bluuebunny/crossref_metadata_2025 huggingface dataset:
Twelve-Month Outcomes of Community-Based Differentiated Models of Multimonth Dispensing of ART Among Stable HIV-Infected Adults in Lesotho: A Cluster-Randomized Noninferiority Trial
Authors: Tukei Betty B. , Fatti Geoffrey , Tiam Appolinaire , Ngorima-Mabhena Nicoletta , Tukei Vincent J. , Tshabalala Itumeleng , Sejana Veronica M. , Muzenda Trish , Mokoroane Lincoln M. , Sehlabo Lebelang , Maotoe Thapelo , Mirembe Justine K. , Membe Ian , Akpan Francis , Maile Khotso , Faturiyele Iyiola , Xulu Thembi , Minior Thomas , Sanne Ian , Chasela Charles ,   for EQUIP Health
Published: July 2020

Background:

Lesotho adopted the test-and-treat approach for HIV treatment in June 2016, which increased antiretroviral treatment (ART) clinic volume. We evaluated community-based vs. facility-based differentiated models of multimonth dispensing of ART among stable HIV-infected adults in Lesotho.

Methods:

Thirty facilities were randomized to 3 arms, facility 3-monthly ART (3MF) (control), community ART groups (3MC), and 6-monthly community distribution points (6MCD). We estimated risk differences (RDs) between arms using population-averaged generalized estimating equations, controlling for baseline imbalances and specifying for clustering. The primary outcome was retention in ART care by intention-to-treat and virologic suppression as a secondary outcome (ClinicalTrials.gov: NCT03438370).

Results:

A total of 5,336 participants were enrolled, with 1898, 1558, and 1880 in 3MF, 3MC, and 6MCD, respectively. Retention in ART care was not different across arms and achieved the prespecified noninferiority limit (−3.25%) between 3MC vs. 3MF (control); 6MCD vs. 3MF; and 6MCD vs. 3MC, adjusted RD = −0.1% [95% confidence interval (CI): −1.6% to 1.5%], adjusted RD = −1.3% (95% CI: −3.0% to 0.5%), and adjusted RD = −1.2% (95% CI: −2.9% to 0.5%), respectively. After 12 months, 98.6% (n = 1503), 98.1% (n = 1126), and 98.3% (n = 1285) were virally load (VL) suppressed in 3MF, 3MC, and 6MCD, respectively. There were no differences in VL between 3MC vs. control and 6MCD vs. control, risk ratio (RR) = 1.00 (95% CI: 0.98 to 1.01) and RR = 1.00 (95% CI: 0.98 to 1.01), respectively.

Conclusions:

There were no differences in retention and VL suppression for stable HIV-infected participants receiving multimonth dispensing of ART within community-based differentiated models when compared with the facility-based standard-of-care model.
Early and Consistent Improvements in Urinary Symptoms and Quality of Life With OnabotulinumtoxinA in Patients With Overactive Bladder and Urinary Incontinence: Results From a Randomized, Placebo-controlled, Phase IV Clinical Trial
Authors: McCammon Kurt , Gousse Angelo , Kohan Alfred , Glazier David , Gruenenfelder Jennifer , Bai Zhanying , Patel Anand , Hale Douglass
Published: July 2020

Objectives

This randomized, multicenter, placebo-controlled, phase IV study assessed the efficacy and tolerability of onabotulinumtoxinA in patients with overactive bladder.

Methods

Patients were randomized 1:1 to onabotulinumtoxinA 100 U or placebo. Assessments over 12 weeks included: change from baseline in urinary incontinence (UI) episodes/day; proportions of patients who achieved 100% and 50% or greater reductions in UI episodes/day; proportion of patients using no incontinence pads in the previous 24 hours; and changes from baseline in micturition frequency, nocturia, urgency UI, Incontinence-Quality of Life, King’s Health Questionnaire, International Consultation on Incontinence Questionnaire—UI Short Form scores and time to request retreatment.

Results

Significant reductions in UI episodes/day were seen with onabotulinumtoxinA versus placebo within week 1 posttreatment (−2.9 vs −2.0, P = 0.005) through week 12 (coprimary endpoint: −3.5 vs −1.6, P < 0.001). Significantly more onabotulinumtoxinA-treated patients achieved 100% (coprimary endpoint) and 50% or greater reductions in UI episodes/day. Decreases in other urinary symptoms were also seen within 1 week with onabotulinumtoxinA that continued through at least week 12. More onabotulinumtoxinA-treated versus placebo-treated patients required no incontinence pads at weeks 1 to 12, and greater improvements in quality of life measurements were seen. Time to request retreatment was significantly longer with onabotulinumtoxinA versus placebo (30.0 weeks vs 13.1 weeks; P < 0.001). No unexpected safety signals were observed. Urinary tract infection was the most commonly observed adverse event.

Conclusions

Urinary symptom and quality of life improvements were observed with onabotulinumtoxinA within 1 week of treatment and were sustained for at least 12 weeks.
Effect of Lomerizine Hydrochloride on Preventing Strokes in Patients With Cerebral Autosomal Dominant Arteriopathy With Subcortical Infarcts and Leukoencephalopathy
Authors: Watanabe-Hosomi Akiko , Mizuta Ikuko , Koizumi Takashi , Yokota Isao , Mukai Mao , Hamano Ai , Kondo Masaki , Fujii Akihiro , Matsui Masaru , Matsuo Koushun , Ito Keita , Teramukai Satoshi , Yamada Kei , Nakagawa Masanori , Mizuno Toshiki
Published: July 2020

Background

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is an orphan disease clinically characterized by migraine, recurrent strokes, and dementia. Currently, there are no disease-modifying therapies, and it is difficult to prevent cerebral ischemic events in CADASIL patients by conventional antithrombotic medication. We hypothesized that an antimigraine agent, lomerizine hydrochloride, may prevent strokes in CADASIL patients, based on its effect on increasing cerebral blood flow.

Subjects and Methods

This was an open-labeled clinical trial in which 30 adult CADASIL patients received lomerizine at 10 mg/d. Numbers of symptomatic strokes during the 2 years after the start of lomerizine administration were compared with those in the 2 years before its initiation. The effect of lomerizine on preventing strokes was evaluated based on the incidence rate ratio (IR) calculated with the Mantel-Haenszel method.

Results

When including all 30 patients (analysis 1), the IR was less than 1 (0.46; 95% confidence interval [CI], 0.19–1.12) but did not reach significance. To evaluate the effect of lomerizine on secondary prevention, subgroups of 15 patients with stroke episodes occurring any time before lomerizine administration (analysis 2) and 10 patients with stroke episodes during the 2 years before lomerizine administration (analysis 3) were analyzed. The IR values were 0.33 (95% CI, 0.12–0.94) in analysis 2 and 0.17 (95% CI, 0.04–0.67) in analysis 3.

Conclusions

Our results suggest the effect of lomerizine on preventing secondary stroke in CADASIL patients.
Social effects on age-related and sex-specific immune cell profiles in a wild mammal
Authors: van Lieshout Sil H. J. , Badás Elisa P. , Mason Michael W. T. , Newman Chris , Buesching Christina D. , Macdonald David W. , Dugdale Hannah L.
Published: July 2020

Evidence for age-related changes in innate and adaptive immune responses is increasing in wild populations. Such changes have been linked to fitness, and knowledge of the factors driving immune response variation is important for understanding the evolution of immunity. Age-related changes in immune profiles may be owing to factors such as immune system development, sex-specific behaviour and responses to environmental conditions. Social environments may also contribute to variation in immunological responses, for example, through transmission of pathogens and stress arising from resource and mate competition. Yet, the impact of the social environment on age-related changes in immune cell profiles is currently understudied in the wild. Here, we tested the relationship between leukocyte cell composition (proportion of neutrophils and lymphocytes [innate and adaptive immunity, respectively] that were lymphocytes) and age, sex and group size in a wild population of European badgers (Meles meles). We found that the proportion of lymphocytes in early life was greater in males in smaller groups compared to larger groups, but with a faster age-related decline in smaller groups. By contrast, the proportion of lymphocytes in females was not significantly related to age or group size. Our results provide evidence of sex-specific age-related changes in immune cell profiles in a wild mammal, which are influenced by the social environment.
Thistledown velvet ants in the Desert Mimicry Ring and the evolution of white coloration: Müllerian mimicry, camouflage and thermal ecology
Authors: Wilson Joseph S. , Sidwell Jeni Sage , Forister Matthew L. , Williams Kevin A. , Pitts James P.
Published: July 2020

Adaptive coloration among animals is one of the most recognizable outcomes of natural selection. Here, we investigate evolutionary drivers of white coloration in velvet ants (Hymenoptera: Mutillidae), which has previously been considered camouflage with the fruit of creosote bush (
Larrea tridentata
). Our analyses indicate instead that velvet ants evolved white coloration millions of years before creosote bush was widespread in North America's hot deserts. Furthermore, velvet ants and the creosote fruit exhibit different spectral reflectance patterns, which appear distinct to potential insectivorous predators. While the white coloration in velvet ants likely did not evolve as camouflage, we find that white-coloured species remain cooler than their red/orange relatives, and therefore we infer the white coloration likely evolved in response to Neogene desertification. This study shows the importance of cross-disciplinary investigation and of testing multiple hypotheses when investigating evolutionary drivers of adaptive coloration.
Temperature and predator cues interactively affect ontogenetic metabolic scaling of aquatic amphipods
Authors: Gjoni V. , Basset A. , Glazier D. S.
Published: July 2020

A common belief is that body mass scaling of metabolic rate results chiefly from intrinsic body-design constraints. However, several studies have shown that multiple ecological factors affect metabolic scaling. The mechanistic basis of these effects is largely unknown. Here, we explore whether abiotic and biotic environmental factors have interactive effects on metabolic scaling. To address this question, we studied the simultaneous effects of temperature and predator cues on the ontogenetic metabolic scaling of amphipod crustaceans inhabiting two different aquatic ecosystems, a freshwater spring and a saltwater lagoon. We assessed effects of phenotypic plasticity on metabolic scaling by exposing amphipods in the laboratory to water with and without fish cues at multiple temperatures. Temperature interacts significantly with predator cues to affect metabolic scaling. Our results suggest that metabolic scaling is highly malleable in response to short-term acclimation. The interactive effects of temperature and predators show the importance of studying effects of global warming in realistic ecological contexts.
Hypoxia inducible factor-1
α
knockout does not impair acute thermal tolerance or heat hardening in zebrafish
Authors: Joyce William , Perry Steve F.
Published: July 2020

The rapid increase in critical thermal maximum (CT
max
) in fish (or other animals) previously exposed to critically high temperature is termed ‘heat hardening’, which likely represents a key strategy to cope with increasingly extreme environments. The physiological mechanisms that determine acute thermal tolerance, and the underlying pathways facilitating heat hardening, remain debated. It has been posited, however, that exposure to high temperature is associated with tissue hypoxia and may be associated with the increased expression of hypoxia-inducible factor-1 (Hif-1). We studied acute thermal tolerance in zebrafish (
Danio rerio
) lacking functional Hif-1
α
paralogs (Hif-1aa and Hif-1ab double knockout; Hif-1
α
−/−
), which are known to exhibit markedly reduced hypoxia tolerance. We hypothesized that Hif-1
α
−/−
zebrafish would suffer reduced acute thermal tolerance relative to wild type and that the heat hardening ability would be lost. However, on the contrary, we observed that Hif-1
α
−/−
and wild-type fish did not differ in CT
max
, and both genotypes exhibited heat hardening of a similar degree when CT
max
was re-tested 48 h later. Despite exhibiting impaired hypoxia tolerance, Hif-1
α
−/−
zebrafish display unaltered thermal tolerance, suggesting that these traits are not necessarily functionally associated. Hif-1
α
is accordingly not required for short-term acclimation in the form of heat hardening.
Thermomagnetic resonance affects cancer growth and motility
Authors: Lucia Umberto , Grisolia Giulia , Ponzetto Antonio , Bergandi Loredana , Silvagno Francesca
Published: July 2020

The fight against a multifaceted incurable disease such as cancer requires a multidisciplinary approach to overcome the multitude of molecular defects at its origin. Here, a new thermophysical biochemical approach has been suggested and associated with the use of electromagnetic fields to control the growth of cancer cells. In particular, thermodynamic analysis of the heat transfer is developed in correlation with cellular parameters such as the volume/area ratio. We propose that the electromagnetic wave, at the specific frequency calculated as the characteristic response time of any cell type to the external thermal perturbation, can affect resonant intracellular molecular oscillations. The biochemical model hypothesizes that microtubules are stabilized, and the impact is predicted on cell growth, migration and mitochondrial activity. Experimental validation of the theoretical results shows that the thermodynamic analysis allows the application of the specific electromagnetic field able to decrease cancer cell invasion and proliferation.
A polycarboxylic/ether composite polymer electrolyte via
in situ
UV-curing for all-solid-state lithium battery
Authors: Wang Wenli , Qiu Ziwen , Wang Qian , Zhou Xiaoyu , Liu Yang , Zhou Jingjing , Guo Bingkun
Published: July 2020

A polycarboxylic/ether composite polymer electrolyte derived from two-arm monomer and polyethylene oxide (PEO) was
in situ
synthesized on the cathode. The composite electrolyte exhibits a high ionic conductivity of 3.6 × 10
−5
S cm
–1
, high oxidation stability, excellent stability towards Li metal and makes Li/LiFePO
4
present good cyclic and rate performance at 25°C.
In silico prediction and in vitro assessment of microbial substrate utilisation: a focus on newly identified health promoting gut bacteria
Authors: Lordan Cathy , Walsh Aaron M. , Paul Ross R. , Cotter Paul D.
Published: July 2020

The contribution of the gut microbiota to health and disease is becoming ever more apparent in the last number of years, due to developments in DNA sequencing technology and more well-defined cultivation techniques. This has resulted in the identification of health-promoting bacteria. Until recently, prebiotics, non-digestible food substrates which are selectively utilised by beneficial bacteria, were employed with a view to increasing the growth of well-established health promoting bacteria, namely Lactobacillus and Bifidobacterium. However, other beneficial bacteria recently revealed may also be targeted to enhance their growth as they establish themselves as the next generation of health-promoting microbes. These include anaerobes such as Akkermansia muciniphila, Faecalibacterium prausnitzii and Eubacterium rectale. Identification of growth substrates/bioactives through the analysis of genome sequence data can aid in elucidating which substrates may best enhance the growth of these microbes which are often difficult to grow.

The phenotypic microbial trait analyser, Traitar, can predict 67 phenotypes based on the genome sequence inputted. Some of these traits include substrates that could potentially be utilised by the bacteria. Another tool, CarveMe, which has been created with the aim of making metabolic modelling more user-friendly, was also used with the same genomes. A select number of substrates identified in both tools have been chosen to be evaluated in vitro in order to establish the accuracy of these predictive tools as well as giving an indication as to how these beneficial microbes can be modulated through dietary components.
Antimicrobial resistance Salmonella isolates recovered from food products of animal origin in the Russian Federation
Authors: Skitovich Galina , Serova Kseniya , Korchagina Yevgenia , Shadrova Natalya
Published: July 2020

The study was aimed at Salmonella isolation from samples of animal food products submitted for testing from various regions of the Central part of the RF and serotyping of the recovered isolates and their testing for antibiotic resistance. A total of 2,342 tests were performed and 87 (3.7%) Salmonella isolates were recovered. Most of them (54 isolates) were recovered from poultry meat and poultry meat preparation samples submitted for testing. Besides, 25 isolates were recovered from pork and pork preparation samples, 7 isolates – from beef samples, 1 isolate – from hard cheese samples. Serotyping of 64 Salmonella isolates showed that the majority of the isolates (57.8%) belonged to О7 group. Also, Salmonella isolates belonging to О9 (21.9%), О8 (9.4%), О4,5 (6.2%) and О10 (4.7%) were detected in food products. S. Enteritidis, (23.3%), and S. infantis (18.7%), were predominant based on the number of detections. Also, the following serovars were identified: S. typhimurium, S. nigeria, S. montevideo, S. derby, S. meleagridis, S. virchov, S. oranienburg. Tests of 87 Salmonella isolates for their antibiotic resistance with disk diffusion method revealed that they were highly resistant to nalidixic acid (70.1%), tetracycline (49.4%), trimethoprim/sulfamethoxazol (40.2%). Moreover, nalidixic acid-resistance was common for all identified isolates. Seventeen isolates (19.5%) demonstrated multiple antibiotic resistance and two isolates were found to be resistant to ≥7 antibiotics. All recovered isolates were susceptible to gentamicin, amikacin, meropenem and imipenem. Obtained results indicate the necessity of Salmonella antibiotic resistance monitoring to gain understanding of Salmonellas’ antibiotic resistance emergence and trends.
Comprehensive evaluation of the antigenic impact of intra-genotypic human papillomavirus variant diversity on recognition by neutralizing monoclonal antibodies raised against lineage a L1 virus like particles
Authors: Godi Anna , Boampong Dulcibella , Elegunde Busayo , Panwar Kavita , Fleury Maxime , Li Shaowei , Zhao Qinjian , Xia Ningshao , Christensen Neil , Beddows Simon
Published: July 2020

Introduction. Naturally-occurring variants of Human papillomavirus (HPV) genotypes have been defined as lineages and sub-lineages, but little is known about the impact of this diversity on protein function. We have previously demonstrated that variation within the major (L1) and minor (L2) capsid proteins impact the susceptibility of HPV to serum antibodies elicited by vaccination and natural infection. Higher resolution mapping of variant residues, however, requires the availability of appropriate tools, such as type-specific monoclonal antibodies (MAbs). These empirical data will improve our understanding of the consequences of natural variation on capsid antigenicity.

Methods. We investigated the susceptibility of 37 representative pseudovirus variants of HPV16, HPV18, HPV31, HPV33, HPV45, HPV52 and HPV58 to neutralization by type-specific murine MAbs raised against the A lineage of their respective genotypes. Homology models derived from available HPV L1 crystal structures were generated to permit mapping of variant residues onto the surface-exposed L1 protein for relevant variants

Results. Type-specific lineage A-specific MAbs demonstrated differential reactivity against some, but not all, variants within its respective genotype. Some of these differences were minor (<4 fold) while some variants displayed orders of magnitude reduced sensitivity. These differences in antigenicity were mapped to a limited number of variant residues on the capsid surface.

Conclusions. These data contribute to our understanding of HPV L1 variant antigenicity and may have implications for seroprevalence or vaccine immunity studies based upon L1 antigens.
Molecular genetics of the virulence plasmids of pathogenic Escherichia coli O104:H4
Authors: Whelan Rachel , McVicker Gareth
Published: July 2020

In 2011 a large outbreak of enterohemorrhagic gastroenteritis and haemolytic uremic syndrome (HUS) throughout Europe resulted in almost 4,000 infections, 845 cases of HUS and 54 fatalities. This was due to a dangerous exchange of mobile genetic elements (MGE) resulting in a hybrid strain of E. coli O104:H4. This strain carried an unusual combination of EAEC- and STEC-associated virulence factors on a plasmid and phage respectively. In vitro the virulence plasmid has exhibited unusual stability under a wide range of environmental stresses, contrasting with rapid plasmid loss in the human gut. This project will characterise plasmid encoded maintenance systems responsible for its unique stability. Current investigations focus on toxin-antitoxin (TA) systems involved in postsegregationalkilling which contribute to plasmid maintenance therefore resulting in increased virulence. By inducing expression of putative TA genes cloned onto lab-made plasmid vectors, we have analysed their function in the cell. Once characterised we will further investigate the effects of various environmental conditions able to disrupt these TA systems, ultimately resulting in plasmid loss. This atypical strain displayed heightened pathogenicity and providedun foreseen treatment challenges. We aim to further our understanding of MGE carriage in O104:H4 as a model to predict and combat future outbreaks of hybrid pathovars.
Viruses in multiple sclerosis pathogenesis
Authors: Tarlinton Rachael , Morandi Elena , Wang Belinda , Gran Bruno , Khaiboullin Timur , Martynova Ekatarina , Rizvanov Albert , Khaiboullina Svetlana
Published: July 2020

Multiple sclerosis (MS) is an extremely debilitating auto-immune disease of people characterised by demyelination of the central nervous system and progressive neurological dysfunction. The etiology of the disease is complex (including factors such as genetics, sex hormones and vitamin D levels). The involvement of viral infections as a risk factor in triggering disease has long been suspected and two classes of viruses in particular, the herpesvirus Epstein-Barr virus (EBV) and the Human endogenous retrovirus “W” family (HERV-W) have been the focus of much recent research. Despite near ubiquitious infection (EBV), or integration into the genome as a repetitive element no longer able to function as a virus (HERV-W) a picture is gradually emerging of how these are involved in MS pathogenesis. In the case of EBV, having had infectious mononucleosis (clinical disease in patients infected post-puberty) increases the risk of developing MS. For HERV-W our recent work has confirmed that RNA is over-expressed in MS patients compared with healthy controls (though basal levels vary with ethnic background) and that EBV infection of B cells triggers expression of HERV-W RNA and proteins. There is a growing body of evidence that expression of HERV-W can trigger innate immune system inflammatory responses. There is also increasing evidence for molecular mimicry between epitopes of the HERV-W env protein, the EBV EBNA1 protein and peptides from brain proteins implicated in MS pathogenesis. Crucially these peptides are also able to bind the HLA-DR2b locus that is the strongest genetic risk factor for MS development.
Intelligent wound dressing for diagnostic & therapeutic applications - critical to wound infection
Authors: Mahmood Zahid , Salisbury Anne-Marie , Chen Rui , Rimmer Stephen , Percival Steven
Published: July 2020

A medical device comprising of biomaterials responsive to biochemical stimuli: channel for indicating the infective states of wounds and ensuring delivery of smart antimicrobial and antibiofilm agents to promote tissue regeneration and healing.

The importance of providing diagnostic wound dressings that can inform healthcare professionals on the state of infection within wounds but also provide some of the treatment required in response to at risk or infected wounds is of key interest. The aim is to investigate an innovative proof of concept diagnostic and detection system, an intelligent hydrogel wound dressing that responds to specific biochemical stimuli in wounds (MMPs and pH) enabling the selective and triggered release of antibiofilm and antimicrobial agents (‘Detect and Treat’)to the trauma site. The dressing is made of a sterile alginate core material covered in a biocompatible dry or hydrated peptide-polymer-complex film and may include a fluorescent dye which upon release during the wound healing process indicates when a change in dressing is necessary. Efficacy studies of the hydrogel dressing were performed within a drip-flow bioreactor in which regression of Pseudomonas aeruginosa biofilm was observed. A 5-log reduction in biofilm was observed in comparison to an untreated control biofilm. The hydrogel dressing indicated a clear response when in contact with biofilms produced only by pathogenic strains of bacteria when analysed. This further confirmed the adequate release and function of the antimicrobial and antibiofilm agents within the peptide-polymer-complex formulation of the hydrogel wound dressing.
Engineered ureolytic Bacillus subtilis and its future in Microbial Induced Calcium Carbonate Precipitation (MICCP)
Authors: Wright Jennifer , Moreland Polly , Wipat Anil , Zhang Meng , Dade-Robertson Martyn
Published: July 2020

As the global population grows there is an urgent need for increased, yet sustainable civil infrastructure. The ability to harness biological processes in order to improve ground stability; as well as creating construction materials without adding to climate damage is necessary. In almost every environment on earth, microorganisms and microbially mediated mineralisation (biomineralisation) processes are active. It is well documented that microbes present in soil can induce the precipitation of calcium carbonate (CaCO3) in both the laboratory and the natural setting through microbial induced calcium carbonate precipitation (MICCP). MICCP utilises microorganisms as a result of their active metabolism, to precipitate CaCO3, strengthening the surrounding matrix. MICCP is used in a variety of different applications such as carbon sequestration, environmental remediation and improving construction materials.

The enzyme urease catalyzes the hydrolysis of urea to ammonia and CO2, and is acknowledged to be instrumental in MICCP. Bacillus subtilis is a model, gram positive, spore-forming soil bacterium that produces a functionally active urease, but with low efficiency, and the activation is not completely understood. Sporosarcina pasteurii is one of the most commonly used MICCP microbes as its urease operon has been well studied and the bacterium has proven to produce ecologically stable bioconstruction materials. The ability to clone the urease operon of S. pasteurii into the model B. subtilis would create an engineered ureolytic organism whose urease activity could be controlled. This control would enable the CaCO3 morphology and material properties to be tailored and would create a truly responsive biomaterial.
Multidrug and efflux transporters of the model microbe Dictyostelium
Authors: T. Ferrara Billy , Mounir Saleh Salma , P. Thompson Elinor
Published: July 2020

The evolutionarily ubiquitous multidrug and toxin efflux (MATE) proteins mediate anticancer and antibiotic resistance, while transporting toxins, ions and flavonoids in plants. MATEs of the model amoeba Dictyostelium discoideum have not been studied although sequences of its pair group with the two Homo sapiensMATEs. Ddmate1 and 2 are both transcribed, Ddmate2 more so, with peaks in vegetative and slug life-cycle stages. Ddmate1 was upregulated in response to a toxin, ethidium bromide, at the lowest concentration tested. Removing MATE function by inhibitor or mutation increased intracellular levels of various compounds, confirming these as efflux transporters. Plasma membrane localisation was revealed using a GFP-MATE1 reporter-line. MATE1 and MATE2 phenotypes indicated roles beyond detoxification: on Klebsiella lawns these mutants produced significantly smaller plaques than WT, and their axenic growth rates were also lower. The transporters’ impact on use of Dictyostelium for novel drug research was tested using flavonoids. LCMS and fluorescence-imaging revealed differential flavonoid uptake. Flavanones such as naringenin did not cross into cells, whereas flavonols localised to mitochondria and cytoplasm. Ddmate1 transcription was upregulated, however, in response to naringenin, which is known to reduce levels of kidney-disease protein PKD2 in both Dictyostelium and animal cells. Increased flavonol intracellular concentrations confirmed that efflux not import was impeded in MATE1 and MATE2, and kaempferol therefore further reduced MATE1-cells’ growth. These D. discoideum MATEs may usefully model the HsMATEs, aid understanding of flavonoids’ effects, and should be considered when using this model eukaryote to screen drugs.
Comparison of the distribution and diversity of antimicrobial resistance genes between wild and commercially available Atlantic Mackerel
Authors: Mompel Daniel , Watts Joy , Hale Michelle
Published: July 2020

The global uncontrolled rise of antimicrobial resistance (AMR) is a major societal threat and it is well documented that AMR is already negatively affecting healthcare and intensive livestock farming systems. Nonetheless, capture fisheries are still essential to the global food supply providing over 50% of the world’s aquatic organism production. To facilitate improved management, it is therefore imperative that we better understand reservoirs of AMR and how gene transmission occurs in the aquatic environment. In order to discern which AMR bacteria and genes are present in the marine environment, sediment and seawater samples were collected and Atlantic Mackerel were captured at the beginning of summer and autumn in the Solent Strait (Portsmouth, U.K). In addition, commercially available Atlantic mackerel were purchased at a local fish market. Using culture-dependent techniques we obtained more than 700 bacterial and 20 fungal isolates from skin, intestinal lining, and intestinal content. Ten different cefotaxime-resistant Pseudomonas spp. were isolated from the seawater and market fish skin samples, and one cefotaxime-resistant Rhanella sp. was isolated from wild fish digesta. Results from ongoing whole-genome shotgun metagenomics analysis will be discussed, as well as the connection between AMR bacteria and AMR gene presence within the marine coastal environment and the local fish markets, which are the last link between capture fisheries and consumers.
Characterisation of the antimicrobial mode of action of gallium maltolate
Authors: Piatek Magdalena , Griffith Darren , Kavanagh Kevin
Published: July 2020

To human health worldwide. Existing treatments are becoming inefficacious and therefore there is an urgent need for the development of treatments with alternative modes of action. The use of gallium as an antimicrobial agent has been of interest due to its unconventional mode of action involving the inhibition of iron acquisition and metabolism. The structural similarity and inability to reduce from a trivalent to divalent form under normal physiological conditions allows gallium to act as an iron mimetic and inhibit many iron-dependent biological pathways, respectively.

The antimicrobial potential of gallium maltolate (GaM), Ga(III) coordination complex of maltol, was investigated on the opportunistic pathogen Pseudomonas aeruginosa. In vitro and in vivo analyses using Galleria mellonella (greater wax moth) larvae demonstrated the potent bacteriostatic and non-toxic effect of the complex. Subsequent analysis of GaM treated P. aeruginosa via label-free quantitative proteomics provided an insight into the intrinsic mechanisms of action of GaM. Increased expression of iron-storage protein Bacterioferritin B, the HemO component of iron-sulfur clusters and several stress response proteins (Chaperone Proteins ClpB, HtpG and DnaJ) indicate cell stress in response to inhibited iron uptake. Decreased expression of LasA Protease and LasB Elastase quorum-sensing proteins and flagellar motility proteins FlgM and FlgG further demonstrate the growth inhibitory effect of GaM. These findings provide a basis for a better understanding of the mode of action of GaM, a requirement for the improvement of synthesis and efficacy of the treatment.
Dehalogenation of brominated phenolic compounds by environmental microorganisms
Authors: Lamb Claire , Watts Joy
Published: July 2020

Halogenated compounds constitute one of the largest groups of environmental pollutants and are a worldwide issue accumulating readily across even remote environments. Contamination by halogenated flame retardants such as polybrominated diphenyl ether (PBDE) is widespread, including marine and freshwater sediments, soil and human tissue. This has been hypothesised to lead to multiple health issues following exposure such as endocrine disruption and immune system alterations. Despite a recent reduction in use, PBDE containing products will continue to leach into the environment for years. Marine sponges are a natural reservoir of brominated compounds and dehalogenation activities of the associated microbiota have been previously observed. It has been postulated that mechanisms for microbial mediated degradation of halogenated compounds also exist within environmental samples commonly contaminated by PBDEs, for example widespread areas of soil sediment. In order to detect and investigate the dehalogenation capabilities of environmental microorganisms, sediment samples from recycling plants have been used to create microcosms with various PBDE congeners (PBDE 47, 99, 153, 209) added, to establish bacterial communities in the laboratory associated with potential PBDE degradation. Once dehalogenation is detected characterisation of debrominating communities from environmental samples will be performed using microbial community 16S rRNA community profiling and QRTPCR. This will provide valuable insight to bacterial communities associated with haloaromatic degradation and further useful information for potential bioremediation of PBDE contaminated soils and sediments.
‘Seq & Destroy’: the full genome sequencing of archived wild type and vaccine rinderpest virus isolates prior to their destruction
Authors: King Simon , Rajko-Nenow Paulina , Ropiak Honorata , Ribeca Paolo , Batten Carrie , D. Baron Michael
Published: July 2020

Rinderpest, a once much feared livestock disease, was declared eradicated in 2011, however virus-containing material is still held in laboratories worldwide. Prior to the destruction of our institute’s stocks, we determined the full genome sequence of the distinct samples of rinderpest virus (RPV) in our repository. This data would decipher the historical epidemiology of RPV and allow for recovery of the virus should the need arise.

For each sample (n=123), sequencing libraries were prepared using either transposon-based fragmentation of cDNA (Nextera XT DNA Library Prep kit) or single primer isothermal amplification (Trio RNA-Seq kit) and sequenced on the Illumina MiSeq. Regions of low or no coverage were re-sequenced using a Sanger sequencing approach.

Examination of the sequences of RPV isolates has shown that the African isolates form a single disparate clade, rather than two separate clades as was previously believed. We have also identified two groups of goat-passaged viruses which have acquired an extra 6 bases in the long untranslated region between the matrix and fusion protein coding sequences, and a group of African isolates where translation of the fusion protein begins from a non-standard start codon (AUA). In addition, the viruses that were force-passaged through alternate hosts such as rabbits or goats, appear to diverge from the clades that represent viruses which were maintained in the wild.

Our unique set of sequence data will be invaluable for forensic epidemiology investigations in the event of an unforeseen outbreak and aid in the understanding of the evolution of related morbilliviruses.
Prevalence of Tinea unguium (Onychomycosis) in Toe Nails of boot wearing group (The Footballers) in Owerri, Imo State. Nigeria
Authors: Ohalete Chinyere , Dike-Ndudim Joy , Njokuobi Treasure
Published: July 2020

Foot mycoses are a frequent disease that represents a public health problem worldwide. This study aims to evaluate the epidemiology of foot mycoses among footballers in Owerri, Imo State, in order to determine the fungal etiological agents and to identify possible risk factors. To investigate the treatment and preventive measures for the susceptible groups. A total of 485 samples were collected; tinea unguium were confirmed in 88.2% of cases. A prospective study of fifty footballers was undertaken during one year (2018-2019). A complete mycological diagnosis was carried out on all footballers. The results obtained showed that out of the 50 toe nails samples of footballers examined, 28(56.0%) had positive cases of the infection on direct microscopy which served as the screening test. The causative pathogens of Onychomycosis isolated from fungal culture are dermatophytes , and the most frequent pathogen was Trichophyton rubrum 15(30.0%), yeast Candida albicans 9(18.0%). Non-dermatophyte molds were observed in 8(16.0%) cases and Fusarium sp. was the frequent genus 14(28.0%)and Aspergillus sp. 4(8.0%). The main predisposing factors of fungal foot infections were practicing ritual washing (56.6%) and frequentation of communal showers (50.5%). Confirmatory test such as germ-tube test was done on the Candida albicans isolate for proper identification. The age group 31- 35 years had the highest prevalence of onychomycosis 12(92.31%) and age group 16-20 years presented the lowest prevalence of onychomycosis 4(28.57%). Proper care of toe nails and boots is necessary to prevent the increasing rate of this infection.
Metagenomic mining of novel/innovative commercial glycoenzymes
Authors: Valancauskaite Mingaile , Black Gary W. , Charnock Simon J.
Published: July 2020

In biological science, metagenomics has revolutionised the process of drug discovery. This is because metagenomics serves as a tool for in depth characterisation by examining, sequencing, replicating and identifying the whole DNA/genome collected from any mixed population (Mahapatra et al., 2019). Metagenomics is used to study Carbohydrate Active Enzymes (CAZymes) containing microbial communities due to molecular-based culture-independent methods (Kunath et al., 2017). CAZymes are made of multiple domains; each domain serves as the key mediator for a specific function for the protein and structure. In the Carbohydrate-Active enZYmes (CAZy) database 20% of all protein domains are identified as domains of unknown function (DUFs). DUFs are mostly ignored due to not being the most abundant in many genomes. However, in a paper by Goodacre 2014, DUFs are shown to be essential and likely related to the organism survival function due to their relation to essential proteins(Goodacre et al., 2014). In the CAZy database multiple DUFs are associated with catalytic CAZyme domains, which could result in them having a similar function or increase their catalytic activity. We present DUFs that are considered to have the capability to help CAZymes break down polysaccharide chains and tools/methods we used to achieve these results.
A comparative approach to understanding selection on extracellular secretion
Authors: Dewar Anna , Thomas Joshua , Ghoul Melanie , Griffin Ashleigh , West Stuart
Published: July 2020

Many bacterial genes encode proteins that are secreted extracellularly. These proteins can be considered cooperative because all surrounding cells can benefit from their production. Therefore, it has been hypothesized that these cooperative genes would more frequently lie on mobile elements, such as plasmids, which can transfer to other cells. This could stabilise cooperation, leading to the prediction that plasmids should carry proportionally more cooperative genes than the less mobile chromosome. However, it is unknown whether this prediction holds across the bacterial tree of life. To address this, we analysed the gene content of the chromosome and plasmid(s) of 1620 genomes comprising 51 diverse bacterial species. We find that across species analysed, plasmids do not carry proportionally more cooperative genes than the chromosome. Contrary to prediction, the role of mobile elements in promoting cooperative behaviour is highly variable across bacterial species.
Uncovering the molecular mechanisms of the Pseudomonas aeruginosa PA14 response to myxobacterial predation
Authors: Sydney Natashia , Whitworth David , Tucker Nicholas
Published: July 2020

Myxobacteria are Gram-negative bacteria, notable for their predatory and antimicrobial activities, which dictate the outcomes of their interactions with neighbouring organisms. They are abundant and widespread in nature, and can significantly affect the microbiome of an environment.

We hypothesise that there are underlying molecular mechanisms in prey specieswhich govern the prey’s susceptibility/resistance to the antimicrobial activity of myxobacteria. In this work we attempt to define the mechanisms by which Pseudomonas aeruginosa PA14 resists predation bythe model myxobacterium Myxococcus xanthus.

Pseudomonas aeruginosa is an opportunistic pathogen of humans and plants. With the rise in antibiotic resistant organisms, Pseudomonas spp. are categorised as World Health Organisation priority 1 antibiotic-resistant bacteria and are our prey of choice in this study.

In collaboration with Dr N. Tucker (Strathclyde), and using a strain of M. xanthus expressing mCherry (courtesy of E. Hoiczyk, Sheffield), we developed 96-well plate assays of predation which measured the optical density of both predator and prey and the florescence of predator at different point intervals. Predation was assayed againsta library of approximately 5700 PA14 mutants to identify strains with increased/decreased susceptibility to predation. Responses of PA14 mutants varied with time and between mutants, allowing us to create a shortlist of candidate genes involved in the prey response to predation.

We are currently performing a preliminary analysis of the data using the Integrated Genomic Viewer and Circos plots to assess the genomic organisation of the prey genes that influence susceptibility and resistance to predation.
Investigating selection for antimicrobial resistance by non-antibiotic drugs (NADs)
Authors: Hayes April , Feil Edward , Kasprzyk-Horden Barbara , Snape Jason , Zhang Lihong , Gaze William , Murray Aimee
Published: July 2020

A recent study screening over 1000 drugs has shown that non-antibiotic drugs (NADs), including human targeted drugs, have been shown to have antimicrobial effects on representative strains of human gut bacteria. NADs are present in both wastewater effluent and freshwater systems, where they may only be partially metabolised. Concentrations of antibiotics found in the environment have been shown to select for resistance in complex microbial communities, and it is thought that concentrations of NADs in the environment may also select for resistance. This project aims to determine if NADs select for antimicrobial resistance, by investigating effects in a complex bacterial community. Pharmaceuticals from 7 different drug classes have been screened for antimicrobial activity. The most potent compounds will be used in exposure experiments to identify any existing antimicrobial resistance genes that confer cross-resistance to both antibiotics and NADs using a metagenomics approach. In addition, changes in community composition will be investigated to determine if there is enrichment for opportunistic pathogens after exposure to NADs. This project ultimately aims to inform on environmental water quality standards and environmental risk assessment of wastewater treatment effluent in order to mitigate the growing problem of environmental antimicrobial resistance.
Next generation sequencing and in vivo pathogenicity study of multidrug-resistance efflux pump genesoqxAB-encoding plasmids in Escherichia coli
Authors: Lau Andes , Cao Huiluo , Chun-Jian Liu Melissa , Tong Man-Ki , Chow Kin-Hung , Ho Pak-Leung
Published: July 2020

Background: Multidrug-resistant efflux pump genes oqxAB-encoding plasmids are wildly disseminated in livestock, and also identified in human samples. Giving the high presence in environment and multidrug-resistant nature of oqxAB, deeper understanding of oqxAB-encoding plasmids is necessary.

Objective: To investigate the prevalence, virulence, and phylogenetic of oqxAB-encoding plasmids.

Method: A total of 43 oqxAB carrying Escherichia coli were isolated from human and livestock from China and Hong Kong, these isolates were characterised by disc-diffusion susceptibility test and PCR. The 43 samples were sequenced using PacBio or Illumina platforms, and analysied with five oqxAB-encoding plasmid sequences extracted from Genbank. in vivo pathogenicity study performed by injecting E. coli J53 transconjugants containing oqxAB plasmid into Galleria mellonella larvae.

Result: Among the 48 oqxAB-encoding plasmids, 27 were IncFII F18 plasmids, 12 F16 plasmids, six F33 plasmids, two F24 plasmids, and one F14 plasmid. Virulence regions in plasmids with same Inc group encoded similar set of virulence factors and antibiotic resistance genes. Co-existence of blaCTX-M, fosA3, and oqxAB genes was identified in all F33 plasmids and one F18 plasmid. in vivo pathogenicity study suggested oqxAB plasmids caused significant health deterioration in larvae but no significant increase in death.

Conclusion: Our data shows similar sets of pathogenic factors are frequently co-carried by oqxAB plasmids of same Inc group, suggesting high correlation between plasmids identified from China and Hong Kong. Co-existence of fosA3, blaCTX-M, and oqxAB suggests resistance to most clinical antibiotics. in vivo test indicates oqxAB plasmid can increase pathogenicity of the host bacteria.
Machine learning models to identify patient and microbial genetic factors associated with carbapenem-resistant Klebsiella pneumoniae infection
Authors: Lapp Zena , Han Jennifer , Lautenbach Ebbing , Snitkin Evan
Published: July 2020

The World Health Organization considers carbapenem-resistant Enterobacteriaceae (CRE) an urgent public health threat due to global prevalence, limited treatment options, and high mortality rates. Carbapenem-resistant Klebsiella pneumoniae (CRKP), the most common CRE species, is especially prevalent in long-term acute care hospitals (LTACHs) in the United States. Among patients colonized with CRKP, only a subset develop clinical infection. We used CRKP whole-genome sequences and associated clinical metadata from unique patient samples from 20 LTACHs (n=366) to (1) identify both clinical and microbial features associated with infection compared to colonization, and (2) evaluate the contribution of microbial features in infection prediction. Modifiable clinical features associated with infection could inform clinical practice, while microbial features could help predict clinical infection. We performed L2 regularized logistic regression 100 times for each feature set. Clinical predictors of infection include having a central line or gastrostomy tube. Genomic predictors of infection include iron scavenging genes (known to be associated with invasive infections in healthy hosts) and the number of antibiotic resistance genes. Furthermore, we found that clinical and genomic features (separate or combined) have similar predictive power (AUROC IQRs: clinical=0.56-0.64, genomic=0.54-0.63, combined=0.59-0.67). This suggests that genomic features may be associated with certain clinical features. These results provide insight into potential clinical and microbial drivers of CRKP infection in LTACH patients and provide a starting point for investigating the biological basis of infection, identifying patients at high risk of infection, and devising targeted strategies to prevent infection.