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.)

Genome sequence comparisons of serial multi-drug-resistant Mycobacterium tuberculosis isolates over 21 years of infection in a single patient

We report a case of chronic pulmonary multi-drug-resistant tuberculosis. Despite 14 years of treatment, Mycobacterium tuberculosis was persistently isolated from sputum. Following treatment cessation the patient remained well, although M. tuberculosis was isolated from sputum for a further 8 years. Genome sequencing of eight serial M. tuberculosis isolates cultured between 1991 and 2011 revealed 17 mutations (0.8 mutations per genome year- 1). Eight of these were persisting mutations and only two mutations were detected in the 7 years following cessation of treatment in 2004. In four isolates there were mixed alleles, suggesting the likely presence of bacterial subpopulations. The initial 1991 isolate demonstrated genotypic resistance to isoniazid (katG W91R), rifampicin (rpoB S531L), ethambutol (embB M306V), streptomycin (gidB L16R), quinolones (gyrA S95T) and P-aminosalicylic acid (thyA T202A). Subsequent resistance mutations developed for pyrazinamide (pncA I31F) and ethionamide (ethA frameshift). Such information might have been instructive when developing a treatment regimen. In retrospect and with the benefit of high-resolution genomic hindsight we were able to determine that the patient received only one or two active anti-tuberculous agents for most of their treatment. Additionally, mutations in bacA and Rv2326c were detected, which may have contributed to the persistent but mild disease course. BacA is likely to be associated with maintenance of chronic infection and Rv2326c with a decreased bacterial metabolic state. These results expand our understanding of M. tuberculosis evolution during human infection and underline the link between antibiotic resistance and clinical persistence

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

Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia.

NoSince 2000, cases of the neglected tropical disease Buruli ulcer, caused by infection with Mycobacterium ulcerans, have increased 100-fold around Melbourne (population 4.4 million), the capital of Victoria, in temperate southeastern Australia. The reasons for this increase are unclear. Here, we used whole-genome sequence comparisons of 178 M. ulcerans isolates obtained primarily from human clinical specimens, spanning 70 years, to model the population dynamics of this pathogen from this region. Using phylogeographic and advanced Bayesian phylogenetic approaches, we found that there has been a migration of the pathogen from the east end of the state, beginning in the 1980s, 300 km west to the major human population center around Melbourne. This move was then followed by a significant increase in M. ulcerans population size. These analyses inform our thinking around Buruli ulcer transmission and control, indicating that M. ulcerans is introduced to a new environment and then expands, rather than it being from the awakening of a quiescent pathogen reservoir.National Health and Medical Research Council of Australia (NHMRC), an NHMRC Senior Research Fellowship to T.P.S. (grant GNT1105525); and an NHMRC Practitioner Fellowship to B.P.H. (GNT1105905). A.H.B. was supported by an Australian Postgraduate Award Ph.D. scholarship

Clinical, Microbiological and Pathological Findings of <i>Mycobacterium ulcerans</i> Infection in Three Australian Possum Species

<div><p>Background</p><p>Buruli ulcer (BU) is a skin disease caused by <i>Mycobacterium ulcerans</i>, with endemicity predominantly in sub-Saharan Africa and south-eastern Australia. The mode of transmission and the environmental reservoir(s) of the bacterium and remain elusive. Real-time PCR investigations have detected <i>M. ulcerans</i> DNA in a variety of Australian environmental samples, including the faeces of native possums with and without clinical evidence of infection. This report seeks to expand on previously published findings by the authors' investigative group with regards to clinical and subclinical disease in selected wild possum species in BU-endemic areas of Victoria, Australia.</p><p>Methodology/Principal Findings</p><p>Twenty-seven clinical cases of <i>M. ulcerans</i> infection in free-ranging possums from southeastern Australia were identified retrospectively and prospectively between 1998–2011. Common ringtail possums (<i>Pseudocheirus peregrinus</i>), a common brushtail possum (<i>Trichosurus vulpecula</i>) and a mountain brushtail possum (<i>Trichosurus cunninghami</i>) were included in the clinically affected cohort. Most clinically apparent cases were adults with solitary or multiple ulcerative cutaneous lesions, generally confined to the face, limbs and/or tail. The disease was minor and self-limiting in the case of both <i>Trichosurus</i> spp. possums. In contrast, many of the common ringtail possums had cutaneous disease involving disparate anatomical sites, and in four cases there was evidence of systemic disease at post mortem examination. Where tested using real-time PCR targeted at IS<i>2404</i>, animals typically had significant levels of <i>M. ulcerans</i> DNA throughout the gut and/or faeces. A further 12 possums without cutaneous lesions were found to have PCR-positive gut contents and/or faeces (subclinical cases), and in one of these the organism was cultured from liver tissue. Comparisons were made between clinically and subclinically affected possums, and 61 PCR-negative, non-affected individuals, with regards to disease category and the categorical variables of species (common ringtail possums <i>v</i> others) and sex. Animals with clinical lesions were significantly more likely to be male common ringtail possums.</p><p>Conclusions/Significance</p><p>There is significant disease burden in common ringtail possums (especially males) in some areas of Victoria endemic for <i>M. ulcerans</i> disease. The natural history of the disease generally remains unknown, however it appears that some mildly affected common brushtail and mountain brushtail possums can spontaneously overcome the infection, whereas some severely affected animals, especially common ringtail possums, may become systemically, and potentially fatally affected. Subclinical gut carriage of <i>M. ulcerans</i> DNA in possums is quite common and in some common brushtail and mountain brushtail possums this is transient. Further work is required to determine whether <i>M. ulcerans</i> infection poses a potential threat to possum populations, and whether these animals are acting as environmental reservoirs in certain geographical areas.</p></div

Data for sub-clinically affected possums.

<p>Data for sub-clinically affected possums.</p

(a): Photomicrograph of a skin lesion obtained from case 16.

<p>The lesion is characterised by proliferative epidermis overlying fibrotic dermal tissue admixed with inflammatory cells, and superficial crust composed of serous exudate and degenerate leukocytes overlying a necrotic base. (H&E stain)) (<b>b</b>): Demonstration of numerous acid-fast bacilli (AFB) in an ulcerated skin lesion of case 16 (modified ZN stain), (<b>c</b>): the liver lesions in this case contained rare AFB, mostly within macrophages (arrow) (modified ZN stain). (Images C. McCowan).</p

Relative real-time IS<i>2404</i> PCR signal from gut contents of possums.

<p>Relative real-time IS<i>2404</i> PCR signal from gut contents of possums.</p

Data for possums with confirmed clinical <i>M. ulcerans</i> infection.

<p>Data for possums with confirmed clinical <i>M. ulcerans</i> infection.</p