Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections

Polyclonal infections occur when at least two unrelated strains of the same pathogen are detected in an individual. This has been linked to worse clinical outcomes in tuberculosis, as undetected strains with different antibiotic resistance profiles can lead to treatment failure. Here, we examine the amount of polyclonal infections in sputum and surgical resections from patients with tuberculosis in the country of Georgia. For this purpose, we sequence and analyse the genomes of Mycobacterium tuberculosis isolated from the samples, acquired through an observational clinical study (NCT02715271). Access to the lung enhanced the detection of multiple strains (40% of surgery cases) as opposed to just using a sputum sample (0-5% in the general population). We show that polyclonal infections often involve genetically distant strains and can be associated with reversion of the patient's drug susceptibility profile over time. In addition, we find different patterns of genetic diversity within lesions and across patients, including mutational signatures known to be associated with oxidative damage; this suggests that reactive oxygen species may be acting as a selective pressure in the granuloma environment. Our results support the idea that the magnitude of polyclonal infections in high-burden tuberculosis settings is underestimated when only testing sputum samples

Predictors of Multidrug- and Extensively Drug-Resistant Tuberculosis in a High HIV Prevalence Community

BACKGROUND: Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) have emerged in high-HIV-prevalence settings, which generally lack laboratory infrastructure for diagnosing TB drug resistance. Even where available, inherent delays with current drug-susceptibility testing (DST) methods result in clinical deterioration and ongoing transmission of MDR and XDR-TB. Identifying clinical predictors of drug resistance may aid in risk stratification for earlier treatment and infection control. METHODS: We performed a retrospective case-control study of patients with MDR (cases), XDR (cases) and drug-susceptible (controls) TB in a high-HIV-prevalence setting in South Africa to identify clinical and demographic risk factors for drug-resistant TB. Controls were selected in a 1:1:1 ratio and were not matched. We calculated odds ratios (OR) and performed multivariate logistic regression to identify independent predictors. RESULTS: We enrolled 116, 123 and 139 patients with drug-susceptible, MDR, and XDR-TB. More than 85% in all three patient groups were HIV-infected. In multivariate analysis, MDR and XDR-TB were each strongly associated with history of TB treatment failure (adjusted OR 51.7 [CI 6.6-403.7] and 51.5 [CI 6.4-414.0], respectively) and hospitalization more than 14 days (aOR 3.8 [CI 1.1-13.3] and 6.1 [CI 1.8-21.0], respectively). Prior default from TB treatment was not a risk factor for MDR or XDR-TB. HIV was a risk factor for XDR (aOR 8.2, CI 1.3-52.6), but not MDR-TB. Comparing XDR with MDR-TB patients, the only significant risk factor for XDR-TB was HIV infection (aOR 5.3, CI 1.0-27.6). DISCUSSION: In this high-HIV-prevalence and drug-resistant TB setting, a history of prolonged hospitalization and previous TB treatment failure were strong risk factors for both MDR and XDR-TB. Given high mortality observed among patients with HIV and drug-resistant TB co-infection, previously treated and hospitalized patients should be considered for empiric second-line TB therapy while awaiting confirmatory DST results in settings with a high-burden of MDR/XDR-TB

Improved supergeometries for type-II Green-Schwarz non-linear sigma-model

SIGLEITItal

Georgian vitis germplasm: usage, conservation and investigation

International audienceGeorgian grapevine germplasm (V. vinifera L.) originated in diverse regions of the country over a long historical period. During the XX century bred varieties enriched it. Georgia is also a place where V. vinifera sylvestris spread in large numbers, provided an important initial impulse to the domestication of grapevine. The main cultivated varieties in Georgia are autochthonous varieties, having high-market value – best of those are also cultivated in East Europe and Middle Asia. Conservation initiatives for Georgian Vitis germplasm started since XIX century and entered into XXI century with some difficulties. However, Georgia was able to establish new field collections and collaborative works, in the framework of international projects and local initiatives. This germplasm is the object of intensive investigations; it attracts international collaborations because of its genetic diversity. Investigations based on SSR fingerprinting and ampelographic methods are used for classification of varieties and understanding their phylogenic relationships.Il germoplasma di vite georgiano (V. vinifera L.) si è originato in differenti aree del paese nel corso di un lungo periodo storico. Durante il XX sec. nuovi vitigni ottenuti per incrocio lo hanno arricchito. La Georgia è un luogo ove è diffusa la V. vinifera sylvestris; si ritiene quindi che le antiche civiltà locali abbiano dato un importante contributo alla domesticazione della vite. Le principali cultivar sono autoctone; quelle più apprezzate sono coltivate anche in Europa orientale e Asia Centrale. In Georgia la consapevolezza dell’importanza della conservazione del germoplasma risale al XIX sec. Entrò in difficoltà per i problemi economici nel XXI sec. Comunque la Georgia è stata in grado di costituire nuove collezioni e attività di collaborazione, internazionali e locali. Il germoplasma georgiano è oggetto di intense attività di ricerca anche perché, a causa della sua diversità genetica suscita interesse internazionale. I marcatori SSR e le moderne tecniche ampelografiche sono utilizzate per la caratterizzazione varietale, la comprensione della relativa struttura genetica e delle relazioni filogenetiche

Stress-metabolite stilbenoids in vine trunk of ojaleshi grape variety (Vitis vinifera L.) under crown gall infection

The trunk stilbenoids of healthy and crown gall infected vines of Ojaleshi variety have been studied and identified as stress-metabolite compounds .Vine samples were taken from a 12-year-old vineyard cultivated on yellow soils type in Martvili region (Western Georgia). The stilbenoids were extracted by ethyl acetate and then separated in a chromatographic column and analyzed by the HPLC/MS method. The following stilbenoids have been detected: cis-piceid, trans-resveratrol, trans-ε-viniferin, cis-miyabenol C, cis-miyabenol. The concentrations were higher in infected vines as compared to the healthy ones. This is the first time that stilbenoids have been investigated in Ojaleshi grape variety

Dynamics of TB mixed infections through space and time

Abstract de la comunicación oral presentada al Scientific Meeting on Mycobacteria. MycoPORTO 2019 Porto (Portugal), 19-20 de septiembre de 2019Pág. 25 del libro de abstracts que se adjunta. Mixed infections happen when at least two unrelated strains of the same pathogen can be detected in an individual. This has been linked to worse clinical outcomes in tuberculosis infections, as undetected strains presenting different antibiotic resistance profiles can lead to treatment failure. Here, we present a study of the extent of mixed infections in Georgia, a high-burden setting in which up to 11% of new TB cases are MDR/RR-TB. We obtained NGS data from cultures derived from surgery and sputum samples from 20 patients. Combined with a customized bioinformatics pipeline we enhanced the detection of multiple strains as opposed to just using a clinical sputum sample, identifying an unprecedented number of mixed infection cases of up to 40% of the patients analyzed. We also characterized transmission using 358 clinical samples and detected transmission clusters, several of which contained a sample from our surgery patients¿ dataset, allowing us to trace the history of several mixed infections. Our results suggest that the magnitude of mixed infections in highburden settings is likely to be underestimated when only using sputum samples and they can be behind discrepancies between DST and WGS predictions if not properly assessed