In this epidemiologically well characterized urban population with a high prevalence of HIV infection, we identified a very high level of strain clustering, indicating substantial ongoing recent TB transmission. Geographic linkage could be detected in a proportion of these clusters. A small group of actively circulating strains accounted for most of the cases of TB transmission.