bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell surface lipid composition and hydrophobicity governs tuberculosis evolution and pathogenicity
Authors: Minnikin David
Published: July 2020

The evolution of tubercle bacilli correlates closely with changes in cell envelope surface lipid composition (Donoghue et al.
Diversity 2017, 9:46; Jankute et al.
Scientific Reports 2017, 7:1315). Smooth, hydrophilic “Mycobacterium canettii” is the first recognisable member of the Mycobacterium tuberculosis complex, but it has reduced pathogenicity and poor aerosol transmission. In contrast, rough M. tuberculosis is very hydrophobic and readily spread in aerosols. Starting from hydrophilic surface lipids in environmental Mycobacterium kansasii, intermediate “M. canettii” adds hydrophobic lipids but retains overall cell hydrophilicity. Eliminating hydrophilic lipooligosaccharides (LOSs) and phenolic glycolipids (PGLs) from “M. canettii” leads to M. tuberculosis with a refined selection of hydrophobic lipids, namely phthiocerol dimycocerosates (PDIMs), pentaacyl trehaloses (PATs) and sulfoglycolipids (SGLs). The relative hydrophobicity of M. tuberculosis is double that of representatives of M. kansasii and “M. canettii”.

The above changes have implications both for the onset of tuberculosis and pinpointing evolutionary hosts. Tuberculosis has not been found in Homo sapiens during the Late Pleistocene, but megafauna are the most likely hosts; characteristic bone lesions have been validated by TB DNA amplification and lipid biomarkers in bison metacarpals up to 17,000 years old. Late Pleistocene enhanced TB hydrophobicity and aerosolisation may have produced megafaunal pandemics, with extinction of bison, mastodons and contemporary taxa. The oldest H. sapiens tuberculosis is from the “Fertile Crescent” back to 9-11ka BP at the start of the Holocene. Naïve humans arriving “Out of Africa” may have encountered newly virulent tubercle bacilli of megafaunal origin, recently refined through a distinct “bottleneck”.
Harnessing microbial science to accelerate the United Nations sustainable development goals
Authors: Fagunwa Omololu , Atinuke Afolake
Published: July 2020

Modernisation has thrown humanity and other forms of life on our planet into ditch of problems. Poverty, climate change, injustice, environmental degradation are few of the shared global problems. The United Nations SDGs are set as blueprint to achieve a better and more sustainable future for all. The SDGs are well structured to address the global challenges we face including poverty, inequalities, hunger, climate change, environmental degradation, peace and justice. The SDGs have been driven mainly by international donors and ‘professional’ international development organisations. The world is left with 10 years to achieve these ambitious goals and targets. Various reviews indicated that little has been achieve on overall, and the SDGs will not be reality if new strategy is not in place to bring inclusion. Microbiology, the scientific discipline of microbes, their effects and practical uses has insightful influence on our day to day living. We present how microbiology and microbiologists could increase the scorecard and accelerate these global goals. Microbiology contribution to peace, justice, gender equality, decent work and economic growth will be also highlighted among others. The pledge of Leave No One Behind will fast track progress and microbiology is better position to make this work.
Characterising the role of Proline Tyrosine Kinase 2 during Adherent-invasive Escherichia coli infection of macrophages
Authors: Li Xiang , Ormsby Michael , Wall Donal
Published: July 2020

Studies have implicated that Adherent-invasive Escherichia coli (AIEC) in the aetiology of Crohn’s Disease (CD), a chronic inflammatory bowel disease (IBD). CD-associated AIEC are characterised by an ability to adhere to and invade intestinal epithelial cells and replicate intracellularly in macrophages. This occurs as AIEC form vacuoles within phagolysosomes, preventing macrophage-mediated killing. However, little is known about the interaction of macrophage proteins with AIEC.

In this study, we used an in vitro infection model to identify macrophage proteins associated with AIEC intracellular replication. We identified the importance of proline-rich tyrosine kinase 2 (PYK2) in AIEC infection. PYK2 is widely expressed in epithelial cells and hematopoietic cells and plays essential roles in tumorigenesis and tumour progression. PYK2 is also overexpressed in patients with intestinal and colorectal cancer (CRC). CRC is one of the major long-term complications of IBD, especially in patients with long disease duration, a large extent of colitis, and uncontrolled inflammation. Moreover, PYK2 has been identified as an IBD risk loci via large scale genome-wide association studies.

Our in vitro models have demonstrated that the addition of PYK2 inhibitor PF-431396 during infection results in a significant decrease in intracellular replication of AIEC. This has been quantified using fluorescence immunostaining and imaging flow cytometry. These results suggest that PYK2 may play a role in intracellular bacteria survive and replication. Our future work aims to further understand the relationship between PYK2, AIEC and CD.
Inter and intra species social exploitation of antimicrobial resistance alters antibiotic efficacy
Authors: Bottery Michael , Friman Ville
Published: July 2020

The widespread use and misuse of antibiotics has led to the global spread of antimicrobial resistance. It is increasingly evident that very low concentrations of antibiotics, well below the MIC of sensitive strains, can select for antimicrobial resistance. However, it is less clear how social interactions within bacterial communities can alter sub-MIC selection dynamics, potentially confounding the outcomes of antibiotic treatments. Here we explore how antimicrobial resistances that inactivate antibiotics can be socially exploited by sensitive members of the microbial community at the inter and intra species level. We first show that a beta-lactamase encoded multi-drug resistance plasmid provides high levels of protection to plasmid-free antibiotic-sensitive cells within single-species populations in a frequency-dependent manner. Second, a similar protection can also occur between different species during polymicrobial infections. Using model Cystic Fibrosis lung communities, we demonstrate that the focal pathogen Pseudomonas aeruginosa can socially exploit antibiotic resistance in the presence of Stenotrophomonas maltophilia bacterium that can hydrolyse imipenem antibiotic. In contrast, the presence of Staphylococcus aureus, another commonly co-occurring CF pathogen, provided P. aeruginosa with no protection, but instead, made P. aeruginosa more susceptible to antibiotic due to intensified competition. These findings reveal that social exploitation of pre-occurring antimicrobial resistance, and inter-specific competition, can have a large effect on the efficacy of antibiotic treatments, highlighting the importance of microbial ecology for understanding antibiotic resistance evolution.
Influence of phosphate dosing on biofilm development on Drinking Water Distribution Systems infrastructure surfaces
Authors: Del Olmo Gonzalo , Rosales Esther , Karunakaran Esther , Jensen Henriette , Calero Carolina , Ahmad Arsland , Gaskin Paul , Douterelo Isabel
Published: July 2020

Phosphate is added to drinking water by UK water companies as a treatment to prevent the corrosion and metal leaching, like lead, in pipes. However, phosphate is a nutrient for microorganisms, and it can favour biofilm formation in Drinking Water Distribution Systems (DWDS), which can alter the water quality and safety. This study analyses the effect of phosphate addition on biofilm formation over different materials and its consequences for drinking water quality by i) using controlled experimental pipeline facility representative of a real-scale DWDS with high-density polyethylene coupons and ii) using a small-scale DWDS biofilm reactors with lead coupons. Biofilms developed over one month were exposed to the effect of different phosphate dosing and compare with UK normal water phosphate concentrations. During the experiment, physico-chemical analysis of water and microbial analysis of biofilms was carried out. Sequencing analysis of the 16s rRNA gene, from extracted DNA obtained from biofilms, provided information on any bacterial changes, and Scanning Electron Microscopy gave information about the biofilm organization. The results indicate that microorganisms find more difficult to establish and develop biofilms under high phosphate dosing, resulting in biofilms with less cells. Also, some physico-chemical parameter seems to be affected by phosphate dosing, like chlorine and lead. It is expected that differences in the biofilm community will be found depending on phosphate dosing. This study will provide information on the effect of phosphate on biofilm development in different pipes materials, which will facilitate to adjust an optimal phosphate dose to prevent plumbosolvency in DWDS.
Explosive intron expansion and fickle rDNA copies within plastid genomes of Euglenophyta
Authors: Maciszewski Kacper , Karnkowska Anna
Published: July 2020

Several eukaryotic lineages gained the ability of photosynthesis by acquiring plastids in the events of primary endosymbiosis with cyanobacteria, or secondary endosymbiosis with plastid-bearing eukaryotes. Plastids possess genomes (ptDNA) with genetic contents considerably reduced as a result of gene losses and transfers to the host’s nucleus. Still, ptDNA encodes components of various metabolic processes, including photosynthesis. Plastid genomes usually retain quadripartite structure with two rDNA-bearing inverted repeats, but the reason for its conservation, and the consequences of its decline, have not been fully understood.

As the model group to study plastid genome evolution, we chose euglenids (Euglenophyta), whose ancestor acquired the secondary plastid by endosymbiosis with a green alga. The organization of ptDNA in this lineage is rather diverse: we have shown that loss of one repeat occurred at least three times, while some species in the genus Euglena possess tandemly repeated rDNA copies. The ptDNA of euglenids is also intron-rich, but we did not confirm the previously proposed strong correlation between the prevalence of introns and quantity of maturases.

Although euglenophytes are predominantly photosynthetic, a few of them lost their photosynthetic capabilities independently. Thus far, only Euglena longa has been shown to possess vestigial plastids with reduced genome; we observed that another strain lost its plastid genome completely. Currently, we are investigating the loss and retention of metabolic functions in the plastids of other non-photosynthetic euglenophytes. This, along with investigation of ptDNA structure, will bring new insights into the evolutionary processes shaping the diversity of eukaryotic plastids.
Host-dependent differences in replication and virion release strategy of the Sulfolobus Spindle-shaped Virus strain SSV9 (a.k.a., SSVK1): Lytic replication in hosts of the family Sulfolobaceae
Authors: Michael Ceballos Ruben , Stacy Carson , Drummond Coyne , Ahmed Yeasin , Parveen Samia , Padilla Crespo Elizabeth , Stedman Kenneth
Published: July 2020

The Sulfolobus Spindle-shaped Virus (SSV) system is a model for studying thermophilic archaeal virus biology. Several factors make the SSV system amenable to studying archaeal genetics and virus-host interactions in extreme environments. It has been shown that populations of Sulfolobus, the natural host, exhibit biogeographic structure. The acidic (pH<4.5) high temperature (65-88°C) habitats have low biodiversity, which diminishes prospects for host switch. SSVs and their hosts are readily cultured in liquid media and on plates. Given the wide geographic separation between various SSV-Sulfolobus habitats, the system is also amenable to studying allopatric versus sympatric virus-host interactions. We previously reported that SSVs exhibit differential infectivity on allopatric and sympatric hosts. We discovered a strikingly broad host-range for strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as “non-lytic” dsDNA viruses that infect species of Sulfolobus and release virus particles via blebbing as a preferred strategy over host lysis (in reported laboratory infections). Here, we show, that SSVs infect more than one genus of the family Sulfolobaceae and, in allopatric hosts, SSV9 does not release virions via blebbing. Instead, SSV9 appears to lyse all susceptible allopatric hosts, while exhibiting canonical non-lytic virion release (historically reported for SSVs) on a single sympatric host. Lytic versus non-lytic virus release does not appear to be driven by multiplicity of infection. Data suggest that SSV9 is more stable than other SSVs in suspension; however, genetic substrates (e.g., CRISPR profiles) underlying non-lytic versus lytic virion release remain unresolved and are the subject of ongoing investigation.
Investigating the mechanisms of BK polyomavirus egress and virus-host interactions
Authors: Ho Sophia , Caller Laura , Beale Rupert , Crump Colin
Published: July 2020

BK polyomavirus (BKPyV) is a small, non-enveloped dsDNA virus that infects 70-90% of the world's population and causes a lifelong, silently persistent infection. In immunocompromised individuals, BKPyV replication can result in serious pathology. Bone marrow transplant patients can develop a haemorrhagic cystitis, and in kidney transplant patients BKPyV replication can provoke a nephropathy that leads to deterioration of allograft function and eventual loss of the transplanted organ. There are currently no antiviral treatments with clinical efficacy against BKPyV associated nephropathy.

While the life cycles of non-enveloped viruses are often assumed to require cell lysis to release progeny virions, we have evidence to suggest that BKPyV exits the cell via non-lytic means using an unconventional secretory pathway. We have investigated the effects of knocking out cellular genes thought to be involved in unconventional secretory pathways that bypass the Golgi apparatus on the release of BKPyV. We observe decreased BKPyV release from cells that have undergone CRISPR-mediated knockout of Golgi Reassembly Stacking Protein (GORASP) 1 or 2. Investigation of BKPyV-induced changes to the plasma membrane of infected cells demonstrated increased cell surface expression of transmembrane proteins normally resident in the endoplasmic reticulum. This appears to be inhibited by the knockout of GORASP1 or 2, suggesting that virions and ER markers are secreted via a common pathway in infected cells. These experiments are uncovering novel virus-host interactions that, when targeted, could help prevent BKPyV-associated nephropathy and allograft loss.
Generation of a bacterial clone for assessing the impact of climatic stress conditions on microbial proliferation
Authors: Attard Juan , Griffin Sholeem , Valdramidis Vasilis
Published: July 2020

Documented increases in atmospheric Carbon Dioxide (CO2) concentrations have contributed to a rise in average global temperatures. Environmental variation due to climate change is expected to affect the growth of microorganisms. Hence, there is a need to assess the induced adaptations of microorganisms, which are common biological contaminants, to environmental changes. Therefore, an enhanced green fluorescent protein (eGFP) expressing Escherichia coli BL21(DE3) clone was generated. Plasmid pAP1698-4 was used as the donor for the eGFP gene and pD454-MBP as the recipient plasmid to produce pD454-MBPeGFP. Expression of eGFP in the clone was confirmed using confocal microscopy. The growth of the clone was characterised by plate counting technique. Variation in the length of the lag phase, λ, and growth rate, μmax, kinetic parameters of the clone was observed, compared to the wildtype BL21(DE3). A live/dead kinetic assay, using eGFP for the quantification of live cells and propidium iodide (PI) as a stain for dead cells, was optimised using a microplate reader with controlled temperature and CO2 conditions. Full growth curves were collected when culture media was inoculated with 4 to 6 Log10CFU.mL-1. The optimal PI concentration was 150 nM; higher concentrations inhibited growth, and lower concentrations gave no signal difference compared to the blank. The growth kinetics of the clone under different environmental conditions; between 400 ppm to 2500 ppm CO2, combined with 37°C to 42°C, were evaluated using the live/dead kinetic assay, allowing assessment of response to induced environmental stress.
Peroxynitrite is essential for the initiation of cytomegalovirus replication in vitro and in vivo
Authors: Sabberwal Pragati , Chapman Lucy , Clement Mathew , Fielding Ceri , Thomas David , Stanton Richard , Humphreys Ian
Published: July 2020

Human cytomegalovirus (HCMV) is a pathogenic beta-herpesvirus that establishes a lifelong infection in hosts. It causes significant morbidity and mortality in the immunocompromised and is associated with a range of birth defects following congenital infection. Current therapeutic approaches that target key viral proteins are toxic and antiviral drug resistance is common. Thus, targeting host genes and cellular pathways essential for HCMV infection offers an alternative strategy for the development of antivirals. Here we show that host oxidative/nitrosative stress responses to CMV are critical for virus replication. Oxidative/nitrosative stress occurs due to accumulation of reactive oxygen/nitrogen species (ROS/RNS). Using a range of ROS/RNS scavengers, we identified that peroxynitrite, a powerful oxidant and nitrating agent, dramatically promoted virus replication in both in vitro and in vivo models of CMV infection. HCMV rapidly induced production of intracellular peroxynitrite upon infection. Inhibition of peroxynitrite within the first 24 hours alleviates efficient HCMV infection in both cell-free and cell-associated infection systems, indicating that peroxynitrite may influence pathways necessary for HCMV entry and/or replication. Furthermore, peroxynitrite inhibition also inhibited HCMV reactivation from latency. Interestingly, the neurotransmitter and naturally-occurring peroxynitrite antagonist 5-hydroxytryptamine, commonly known as serotonin, also impinged on HCMV-induced peroxynitrite production and exhibited anti-HCMV activity. Thus, overall, our study demonstrates a novel role for intracellular peroxynitrite in CMV pathogenesis and implies that peroxynitrite could be targeted as a novel approach to inhibiting CMV infection.
Characterisation and identification of STEC O157 pathogenicity using machine learning
Authors: Khatun Suniya , J. Dallman Timothy , Jenkins Claire
Published: July 2020

Shiga toxin-producing Escherichia coli O157: H7 (STEC) is a zoonotic pathogen that is globally dispersed, causing severe gastroenteritis when transmitted from ruminants to humans through direct or indirect contact with animals, their environment or contaminated food. Symptoms are varied in severity; from mild to bloody diarrhoea with more serious sequalae including hemolytic uremic syndrome (HUS) which can be fatal. Although there is compelling evidence that the Shiga toxin sub-type is a key predictor of disease severity, differences in virulence potential of strains with the same Shiga toxin profile are often observed. In this study, we employ machine learning algorithms to explore the relationship between the STEC genome with clinical outcome.

Kmer-counts of variable length (9-100 base pair) from 1148 isolates of STEC O157:H7, representing two years of routine surveillance in England, were matched to their respective clinical outcome data. A Random Forest classifier was developed and validated with the objective of inferring the clinical symptoms associated with a given STEC genome. Clinical outcomes were categorised into asymptomatic, diarrhoea, bloody diarrhoea and HUS. The model correctly classified 160 out of 190 cases of bloody diarrhoea, 81 out of 128 cases of diarrhoea and 7 out of 12 cases of HUS, with average AUC ROC score of 90%. Kmers deemed important for distinct classification were characterised and matches related to Shiga toxin 2a phage integration and excision genes and adhesion and transporter proteins were identified. This is consistent with reported virulence factors in the literature, supporting this approach of de novo pathogen characterisation.
Effects of trimethylamine N-oxide on the growth and metabolism of gut bacteria
Authors: Dawson Samuel , McLean Samantha , Hoyles Lesley
Published: July 2020

Trimethylamine N-oxide (TMAO) is an osmolyte that enters the bloodstream directly through consumption of fish, or through microbial metabolism of it and other dietary methylamines such as carnitine and choline, producing trimethylamine (TMA). TMA produced by microbes enters the blood and is transported to the liver, where it is converted back to TMAO by flavin-containing monooxygenases before being excreted in the urine. TMAO has been shown to potentially have beneficial effects on metabolic health and the gut-brain axis at normal physiological levels, while elevated serum levels are associated with cardiometabolic disease in Western patients. Bacteria in the family Enterobacteriaceae exhibit changes in their growth and metabolome in the presence of TMAO but why this occurs is not known. Growth experiments show that a caecal isolate of Klebsiella pneumoniae, a member of the Enterobacteriaceae, experience a more rapid growth rate, when grown anaerobically in the presence of TMAO, but may require oxygen to be present to produce TMA. K. pneumoniae will be subjected to differing concentrations of TMAO and oxygen to examine the effects on the metabolites produced, the genes expressed, and the rate of growth. This will be done by analysing spent media using GC-MS, qPCR targeting genes involved in anaerobic respiration, and measuring the turbidity of cultures over time. By understanding how bacteria in the gut interact with TMAO new insights can be gained as to how gut bacteria and their metabolites influence human health.
Interreg 2 seas Project: Health For Dairy Cows, H4DC
Authors: A. Ribeiro Claudia , Pinto Pedro , J. Warren Christopher , Vlandas Alexis , Vuylsteke Isabelle , Canniere Evi , Dellevoet Martine , Roemen Janine , Bourgeois Anne , Leruste Helene , Roblin Maud , Windal Feryal , Benhabiles Halim , Hammouma O. , Deweer Caroline , Robinson Gary
Published: July 2020

Cryptosporidium spp. are microbial parasites that infect the gastrointestinal tract of humans and many animals, causing cryptosporidiosis, a disease characterised by acute watery diarrhoea. In dairy farms, C. parvum is the most common species in calves, leading to high mortality rate, stunted growth, and consequently high economic losses. Trade between farms and breeding centres is a major risk factor in the spread of such parasites, posing a threat to other farms worldwide as well as to human health. This problem is aggravated by the lack of good breeding practices, efficient detection tools, and lack of effective anti-cryptosporidial drugs.

To address cryptosporidiosis in dairy farms, we have established the ‘Health For Dairy Cows (H4DC)’ consortium in order to tackle some of the aforementioned issues.

Herein, we will present preliminary data from a 3-step strategy:

1)Dissemination of pilot farms in France, Belgium, The Netherlands and England. This collaboration will serve to test the effect of new husbandry practices in the occurrence of Cryptosporidium, which will aim to decrease Cryptosporidium incidence and ultimately decrease the economic burden of cryptosporidiosis.

2)These pilot farms will later be used as testing-grounds of the low-cost and easy-to-use in-situ C. parvum detection tool that will be developed during this project.

3)Development of a cell-based drug-screening system which will be used to screen various drugs and compounds for anti-Cryptosporidium activity.

Finally, data from these findings will be used to establish model and strategies in order to transfer the developed technologies to both farmers and biotech/pharmaceutical companies.
The complete sequence, annotation and comparative analysis of the Escherichia coli IncFII family plasmid pMccB17, encoding biosynthetic and immunity functions for the antimicrobial peptide microcin B17
Authors: Ajeigbe Mayokun , Bingle Lewis
Published: July 2020

Microcin B17 (Mcb17) is a ribosomally synthesized and post-translationally modified peptide (RiPP), produced by Escherichia coli, that inhibits bacterial DNA gyrase in a similar way to quinolones. The Mcb17 operon, consisting of seven genes encoding biosynthetic and immunity/export functions, was originally found on a plasmid, pMccB17. This circular plasmid, previously known as pRYC17, was originally found in Escherichia coli strain LP17, isolated from the intestinal tract of a healthy newborn at Hospital La Paz, Spain and was transferred by conjugation to E. coli K-12 [Baquero et al. (1978) J. Bacteriol. 135: 342]. pMccB17 is a low copy number IncFII plasmid in the same incompatibility group as R100 and R1. Not much is known about this plasmid aside from the facts that it carries the Mcb17 operon, does not possess any conventional antibiotic resistance markers and its size was estimated to be approximately 70 kb.

We extracted the plasmid from E. coli K-12 strain RYC1000 [pMccB17] and sequenced it twice using an Illumina short-read method, firstly together with the host bacterial chromosome, then plasmid DNA was purified and sequenced separately. PCR primers were designed to close the single remaining gap via Sanger sequencing. The resulting complete sequence has 83 predicted genes, initially identified by Prokka and subsequently manually reannotated using BLAST. Comparison to other IncFII plasmids shows a large proportion of shared genes, especially in the conjugative plasmid backbone. However, pMccB17 which is a MOBF12 plasmid lacks transposable elements and in addition to the Mcb17 operon, this plasmid carries 25 genes of unknown function.
The investigation of virus-driven intrahepatic cholangiocarcinoma through dysregulated hepatic differentiation
Authors: Kilvington Alexandria , Matthews Laura , Griffin Stephen
Published: July 2020

Intrahepatic Cholangiocarcinoma (iCCA), bile duct cancer, is increasing in incidence worldwide. Infection with hepatitis C virus (HCV) is a known risk factor for developing iCCA. Recent studies of HCV associated hepatocellular carcinoma (HCC) have demonstrated that HCV infection induces oncogenic gene expression patterns resulting from altered epigenetic profiles. Importantly, whilst ∼90% of patients treated with new direct acting antivirals (DAAs) attain a sustained virological response, the risk of HCC and other malignancies is not reduced by the same extent as previous interferon therapies. We, and others, have shown that this may be related to an imprinted gene expression pattern persisting post-treatment.

The cellular origin of primary liver cancers can vary due to liver cell plasticity. However, the incidence of mixed iCCA-HCC tumour phenotypes and the dual iCCA/HCC risk associated with HCV infection led us to hypothesise that virus-infected hepatic progenitor cells (HPC) might be the source of virus-driven malignancies. Accordingly, we demonstrated that adult HPCs were susceptible to HCV infection ex vivo. Moreover, models of hepatic differentiation revealed that HCV disrupts this process via hijacking the HIPPO signalling pathway with oncogenic hallmarks persisting following viral cure.

To explore HCV-induced alterations during cholangiocyte-specific differentiation, we have chosen to exploit the immortalised non-transformed HPC line, HepaRG and induced pluripotent stem cell derived HPCs. We will describe endeavours to develop a robust model of HCV-mediated perturbation of cholangiocyte-specific differentiation in order to identify new treatments that complement DAA therapy in order to eliminate the risk of malignancy.
Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa
Authors: Foster-Nyarko Ebenezer , Alikhan Nabil-Fareed , Ravi Anuradha , Thomson Nicholas , Jarju Sheikh , Secka Arss , Antonio Martin , J. Pallen Mark
Published: July 2020

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from ten chickens and nine guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (four of them novel), of which ST155 was the most common (22/68, 32%). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64%) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates sit within a tight genomic cluster (100 alleles difference) of strains from poultry and livestock in sub-Saharan Africa (the Gambia, Uganda and Kenya). Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted.
Isolation of thermophilic Actinobacteria from compost and identification of bioactive compounds with antimicrobial properties
Authors: Halket Gillian , Herron Paul , Munro Carol
Published: July 2020

To combat the problem of antimicrobial resistance, we are testing the hypothesis that thermophilic Actinobacteria produce novel antimicrobials at higher temperatures, with potential activity against life-threatening infections like invasive aspergillosis caused by the fungus Aspergillus fumigatus. Samples from “windrows” at a green waste processing facility yielded 36 potential thermophilic Actinobacterial strains isolated at 50oC, as well as strains of A. fumigatus. The phylogeny and identities of the bacterial strains were determined by 16S rDNA sequencing. Three strains - DJT 15 Streptomyces thermoviolaceus subsp. apingens, DJT 32 Saccharomonospora viridis and DJT 36 Saccharomonospora glauca - have shown inhibitory activity in bioassays against the ESKAPE pathogens, two of which (DJT 32 and 36) also inhibited the growth of the fungal pathogen Aspergillus fumigatus isolated from the same compost. Strain DJT 32 has also been shown to have an inhibitory effect against azole resistant human pathogenic strains of A. fumigatus. Whole genome Sequencing data of DJT 15 and 32 have been used to identify possible biosynthetic gene clusters for antimicrobial compounds (novel or otherwise) through AntiSmash analysis. Alongside this, bioactive compounds have been extracted from broth cultures of each strain using HP-20 Resin method, and the metabolites will be identified using LC:MS combined with metabolic profiling. Extraction and identification of novel metabolites will provide a path for the development of new antimicrobials for clinical use. This study has shown that thermophilic Actinobacteria produce antimicrobial compounds at higher temperatures, against Staphylococcus aureus and against the highly pathogenic fungus, A. fumigatus.
Characterization of a multi-modular bacterial enzyme with binding and hydrolysis activities on fungal cell wall components: Insights into bacterial-fungal interactions in the soil
Authors: Lu Zijia , Inman Annie , Kask Josefin , Sara McKee Lauren
Published: July 2020

Bacteria from the phylum Bacteroidetes is known as good degraders because of their abilities in secreting glycoside hydrolases (GHs). As a member in Bacteroidetes, Chitinophaga pinensis is capable to hydrolyze several glycans (McKee et al., 2019). We found that a multi-modular CAZyme produced by C. pinensis contains not only two GHs but also two uncharacterized domains. Although it is common for CAZmes to have non-catalytic modules like carbohydrate-binding domains (CBMs), the domains in this protein are uncommon, and their functions unknown.

Our enzyme contains five domains – a GH5_46 enzyme, a GH18 enzyme, two non-identical uncharacterized domains, and a Por C-terminal secretion domain. I have shown that the GH5 can specifically degrade pustulan (β-1,6-glucan), and is the only β-1,6-glucanase found in its sub-family. The GH18 is a chitinase that reacts with β-chitin. Interestingly, the two uncharacterized domains both bind polysaccharides, and improve enzyme stability. However, they do not necessarily bind the same glycan as their GH partners. Our result demonstrates how two distinct polysaccharide-degrading modules within one protein can cooperate. We also discuss the impact of the binding domains on the GH activity.

We anticipate our research can stimulate the exploration of β-1,6-glucanase activity in family GH5, and expand the database of carbohydrate specificities in bacteria. The two unusual binding domains we have characterized suggest an unexplored aspect of bacterial physiology in the soil.

References:

McKee, L.S., et al., 2019. Focused metabolism of β-Glucans by the soil Bacteroidetes species Chitinophaga pinensis. Appl. Environ. Microbiol., 85(2), pp.e02231-18.
Using structural biology of methanogen enzymes to aid our understanding of methane formation
Authors: Ronimus Ron , Schofield Linley , Carbone Vince , Sang Carrie , Sutherland-Smith Andrew
Published: July 2020

Methane is a potent greenhouse gas (28-fold more potent than carbon dioxide) and is a significant gas contributing to global climate change. Approximately a billion tons of methane are produced each year by methanogenic archaea in ruminants. These archaea possess a number of unusual traits such as isoprenoid-based lipids, unusual cell wall chemistry and a unique energy metabolism (methanogenesis) that requires six methanogen-specific cofactors. Many of the enzymes involved in these processes have no direct analogues in the host animal. To gain insights into the fundamental biology of rumen methanogens we have determined crystal structures of key enzymes with archaeal-specific traits. Over 600 enzymes were targeted for structure determination which produced approximately 200 purified soluble enzymes for crystallographic screening. More than 50 different enzymes have produced crystals and 30 structures have been solved for individual enzymes to date. The results have helped illuminate our understanding of methane formation at this critical juncture in the world’s history.
Novel intraoperative online functional mapping of somatosensory finger representations for targeted stimulating electrode placement
Authors: McMullen David P. , Thomas Tessy M. , Fifer Matthew S. , Candrea Daniel N. , Tenore Francesco V. , Nickl Robert W. , Pohlmeyer Eric A. , Coogan Christopher , Osborn Luke E. , Schiavi Adam , Wojtasiewicz Teresa , Gordon Chad , Cohen Adam B. , Ramsey Nick F. , Schellekens Wouter , Bensmaia Sliman J. , Cantarero Gabriela L. , Celnik Pablo A. , Wester Brock A. , Anderson William S. , Crone Nathan E.
Published: July 2020

Defining eloquent cortex intraoperatively, traditionally performed by neurosurgeons to preserve patient function, can now help target electrode implantation for restoring function. Brain-machine interfaces (BMIs) have the potential to restore upper-limb motor control to paralyzed patients but require accurate placement of recording and stimulating electrodes to enable functional control of a prosthetic limb. Beyond motor decoding from recording arrays, precise placement of stimulating electrodes in cortical areas associated with finger and fingertip sensations allows for the delivery of sensory feedback that could improve dexterous control of prosthetic hands. In our study, we demonstrated the use of a novel intraoperative online functional mapping (OFM) technique with high-density electrocorticography (ECoG) to localize finger representations in human primary somatosensory cortex. In conjunction with traditional pre- and intraoperative targeting approaches, this technique enabled accurate implantation of stimulating microelectrodes, which was confirmed by post-implantation intra-cortical stimulation of finger and fingertip sensations. This work demonstrates the utility of intraoperative OFM and will inform future studies of closed-loop BMIs in humans.
Maternal and perinatal characteristics and outcomes of pregnancies complicated with COVID-19 in Kuwait
Authors: Ayed Amal , Embaireeg Alia , Benawath Asma , Al-Fouzan Wadha , Hammoud Majdeda , Al-Hathal Monif , Alzaidai Abeer , Ayed Mariam
Published: July 2020

Background

In late December of 2019, a novel coronavirus (SARS-CoV-2) was identified in the Chinese city Wuhan among a cluster of pneumonia patients. While it is known that pregnant women have reduced immunity and they are at risk for COVID-19 infection during the current pandemic, it is not clear if the disease manifestation would be different in pregnant women from non-pregnant women.

Objectives

To describe the maternal and neonatal clinical features as well as outcome of pregnancies complicated with SARS-CoV-2 infection.

Methods

In this retrospective national-based study, we analyzed the medical records of all SARS-CoV-2 positive pregnant patients and their neonates who were admitted to New-Jahra Hospital, Kuwait, between March 15th 2020 and May 31st 2020. The outcomes of pregnancies were assessed until the end date of follow-up (June 15th 2020).

Results

A total of 185 pregnant women were enrolled with a median age of 31 years (interquartile range, IQR: 27.5-34), and median gestational age at diagnosis was 29 weeks (IQR: 18-34). The majority (88%) of the patients had mild symptoms, with fever (58%) being the most common presenting symptom followed by cough (50.6%). During the study period, 141 (76.2%) patients continued their pregnancy, 3 (1.6%) had a miscarriage, 1 (0.5%) had intrauterine fetal death and only 2 (1.1%) patients developed severe pneumonia and required intensive care. Most of the neonates were asymptomatic, and only 2 (5%) of them tested positive on day 5 by nasopharyngeal swab testing.

Conclusion

Pregnant women do not appear to be at higher risk to the COVID-19 than the general population. The clinical features of pregnant women with SARS-CoV-2 infection were similar to those of the general population having SARS-CoV-2 infection. Favorable maternal and neonatal outcomes reinforce the existing evidence and may guide healthcare professionals in the management of pregnancies complicated with SARS-CoV-2 infection.
The Efficacy of IL-6 Inhibitor Tocilizumab in Reducing Severe COVID-19 Mortality: A Systematic Review
Authors: Kaye Avi , Siegel Robert
Published: July 2020

In the absence of highly effective antiviral therapies against SARS-CoV-2, it is crucial to counter the known pathophysiological causes of severe COVID-19. Evaluating the efficacy existing drugs may expedite the development of such therapeutics. Severe COVID-19 is largely the result of a dysregulated immune response characterized by lymphocytopenia, neutrophilia and critical hypercytokinemia, or “cytokine storm,” which is largely mediated by the cytokine interleukin-6 (IL-6). The IL-6 inhibitor tocilizumab (TCZ) could potentially suppress the effects of the pro-inflammatory cytokine and thereby lower mortality from the disease. This systematic analysis aimed to investigate and synthesize existing evidence for the efficacy of TCZ in reducing COVID-19 mortality. PubMed and SearchWorks searches were performed to locate clinical studies with primary data on TCZ treatment for severe COVID-19. Sixteen case-control studies comparing mortality between TCZ and standard of care (SOC) were identified for quantitative synthesis. Combined mortality for the TCZ-treated and SOC groups were 26.0% and 43.4% respectively. In all but one of the studies, the odds ratio of mortality from COVID-19 pointed towards lower fatality with TCZ versus the SOC. A combined random effects odds ratio calculation yielded an odds ratio of 0.453 (95% CI 0.376-0.547, p<0.001). Additionally, eighteen uncontrolled trials were identified for qualitative analysis producing a raw combined mortality rate of 16.0%. Important caveats to this research include the lack of prospective randomized control trials (RCTs) and the absence of data from the large COVATA study from the published literature. However, results from this systematic analysis of published research provide positive evidence for the potential efficacy of TCZ to treat severe COVID-19, validating the ethical basis and merit of ongoing randomized controlled clinical trials.
Impact of meteorological parameters on the Covid-19 incidence. The case of the city of Oran, Algeria
Authors: Rahal Farid , Rezak Salima , Baba Hamed Fatima Zohra
Published: July 2020

Several studies have confirmed the impact of weather conditions on the evolution of the Covid-19 pandemic. We wanted to verify this phenomenon in the city of Oran in Algeria, which experienced its first case of Covid19 on March 19, 2020.

The data studied are the new Covid19 cases, the average, minimum and maximum temperatures, as well as the relative humidity rate.

A first analysis of the data with a Spearman rank correlation test did not yield significant results. Taking into account the average incubation period to adjust the data made it possible, during a second analysis, to show that the minimum temperature is significantly correlated with the new cases of Covid19 in Oran. This study can help establish prevention policies against Covid19, especially during fall in temperatures in autumn and winter.
Impact of COVID-19 Lockdown Policy on Homicide, Suicide, and Motor Vehicle Deaths in Peru
Authors: Calderon-Anyosa Renzo JC , Kaufman Jay S
Published: July 2020

Introduction

Although lockdown measures to stop COVID-19 have direct effects on disease transmission, their impact on violent and accidental deaths remains unknown. Our study aims to assess the early impact of COVID-19 lockdown on violent and accidental deaths in Peru.

Methods

Based on data from the Peruvian National Death Information System, an interrupted time series analysis was performed to assess the immediate impact and change in the trend of COVID-19 lockdown on external causes of death including homicide, suicide, and traffic accidents. The analysis was stratified by sex and the time unit was every 15 days.

Results

All forms of deaths examined presented a sudden drop after the lockdown. The biggest drop was in deaths related to traffic accidents, with a reduction of 12.66 deaths per million men per month (95% CI: −15.56, −9.76) and 3.64 deaths per million women per month (95% CI:-5.25, −2.03). Homicide and suicide presented similar level drop in women, while the homicide reduction was twice the size of the suicide reduction in men. The slope in suicide in men during the lock-down period increased by 3.62 deaths per million men per year (95% CI:0.06, 7.18). No other change in slope was detected.

Conclusions

Violent and accidental deaths presented a sudden drop after the lockdown was implemented and an increase in suicide in men was observed. Falls in mobility have a natural impact on traffic accidents, however, the patterns for suicide and homicide are less intuitive and reveal important characteristics of these events, although we expect all of these changes to be transient.
Effects of Smoking and Smoking Cessation on the Intestinal Microbiota
Authors: Sublette Marcus G. , Cross Tzu-Wen L. , Korcarz Claudia E. , Hansen Kristin M. , Murga-Garrido Sofia M. , Hazen Stanley L. , Wang Zeneng , Oguss Madeline K. , Rey Federico E. , Stein James H.
Published: July 2020

Introduction

We evaluated associations of smoking heaviness markers and the effects of smoking cessation on the intestinal microbiota and cardiovascular disease risk factors in current smokers undertaking a quit attempt.

Methods and Results

Participants were current smokers enrolled in a randomized clinical trial of smoking cessation therapies with visits, risk factor measurements, and fecal collections at baseline, 2, and 12 weeks after starting a quit attempt. Genomic DNA was extracted from fecal samples followed by 16S rRNA gene sequencing and analysis using the QIIME2 software workflow. Relative abundances of bacterial taxa and alpha- and beta-diversity measures were compared.

Longitudinal changes in bacterial taxa abundances were compared using analysis of covariance (ANCOVA). The 36 smokers were (mean [standard deviation]) 51.5 (11.1) years old (42% male) and smoked 15.1 (6.4) cigarettes per day for 22.7 (11.9) pack-years. Their exhaled carbon monoxide (CO) levels were 17.6 (9.3) ppm. At baseline, relative abundances of the phylum Actinobacteria were correlated inversely with pack-years (rho=-0.44, p=0.008) and Cyanobacteria were correlated positively with CO levels (rho=0.39, p=0.021). After 12 weeks, abundances of the phylaBacteroidetes increased (pANCOVA=0.048) and Firmicutes decreased (pANCOVA=0.036) among abstainers compared to continuing smokers. Increases in alpha-diversity were associated with lower heart rates (rho=-0.59, p=0.037), systolic blood pressures (rho=-0.58, p=0.043), and C-reactive protein levels (rho=-0.60, p=0.034).

Conclusions

Smoking cessation leads to minor changes in the intestinal microbiota. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota and if such changes affect cardiovascular disease risk.

Implications

In the largest prospective study of current smokers making a quit attempt to date, we showed that smoking cessation has minor effects on the composition of the gut microbiome. In successful abstainers, relative abundances of the phyla Bacteroidetes increased and Firmicutes decreased, a pattern of uncertain clinical significance. We did not observe significant changes in alpha- or beta-diversity with smoking cessation. It is unclear if the proven health benefits of smoking cessation lead to salutary changes in the intestinal microbiota and if such changes affect cardiovascular disease risk.