Acid-adaption by a medic microsymbiont: new insights from the genome of Sinorhizobium medicae WSM419

The poor availability of nitrogen is one of the principal factors limiting global biomass. Legumes are vital components of agricultural systems because of their ability to associate symbiotically with root nodule bacteria (RNB) and subsequently fix atmospheric nitrogen to a form that can be utilised by the plant partner. Furthermore, this symbiotic relationship provides available soil nitrogen for subsequent non-leguminous crops. This RNB-legume interaction is affected by a number of environmental factors. Progressive acidification of agricultural soils is one of the big challenges in agriculture as soil acidity negatively impacts legume productivity. One genus of RNB, Sinorhizobium, is particularly acid-sensitive causing a major reduction in Medicago productivity in acidic soils. Due to the importance of Medic pasture production, alternative strains have been captured, and are still being captured, from the genetic pool that display superior acid tolerance characteristics. This presentation will focus on the acid-tolerant species S. medicae (previously known as S. meliloti) and in particular on the previously used commercial inoculant WSM419

Genome sequence of <i>Ensifer medicae</i> strain WSM1369; an effective microsymbiont of the annual legume <i>Medicago sphaerocarpos</i>

Ensifer medicae WSM1369 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1369 was isolated in 1993 from a nodule recovered from the roots of Medicago sphaerocarpos growing at San Pietro di Rudas, near Aggius in Sardinia (Italy). WSM1369 is an effective microsymbiont of the annual forage legumes M. polymorpha and M. sphaerocarpos. Here we describe the features of E. medicae WSM1369, together with genome sequence information and its annotation. The 6,402,557 bp standard draft genome is arranged into 307 scaffolds of 307 contigs containing 6,656 protein-coding genes and 79 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project

Sofosbuvir and Velpatasvir for HCV Genotype 2 and 3 Infection

BACKGROUND: In phase 2 trials, treatment with the combination of the nucleotide polymerase inhibitor sofosbuvir and the NS5A inhibitor velpatasvir resulted in high rates of sustained virologic response in patients chronically infected with hepatitis C virus (HCV) genotype 2 or 3. METHODS: We conducted two randomized, phase 3, open-label studies involving patients who had received previous treatment for HCV genotype 2 or 3 and those who had not received such treatment, including patients with compensated cirrhosis. In one trial, patients with HCV genotype 2 were randomly assigned in a 1:1 ratio to receive sofosbuvir-velpatasvir, in a once-daily, fixed-dose combination tablet (134 patients), or sofosbuvir plus weight-based ribavirin (132 patients) for 12 weeks. In a second trial, patients with HCV genotype 3 were randomly assigned in a 1:1 ratio to receive sofosbuvir-velpatasvir for 12 weeks (277 patients) or sofosbuvir-ribavirin for 24 weeks (275 patients). The primary end point for the two trials was a sustained virologic response at 12 weeks after the end of therapy. RESULTS: Among patients with HCV genotype 2, the rate of sustained virologic response in the sofosbuvir-velpatasvir group was 99% (95% confidence interval [CI], 96 to 100), which was superior to the rate of 94% (95% CI, 88 to 97) in the sofosbuvir-ribavirin group (P=0.02). Among patients with HCV genotype 3, the rate of sustained virologic response in the sofosbuvir-velpatasvir group was 95% (95% CI, 92 to 98), which was superior to the rate of 80% (95% CI, 75 to 85) in the sofosbuvir-ribavirin group (P CONCLUSIONS: Among patients with HCV genotype 2 or 3 with or without previous treatment, including those with compensated cirrhosis, 12 weeks of treatment with sofosbuvir-velpatasvir resulted in rates of sustained virologic response that were superior to those with standard treatment with sofosbuvir-ribavirin. (Funded by Gilead Sciences; ASTRAL-2 ClinicalTrials.gov number, NCT02220998; and ASTRAL-3, NCT02201953.)

The influence of HIV infection on the natural history of hepatocellular carcinoma: results from a global multi-cohort study

Purpose. Conflicting evidence indicates HIV-seropositivity to influence the outcome of patients with hepatocellular carcinoma (HCC), a leading cause of mortality in people with HIV. We aimed to verify whether HIV affected the overall survival (OS) of patients with HCC independent of treatment and geographic origin. Patients and Methods: We designed an international multi-cohort study of HCC patients who did not receive any anticancer treatment accrued from four continents. We estimated the effect of HIV-seropositivity on patients’ OS while accounting for common prognostic factors and demographic characteristics in uni- and multi-variable models. Results: A total of 1588 patients were recruited, 132 of whom were HIV-positive. Most patients clustered within Barcelona Clinic Liver Cancer (BCLC) C/D criteria (n=1168, 74%), Child-Turcotte-Pugh (CTP) Class B (median score 7, IQR 3). At HCC diagnosis the majority of HIV-positive patients (n=65, 64%) had been on anti-retrovirals for a median duration of 8.3 years (IQR 8.59) and had median CD4+ cell counts of 256 (IQR 284) with undetectable HIV RNA (n=68, 52%). OS significantly reduced throughout BCLC stages 0-D (16, 12, 7.5, 3.1 and 3 months, p<0.001). Median OS of HIV-positive patients was half that of HIV-uninfected counterparts: 2.2 months, (bootstrap 95%CI 1.2-3.1) versus 4.1 months (95%CI 3.6-4.4). In adjusted analyses HIV-seropositivity increased the hazard of death by 24% (p=0.0333) independent of BCLC (p<0.0001), CTP (p<0.0001), alpha-fetoprotein (AFP) (p<0.0001), geographical origin (p<0.0001) and male gender (p=0.0016). Predictors of worse OS in HIV-positive patients included CTP (p=0.0071) and AFP (p<0.0001). Conclusions. Despite adequate antiretroviral treatment, HIV-seropositivity is associated with decreased survival in HCC independent of stage, anti-cancer treatment and geographical origin. Mechanistic studies investigating the immuno-biology of HIV-associated HCC are urgently required

Ledipasvir and sofosbuvir for untreated HCV genotype 1 infection.

BACKGROUND: In phase 2 studies, treatment with the all-oral combination of the nucleotide polymerase inhibitor sofosbuvir and the NS5A inhibitor ledipasvir resulted in high rates of sustained virologic response among previously untreated patients with hepatitis C virus (HCV) genotype 1 infection. METHODS: We conducted a phase 3, open-label study involving previously untreated patients with chronic HCV genotype 1 infection. Patients were randomly assigned in a 1:1:1:1 ratio to receive ledipasvir and sofosbuvir in a fixed-dose combination tablet once daily for 12 weeks, ledipasvir-sofosbuvir plus ribavirin for 12 weeks, ledipasvir-sofosbuvir for 24 weeks, or ledipasvir-sofosbuvir plus ribavirin for 24 weeks. The primary end point was a sustained virologic response at 12 weeks after the end of therapy. RESULTS: Of the 865 patients who underwent randomization and were treated, 16% had cirrhosis, 12% were black, and 67% had HCV genotype 1a infection. The rates of sustained virologic response were 99% (95% confidence interval [CI], 96 to 100) in the group that received 12 weeks of ledipasvir-sofosbuvir; 97% (95% CI, 94 to 99) in the group that received 12 weeks of ledipasvir-sofosbuvir plus ribavirin; 98% (95% CI, 95 to 99) in the group that received 24 weeks of ledipasvir-sofosbuvir; and 99% (95% CI, 97 to 100) in the group that received 24 weeks of ledipasvir-sofosbuvir plus ribavirin. No patient in either 12-week group discontinued ledipasvir-sofosbuvir owing to an adverse event. The most common adverse events were fatigue, headache, insomnia, and nausea. CONCLUSIONS: Once-daily ledipasvir-sofosbuvir with or without ribavirin for 12 or 24 weeks was highly effective in previously untreated patients with HCV genotype 1 infection. (Funded by Gilead Sciences; ION-1 ClinicalTrials.gov number NCT01701401.)

Tocilizumab in patients hospitalised with COVID-19 pneumonia: efficacy, safety, viral clearance, and antibody response from a randomised controlled trial (COVACTA)

Background: In COVACTA, a randomised, placebo-controlled trial in patients hospitalised with coronavirus disease-19 (COVID-19), tocilizumab did not improve 28-day mortality, but shortened hospital and intensive care unit stay. Longer-term effects of tocilizumab in patients with COVID-19 are unknown. Therefore, the efficacy and safety of tocilizumab in COVID-19 beyond day 28 and its impact on Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) clearance and antibody response in COVACTA were investigated. Methods: Adults in Europe and North America hospitalised with COVID-19 (N = 452) between April 3, 2020 and May 28, 2020 were randomly assigned (2:1) to double-blind intravenous tocilizumab or placebo and assessed for efficacy and safety through day 60. Assessments included mortality, time to hospital discharge, SARS-CoV-2 viral load in nasopharyngeal swab and serum samples, and neutralising anti-SARS-CoV-2 antibodies in serum. ClinicalTrials.gov registration: NCT04320615. Findings: By day 60, 24·5% (72/294) of patients in the tocilizumab arm and 25·0% (36/144) in the placebo arm died (weighted difference –0·5% [95% CI –9·1 to 8·0]), and 67·0% (197/294) in the tocilizumab arm and 63·9% (92/144) in the placebo arm were discharged from the hospital. Serious infections occurred in 24·1% (71/295) of patients in the tocilizumab arm and 29·4% (42/143) in the placebo arm. Median time to negative reverse transcriptase–quantitative polymerase chain reaction result in nasopharyngeal/oropharyngeal samples was 15·0 days (95% CI 14·0 to 21·0) in the tocilizumab arm and 21·0 days (95% CI 14·0 to 28·0) in the placebo arm. All tested patients had positive test results for neutralising anti–SARS-CoV-2 antibodies at day 60. Interpretation: There was no mortality benefit with tocilizumab through day 60. Tocilizumab did not impair viral clearance or host immune response, and no new safety signals were observed. Future investigations may explore potential biomarkers to optimize patient selection for tocilizumab treatment and combination therapy with other treatments. Funding: F. Hoffmann-La Roche Ltd and the US Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, Biomedical Advanced Research and Development Authority, under OT number HHSO100201800036C

Methods for isolation of plant growth promoting rhizo-bacteria (PGPR) from Western Australian soils

There is a substantial and increasing effort in industrial microbiology and biotechnology to develop microbial inoculants as a means to improve the sustainability and profitability of rural activities whilst increasing productivity. Inoculants are being developed for use as microbial biofertilizers, biocontrol agents for weed suppression, biopesticides and bioremediation agents. All of these require the addition of microorganisms to complex microbial communities. Plant Growth Promoting Rhizosphere organisms (PGPRs) are good examples of microbes that might have important roles in agriculture. PGPRs inhabit plant root rhizospheres and can affect plant growth directly by nutrient solubilisation (P, Nand K) and production of plant growth regulators, and indirectly by suppression of plant pathogens by competition, release of antibiotics or siderophores

Development of plant growth promoting rhizosphere organisms to enhance productivity of cereals and legumes in dry-land farming in South Australia

There is a substantial and increasing effort to develop microorganisms for agricultural purposes to improve the sustainability and profitability of rural activities whilst increasing productivity. These are generically termed Plant Growth Regulating Rhizosphere organisms (PGPR), and the number of research groups that are involved in their isolation and/or characterisation is growing. Examples of PGPR organisms that have been shown to be beneficial include microbial biofertilisers, biocontrol agents for weed suppression, ana plant stimulants from Actinomycetes, and the fungal and bacterial genera Trichoderma, Penicillium, Pseudomonas, Agrobacterium, Azospirillum, Azotobacter, Acetobacter and Bacillus. The use of these organisms is now seen in the fields of agriculture, horticulture, forestry and environmental restoration. The specific 'mechanisms of plant growth enhancement by PGPR have not been well characterised but their modes of action are broadly divided into two categories, viz. enhancement of plant growth by indirect and enhancement of plant growth by direct means