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Evolution and tuberculosis

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https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#1
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785015/frequent-transmission-of-the-mycobacterium-tuberculosis-beijing-lineage-and-positive-selection-for-the-esxw-beijing-variant-in-vietnam
#2
Kathryn E Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha, Nguyen Ngoc Lan, Nguyen Huu Lan, Nguyen Thi Quynh Nhu, Hoang Thanh Hai, Vu Thi Ngoc Ha, Guy Thwaites, David J Edwards, Artika P Nath, Kym Pham, David B Ascher, Jeremy Farrar, Chiea Chuen Khor, Yik Ying Teo, Michael Inouye, Maxine Caws, Sarah J Dunstan
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29779780/on-sunspots-click-science-and-molecular-iconography
#3
Igor Mokrousov
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29763750/genome-sequence-and-analysis-of-mycobacterium-tuberculosis-strain-swlpk
#4
Muhammad Ibrahim, Asma Muhammad Yar, Ghunva Zaman, Changhui Yan, Muhammad Khurshid, Habib Bokhari
OBJECTIVES: Multidrug resistant Mycobacterium tuberculosis poses a global threat, particularly in developing countries such as Pakistan. Genome sequencing, comparative genomic analysis, and drug resistance gene analysis, could be beneficial for understanding and monitoring M. tuberculosis disease severity in Pakistan by elucidating the biology of M. tuberculosis. METHODS: In this study, we sequenced, assembled, and annotated a draft genome of M. tuberculosis strain swlpk using the Illumina MiSeq 300PE throughput 2M system...
May 12, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29763423/from-one-incision-to-one-port-the-surgical-technique-and-the-evolution-of-segmentectomy-in-patients-with-pulmonary-tuberculosis
#5
Yau-Lin Tseng, Chao-Chun Chang, Ying-Yuan Chen, Yi-Sheng Liu, Lili Cheng, Jia-Ming Chang, Ming-Ho Wu, Yi-Ting Yen
OBJECTIVES: We retrospectively reviewed the evolution of segmentectomy for pulmonary tuberculosis (TB) and the feasibility of multi- and single-incision video-assisted thoracoscopic segmentectomy. METHODS: Of 348 patients undergoing surgery for TB, the medical records of 121 patients undergoing segmentectomy between January 1996 and November 2015 were reviewed. Clinical information and computed tomography (CT) image characteristics were investigated and analyzed...
2018: PloS One
https://www.readbyqxmd.com/read/29756725/-tuberculosis-by-multiresistant-mycobacterium-africanum-pediatric-clinical-case
#6
Júlia Morata Alba, Paloma Beltrán Catalá, Nelson Orta Sibú
Tuberculosis, considered since 2003 by the World Health Organization a global health emergency, causes annual mortality of approximately 2 million people, mainly in developing countries. In the Spanish pediatric population, the incidence is 5 cases/100 000 children between 5 and 14 years and 13 cases/100 000 children between 0 and 4 years. The infection is transmitted through the respiratory tract by baciliferous patients. Children eliminate few bacilli in respiratory secretions and do not usually transmit the infection...
June 1, 2018: Archivos Argentinos de Pediatría
https://www.readbyqxmd.com/read/29745901/review-of-the-systems-biology-of-the-immune-system-using-agent-based-models
#7
REVIEW
Snehal B Shinde, Manish P Kurhekar
The immune system is an inherent protection system in vertebrate animals including human beings that exhibit properties such as self-organisation, self-adaptation, learning, and recognition. It interacts with the other allied systems such as the gut and lymph nodes. There is a need for immune system modelling to know about its complex internal mechanism, to understand how it maintains the homoeostasis, and how it interacts with the other systems. There are two types of modelling techniques used for the simulation of features of the immune system: equation-based modelling (EBM) and agent-based modelling...
June 2018: IET Systems Biology
https://www.readbyqxmd.com/read/29739036/pathogenic-gene-screening-of-mycobacterium-tuberculosis-by-literature-data-mining-and-information-pathway-enrichment-analysis
#8
Guangyu Xu, Simin Wen, Yuchen Pan, Nan Zhang, Yuanyi Wang
BACKGROUND: Recent studies have unraveled mutations which have led to changes in the original conformation of functional proteins targeted by frontline drugs against Mycobacterium tuberculosis. These mutations are likely responsible for the emergence of drug-resistant strains of M. tuberculosis. Identification of new therapeutic targets is fundamental to the development of novel anti-TB drugs. METHODS: Boost evolution analysis of interactome data with use of high-throughput biological experimental technologies provides opportunities for identification of pathogenic genes and for screening out novel therapeutic targets...
May 1, 2018: Clinical Laboratory
https://www.readbyqxmd.com/read/29664901/genetic-profiling-of-mycobacterium-bovis-strains-from-slaughtered-cattle-in-eritrea
#9
Michael Kahsay Ghebremariam, Tiny Hlokwe, Victor P M G Rutten, Alberto Allepuz, Simeon Cadmus, Adrian Muwonge, Suelee Robbe-Austerman, Anita L Michel
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely.Spoligotyping, VNTR profiling, and whole genome sequencing (WGS)ofM. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea's largest slaughterhouse in the capital Asmara, were conducted...
April 17, 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29628767/interaction-between-rpsl-and-gyra-mutations-affects-the-fitness-and-dual-resistance-of-mycobacterium-tuberculosis-clinical-isolates-against-streptomycin-and-fluoroquinolones
#10
Honghu Sun, Jumei Zeng, Song Li, Pengkuan Liang, Chao Zheng, Yong Liu, Tao Luo, Nalin Rastogi, Qun Sun
Background: The interaction between different drug-resistant mutations is important to the development of drug resistance and its evolution. In this study, we aimed to reveal the potential relationships between mutations conferring resistance to two important antituberculosis drugs streptomycin (STR) and fluoroquinolones (FLQ). Materials and methods: We used an in vitro competitive fitness assay to reveal the interactions between different mutations of rpsL and gyrA in drug-resistant Mycobacterium smegmatis , followed by the analysis of the frequency of rpsL and gyrA mutation combinations in 213 STR-FLQ dual-resistant clinical Mycobacterium tuberculosis isolates from Sichuan region, which was also investigated by the whole genome data from 3,056 global clinical M...
2018: Infection and Drug Resistance
https://www.readbyqxmd.com/read/29550921/genotyping-of-mycobacterium-tuberculosis-using-whole-genome-sequencing
#11
REVIEW
Jana Amlerova, Ibrahim Bitar, Jaroslav Hrabak
Tuberculosis (TB) is considered one of the most serious infectious diseases worldwide. Effective control of tuberculosis infection involves multiple steps, such as reliable detection, treatment, an epidemiological control as a part of case management, and further surveillance and monitoring of TB spread in the human population. Due to the accelerating advances in molecular biology, especially in DNA sequencing, in the past decade, the application of these methods has become crucial for TB evolution studies, differentiation of Mycobacterium tuberculosis genotypes, and their distribution...
March 17, 2018: Folia Microbiologica
https://www.readbyqxmd.com/read/29524441/modelling-the-effects-of-bacterial-cell-state-and-spatial-location-on-tuberculosis-treatment-insights-from-a-hybrid-multiscale-cellular-automaton-model
#12
Ruth Bowness, Mark A J Chaplain, Gibin G Powathil, Stephen H Gillespie
If improvements are to be made in tuberculosis (TB) treatment, an increased understanding of disease in the lung is needed. Studies have shown that bacteria in a less metabolically active state, associated with the presence of lipid bodies, are less susceptible to antibiotics, and recent results have highlighted the disparity in concentration of different compounds into lesions. Treatment success therefore depends critically on the responses of the individual bacteria that constitute the infection. We propose a hybrid, individual-based approach that analyses spatio-temporal dynamics at the cellular level, linking the behaviour of individual bacteria and host cells with the macroscopic behaviour of the microenvironment...
June 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29506609/people-and-patient-centred-care-for-tuberculosis-models-of-care-for-tuberculosis
#13
A Odone, B Roberts, M Dara, M van den Boom, H Kluge, M McKee
SETTING: The first pillar in the World Health Organisation's (WHO's) End TB strategy is 'Integrated, patient-centred tuberculosis (TB) care and prevention'. However, what are patient- and people-centred care, and why are they important for TB care and prevention? OBJECTIVE AND RATIONALE: To define the concept of patient-centred care, the rationale for it, and its evolution into people-centred care; and to explore evidence on whether people-centred approaches work for TB and present key areas where continuous efforts are needed to support their implementation...
February 1, 2018: International Journal of Tuberculosis and Lung Disease
https://www.readbyqxmd.com/read/29502894/-thoracic-endometriosis-complicated-with-pneumopericard-and-iterative-pneumothorax-due-to-bullous-dystrophy
#14
A Kienlen, C Fernandez, Z Henni-Laleg, M Andre, V Gazaille, N Coolen-Allou
Thoracic endometriosis is a rare entity characterized by presence of endometrial tissue in pleura, lung parenchyma or airways. Most frequent manifestations are catamenial pneumothorax, hemothorax, hemoptysis and pulmonary nodules. We report here a rare case of a woman with thoracic endometriosis who developed iterative pneumothorax and pneumopericardium on bilateral bullous pulmonary dystrophy. She was a 37-year-old woman without any tobacco exposure and with previous history of pleural tuberculosis treated 5 years earlier...
April 2018: Revue de Pneumologie Clinique
https://www.readbyqxmd.com/read/29501678/comparative-genomics-of-mycobacterium-reveals-evolutionary-trends-of-m-avium-complex
#15
Mousumi Sarkar Saha, Shilpee Pal, Indrani Sarkar, Ayan Roy, Pradeep K Das Mohapatra, Arnab Sen
Mycobacterium is gram positive, slow growing, disease causing Actinobacteria. Beside potential pathogenic species, Mycobacterium also contains opportunistic pathogens as well as free living non-pathogenic species. Disease related various analyses on Mycobacterium tuberculosis are very widespread. However, genomic study of overall Mycobacterium species for understanding the selection pressure on genes as well as evolution of the organism is still illusive. MLSA and 16s rDNA based analysis has been generated for 241 Mycobacterium strains and a detailed analysis of codon and amino acid usage bias of mycobacterial genes, their functional analysis have been done...
February 28, 2018: Genomics
https://www.readbyqxmd.com/read/29491462/gene-expression-models-based-on-a-reference-laboratory-strain-are-poor-predictors-of-mycobacterium-tuberculosis-complex-transcriptional-diversity
#16
Álvaro Chiner-Oms, Fernando González-Candelas, Iñaki Comas
Every year, species of the Mycobacterium tuberculosis complex (MTBC) kill more people than any other infectious disease caused by a single agent. As a consequence of its global distribution and parallel evolution with the human host the bacteria is not genetically homogeneous. The observed genetic heterogeneity has relevance at different phenotypic levels, from gene expression to epidemiological dynamics. However, current systems biology datasets have focused on the laboratory reference strain H37Rv. By using large expression datasets testing the role of almost two hundred transcription factors, we have constructed computational models to grab the expression dynamics of Mycobacterium tuberculosis H37Rv genes...
February 28, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29488183/variations-on-a-theme-evolution-of-the-phage-shock-protein-system-in-actinobacteria
#17
Janani Ravi, Vivek Anantharaman, L Aravind, Maria Laura Gennaro
The phage shock protein (Psp) stress-response system protects bacteria from envelope stress through a cascade of interactions with other proteins and membrane lipids to stabilize the cell membrane. A key component of this multi-gene system is PspA, an effector protein that is found in diverse bacterial phyla, archaea, cyanobacteria, and chloroplasts. Other members of the Psp system include the cognate partners of PspA that are part of known operons: pspF||pspABC in Proteobacteria, liaIHGFSR in Firmicutes, and clgRpspAMN in Actinobacteria...
May 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29456241/ecology-and-evolution-of-mycobacterium-tuberculosis
#18
REVIEW
Sebastien Gagneux
Tuberculosis (TB) is the number one cause of human death due to an infectious disease. The causative agents of TB are a group of closely related bacteria known as the Mycobacterium tuberculosis complex (MTBC). As the MTBC exhibits a clonal population structure with low DNA sequence diversity, methods (such as multilocus sequence typing) that are applied to more genetically diverse bacteria are uninformative, and much of the ecology and evolution of the MTBC has therefore remained unknown. Owing to recent advances in whole-genome sequencing and analyses of large collections of MTBC clinical isolates from around the world, many new insights have been gained, including a better understanding of the origin of the MTBC as an obligate pathogen and its molecular evolution and population genetic characteristics both within and between hosts, as well as many aspects related to antibiotic resistance...
April 2018: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/29404424/signatures-of-selection-at-drug-resistance-loci-in-mycobacterium-tuberculosis
#19
Tatum D Mortimer, Alexandra M Weber, Caitlin S Pepperell
Tuberculosis (TB) is the leading cause of death by an infectious disease, and global TB control efforts are increasingly threatened by drug resistance in Mycobacterium tuberculosis . Unlike most bacteria, where lateral gene transfer is an important mechanism of resistance acquisition, resistant M. tuberculosis arises solely by de novo chromosomal mutation. Using whole-genome sequencing data from two natural populations of M. tuberculosis , we characterized the population genetics of known drug resistance loci using measures of diversity, population differentiation, and convergent evolution...
January 2018: MSystems
https://www.readbyqxmd.com/read/29386541/genome-wide-associations-identify-novel-candidate-loci-associated-with-genetic-susceptibility-to-tuberculosis-in-wild-boar
#20
João Queirós, Paulo Célio Alves, Joaquín Vicente, Christian Gortázar, José de la Fuente
Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture...
January 31, 2018: Scientific Reports
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