The availability of effective, reliably accessible, and affordable treatments for snakebite envenoming is a critical and long unmet medical need. Recently, small, synthetic toxin-specific inhibitors ...with oral bioavailability used in conjunction with antivenom have been identified as having the potential to greatly improve outcomes after snakebite. Varespladib, a small, synthetic molecule that broadly and potently inhibits secreted phospholipase A2 (sPLA2s) venom toxins has renewed interest in this class of inhibitors due to its potential utility in the treatment of snakebite envenoming. The development of varespladib and its oral dosage form, varespladib-methyl, has been accelerated by previous clinical development campaigns to treat non-envenoming conditions related to ulcerative colitis, rheumatoid arthritis, asthma, sepsis, and acute coronary syndrome. To date, twenty-nine clinical studies evaluating the safety, pharmacokinetics (PK), and efficacy of varespladib for non-snakebite envenoming conditions have been completed in more than 4600 human subjects, and the drugs were generally well-tolerated and considered safe for use in humans. Since 2016, more than 30 publications describing the structure, function, and efficacy of varespladib have directly addressed its potential for the treatment of snakebite. This review summarizes preclinical findings and outlines the scientific support, the potential limitations, and the next steps in the development of varespladib's use as a snakebite treatment, which is now in Phase 2 human clinical trials in the United States and India.
Genomic surveillance is an essential part of effective disease control, enabling identification of emerging and expanding strains and monitoring of subsequent interventions. Whole-genome sequencing ...was used to analyze the genomic diversity of all Neisseria meningitidis isolates submitted to the New Zealand Meningococcal Reference Laboratory during 2013-2018. Of the 347 isolates submitted for whole-genome sequencing, we identified 68 sequence types belonging to 18 clonal complexes (CC). The predominant CC was CC41/44; next in predominance was CC11. Comparison of the 45 New Zealand group W CC11 isolates with worldwide representatives of group W CC11 isolates revealed that the original UK strain, the 2013 UK strain, and a distinctive variant (the 2015 strain) were causing invasive group W meningococcal disease in New Zealand. The 2015 strain also demonstrated increased resistance to penicillin and has been circulating in Canada and several countries in Europe, highlighting that close monitoring is needed to prevent future outbreaks around the world.
Research data is optimized when it can be freely accessed and reused. To maximize research equity, transparency, and reproducibility, policymakers should take concrete steps to ensure that research ...software is openly accessible and reusable.
•The effect of simple virus enrichment methods were tested on a metagenomics dataset.•Centrifugation, filtration or nuclease-treatment was evaluated.•A multi-step enrichment method increased the ...proportion of virus sequences.•This evaluation guides researchers in their choice of enrichment methodology.
The discovery of new or divergent viruses using metagenomics and high-throughput sequencing has become more commonplace. The preparation of a sample is known to have an effect on the representation of virus sequences within the metagenomic dataset yet comparatively little attention has been given to this. Physical enrichment techniques are often applied to samples to increase the number of viral sequences and therefore enhance the probability of detection. With the exception of virus ecology studies, there is a paucity of information available to researchers on the type of sample preparation required for a viral metagenomic study that seeks to identify an aetiological virus in an animal or human diagnostic sample. A review of published virus discovery studies revealed the most commonly used enrichment methods, that were usually quick and simple to implement, namely low-speed centrifugation, filtration, nuclease-treatment (or combinations of these) which have been routinely used but often without justification. These were applied to a simple and well-characterised artificial sample composed of bacterial and human cells, as well as DNA (adenovirus) and RNA viruses (influenza A and human enterovirus), being either non-enveloped capsid or enveloped viruses. The effect of the enrichment method was assessed by both quantitative real-time PCR and metagenomic analysis that incorporated an amplification step. Reductions in the absolute quantities of bacteria and human cells were observed for each method as determined by qPCR, but the relative abundance of viral sequences in the metagenomic dataset remained largely unchanged. A 3-step method of centrifugation, filtration and nuclease-treatment showed the greatest increase in the proportion of viral sequences. This study provides a starting point for the selection of a purification method in future virus discovery studies, and highlights the need for more data to validate the effect of enrichment methods on different sample types, amplification, bioinformatics approaches and sequencing platforms. This study also highlights the potential risks that may attend selection of a virus enrichment method without any consideration for the sample type being investigated.
HPV testing is replacing cytology for cervical cancer screening because of greater sensitivity and superior reassurance following negative tests for the dozen HPV genotypes that cause cervical ...cancer. Management of women testing positive is unresolved. The need for identification of individual HPV genotypes for clinical use is debated. Also, it is unclear how long to observe persistent infections when precancer is not initially found.
In the longitudinal NCI-Kaiser Permanente Northern California Persistence and Progression (PaP) Study, we observed the clinical outcomes (clearance, progression to CIN3+, or persistence without progression) of 11,573 HPV-positive women aged 30–65 yielding 14,158 type-specific infections.
Risks of CIN3+ progression differed substantially by type, with HPV16 conveying uniquely elevated risk (26% of infections with seven-year CIN3+ risk of 22%). The other carcinogenic HPV types fell into 3 distinct seven-year CIN3+ risk groups: HPV18, 45 (13% of infections, risks >5%, with known elevated cancer risk); HPV31, 33, 35, 52, 58 (39%, risks >5%); and HPV39, 51, 56, 59, 68 (23%, risks <5%). In the absence of progression, HPV clearance rates were similar by type, with 80% of infections no longer detected within three years; persistence to seven years without progression was uncommon. The predictive value of abnormal cytology was most evident for prevalent CIN3+, but less evident in follow-up. A woman's age did not modify risk; rather it was the duration of persistence that was important.
HPV type and persistence are the major predictors of progression to CIN3+; at a minimum, distinguishing HPV16 is clinically important. Dividing the other HPV types into three risk-groups is worth considering.
During 1998-2012, an extended outbreak of Salmonella enterica serovar Typhimurium definitive type 160 (DT160) affected >3,000 humans and killed wild birds in New Zealand. However, the relationship ...between DT160 within these 2 host groups and the origin of the outbreak are unknown. Whole-genome sequencing was used to compare 109 Salmonella Typhimurium DT160 isolates from sources throughout New Zealand. We provide evidence that DT160 was introduced into New Zealand around 1997 and rapidly propagated throughout the country, becoming more genetically diverse over time. The genetic heterogeneity was evenly distributed across multiple predicted functional protein groups, and we found no evidence of host group differentiation between isolates collected from human, poultry, bovid, and wild bird sources, indicating ongoing transmission between these host groups. Our findings demonstrate how a comparative genomic approach can be used to gain insight into outbreaks, disease transmission, and the evolution of a multihost pathogen after a probable point-source introduction.
Nitrification inhibitors, such as dicyandiamide (DCD), have been shown to decrease leaching from urea- and ammonium-based fertilisers and from urine patches in grazed pastures. To date there have ...been few studies on effects of nitrification inhibitors on non-target soil microbiota. This pot trial examined the short-term effects of DCD on the activity and diversity of both target (ammonium-oxidising bacteria and archaea) and non-target soil microbial populations. Bovine urine at a rate equivalent to 600kgurine-Nha−1 with or without DCD at 30kgha−1 was applied to pots planted with perennial ryegrass. This rate of DCD was typical of the amount applied to pasture in New Zealand, although this annual rate may be spread over several applications carried out over 2–3 months. The single high rate application was used to provide a “worst case scenario” to assist detection of potential impacts of DCD application to non-target soil microflora. Treatments also included DCD alone and untreated control pots. Soil used was a Horotiu sandy loam and pots were maintained at 80% WHC in a controlled-environment room at 12°C/16h (day) and 8°C/8h (night). Soil mineral N, hot water extractable C and N concentrations, soil pH, microbial biomass C and N, and DCD persistence were measured at regular intervals. Diversity and composition of the overall soil bacterial community were analysed by serial analysis of ribosomal sequence tags (SARST). Effects on ammonium-oxidising bacterial and archaeal communities were monitored more closely by determining the size of these populations using real-time PCR and their transcriptional activity by comparing RNA-denaturing gradient gel electrophoresis (DGGE) profiles following RT-PCR of the amoA gene. Changes in soil pH and mineral N following application of urine in the pot trial reflected patterns typically demonstrated in the field. Application of DCD to soil did not change the diversity of the soil bacterial community, with the four predominant phyla (Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes) remaining in proportions that were similar to control soils. In contrast, urine application to soil resulted in a significant increase in members of Firmicutes, some of which are relatively stress tolerant. In line with the SARST results, shifts in the structure of the active component of the general soil bacterial community were detected in the urine and urine+DCD treatments only, further suggesting DCD had little impact on the overall soil bacterial activity. In contrast the microbes targeted by DCD, the ammonium-oxidising bacteria, were significantly affected by DCD with reductions in population size and altered activity. Ammonium-oxidising archaea, however, showed no response to application of DCD to soil, and were only minimally affected by application of urine. The results suggest that application of DCD to pasture is a relatively benign intervention that has an important role to play in mitigating the environmental hazards imposed by ongoing land use intensification.
Continuing, severe outbreaks of mountain pine beetle (
Dendroctonus ponderosae) across western North America have resulted in widespread mortality of lodgepole pine (
Pinus contorta). Multiple ...studies have used high spatial resolution satellite data to map areas of beetle kill; these studies have largely focused on mapping red canopy cover associated with recent tree mortality and have not examined mapping gray canopy cover that occurs after red needles have dropped. The work presented here examines the use of newly available GeoEye-1 data for mapping both red and gray canopy area in southeastern Wyoming lodgepole pine forest. A 0.5
m spatial resolution, pan-sharpened GeoEye-1 image was used to classify areas of green, red, and gray canopy cover. Reference data were collected at twelve 500
m
2 field plots. Shadow-normalized green, red, and gray canopy area from classified GeoEye-1 data closely agreed with field-estimated green, red, and gray canopy area. Mean absolute error in canopy cover for the twelve sample plots was 8.3% for the green class, 5.4% for the red class, and 7.2% for the gray class. When all twelve plots were aggregated, remotely sensed estimates of green, red, and gray cover were within 1.7% of the field-estimated cover. Our results demonstrate that high spatial resolution spaceborne multispectral data are a promising tool for mapping canopy mortality caused by mountain pine beetle outbreaks.
•DT160 and DT56v shared an estimated date of common ancestor between 1769 and 1821.•DT160 replicated at a faster rate than DT56v in vitro.•Neither DT160 nor DT56v were lysed by phage released by the ...other strain.•A linear plasmid was detected in a DT56v isolate representing the first reported pBSSB1 plasmid isolated from S. Typhimurium.•DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that possibly contributed to its higher prevalence.
Salmonella enterica serovar Typhimurium DT160 was the predominant cause of notified human salmonellosis cases in New Zealand from 2000 to 2010, before it was superseded by another S. Typhimurium strain, DT56 variant (DT56v). Whole genome sequencing and phenotypic testing were used to compare 109 DT160 isolates with eight DT56v isolates from New Zealand animal and human sources. Phylogenetic analysis provided evidence that DT160 and DT56v strains were distantly related with an estimated date of common ancestor between 1769 and 1821. The strains replicated at different rates but had similar antimicrobial susceptibility profiles. Both strains were resistant to the phage expressed from the chromosome of the other strain, which may have contributed to the emergence of DT56v. DT160 contained the pSLT virulence plasmid, and the sseJ and sseK2 genes that may have contributed to the higher reported prevalence compared to DT56v. A linear pBSSB1-family plasmid was also found in one of the DT56v isolates, but there was no evidence that this plasmid affected bacterial replication or antimicrobial susceptibility. One of the DT56v isolates was also sequenced using long-read technology and found to contain an uncommon chromosome arrangement for a Typhimurium isolate. This study demonstrates how comparative genomics and phenotypic testing can help identify strain-specific elements and factors that may have influenced the emergence and supersession of bacterial strains of public health importance.
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