Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways

We thank Jose Munoz for his input on the analysis of the mouse RNA-seq enrichment. R.A.F. was supported by a Wellcome Trust-Massachusetts Institute of Technology (MIT) Postdoctoral Fellowship. M.C.F. and J.R. were supported by Medical Research Council grant MR/K000373/1. R.C.M. is supported by a Wolfson Royal Society Research Merit Award and by funding from the European Research Council under the European Union’s Seventh Framework Program (FP/2007-2013)/ERC (grant agreement no. 614562). This work was funded in part by NIAID grant U19AI110818 to the Broad Institute.Peer reviewedPublisher PD

Characterisation of chemical composition and structural features of novel antimicrobial nanoparticles

© 2017 by the authors. Licensee MDPI, Basel, Switzerland. This is an open access article distributed under the Creative Commons Attribution License (CC BY 4.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Three antimicrobial nanoparticle types (AMNP0, AMNP1 and AMNP2) produced using the TesimaTM thermal plasma technology were investigated and their compositions determined using a combination of analytical methods. Scanning electron micrograph provided the morphology of these particles with observed sizes ranging from 10 – 50 nm. Whilst FTIR spectra confirmed the absence of polar bonds and organic impurities, strong Raman active vibrational bands at ca. 1604 and 1311 cm-1 ascribed to C-C vibrational motions were observed. Carbon signals resonated at δC126 ppm in solid state NMR spectra confirmed sp2 hybridised carbons were present in high concentration in two of the nanoparticle types (AMNP1 and AMNP2). X-ray powder diffraction suggested AMNP0 contains single phase WC in a high state of purity and multiple phases of WC/WC1-x were identified in both AMNP1 and AMNP2. Finally, XPS surface analyses revealed and quantified the elemental ratios in these composite formulations.Peer reviewe

A fast extraction-free isothermal LAMP assay for detection of SARS-CoV-2 with potential use in resource-limited settings

BACKGROUND: To retain the spread of SARS-CoV-2, fast, sensitive and cost-effective testing is essential, particularly in resource limited settings (RLS). Current standard nucleic acid-based RT-PCR assays, although highly sensitive and specific, require transportation of samples to specialised laboratories, trained staff and expensive reagents. The latter are often not readily available in low- and middle-income countries and this may significantly impact on the successful disease management in these settings. Various studies have suggested a SARS-CoV-2 loop mediated isothermal amplification (LAMP) assay as an alternative method to RT-PCR. METHODS: Four previously published primer pairs were used for detection of SARS-CoV-2 in the LAMP assay. To determine optimal conditions, different temperatures, sample input and incubation times were tested. Ninety-three extracted RNA samples from St. George's Hospital, London, 10 non-extracted nasopharyngeal swab samples from Great Ormond Street Hospital for Children, London, and 92 non-extracted samples from Queen Elisabeth Central Hospital (QECH), Malawi, which have previously been tested for SARS-Cov-2 by quantitative reverse-transcription RealTime PCR (qRT-PCR), were analysed in the LAMP assay. RESULTS: In this study we report the optimisation of an extraction-free colourimetric SARS-CoV-2 LAMP assay and demonstrated that a lower limit of detection (LOD) between 10 and 100 copies/µL of SARS-CoV-2 could be readily detected by a colour change of the reaction within as little as 30 min. We further show that this assay could be quickly established in Malawi, as no expensive equipment is necessary. We tested 92 clinical samples from QECH and showed the sensitivity and specificity of the assay to be 86.7% and 98.4%, respectively. Some viral transport media, used routinely to stabilise RNA in clinical samples during transportation, caused a non-specific colour-change in the LAMP reaction and therefore we suggest collecting samples in phosphate buffered saline (which did not affect the colour) as the assay allows immediate sample analysis on-site. CONCLUSION: SARS-CoV-2 LAMP is a cheap and reliable assay that can be readily employed in RLS to improve disease monitoring and management

SARS-CoV-2 infection and antibody seroprevalence in routine surveillance patients, healthcare workers and general population in Kita region, Mali: an observational study 2020–2021

Objective: To estimate the degree of SARS-CoV-2 transmission among healthcare workers (HCWs) and general population in Kita region of Mali. Design: Routine surveillance in 12 health facilities, HCWs serosurvey in five health facilities and community serosurvey in 16 villages in or near Kita town, Mali. Setting: Kita region, western Mali; local health centres around the central (regional) referral health centre. Participants: Patients in routine surveillance, HCWs in local health centres and community members of all ages in populations associated with study health centres. Main outcome measures: Seropositivity of ELISA test detecting SARS-CoV-2-specific total antibodies and real-time RT-PCR confirmed SARS-CoV-2 infection. Results: From 2392 routine surveillance samples, 68 (2.8%, 95% CI: 2.2% to 3.6%) tested positive for SARS-CoV-2 by RT-PCR. The monthly positivity rate was 0% in June–August 2020 and gradually increased to 6% by December 2020 and 6.2% by January 2021, then declined to 5.5%, 3.3%, 3.6% and 0.8% in February, March, April and May 2021, respectively. From 397 serum samples collected from 113 HCWs, 175 (44.1%, 95% CI: 39.1% to 49.1%) were positive for SARS-CoV-2 antibodies. The monthly seroprevalence was around 10% from September to November 2020 and increased to over 40% from December 2020 to May 2021. For community serosurvey in December 2020, overall seroprevalence of SARS-CoV-2 antibodies was 27.7%. The highest age-stratified seroprevalence was observed in participants aged 60–69 years (45.5%, 95% CI: 32.3% to 58.6%). The lowest was in children aged 0–9 years (14.0%, 95% CI: 7.4% to 20.6%). Conclusions: SARS-CoV-2 in rural Mali is much more widespread than assumed by national testing data and particularly in the older population and frontline HCWs. The observation is contrary to the widely expressed view, based on limited data, that COVID-19 infection rates were lower in 2020–2021 in West Africa than in other settings

Testing the effects of mass drug administration of azithromycin on mortality and other outcomes among 1–11-month-old infants in Mali (LAKANA) : study protocol for a cluster-randomized, placebo-controlled, double-blinded, parallel-group, three-arm clinical trial

Background: Mass drug administration (MDA) of azithromycin (AZI) has been shown to reduce under-5 mortality in some but not all sub-Saharan African settings. A large-scale cluster-randomized trial conducted in Malawi, Niger, and Tanzania suggested that the effect differs by country, may be stronger in infants, and may be concentrated within the first 3 months after treatment. Another study found no effect when azithromycin was given concomitantly with seasonal malaria chemoprevention (SMC). Given the observed heterogeneity and possible effect modification by other co-interventions, further trials are needed to determine the efficacy in additional settings and to determine the most effective treatment regimen. Methods: LAKANA stands for Large-scale Assessment of the Key health-promoting Activities of two New mass drug administration regimens with Azithromycin. The LAKANA trial is designed to address the mortality and health impacts of 4 or 2 annual rounds of azithromycin MDA delivered to 1–11-month-old (29–364 days) infants, in a high-mortality and malaria holoendemic Malian setting where there is a national SMC program. Participating villages (clusters) are randomly allocated in a ratio of 3:2:4 to three groups: placebo (control):4-dose AZI:2-dose AZI. The primary outcome measured is mortality. Antimicrobial resistance (AMR) will be monitored closely before, during, and after the intervention and both among those receiving and those not receiving MDA with the study drugs. Other outcomes, from a subset of villages, comprise efficacy outcomes related to morbidity, growth and nutritional status, outcomes related to the mechanism of azithromycin activity through measures of malaria parasitemia and inflammation, safety outcomes (AMR, adverse and serious adverse events), and outcomes related to the implementation of the intervention documenting feasibility, acceptability, and economic aspects. The enrolment commenced in October 2020 and is planned to be completed by the end of 2022. The expected date of study completion is December 2024. Discussion: If LAKANA provides evidence in support of a positive mortality benefit resulting from azithromycin MDA, it will significantly contribute to the options for successfully promoting child survival in Mali, and elsewhere in sub-Saharan Africa. Trial registration: ClinicalTrials.gov NCT04424511. Registered on 11 June 2020.publishedVersionPeer reviewe

Antimicrobial resistance as a super wicked problem: how do we engage the public to be part of the solution

Summary: Antimicrobial resistance (AMR) is now regarded as one of the greatest global challenges of the 21st century. The complexity, urgent timeframe, and lack of clear solution to AMR have contributed to its classification as a ‘super wicked problem’. Yet knowledge surveys of the general public have found that they still harbour numerous misconceptions linked to both the sources and impact of AMR. This confusion is compounded by AMR being a One Health issue, and therefore a factor in not just human health but in other industries, such as farming. This can further inhibit understanding and knowledge transfer around AMR for those without a prior knowledge base.In order to address the escalating risk that AMR presents, however, it is essential to address this knowledge gap and engage with the public to support wide scale changes in behaviour and consumer choice. The WHO now requires national action plans tackling AMR to include patient and public involvement/engagement (PPI/E) to support changing the trajectory of AMR. Despite this, little detail is available as part of strategic plans on how PPI/E should be undertaken in order to aid implementation. This paper discusses a number of approaches to support the design and delivery of PPI/E in relation to AMR, including the different social behaviour models underlying successful PPI/E strategies, and key considerations linked to specific activity types. The framework produced includes features for steps from initial planning and design through to evaluation. The aim is to help improve the ability of scientists and healthcare professionals to produce high quality AMR PPI/E

Healthcare Environments and Spatial Variability of Healthcare Associated Infection Risk: Cross-Sectional Surveys

International audiencePrevalence of healthcare associated infections remains high in patients in intensive care units (ICU), estimated at 23.4% in 2011. It is important to reduce the overall risk while minimizing the cost and disruption to service provision by targeted infection control interventions. The aim of this study was to develop a monitoring tool to analyze the spatial variability of bacteriological contamination within the healthcare environment to assist in the planning of interventions. Within three cross-sectional surveys, in two ICU wards, air and surface samples from different heights and locations were analyzed. Surface sampling was carried out with tryptic Soy Agar contact plates and Total Viable Counts (TVC) were calculated at 48hrs (incubation at 37°C). TVCs were analyzed using Poisson Generalized Additive Mixed Model for surface type analysis, and for spatial analysis. Through three cross-sectional survey, 370 samples were collected. Contamination varied from place-to-place, height-to-height, and by surface type. Hard-to-reach surfaces, such as bed wheels and floor area under beds, were generally more contaminated, but the height level at which maximal TVCs were found changed between cross-sectional surveys. Bedside locations and bed occupation were risk factors for contamination. Air sampling identified clusters of contamination around the nursing station and surface sampling identified contamination clusters at numerous bed locations. By investigating dynamic hospital wards, the methodology employed in this study will be useful to monitor contamination variability within the healthcare environment and should help to assist in the planning of interventions