Molecular epidemiology of tuberculosis in Tasmania and genomic characterisation of its first known multi-drug resistant case

Background:The origin and spread of tuberculosis (TB) in Tasmania and the types of strains of Mycobacteriumtuberculosis complex (MTBC) present in the population are largely unknown.Objective:The aim of this study was to perform the first genomic analysis of MTBC isolates from Tasmaniato better understand the epidemiology of TB in the state.Methods:Whole-genome sequencing was performed on cultured isolates of MTBC collected from2014–2016. Single-locus variant analysis was applied to determine the phylogeny of the isolatesand the presence of drug-resistance mutations. The genomic data were then cross-referencedagainst public health surveillance records on each of the cases.Results:We determined that 83.3% of TB cases in Tasmania from 2014–2016 occurred in non-Australianborn individuals. Two possible TB clusters were identified based on single locus variantanalysis, one from November-December 2014 (n = 2), with the second from MayAugust2015 (n = 4). We report here the first known isolate of multi-drug resistant (MDR)M. tuberculosis in Tasmania from 2016 for which we established its drug resistance mutationsand potential overseas origin. In addition, we characterised a case of M. bovis TB in aTasmanian-born person who presented in 2014, approximately 40 years after the last confirmedcase in the state’s bovids.Conclusions:TB in Tasmania is predominantly of overseas origin with genotypically-unique drug-susceptibleisolates of M. tuberculosis. However, the state also exhibits features of TB that areobserved in other jurisdictions, namely, the clustering of cases, and drug resistance. Earlydetection of TB and contact tracing, particularly of overseas-born cases, coordinated withrapid laboratory drug-susceptibility testing and molecular typing, will be essential for Tasmaniato reach the World Health Organisation’s TB eradication goals for low-incidencesettings

Mycobacterium tuberculosis lineage 4 comprises globally distributed and geographically restricted sublineages

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most common generalist sublineage. Hence, the global success of lineage 4 reflects distinct strategies adopted by different sublineages and the influence of human migration.We thank S. Lecher, S. Li and J. Zallet for technical support. Calculations were performed at the sciCORE scientific computing core facility at the University of Basel. This work was supported by the Swiss National Science Foundation (grants 310030_166687 (S.G.) and 320030_153442 (M.E.) and Swiss HIV Cohort Study grant 740 to L.F.), the European Research Council (309540-EVODRTB to S.G.), TB-PAN-NET (FP7-223681 to S.N.), PathoNgenTrace projects (FP7-278864-2 to S.N.), SystemsX.ch (S.G.), the German Center for Infection Research (DZIF; S.N.), the Novartis Foundation (S.G.), the Natural Science Foundation of China (91631301 to Q.G.), and the National Institute of Allergy and Infectious Diseases (5U01-AI069924-05) of the US National Institutes of Health (M.E.)

Molecular Characterization of Isoniazid-Resistant Mycobacterium tuberculosis Isolates Collected in Australia

Elucidation of the molecular basis of isoniazid (INH) resistance in Mycobacterium tuberculosis has led to the development of different genotypic approaches for the rapid detection of INH resistance in clinical isolates. Mutations in katG, in particular the S315T substitution, are responsible for INH resistance in a large proportion of tuberculosis cases. However, the frequency of the katG S315T substitution varies with population samples. In this study, 52 epidemiologically unrelated clinical INH-resistant M. tuberculosis isolates collected in Australia were screened for mutations at katG codon 315 and the fabG1-inhA regulatory region. Importantly, 52 INH-sensitive isolates, selected to reflect the geographic and genotypic diversity of the isolates, were also included for comparison. The katG S315T substitution and fabG1-inhA −15 C-to-T mutation were identified in 34 and 13 of the 52 INH-resistant isolates, respectively, and none of the INH-sensitive isolates. Three novel katG mutations, D117A, M257I, and G491C, were identified in three INH-resistant strains with a wild-type katG codon 315, fabG1-inhA regulatory region, and inhA structural gene. When analyzed for possible associations between resistance mechanisms, resistance phenotype, and genotypic groups, it was found that neither the katG S315T nor fabG1-inhA −15 C-to-T mutation clustered with any one genotypic group, but that the −15 C-to-T substitution was associated with isolates with intermediate INH resistance and isolates coresistant to ethionamide. In total, 90.4% of unrelated INH-resistant isolates could be identified by analysis of just two loci: katG315 and the fabG1-inhA regulatory region

Epidemiology and control of tuberculosis in Victoria, a low-burden state in south-eastern Australia, 2005-2010

SETTING: Victoria, Australia. OBJECTIVE: To describe the epidemiology and control of tuberculosis (TB) in Victoria, 2005-2010. DESIGN: Retrospective review of laboratory-confirmed TB in Victoria, 2005-2010. State TB reference laboratory records were matc

First case of Mycobacterium ulcerans disease (Bairnsdale or Buruli ulcer) acquired in New South Wales

Mycobacterium ulcerans is a slow-growing environmental bacterium that causes Buruli ulcer (also known as Bairnsdale ulcer in Victoria and Daintree ulcer in northern Queensland). We describe two patients with laboratory-confirmed Buruli ulcer who were infected either in New South Wales or overseas. A molecular epidemiological investigation demonstrated that, while one case was probably acquired in Papua New Guinea, the other was most likely to have been acquired in southern NSW. To our knowledge, this is the first case of M. ulcerans infection acquired in NSW

Demographic and specimen information for tuberculosis cases (<i>n</i> = 18) in Tasmania from 2014 to 2016.

<p>Demographic variables on the TB cases and specimen types were recorded. Cases were 72.2% male and 27.8% female. The mean TB patient age was 33.6 years (range 0–70 years).</p

Genome sequence comparisons of serial multi-drug resistant Mycobacterium tuberculosis isolates

<p>Supplementary table S1 as published in <em>Microbial Genomics</em> in the following article: Genome sequence comparisons of serial multi-drug resistant Mycobacterium tuberculosis isolates over 21 years of infection in a single patient [10.1099/mgen.0.000037]</p

Mutations detected in the genome of the TASMDR1 isolate that confer resistance to anti-tubercular drugs.

<p>Six mutations that have been associated with anti-tubercular drug resistance were identified. The mutations listed in the <i>rpoB</i>, <i>katG</i>, <i>pncA</i>, and <i>embB</i> genes were classified as high confidence SNPs with respect to resistance to rifampicin, isoniazid, pyrazinamide and ethambutol, respectively, by the PhyResSE database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192351#pone.0192351.ref012" target="_blank">12</a>]. In addition, an A/C substitution was detected at position 514 of the 16S rRNA gene, <i>rrs</i> (MTB000019) that is associated with streptomycin resistance [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192351#pone.0192351.ref033" target="_blank">33</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192351#pone.0192351.ref034" target="_blank">34</a>].</p

Distribution of <i>in silico</i> generated spoligotypes across the culture-positive Tasmanian TB isolates analysed from 2014–2016.

<p>^aThe <i>in silico</i> derived spoligotype of the four Tasmanian Lineage 3 cluster isolates (RHH3, RHH11, RHH13, RHH14) and a fifth Lineage 3 isolate (RHH10) matched Spoligotype International Type 26 of the CAS1_Delhi spoligotyping family which accounted for approximately 50% of Lineage 3 <i>M</i>. <i>tuberculosis</i> isolates in Nepal in a previous analysis [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192351#pone.0192351.ref021" target="_blank">21</a>]. ^bThe <i>in silico</i> derived spoligotype of the <i>M</i>. <i>bovis</i> isolate (TASMB14) matches that of human <i>M</i>. <i>bovis</i> cases that were reported in other Australian states/territories between 1977 and 1989 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0192351#pone.0192351.ref022" target="_blank">22</a>].</p