Browsing by Subject "bacteria"

Now showing 1 - 4 of 4
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    Open Access
    Extinctions: Past and Present Week 1 - An abundance of bacteria
    (2017-03-17) Chinsamy-Turan, Anusuya; Rybicki, Ed
    In this video, Professor Anusaya Chinsamy-Turan interviews Professor Ed Rybicki, a microbiologist based in the Department of Molecular and Cell Biology at UCT. They discuss the history and diversity of microbes on earth and how they played a key role in the development of oxygen in the atmosphere. Professor Rybicki also outlines how essential microbes are for our survival, as they help us to digest food, produce vitamins, and fight off disease.
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    Microbial solvent formation revisited by comparative genome analysis
    (2017) DYrre, Peter
    Abstract Background Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today. Results The genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected. Conclusions Our findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.
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    The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
    (2017) Trauner, Andrej; Liu, Qingyun; Via, Laura E; Liu, Xin; Ruan, Xianglin; Liang, Lili; Shi, Huimin; Chen, Ying; Wang, Ziling; Liang, Ruixia; Zhang, Wei; Wei, Wang; Gao, Jingcai; Sun, Gang; Brites, Daniela; England, Kathleen; Zhang, Guolong; Gagneux, Sébastien; Barry, Clifton E; Gao, Qian
    BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. RESULTS: By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. CONCLUSIONS: Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.
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    The yield of nasopharyngeal bacteria from culture compared to polymerase chain reaction in South African children with lower respiratory tract infection
    (2022) Pillay, Vashini; Zar, Heather
    Background Lower respiratory tract infection (LRTI) is a major cause of morbidity and mortality in children under 5 years of age. Bacterial pathogens contribute significantly to this process. Culture of respiratory tract specimens is labour-intensive and slow. Polymerase chain reaction (PCR) is comparatively, a rapid, sensitive method of detecting low levels of nucleic acid for clinically relevant bacteria. This study compares the yield of bacteria obtained from culture and the FTDResp33 multiplex PCR of nasopharyngeal swabs (NPs) during LRTI episodes in children, in the Drakenstein Child Health Study. Methods At each episode of LRTI, 2 NPs were obtained, one for culture and one for PCR testing. Bacterial yields and concordance for the 5 commonest bacteria were compared using frequencies and proportions. Results From 13th August 2012 to 23rd November 2020, there were 859 episodes of LRTI in 434 children [median age 9.2 (IQR 3.8; 18.9) months; 0.2% HIV-infected]. S. pneumoniae, S. aureus, M. catarrhalis, H. influenzae and K. pneumoniae were the predominant bacteria detected by either method. Concordance between culture and PCR for S. pneumoniae, S. aureus, and K. pneumoniae was 84.9%, 89.7% and 86.3% respectively. Culture and PCR for H. influenzae had a concordance of 76.9%. The greatest discordance between culture and PCR was for the detection of M. catarrhalis (34.4%). Median bacterial loads on PCR for all 5 organisms were significantly associated with semi-quantitative culture results (p<0.001 for each). Adjusting for age and hospitalization, children on antibiotics at the time of sampling, had a reduced chance of having a positive culture (OR 0.1; 95% CI 0.1-0.4), and a reduction in PCR yield (OR 0.8; 95% CI 0.4-1.6). Conclusion: Significant concordance existed between PCR and culture for 4 of the 5 common bacteria, affirming PCR as a comparable method of testing to culture.