bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibacterial Action of Visible 405-nm light for Bacterial Reduction in Blood Plasma
Authors: Stewart Caitlin Fiona , Ralston Heather , MacPherson Ruairidh , Wilson Mark , MacGregor Scott , Atreya Chintamani , Maclean Michelle
Published: May 2022

The introduction of risk prevention measures, such as blood screening and donor deferrals have dramatically reduced the incidence of transfusion-transmitted viral infections. Nevertheless, bacterial contamination of blood transfusion products remains a concern to patient health, and a range of pathogen reduction technologies have been developed to reduce this risk. Visible violet-blue light, in the region of 405-nm, has recently demonstrated potential for in situ treatment of ex vivo stored plasma and platelet products, without the need for additional photosensitizers.

This study assessed the broad-spectrum efficacy of 405-nm light against a range of bacteria implicated in transfusion-transmitted infections: Staphylococcus aureus, Staphylococcus epidermidis, Bacillus cereus, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniaeandYersinia enterocolitica. Plasma was seeded with clinically-relevant low-level bacterial contamination (102-103CFUmL-1) and exposed to a 405-nm light dose of 360 Jcm-2 (1-hr at 100mWcm-2) using a small-scale exposure system. Broad spectrum antibacterial efficacy was observed, with 99.0 – 100% inactivation achieved for all bacterial species tested. Bacterial inactivation tests were then scaled-up to expose large volumes of prebagged plasma seeded with S. aureusat ~103 CFUmL-1, to 22mWcm-2 405-nm light, under agitation, (≤396 Jcm-2). Successful bacterial inactivation was observed using the large-scale exposure system, with a dose of 238 Jcm-2 (3-hr at ~22mWcm-2) achieving complete (3.5-log10) reductions in prebagged bacterial-seeded plasma (P=0.001). Results from this study support further development of visible 405-nm light technology as a bactericidal tool for application in transfusion medicine.

This abstract reflects the views of the author and should not be construed to represent FDA’s views or policies.
Diversity and dynamics of particle-associated and free-living bacteria in eelgrass (Zostera marina) bed along the coast of Japan
Authors: Iqbal Md Mehedi , Nishimura Masahiko , Sano Masayoshi , Yoshizawa Susumu
Published: May 2022

As the seagrass leaves remain underwater, the primary source of leaf microbes is considered to be seawater heterotrophic bacterioplankton, which possess the ability to degrade biopolymers and are known to attach to surface and form biofilms. In this study, 16S rRNA gene amplicon sequencing was used to assess bacterial diversity and dynamics of the particle associated (PA) and free-living (FL) fraction of the seagrass-covering seawater (inside) and bulk seawater (outside) among different seagrass bed around Japan. Samples were collected from the three Zostera marinabeds (Ikuno-shima Is., Hiroshima; Nanao Bay, Ishikawa; Mutsu Bay, Aomori Prefecture) around Japan during summer (June-August 2015; July 2016). Prokaryotic DNA was extracted from samples using a FastDNA spin kit according to the manufacturer’s protocol. After extracting DNA, 16S ribosomal RNA (16S rRNA) genes were sequenced by Illumina Miseq platform. The Results showed that PA bacterial communities had a higher (p <0.001) diversity than FL ones. Compared to the outside of the seagrass bed, the inside had lower diversity both in PA and FL fraction. Taxonomic analysis revealed a different community composition between lifestyle (PA vs FL) and sampling point (inside vs outside). Differential abundance analysis showed that PA were significantly enriched in a diversity of Cyanobacteria (Synechococcaceae), Saprospiraceae and Hyphomonadaceae. Conversely, FL were more abundant in Gammaproteobacteria (including Halomonadaceae, Alteromonadaceae), Microbacteriaceae, Campylobacteraceae, Pelagibacteraceae,Acidimicrobiia(OCS155). The present data provide a comprehensive description of the PA and FL microbial community in the seagrass bed and can be useful for better understanding the seagrass microbe interactions.
Synergistic biodegradation of a compostable film by a marine microbial community
Authors: Meyer-Cifuentes Ingrid E. , Öztürk Başak
Published: May 2022

Background

The need for replacing conventional plastics has led to an increase of the use biodegradable plastics. Most biodegradable plastic materials are certified for compostability, and their degradation mechanisms by marine bacterial communities, are still largely unknown.

Methods

Bacterial communities that degrade a poly (butylene adipate-co-terephthalate)-based biodegradable film (PF) were enriched from marine samples. DNA, RNA and proteins were extracted simultaneously from the biofilm and free-living bacteria. Genes of hydrolases similar to the ones involved in polyethylene terephthalate (PET) and monoester mono-2-hydroxyethyl terephthalate (MHET) degradation (PETase and MHETases, respectively) were detected. A MHETase-like gene (Mle046) was then recombinantly expressed. The activity of Mle046 was tested against the end product of PET and PF degradation: MHET and 4-(4-hydroxybutoxycarbonyl) benzoic acid (Bte), respectively. The optimal incubation temperature and pH of Mle046 activity was determined.

Results

PETase-like (Ples) and MHETase-like (Mles) hydrolases and other enzymes needed for PF degradation were expressed within the microbial community. Within the biofilm, Ples were abundant and upregulated while Mles and terephthalate dioxygenases were abundant in the free-living fraction. Mle046 was the only Mle produced in this fraction and it was highly expressed. The purified Mle046 could degrade MHET and Bte. The optimum temperature of Mle046 activity was 20°C.

Conclusion

PF degradation is achieved synergistically by labour division among film-attached and free-living bacteria. Understanding the biodegradability of these plastics will facilitate the development of more degradable materials. In addition, the discovery of new PETases- and MHETases-like enzymes will enable their future use in plastic recycling.
Examining Phosphate Physiology in Coccolithophore Life Cycle Stages
Authors: Sturm Daniela , Wheeler Glen , Brownlee Colin , Tyrell Toby
Published: May 2022

Despite the significance of coccolithophores for biogeochemical cycling, much of their ecology remains poorly understood. In particular, their elusive haplo-diplontic life cyclehas been given little attention in the literature. Yet, it significantly impacts the extent of coccolithophore calcification, their vertical and horizontal distribution in the ocean, and potentially their global success.

The aim of this project is to establish physiological differences between the life cycle stages of the ecologically important coccolithophores Coccolithus braarudiiandCalcidiscus leptoporus in response to changes in the essential macronutrient phosphorus (P). Haploid coccolithophores are more commonly found in P-limited environments, raising the question which underlying mechanisms cause this variable distribution between life stages.

An initial investigation of growth, photophysiology, calcification, and storage of polyphosphate under P-limited conditions will determine which parts of coccolithophore physiology are heavily impacted by P-limitation. An in silicoanalysis of P acquisition and transport genes in coccolithophores and other closely related eukaryotes will highlight differences in P physiology among these groups. Comparing proteins expressed in haploid and diploid coccolithophores under P-limitation will then be used to reveal whether P acquisition strategies differ between the two life stages.

These results will further shed light on potential adaptations of haploid and diploid coccolithophores to different ecological niches. A profound understanding of coccolithophore physiology is vital to revealing their evolutionary success and their impact on ocean biogeochemistry and ecology.
Polyesterase activities in bacterial isolates from seaweed and sponges, with potential utility in polyethylene terephthalate plastic and nanoparticle hydrolysis
Authors: Carr Clodagh M. , Clarke David J. , Dobson Alan D. W.
Published: May 2022

Many marine bacteria have evolved to produce a range of extracellular enzymes which facilitate their growth and survival in the harsh, oligotrophic conditions often present in marine environments. Marine sponge derived Streptomycesstrains have previously been reported to produce polyesterase enzymes, which are of interest for several biotechnological applications, including polyethylene terephthalate (PET) plastic hydrolysis.

Bacteria isolated from sponges and seaweed were screened for polyester hydrolysis activities using plate-clearing assays. Lipolytic and polyesterolytic activities were initially identified by employing tributyrin and polycaprolactone diol agar-based assay systems, respectively. Polyesterase activity was subsequently confirmed on both polycaprolactone and on PET-nanoparticle agar plates, resulting in the prioritisation of six isolates for Illumina next-generation genome sequencing.

These include three Bacillusspp., isolated from the brown seaweed Ascophyllum nodosum,and from marine lake sponges Stelligera stuposaand Eurypon major, together with a Maribacterstrain again isolated from S. stuposa, and Brachybacteriumsp. and Micrococcussp. isolates of deep-sea sponges Pheronemasp. and Inflatella pellicula, that were sampled at depths of 2129m and 2900m, respectively. Genome mining and comparative genomic analysis of these isolates is currently underway to identify genes encoding the observed activities and to assess homology with known PET hydrolases.

Microbes found living in association with filter-feeding sponges may have increased exposure to the plastics and microplastics that widely contaminate our marine ecosystems, thus representing a promising source of degradative activities towards synthetic polymers that could contribute to new plastic waste management strategies.
Beyond fluorescein: Use of fluorescent protein calibrants for direct and absolute quantification of protein production in synthetic biology
Authors: Csibra Eszter , Stan Guy-Bart
Published: May 2022

While inter-lab calibration standards are approaching mainstream usage in synthetic biology, such calibrations are not in fact sufficient for absolute protein quantification required for modelling synthetic circuits. Fluorescein-based calibration of plate reader and flow cytometry instruments allows the measurement of green fluorescent protein (GFP) in synthetic cells to graduate from arbitrary units to calibrated units, but retains important caveats. Fluorescein is only a good calibrant for green FPs, leaving other FPs uncalibrated, and only provides conversions to units of brightness, not to molecule numbers.

Ideal assay calibrants in molecular biology consist of the same molecule as the one to be measured – in this case, a purified preparation of the appropriate fluorescent protein. Here we show that by using purified FP calibrants, all protein species in a synthetic circuit can be quantified in absolute terms using no advanced instrumentation. We develop a SEVA (Standardised European Vector Architecture)-based expression vector that allows the high-level production of soluble protein and describe a straightforward 2-day protocol for the purification of micrograms of FP, followed by a calibration that relates fluorescence activity to protein mass.

We validate this protocol by calculating conversion factors for a panel of commonly-used FPs including superfolder GFP, mCherry, mScarlet-I and mTagBFP2 on multiple laboratory instruments, and use these calibrations to debug synthetic circuits. We also demonstrate that the suspected bias of the presence of mCherry on OD600 measurements is real, but in practice requires extreme overexpression (~100,000 proteins per cell) to have a meaningful impact on cell density estimates.
4000 metres closer to novel antibiotics: a bioprospecting tale of three Streptomyces strains from the Andes
Authors: Pintor-Escobar L. , Zambrano M. M. , Fernández-Martínez L. T.
Published: May 2022

Bioprospecting of underexplored environments and microbiomes remains one of the core strategies for drug discovery. Páramos, a high-altitude ecosystem and evolutionary hotspot in the northern Andes of South America, harbour microbial diversity yet to be studied for its potential for antibiotic production. In this project, three strains (CG885, CG893 and CG926) isolated from a páramo in Colombia were explored using phylogenetic and genome mining tools to uncover their potential for novel antimicrobials. Taxonomic characterisation of three isolates suggested strains CG885 and CG893 can be classified as Streptomyces pratensis while strain CG926 is likely to be a new Streptomyces species. All three strains showed the biosynthetic coding capacity characteristic of streptomycetes and a diverse repertoire of biosynthetic gene cluster types likely to encode for novel specialised metabolites. One cluster in the strain CG926, for instance, is predicted to encode for a new halogenated compound containing the unusual nonproteinogenic amino acid piperazic acid with no known analogue. Integration of these results with phenotypic and metabolomic data will enable the assessment of these molecules and their antimicrobial activity. Overall, these results demonstrated that these three strains from an underexplored environment harbour the potential to become producers of novel antibiotics.
Insights into Otitis Media: Dissecting the interaction of C-Reactive Protein with Non-Typeable Haemophilus influenzae
Authors: Bharj Gurpreet , Vikhe Pratik , Brown Steve , Hood Derek
Published: May 2022

Otitis Media (OM) is the inflammation of the middle ear (ME). Non-typeable Haemophilus influenzae (NTHi) is one of the leading otopathogens in causing OM. Phosphocholine (PCho) on the NTHi lipopolysaccharide influences host-pathogen interaction. C-Reactive Protein (CRP), an acute phase protein recognizes PCho, and can mediate bacterial killing. However, some strains of NTHi survive even in the presence of CRP. We aim to study the interaction of CRP with NTHi to understand its role in bacterial survival and OM.

NTHi can efficiently infect the Junbo mouse, a characterised model of chronic and acute OM. CRP levels were highest 1 day post-intranasal inoculation in the ME fluid (MEF) and nasal passage (NP) washes. We show CRP is a localized response to NTHi as serum CRP levels were unaffected in NTHi inoculated and non-inoculated mice at 1, 3 and 7-day post intranasal inoculation. Further, we confirm the presence of NTHi influences CRP levels in the MEF and NP washes. We show CRP binding is influenced by the position and expression of PCho on the NTHi surface. Serum bactericidal assays indicate that the expression and position of PCho affects NTHi survival. The removal of CRP from the serum restores NTHi survival. The expression of PCho also influences opsonophagocytosis activity in macrophages, thereby confirming the importance of PCho in NTHi survival.

The CRP-NTHi interaction is currently under investigation to advance our understanding of its role in the complex biological processes that influence bacterial killing and the onset, progression and resolution of OM caused by NTHi.
A potential new paradigm of denitrification in Neisseria gonorrhoeae
Authors: Bolton Jack , Djoko Karrera
Published: May 2022

Metals are bacterial nutrients. Upon infection by microorganisms, the animal host innate immune system typically reduces the availability of metals. In response, bacterial pathogens can activate pathways for metal uptake to avoid metal starvation. This competition for metals at the host-pathogen interface is termed “nutritional immunity”.

We are interested in how the obligate human pathogen Neisseria gonorrhoeae acquires nutrient copper (Cu). This Gram-negative bacterium expresses several respiratory cuproenzymes that are required for growth and metabolism in both aerobic and anaerobic conditions. These cuproenzymes include the putative nitrous oxide reductase (NosZ). NosZ contains 12 Cu atoms per functional dimer and it catalyses the reduction of nitrous oxide (N2O) to dinitrogen (N2). This reduction is an intermediate step in the denitrification pathway, in which nitrite (NO2-) is used as the terminal electron acceptor for respiration instead of O2. In this project, we will determine whether NosZ is expressed as a functional enzyme in N. gonorrhoeae. We will then examine how this enzyme acquires nutrient Cu and subsequently assembles its active site.

Given the rise in antibiotic resistance and the worldwide recognition of multidrug-resistant N. gonorrhoeae as a major threat to public health, we hope that a fundamental understanding of the physiology and metabolism of this organism will yield new strategies for anti-infectives, for instance by manipulating Cu availability at the site of infection.
Cell-to-cell ATP differences can modulate cellular decision-making
Authors: Kerr Ryan , Jabbari Sara , Johnston Iain
Published: May 2022

Cells generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. Functionally vital cell fate decisions from a range of phenotypic choices are made by regulatory networks, the dynamics of which rely on gene expression and hence depend on the cellular energy budget (and particularly ATP levels). However, despite pronounced cell-to-cell ATP differences observed across biological systems, the influence of energy availability on regulatory network dynamics is often overlooked as a cellular decision-making modulator, limiting our knowledge of how energy budgets affect cell behaviour. Here, we consider a mathematical model of a highly generalisable, ATP-dependent, decision-making regulatory network, and show that cell-to-cell ATP variability changes the sets of decisions a cell can make. Our model shows that increasing intracellular energy levels can increase the number of supported stable phenotypes, corresponding to increased decision-making capacity. Model cells with sub-threshold intracellular energy are limited to a singular phenotype, forcing the adoption of a specific cell fate. We suggest that energetic differences between cells may be an important consideration to help explain observed variability in cellular decision-making across a broad range of biological systems, including bacteria and the blood stem cell system.

*NOTE: Our work is highly interdisciplinary and if you believe it would be better suited to another topic area, then I would be delighted to discuss that further.
Regulatory mutants of Serratia with modulated antibiotic production due to intergenic transposon insertions
Authors: Plaza Daniel , Salmond George
Published: May 2022

Antibiotic resistance is an increasing problem, exacerbated by global dissemination of drug resistance genes under selection pressure. Moreover, the rate of new antibiotic discovery declined over previous decades and so there is a growing need for new antibiotic discovery and a deeper appreciation of the various genetic and physiological factors that influence antibiotic biosynthesis.

The enterobacterium Serratia sp. ATCC 39006 (Serratia) is a useful model for studies on the biosynthesis and regulation of bioactive secondary metabolites, including two antibiotics - a carbapenem and prodigiosin. Both compounds are tightly regulated in response to various physiological and environmental signals, including quorum sensing.

We have identified novel regulators of antibiotic production after random transposon mutagenesis. Multiple regulatory mutations mapped to a small locus defining an intergenic region (IGR). These IGR insertion mutants display elevated production of both the carbapenem and prodigiosin antibiotics and they also exhibit reduced motility, confirming pleiotropic impacts. Exploiting phage transduction, we constructed double mutants with 15 known Serratia regulators and showed that the IGR mutant phenotype was epistatic over several of these. Further analysis suggested the presence of a putative gene encoded within the IGR locus, which may play an impactful role in the intricate regulatory network. Functional characterisation of the IGR region and its physiological impacts in both the modulation of antibiotic production and in wider pleiotropy were dissected. Mechanistic understanding of the regulatory mechanisms involved may prove exploitable in enhancing controlled antibiotic hyperproduction.
Localization dynamics of N-acetylglucosamine transporter, Ngt1 in Candida albicans
Authors: Roy Kasturi , Ghosh Swagata
Published: May 2022

The amino sugar N-acetylglucosamine (GlcNAc), widely present in multiple cell-surfaces is efficiently utilized by human pathogen Candida albicans at the sites of infection as a survival strategy in different host niches. GlcNAc import inside the cell is mediated by GlcNAc transporter, Ngt1. In this present study, to investigate the Ngt1 dynamics, we have checked the sensitivity of Ngt1 for GlcNAc, expression kinetics and dynamics of Ngt1, stability of Ngt1 in the presence of unrelated carbon source like, glucose and endocytic trafficking of Ngt1. For this study we have used epi-fluorescence microscopy, Western blot and Northern blot analysis. We have observed that Ngt1 expression is prolific and highly sensitive to even minute amount (<2 μM) of GlcNAc. Ngt1 maintains its turnover in the plasma membrane by sugar stimulated endocytosis via UBI4 (polyubiquitin encoding locus) mediated ubiquitylation. Co-localization studies with different sub-cellular markers have revealed that Ngt1 follows a trafficking route via early endosome-late endosome-multi vesicular body (MVB)-Trans Golgi network for degradation. In conclusion, the study will provide a better understanding of endosomal trafficking for other membrane proteins in particular sugar transporters and also will open new therapeutic aspects in Candida albicans.
Back to soil: Awakening the production of cryptic antibiotics in Streptomyces
Authors: Schniete Jana Katharina , Paros Joseph , Fernández-Martínez Lorena
Published: May 2022

Most of the antibiotic biosynthetic gene clusters (BGCs) in Streptomyces are not expressed under laboratory conditions, however these clusters are maintained in the genomes, therefore indicating that they must play important roles in adaptation and survival within their ecological niches.

Understanding the global regulation patterns that affect transcription of antibiotic BGCs in soil conditions versus laboratory conditions allows us to identify novel routes for up- or down- regulation in order to trigger expression of these BGCs and therefore production of these antibiotics under controlled laboratory and fermentation conditions. Cryptic pathways represent an untapped resource in terms of new metabolites that could be very useful in the clinic if we can awaken their expression and production.

We are using RNA sequencing to analyse global transcriptional patterns of S. venezuelae and S. rimosus grown in sterile soil, non-sterile soil and standard laboratory solid medium, as well as using an unbiased metabolomics approach to identify compounds produced in soils. These results will enable the identification of global regulatory pathways that activate cryptic clusters in nature and lead to the production of these compounds in soil.

This will enable us to generate genetically modified strains engineered to increase the yield of both well characterised and cryptic clusters which encode potentially novel compounds under industrial fermentation conditions. It is worth noting that the transcriptional data may also help shed light on the complex regulation of the life cycle of these Streptomyces strains in an ecologically relevant environment.
How do Streptomyces coordinate DNA repair and cell division following DNA damage?
Authors: Stratton Kathryn , Bush Matthew , Chandra Govind , Findlay Kim , Schlimpert Susan
Published: May 2022

DNA damage often results in a pause of cell division until damage is repaired. In bacteria, a widely conserved response to DNA damage is the SOS response which relies on two proteins: the multifunctional recombinase RecA and the transcriptional repressor LexA. Under DNA-damaging conditions, this response activates proteins involved in DNA repair and the inhibition of cell division which in most unicellular bacteria results in temporarily filamentous growth. However, it is unknown how naturally filamentous growing bacteria like Streptomyces cope with DNA damage and how DNA damage repair is coordinated with cell division.

To identify novel regulators of cell division in Streptomyces that specifically function during DNA damaging growth conditions, we investigated the global response of Streptomyces venezuelae to several genotoxic agents, including mitomycin C, ciprofloxacin and methane methylsulfonate. To this end we have performed ChIP-seq experiments to identify the LexA regulon in Streptomycesandconducted RNA-seq experiments to determine the global response to DNA damaging agents in the wildtype and a recA mutant. The combined analysis of the available data sets has allowed us to obtain a comprehensive overview about the genes involved in the SOS response in Streptomycesand further analysis will enable us to understand how damage repair and cell division are coordinated in these bacteria.
Global diversity and potential functioning of prophages in plant pathogenic Ralstonia solanacearum bacterium
Authors: Greenrod Samuel , Stoycheva Martina , Friman Ville-Petri
Published: May 2022

Ralstonia solanacearum is a destructive plant pathogenic bacterium which harbours a wide variety of virulence genes allowing it to infect over 200 plant species worldwide. Its virulence is also affected by the presence of integrated bacteriophages, termed prophages. While several such prophages have been identified, the global distribution and diversity of R. solanacearum prophages is unknown.

To study this, we first identified prophages present in a diverse collection of 192 assembled R. solanacearum genomes. Prophage diversity was explored by calculating prophage genetic distances and clustering with characterised prophages in a neighbour-joining tree. Prophage clusters were further verified by assessing gene content, GC content, and prophage length. Prophage identities were determined using the NCBI Virus database, and prophage-encoded virulence genes identified by analysing pangenome content.

343 intact prophages were identified, forming ten prophage clusters with distinct gene content, GC content, and length profiles. Five prophage clusters, containing 159 prophages, belonged to the Inoviridae, Myoviridae, and Siphoviridae phage families. The remaining 184 prophages were uncharacterised and may therefore represent novel prophages. Transcriptional regulators with potential virulence effects were identified in three prophage clusters, including one uncharacterised cluster. These prophage clusters were unequally distributed throughout the R. solanacearum population being host genotype specific.

This research demonstrates that R. solanacearum contains a high level of uncharacterised prophage diversity and highlights novel prophages that could contribute to pathogen virulence. Given their potential host-genotype-specific virulence effects, R. solanacearumprophages could be co-evolving with their hosts, and may contribute to global variation in R. solanacearum virulence.
An interdisciplinary approach to reveal the dynamics of generalized transduction of antimicrobial resistance genes
Authors: Leclerc Quentin , Gupta Arya , Lindsay Jodi , Knight Gwenan
Published: May 2022

Background

Antimicrobial resistance (AMR) genes can spread between bacteria by “generalized transduction”, where phages act as vectors to transfer them. However, our knowledge of the dynamics of transduction and how to best represent them is limited. We aimed to fill this gap through an interdisciplinary approach, generating microbiological data and using mathematical models to clarify the underlying transduction dynamics.

Methods

We co-cultured two library strains of Methicillin-resistantStaphylococcus aureus, each harbouring a resistance gene for a different antibiotic, with 80α generalized transducing phage. We recorded numbers of bacteria and phages at multiple time-points over 24h, using the presence of bacteria resistant to both antibiotics as evidence that transduction occurred. We developed and compared mathematical models of transduction based on how well they fit to the lab data.

Results

After a growth phase of 8h, bacteria and phage surprisingly coexisted at a stable equilibrium in our culture, the level of which was dependent on the initial concentration of phage. The rate of transducing phage generation was approximately 10-6per lytic phage, sufficient to consistently generate double resistant bacteria, detectable after only 7h. Dynamics of transduction were best captured by a mathematical model in which the rate of phage infection slows as the bacteria population approaches carrying capacity.

Conclusions

The novel data and models generated provide valuable insights into the dynamics of transduction of AMR. This interdisciplinary framework could be extended to other bacterial species, and is the first step towards evaluating the impact of transduction on the overall public health consequences of AMR.
Immuno-proteomics of sera from gonorrhoea patients identified potential vaccine candidates
Authors: Dijokaite-Guraliuc Aiste , Humbert Victoria Maria , Skipp Paul , Christodoulides Myron
Published: May 2022

Gonorrhea is a sexually transmitted disease caused by Neisseria gonorrhoeae and is one of the leading reportable STDs in adults, with ~87 million cases annually and globally. Gonorrhoea remains a major global public health concern not only because of rising incidence each year, but also because of rising antimicrobial resistance. There is an urgent need for long-term solutions to prevent gonorrhoea such as vaccines, but none currently existand research is focused on identifying potential antigens for inclusion in new vaccines. In our study, we used an immuno-proteomics approach to try and identify potential vaccine candidates.

A heterologous N. gonorrhoeae strain P9-17 was grown under iron-limiting conditions and whole cell lysates prepared. These were separated by isoelectric focusing (pH 3-10 range) and fractions were separated by SDS-PAGE. Western blots were prepared and reacted with sera from 20 patients with uncomplicated gonorrhoea and with sera from 5 controls with no history of gonorrhoea. Immuno-reactive bands were excised from the corresponding gels and subjected to mass spectrometry, which provided a profile of gonococcal proteins. After comparing patterns of reactivity, we identified 180 bands in sera from gonorrhoea patients. Using a bio-informatics approach we refined the list to 18 bands of interest and identified 13 novel proteins associated with an increase in immuno-reactivity with gonococci.

In summary, we have identified a unique set of gonococcal proteins that have not yet been investigated as potential vaccine antigens and that are the focus of current studies to develop a gonococcal vaccine.
Investigation of the impact of food preservatives on avian pathogenicEscherichia coli(APEC) and their role in driving zoonotic disease
Authors: Fallata Ghaith , Wall Donal
Published: May 2022

The excessive use of antibiotics in agriculture is routinely described as a major contributor to bacterial antimicrobial resistance. Globally, antibiotics are also widely used as growth supplements in livestock. This has led to concerns regarding use of human-use antibiotics in food and food-producing animals. In more recent times organic acids such as propionic acid (PA) and formic acid (FA) have been used as alternative antimicrobials or preservatives in place of antibiotics.

PA is a short chain fatty acid naturally abundant in the human and animal intestine as a breakdown product of non-digestible carbohydrates. In the human intestine it plays important roles in regulating the immune response in the human body. Recently, a study has shown that exposure of a Crohn’s Disease associated bacterial pathotype, adherent-invasive Escherichia coli(AIEC),to PA significantly altered its phenotype resulting in increased adhesion and invasion of epithelial cells and increased persistence through biofilm-formation.

AIEC are both evolutionarily and phylogenetically related to avian pathogenicEscherichia coli (APEC). PA and FA use is widespread in chickens a known source of zoonotic disease. Our results indicate that virulence of some APEC strains is increased by exposure to alternative antimicrobials such as PA and FA. This included increased adhesion of APEC strain E. coli 601 to human intestinal epithelial cells after exposure to FA which could be a potential risk of zoonotic disease. Further investigation of APEC strains is currently underway in a fermentation model of the poultry gut. This approach will improve our understanding of how commonly used.
HCMV UL148 and UL148D regulate multiple immune pathways by impairing expression of ADAM17
Authors: Rubina Anzelika , Patel Mihil , Nightingale Katie , Fielding Ceri , Forbes Simone , Lau Betty , Nobre Luis , Miners Kelly , Price David , Roberts Dawn , Vlahava Virginia-Maria , Vojtesek Borivoj , Davison Andrew , Weekes Michael , Wilkinson Gavin , Stanton Richard , Tomasec Peter , Wang Eddie
Published: May 2022

Human cytomegalovirus (HCMV) is one of the most widespread, highly successful herpesviruses, establishing a life-long viral infection in humans. HCMV has been described as a paradigm of immune evasion able to manipulate many immune functions in the host. Here, we describe a novel, post-translational mechanism in which HCMV downregulates a disintegrin and metalloproteinase 17 (ADAM17), a ‘sheddase’ that cleaves and releases over 80 membrane-anchored cytokines, cell adhesion molecules and other receptors. A screen of HCMV deletion mutants identified UL148 and UL148D as the HCMV genes responsible for ADAM17 downregulation, working synergistically to alter ADAM17 levels in infected cells. We demonstrate that UL148/UL148D interfere with ADAM17 maturation, resulting in expression of only the intracellular immature precursor, and absence of mature ADAM17 on the surface of wildtype HCMV-infected cells. The consequences of ADAM17 downregulation by HCMV were analysed using proteomics and validated using biochemical and flow cytometric techniques, revealing impact on multiple cell surface and secreted host proteins. This included stabilisation of surface TNF Receptor 2, as well as Vasorin and Jagged1, which have recognised roles in Treg development. Other known ADAM17 targets were not stabilised, suggesting specific control by HCMV. Vaccinia virus, another paradigm of immune evasion, also impaired surface ADAM17 expression, suggesting that manipulation of ADAM17 may represent a novel immunoregulatory hub targeted by large DNA viruses.
The mutational variety of the live-attenuated influenza vaccine proteome
Authors: McConnell Megan , Meyer Léa , Hutchinson Edward
Published: May 2022

Influenza viruses evolve rapidly, and for this reason the influenza vaccine needs to be updated every year. It is therefore important to identify where new mutations could be tolerated. To assess this, we asked which mutations could be identified in the proteins that had passed quality checks by being correctly folded, transported and assembled into influenza virus particles. We re-analysed mass spectrometry proteomics data obtained from the virus particles of genetically well-defined vaccine strains and identified point mutations within viral proteins. Point mutations were tolerated in virus particles at appreciable frequencies in proteins of both influenza A and B viruses, including HA, NA, M1, NP, NS1, PA and PB2. Structural analyses were used to assess the likely impact of this protein diversity on the molecular biology of the virus. As would be expected, mutations that were tolerated the virus particle generally occurred at sites that would not be expected to perturb protein function. We suggest that using proteomics to identify sites in viral proteins that either can or cannot tolerate mutations could inform influenza vaccine development by highlighting areas that have the potential for antigenic drift.
Development of CRISPR/Cas9-based Novel Vaccines against Poultry Viruses
Authors: Vilela Julianne , Munir Muhammad
Published: May 2022

Vaccines remain the primary means of disease prevention throughimmunisationschemes in the poultry sector. Novel approaches in vaccine development, such as reverse genetic systems and genome editing technologies (i.e. CRISPR/Cas9), are currently being utilized to overcome challenges in establishing an immunogenic platform that is safe and capable of inducing long-term immunity. The CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats associated protein nuclease 9) technology offers an effective, fast and simple novel approach to edit genomes for the development of viral vectors against poultry diseases such as Newcastle disease (ND), avian influenza (AI) and infectious bronchitis (IB). In this study, we demonstrate the application of CRISPR/Cas9-based genome editing to generate recombinant viral vectors that express the F gene of NDV. Validation of gene integration, protein expression, and insert stability was carried out by PCR, immunostaining and Western blot analysis, respectively. This approach offers an efficient platform for the generation of multivalent recombinant vaccines that can provide simultaneous protection against major poultry diseases.
Respiratory pathogens co-infection in patients with COVID-19 pneumonia in Kazakhstan
Authors: Lavrinenko Alyona , Kolesnichenko Svetlana , Turmukhambetova Anar , Kadyrova Irina
Published: May 2022

Background

Clinical evidence of the presence of bacterial co-infection in patients with SARS-CoV-2 pneumonia is important for an adequate treatment with antibacterial drugs. Objectives: to determine the secondary bacterial flora in patients with COVID pneumonia in patients in the Republic of Kazakhstan.

Methods

Prospective, microbiological, multicenter study, which was conducted at the Medical University of Karaganda in the Shared Resource Laboratory. Sputum samples were collected from three cities of Kazakhstan with the worst SARS-CoV-2 epidemiological situation. Microbiological examination was carried out using classical methods. All investigated isolates were identified to species by MALDI-TOF mass spectrometry. Susceptibility to antibiotics was performed by the disk diffusion method in accordance with the CLSI 2019 recommendations.

Results

133 patients were included with a mean age of 60.9±12.7 years old, 53/133 (39.8%) had confirmed SARS-CoV-2 PCR test. Microbiological examination showed the growth of normal microflora in 31.45%. Difference in secondary bacterial co-infection etiology in COVID-19 positive and negative patients was not found. The leading place in general etiological structure belonged to K.pneumoniae - 22.64%, E.coli - 11.95% and A.baumannii - 11.32%. A significant relationship (p = 0.003) between such parameters as the use of antibacterial drugs and the isolated microflora was found.

Conclusions

Isolated microorganisms are etiologically significant and are pathogens of the ESKAPE group. It is important to limit the risk of infection and spread of resistant microorganisms by closely monitoring nosocomial infections and drawing attention to secondary infections caused by resistant bacteria that can increase the mortality rate of patients with COVID-19.
Signatures of defective DNA repair and replication in early-onset renal cancer patients referred for germline genetic testing
Authors: Demidova Elena V. , Serebriiskii Ilya G. , Vlasenkova Ramilia , Kelow Simon , Andrake Mark D. , Hartman Tiffiney R. , Kent Tatiana , Pomerantz Richard T. , Dunbrack Roland L. , Golemis Erica A. , Hall Michael J. , Chen David Y.T. , Daly Mary B. , Arora Sanjeevani
Published: May 2022

Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined. Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes. We performed whole-exome sequencing (WES) and found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of γH2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate PGVs in Caki RCC cells increased γH2AX foci. Immortalized patient-derived B cells bearing candidate PGVs in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities. Together, these results suggest that constitutional defects in DNA repair such as DNA replication repair underlie a subset of eoRCC cases. These findings may provide opportunities for use of the DNA repair targeting agents for eoRCC treatment. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs.

Significance Statement

Screening for DNA repair variation may provide a more comprehensive risk assessment for eoRCC patients. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.
Behavioral Responses to Fevers and Other Medical Events in Children With and Without ASD
Authors: Byrne Katherine , Zheng Shuting , Bishop Somer , Boucher Juliana , Ghods Sheila , Kim So Hyun , Lord Catherine
Published: May 2022

Objective

Anecdotal reports and a small number of research studies suggest possible behavioral improvements in children with autism spectrum disorders (ASD) during a fever. However, previous studies rely largely on retrospective reports of this phenomenon. Establishing a robust association between fever and reduction of ASD-related symptoms would promote opportunities for the development of innovative therapeutic interventions for children with ASD.

Methods

Prospective data were collected from 141 children with ASD and 103 typically developing (TD) controls using parent responses to an 11-item behavioral survey. Behaviors when no illness was present, during a fever, the week after a fever, and during non-febrile illnesses for TD and ASD children were compared. Profiles of cases in which caregivers reported consistent behavioral improvements during fever are described.

Results

Data indicated worsening social, emotional/behavioral, and somatic symptoms during a fever regardless of diagnosis, with children with ASD demonstrating greater worsening of behaviors during a fever than TD children. Three children (all with ASD) out of 244 demonstrated consistent behavioral improvements during a fever; these children had a range of cognitive and adaptive skills.

Conclusions

Children with ASD had stronger negative responses to fever than TD children. These findings contradict previous literature suggesting behavioral improvements for children with ASD. While improvements may occur for some children, it does not appear to be a common phenomenon. Additional research is needed to elucidate the nature of behavioral improvements in the subset of children with ASD who may respond positively to fever.

Article Summary

This study examines behavioral changes during fever and other medical events in children with autism compared to behavioral changes in a typically developing control group.

What’s Known on this Subject

Previous research and consistent anecdotal reports suggest the possibility of behavioral improvements for children with autism during a fever. There is a dearth of prospectively collected data examining these effects.

What This Study Adds

Children with autism consistently had stronger and more frequent negative behavior changes during fever than typical children who also primarily showed worsening of behavior during fevers. Three autistic children, and no typical children, showed improvements in varied areas during fevers.
Both vascular risk factors and common genetic variants influence penetrance of variants causing monogenic stroke
Authors: Cho Bernard PH , Harshfield Eric L , Al-Thani Maha , Tozer Daniel J , Bell Steven , Markus Hugh S
Published: May 2022

Monogenic forms of stroke have been thought to be rare with high penetrance. However, recent studies have reported typical monogenic stroke pathogenic variants are much commoner than expected in the general population. Whether such variants are associated with disease, and why the phenotype of these variants varies so widely remain unclear. In 454,787 individuals in UK Biobank, we identified typical pathogenic variants in NOTCH3, HTRA1 and COL4A1/2 genes in 1 in 467, 1 in 832 and 1 in 1353 subjects, respectively. Variants in all three genes were associated with stroke risk, and NOTCH3 and HTRA1 with dementia risk. Cardiovascular risk (assessed by Framingham cardiovascular risk score), polygenic risk (assessed by a polygenic stroke risk score), and variant location within each gene, were all associated with penetrance of NOTCH3 and HTRA1 variants. Our results suggest intensive cardiovascular risk factor modification may reduce stroke and dementia risk in individuals with such variants.
Concurrent malaria and dengue fever in (sub-Saharan) Africa: a systematic review and meta-analysis
Authors: Gebremariam Tewelde T. , Mekonnen Zeleke , Danquah Jonas B.
Published: May 2022

Objectives

To determine the prevalence of concurrent malaria and dengue fever, aetiologies, and the association between the two infections in Africa.

Methods

We assessed evidence from previous studies in Africa that were available in MEDLINE and EMBASE databases between January 01, 2005, and March 30, 2022.

Results

A total of 3942 studies were identified from the databases of which 30 studies from 13 African countries, including 25,241 febrile patients, were included in the meta-analysis. The result of the meta□analysis showed a 4.0% pooled prevalence of concurrent malaria and dengue fever in (sub-Saharan) Africa, and the highest rate was recorded in Central Africa (5.8%) followed by East Africa (4.7%) and West Africa (2.8%). Children <18 years old (57%) and females (52.8%) were more affected by the co-infection than adults and females, respectively. The dengue virus serotypes identified were DENV-2, DENV-3, DENV-1, and DENV-4 in descending order with a proportion of 39%, 31%, 27%, and 3%, respectively. Moreover, Plasmodium falciparum was the only specified malaria parasite in the co-infection among the included studies. Significantly higher odds of malaria infection were documented due to dengue fever when compared with malaria mono-infection. However, no significant odds of acute dengue co-infection were recorded due to malaria in contrast to dengue mono-infection.

Conclusion

This study showed a high prevalence of concurrent malaria and dengue fever in Africa. Healthcare workers should bear in mind the possibility of dengue infection as differential diagnoses for acute febrile illness as well as the possibility of co-existent malaria and dengue in endemic areas. Also, high-quality multi-centre studies are required to verify the above conclusions.

Protocol registration number: CRD42022311301.