Biology subjects

Simmons, B.

Publications and source records attributed to Simmons, B..

6 recordsLinked to original sources

bioRxiv2023

Genomic epidemiology of European Aspergillus fumigatus causing COVID-19-associated pulmonary aspergillosis in Europe

The opportunistic fungus Aspergillus fumigatus has been found to cause coinfections in patients with severe SARS-CoV-2 virus infection, leading to COVID-19-associated pulmonary aspergillosis (CAPA). The CAPA all-cause mortality rate is approximately 50% and may be complicated by azole-resistance. Genomic epidemiology can help shed light on the genetics of A. fumigatus causing CAPA including the prevalence of alleles that are associated with azole-resistance. Here, a population genomic analysis of 21 CAPA isolates from four European countries is presented. The CAPA isolates were compared with A. fumigatus from a wider population of 167 non-CAPA clinical isolates and 73 environmental isolates. Bioinformatic analysis and antifungal susceptibility testing were performed to quantify resistance and identify possible genetically-encoded azole-resistant mechanisms. Phylogenetic analysis of the 21 CAPA isolates showed a lack of genetic distinction from the wider A. fumigatus population, with isolates distributed within two distinct clades (A and B), with the majority of the CAPA isolates in clade B (71.4%). The prevalence of phenotypic azole-resistance in CAPA was 14.3% (n=3/21); all three CAPA isolates contained a known resistance-associated cyp51A polymorphism. CAPA isolates are drawn from the wider A. fumigatus population rather than forming a unique genetic background showing that COVID-19 patients are susceptible to the entire A. fumigatus population. However, the relatively high prevalence of azole-resistance alleles that we document poses a threat to treatment success rates, warranting enhanced detection and surveillance of A. fumigatus genotypes in these patients. Furthermore, potential changes to antifungal first-line treatment guidelines may be needed to improve patient outcomes.

microbiology↗

bioRxiv2022

Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater

Plasmids are mobile genetic elements that can act as mutualists or parasites to their bacterial hosts depending on their accessory genes and environment. Ecological network theory predicts that mutualists, such as plasmids with antimicrobial resistance (AMR) genes in the presence of antimicrobials, should act as generalists, while plasmids without beneficial genes are expected to be more specialised. Therefore, whether the relationship between plasmid and host is mutualistic or antagonistic is likely to have a strong impact on the formation of interaction network structures and the spread of AMR genes across microbial networks. Here we re-analyse Hi-C metagenome data from wastewater samples and identify plasmid signatures with machine learning to generate a natural host-plasmid network. We found that AMR-carrying plasmids indeed interacted with more hosts than non-AMR plasmids (on average 14 versus 3, respectively). The AMR plasmid-host subnetwork showed a much higher connectedness and nestedness than the subnetwork associated with non-AMR plasmids. The overall network was clustered around Proteobacteria and AMR-carrying plasmids giving them a crucial role in network connectivity. Therefore, by forming mutualistic networks with their hosts, beneficial AMR plasmids lead to more connected network structures that ultimately share a larger gene pool of AMR genes across the network.

microbiology↗

bioRxiv2020

Iron Chelator-Mediated Anoxic Biotransformation of Lignin by Novel sp., Tolumonas lignolytica BRL6-1

Lignin is the second most abundant carbon polymer on earth and despite having more fuel value than cellulose, it currently is considered a waste byproduct in many industrial lignocellulose applications. Valorization of lignin relies on effective and green methods of delignification, with a growing interest in the use of microbes. Here we investigate the physiology and lignin biotransformation mechanisms of the novel facultative anaerobic bacterium, Tolumonas lignolytica BRL6-1, under anoxic conditions. Physiological and biochemical changes were compared between cells grown anaerobically in either lignin-amended or unamended conditions. In the presence of lignin, BRL6-1 had a higher biomass and shorter lag phase compared to unamended conditions, and 14% of the proteins determined to be significantly higher in abundance by log2 fold-change of 2 or greater were related to Fe(II) transport in early exponential phase. Ferrozine assays of the supernatant (<10 kDa fraction) confirmed that Fe(III) was bound to lignin and reduced to Fe(II) only in the presence of BRL6-1, suggesting redox activity by the cells. LC-MS/MS analysis of the secretome showed an extra band at 20 kDa in lignin-amended conditions. Protein sequencing of this band identified a protein of unknown function with homology to enzymes in the radical SAM superfamily. Expression of this protein in lignin-amended conditions suggests its role in radical formation. From our findings, we suggest that BRL6-1 is using a protein in the radical SAM superfamily to interact with the Fe(III) bound to lignin and reducing it to Fe(II) for cellular use, increasing BRL6-1 yield under lignin-amended conditions. This interaction potentially generates organic free radicals and causes a radical cascade which could modify and depolymerize lignin. Further research should clarify the extent to which this mechanism is similar to previously described aerobic chelator-mediated Fenton chemistry or radical producing lignolytic enzymes, such as lignin peroxidases, but under anoxic conditions.

microbiology↗

bioRxiv2019

Evaluation of the psychometric properties of the HIV Disability Questionnaire among adults living with HIV in the United Kingdom

ObjectiveTo evaluate the psychometric properties of the HIV Disability Questionnaire (HDQ) among adults living with HIV in London, United Kingdom (UK). MethodsThis is a cross-sectional measurement study. We recruited and administered the self-reported HDQ, seven criterion measures, and a demographic questionnaire with adults living with HIV accessing HIV care. We determined median and interquartile ranges (IQR) for disability presence, severity and episodic scores (range 0-100). We calculated Cronbachs alpha () Kuder-Richardson-20 (KR-20) statistics for disability and episodic scores respectively (internal consistency reliability), smallest detectable change (SDC) for each HDQ severity item and domain (precision), and tested 36 a priori hypotheses assessing correlations between HDQ and criterion scores (construct validity). ResultsOf N=243 participants, all were male, median age 40 years, 94% currently taking antiretroviral therapy, and 22% living with [≥]2 concurrent health conditions. Median HDQ domain scores ranged from 0 (IQR: 0,7) (difficulties with day-to-day activities domain) to 27 (IQR: 14, 41) (uncertainty domain). Cronbachs alpha for the HDQ severity scale ranged from 0.85 (95% Confidence Interval (CI): 0.80-0.90) in the cognitive domain to 0.93 (95%CI: 0.91-0.94) in the mental-emotional domain. The KR-20 statistic for the HDQ episodic scale ranged from 0.74 (95%CI: 0.66-0.83) in the cognitive domain to 0.91 (95%CI: 0.89-0.94) in the uncertainty domain. SDC ranged from 7.3-15.0 points on the HDQ severity scale for difficulties with day-to-day activities and cognitive symptoms domains, respectively. The majority of the construct validity hypotheses (n=30/36, 83%) were confirmed. ConclusionsThe HDQ possesses internal consistency reliability and construct validity with varied precision when administered to males living with HIV in London, UK. Clinicians and researchers may use the HDQ to measure the nature and extent of disability experienced by PLHIV in the UK, and to inform HIV service provision to address the health-related challenges among PLHIV.

epidemiology↗

bioRxiv2017

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

The basidomycete yeast Rhodosporidium toruloides (a.k.a. Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions into the R. toruloides genome. We identified 1337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We found that both mitochondrial and peroxisomal enzymes were required for growth on fatty acids, with different peroxisomal enzymes required on different fatty acids. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, as well as genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species, identify key biological processes to be further explored and optimized for production of lipid-based bioproducts, and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi.

systems biology↗

bioRxiv2017

Rhodosporidium toruloides: A new platform organism for conversion of lignocellulose into terpene biofuels and bioproducts

BackgroundEconomical conversion of lignocellulosic biomass into biofuels and bioproducts is central to the establishment of a robust bioeconomy. This requires a conversion host that is able to both efficiently assimilate the major lignocellulose-derived carbon sources and divert their metabolites toward specific bioproducts.\n\nResultsIn this study, the carotenogenic yeast Rhodosporidium toruloides was examined for its ability to convert lignocellulose into two non-native sesquiterpenes with biofuel (bisabolene) and pharmaceutical (amorphadiene) applications. We found that R. toruloides can efficiently convert a mixture of glucose and xylose from hydrolyzed lignocellulose into these bioproducts, and unlike many conventional production hosts, its growth and productivity were enhanced in lignocellulosic hydrolysates relative to purified substrates. This organism was demonstrated to have superior growth in corn stover hydrolysates prepared by two different pretreatment methods, one using a novel biocompatible ionic liquid (IL) choline -ketoglutarate, which produced 261 mg/L of bisabolene at bench-scale, and the other using an alkaline pretreatment, which produced 680 mg/L of bisabolene in a high gravity fed-batch bioreactor. Interestingly, R. toruloides was also observed to assimilate p-coumaric acid liberated from acylated grass lignin in the IL hydrolysate, a finding we verified with purified substrates. R. toruloides was also able to consume several additional compounds with aromatic motifs similar to lignin monomers, suggesting that this organism may have the metabolic potential to convert depolymerized lignin streams alongside lignocellulosic sugars.\n\nConclusionsThis study highlights the natural compatibility of R. toruloides with bioprocess conditions relevant to lignocellulosic biorefineries and demonstrates its ability to produce non-native terpenes.

bioengineering↗