Multi-species integrative biclustering

We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surprisingly high degree of conservation of regulatory modules across these three species and allows data and insights from well-studied organisms to complement the analysis of related but less well studied organisms

Do anti-malarials in Africa meet quality standards? The market penetration of non quality-assured artemisinin combination therapy in eight African countries

BACKGROUND: Quality of artemisinin-based combination therapy (ACT) is important for ensuring malaria parasite clearance and protecting the efficacy of artemisinin-based therapies. The extent to which non quality-assured ACT (non-QAACT), or those not granted global regulatory approval, are available and used to treat malaria in endemic countries is poorly documented. This paper uses national and sub-national medicine outlet surveys conducted in eight study countries (Benin, Kinshasa and Kantanga [Democratic Republic of the Congo, DRC], Kenya, Madagascar, Nigeria, Tanzania, Uganda and Zambia) between 2009 and 2015 to describe the non-QAACT market and to document trends in availability and distribution of non-QAACT in the public and private sector. RESULTS: In 2014/15, non-QAACT were most commonly available in Kinshasa (83%), followed by Katanga (53%), Nigeria (48%), Kenya (42%), and Uganda (33%). Non-QAACT accounted for 20% of the market share in the private sector in Kenya, followed by Benin and Uganda (19%), Nigeria (12%) and Zambia (8%); this figure was 27% in Katanga and 40% in Kinshasa. Public sector non-QAACT availability and distribution was much lower, with the exception of Zambia (availability, 85%; market share, 32%). Diverse generics and formulations were available, but non-QAACT were most commonly artemether-lumefantrine (AL) or dihydroartemisinin-piperaquine (DHA PPQ), in tablet formulation, imported, and distributed in urban areas at either pharmacies or drug stores. The number of unique manufacturers supplying non-QAACT to each country ranged from 9 in Uganda to 92 in Nigeria. CONCLUSIONS: Addressing the availability and distribution of non-QAACT will require effective private sector engagement and evidence-based strategies to address provider and consumer demand for these products. Given the variation in non-QAACT markets observed across the eight study countries, active efforts to limit registration, importation and distribution of non-QAACT must be tailored to the country context, and will involve addressing complex and challenging aspects of medicine registration, private sector pharmaceutical regulation, local manufacturing and drug importation. These efforts may be critical not only to patient health and safety, but also to effective malaria control and protection of artemisinin drug efficacy in the face of spreading resistance

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation

Convalescent plasma in patients admitted to hospital with COVID-19 (RECOVERY): a randomised controlled, open-label, platform trial

SummaryBackground Azithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatoryactions. We aimed to evaluate the safety and efficacy of azithromycin in patients admitted to hospital with COVID-19.Methods In this randomised, controlled, open-label, adaptive platform trial (Randomised Evaluation of COVID-19Therapy [RECOVERY]), several possible treatments were compared with usual care in patients admitted to hospitalwith COVID-19 in the UK. The trial is underway at 176 hospitals in the UK. Eligible and consenting patients wererandomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once perday by mouth or intravenously for 10 days or until discharge (or allocation to one of the other RECOVERY treatmentgroups). Patients were assigned via web-based simple (unstratified) randomisation with allocation concealment andwere twice as likely to be randomly assigned to usual care than to any of the active treatment groups. Participants andlocal study staff were not masked to the allocated treatment, but all others involved in the trial were masked to theoutcome data during the trial. The primary outcome was 28-day all-cause mortality, assessed in the intention-to-treatpopulation. The trial is registered with ISRCTN, 50189673, and ClinicalTrials.gov, NCT04381936.Findings Between April 7 and Nov 27, 2020, of 16 442 patients enrolled in the RECOVERY trial, 9433 (57%) wereeligible and 7763 were included in the assessment of azithromycin. The mean age of these study participants was65·3 years (SD 15·7) and approximately a third were women (2944 [38%] of 7763). 2582 patients were randomlyallocated to receive azithromycin and 5181 patients were randomly allocated to usual care alone. Overall,561 (22%) patients allocated to azithromycin and 1162 (22%) patients allocated to usual care died within 28 days(rate ratio 0·97, 95% CI 0·87–1·07; p=0·50). No significant difference was seen in duration of hospital stay (median10 days [IQR 5 to >28] vs 11 days [5 to >28]) or the proportion of patients discharged from hospital alive within 28 days(rate ratio 1·04, 95% CI 0·98–1·10; p=0·19). Among those not on invasive mechanical ventilation at baseline, nosignificant difference was seen in the proportion meeting the composite endpoint of invasive mechanical ventilationor death (risk ratio 0·95, 95% CI 0·87–1·03; p=0·24).Interpretation In patients admitted to hospital with COVID-19, azithromycin did not improve survival or otherprespecified clinical outcomes. Azithromycin use in patients admitted to hospital with COVID-19 should be restrictedto patients in whom there is a clear antimicrobial indication

Adverse drug events resulting from use of drugs with sulphonamide-containing anti-malarials and artemisinin-based ingredients: findings on incidence and household costs from three districts with routine demographic surveillance systems in rural Tanzania.

BACKGROUND: Anti-malarial regimens containing sulphonamide or artemisinin ingredients are widely used in malaria-endemic countries. However, evidence of the incidence of adverse drug reactions (ADR) to these drugs is limited, especially in Africa, and there is a complete absence of information on the economic burden such ADR place on patients. This study aimed to document ADR incidence and associated household costs in three high malaria transmission districts in rural Tanzania covered by demographic surveillance systems. METHODS: Active and passive surveillance methods were used to identify ADR from sulphadoxine-pyrimethamine (SP) and artemisinin (AS) use. ADR were identified by trained clinicians at health facilities (passive surveillance) and through cross-sectional household surveys (active surveillance). Potential cases were followed up at home, where a complete history and physical examination was undertaken, and household cost data collected. Patients were classified as having 'possible' or 'probable' ADR by a physician. RESULTS: A total of 95 suspected ADR were identified during a two-year period, of which 79 were traced, and 67 reported use of SP and/or AS prior to ADR onset. Thirty-four cases were classified as 'probable' and 33 as 'possible' ADRs. Most (53) cases were associated with SP monotherapy, 13 with the AS/SP combination (available in one of the two areas only), and one with AS monotherapy. Annual ADR incidence per 100,000 exposures was estimated based on 'probable' ADR only at 5.6 for AS/SP in combination, and 25.0 and 11.6 for SP monotherapy. Median ADR treatment costs per episode ranged from US$2.23 for those making a single provider visit to US$146.93 for patients with four visits. Seventy-three per cent of patients used out-of-pocket funds or sold part of their farm harvests to pay for treatment, and 19% borrowed money. CONCLUSION: Both passive and active surveillance methods proved feasible methods for anti-malarial ADR surveillance, with active surveillance being an important complement to facility-based surveillance, given the widespread practice of self-medication. Household costs associated with ADR treatment were high and potentially catastrophic. Efforts should be made to both improve pharmacovigilance across Africa and to identify strategies to reduce the economic burden endured by households suffering from ADR

Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in <i>Bacillus subtilis</i>

<div><p>Gene expression during spore development in <i>Bacillus subtilis</i> is controlled by cell type-specific RNA polymerase sigma factors. σ^Fand σ^E control early stages of development in the forespore and the mother cell, respectively. When, at an intermediate stage in development, the mother cell engulfs the forespore, σ^F is replaced by σ^G and σ^E is replaced by σ^K. The anti-sigma factor <i>CsfB</i> is produced under the control of σ^F and binds to and inhibits the auto-regulatory σ^G, but not σ^F. A position in region 2.1, occupied by an asparagine in σ^G and by a glutamate in ο^F, is sufficient for CsfB discrimination of the two sigmas, and allows it to delay the early to late switch in forespore gene expression. We now show that following engulfment completion, <i>csfB</i> is switched on in the mother cell under the control of σ^K and that CsfB binds to and inhibits σ^E but not σ^K, possibly to facilitate the switch from early to late gene expression. We show that a position in region 2.3 occupied by a conserved asparagine in σ^E and by a conserved glutamate in σ^K suffices for discrimination by CsfB. We also show that CsfB prevents activation of σ^G in the mother cell and the premature σ^G-dependent activation of σ^K. Thus, CsfB establishes negative feedback loops that curtail the activity of σ^E and prevent the ectopic activation of σ^G in the mother cell. The capacity of CsfB to directly block σ^E activity may also explain how CsfB plays a role as one of the several mechanisms that prevent σ^E activation in the forespore. Thus the capacity of CsfB to differentiate between the highly similar σ^F/σ^G and σ^E/σ^K pairs allows it to rinforce the cell-type specificity of these sigma factors and the transition from early to late development in B. subtilis, and possibly in all sporeformers that encode a CsfB orthologue.</p></div

Role of CsfB in the mother cell.

<p><b>A</b>: microarrays were used to assess the impact of mutational inactivation of the σ^G-dependent promoter for the <i>csfB</i> gene (P_<i>sigF</i> strain) on sporulation-specific gene expression. The panel represents the percentage of genes in each of the sporulation-specific sigma regulons, whose expression was increased (green bars) or unaffected (grey bars) in the P_<i>sigF</i> mutant relative to the wild type. Genes, repressed (“R”) by or dependent (“D”) on the following ancillary transcription factors, are shown: D, SpoIIID; R, GerR; VT, SpoVT; E, GerE. <b>B</b>: the panel illustrates the results of a fluorescence <i>in situ</i> hybridization (FISH) experiment to localize the <i>sspE</i> mRNA, produced under σ^G control, in a wild type strain and in the P_<i>sigF</i> mutant. The mRNA was localized using a fluorescein-labelled anti-sense oligonucleotide and fluorescence microscopy. PC, phase contrast. The graph on the right shows the length (in μm) distribution of the fluorescence signal measured along the longitudinal axis of the cells. <b>C</b>: immunoblot analysis of pro-σ^K and σ^K. Samples from cultures of the wild type and P_<i>sigF</i>-<i>csfB</i> strain were collected at the indicated times (in minutes) after the induction of sporulation by re-suspension. Whole cell extracts were prepared, proteins (15 μg) electrophoretically resolved and immunobloted with anti-σ^K and anti-σ^A (as a loading control) antibodies. Arrows indicate the position of pro-σ^K (in black) and σ^K (red).</p

The sporulation network and the action of CsfB on σ^G.

<p><b>A</b>: the main morphological stages of sporulation are represented, with the main regulatory proteins active in the indicated cells. Pd, pre-divisional cell; Mc, mother cell; Fs, forespore; Sp, mature spore. <b>B</b>: organization of the transcriptional network of sporulation. The broken blue lines represent cell-cell signalling pathways. First, σ^F drives production of a protein, SpoIIR, secreted to the intermembrane space. SpoIIR then activates a membrane-embedded protease that triggers the proteolytic activation of pro-σ^E [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005104#pgen.1005104.ref018" target="_blank">18</a>]. σ^E and σ^F activity are required for the assembly of a cell-cell secretion system (the SpoIIQ-SpoIIIAH channel in the figure) that, following engulfment completion, allows the mother cell to nourish the isolated forespore, thus enabling continued macromoelcualr synthesis and activation of the σ^G auto-regulatory loop [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005104#pgen.1005104.ref067" target="_blank">67</a>]. Lastly, σ^G controls production of a signaling protein, SpoIVB, secreted into the intermembrane space that activates the machinery responsible for the proteolytical activation of σ^K [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005104#pgen.1005104.ref018" target="_blank">18</a>]. The negative feedback loop through which σ^K limits production of σ^E is omitted for simplicity. <b>C</b>: the panel represents the composite negative feedback loop that operates in pre-divisional cells, and possibly also in the forespore prior to engulfment completion, to prevent activation of the σ^G positive auto-regulatory loop. Transcriptional and protein-protein interactions are shown in black and red, respectively. <b>D</b>: a single amino acid residue in region 2.1 (purple sector) allows CsfB to discriminate between the highly similar forespore sigma factors σ^F and σ^G: N45 of <i>B</i>. <i>subtilis</i> σ^G allows binding by CsfB, whereas a glutamate at the same position precludes binding. Conversely, a glutamate at the homologous position of σ^F (E39) impedes binding by CsfB whereas an asparagine at the same position is sufficient for binding. N45 and E39 are conserved among <i>Bacillus</i> orthologues of σ^G and σ^F.</p