bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomic analysis of gastroenteritis-associated Clostridium perfringens identifies isogenic strains in multiple outbreaks and novel virulence-related features
Authors: Kiu Raymond , Caim Shabhonam , Pickard Derek , Dougan Gordon , Painset Anais , Swift Craig , Mather Alison , Amar Corinne , Hall Lindsay 
Published: April 2019

Background
Clostridium perfringensis a major enteric pathogen known to cause gastroenteritis in humans. Although major outbreak cases are frequently reported, to date no Whole Genome Sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of C. perfringens-associated outbreak strains.

Methods
We have applied both genomic and phylogenetic analyses on a sub-set of 109 newly-sequenced C. perfringens strains isolated from gastroenteritis-associated disease cases (including food-poisoning and care-home diarrhoea) from England and Wales between 2011 – 2017 to probe virulence profiles including toxin and AMR genes, plasmid features and genomic epidemiology of these case isolates.

Results
Our data identified that highly-similar C. perfringens strains were associated with 9 care home-associated individual outbreaks over a 5 year interval, indicating potential common sources linked to these distinct outbreaks. Enterotoxin gene cpe was encoded in all but 4 isolates (96.4 % type-F strains), and it was further determined that virulence plasmids encoding cpe were extensively distributed in the isolates (97 % care-home isolates carry pCPF5603 plasmid; 60 % food-poisoning isolates carry pCPF4969 plasmid). Further virulence factors, such as β2-toxin, were enriched in these isolates (46.7 %). Phage proteins were also commonly identified, with additional analysis indicating phages may contribute to spread of virulence determinants.

Conclusion
This study highlights the genotypic and epidemiological relatedness of a large collection of C. perfringens strains isolated from gastroenteritis-associated cases from across the UK and Wales. Key points revealed include the potential circulation of disease-associated strains, and impact of cpe-encoding-plasmid disseminations, linked to outbreak cases.
Characterising the inhibition profile of an antimicrobial produced by Enterococcus
Authors: Cole Nathaniel , Walsh Fiona 
Published: April 2019

Introduction
Antibiotic resistance is one of the greatest problems facing the 21st century with few new classes of antibiotics being discovered. The forefront of antibiotic discovery has been the soil microbiome and it is still a valuable resource for identifying microbes with possible antibiotic producing capabilities leading to novel classes of antibiotics. This justifies continuing investigation into the soil microbiome for antibiotic producing bacteria, to help tackle the growing trend in antibiotic resistance. A bacterial soil isolate was found to inhibit Enterococcus faecalis ATCC 29212 and the aim of this work was to further characterise the inhibition profile of the antibacterial.

Methods
Bacterial plug and supernatant assays were used to access the inhibition ability of a soil bacterial isolate against the WHO ‘priority pathogens’. Identification of the bacteria was carried out using 16S rRNA and whole genome sequencing. Synergy tests were carried out using broth dilution assays.

Results
The soil isolate (N5) was identified as Enterococcus and showed antibacterial activity against Staphylococcus aureus MRSA and E. faecalis VanA. This antibacterial is secreted into the supernatant which still showed inhibitory activity against MRSA and VRE. Synergy with N5 and ciprofloxacin (0.2  µg ml−1) against E. faecalis ATCC 29212 was also observed.

Conclusion
Both VRE and MRSA are important players in nosocomial infections and are displaying high levels of resistance. Further study of this antibacterial could lead to the development of a new compound to help overcome resistance mechanisms or a novel antimicrobial.
Clinical evaluation of the novel molecular bacterial load assay for real-time monitoring of tuberculosis treatment response
Authors: Mtafya Bariki , Sabiiti Wilber , Sabi Issa , Msuya Yahya , Ntinginya Nyanda 
Published: April 2019

Background
Monitoring the treatment of tuberculosis (TB) relies on less sensitive smear microscopy (SM) and culture methods which are very slow. We evaluated the novel Molecular bacterial load assay (MBLA) for implimentability and real-time monitoring of TB treatment in a clinical setting.

Methods
Therapy naive (Xpert MTB/RIF confirmed) TB positive patients were enrolled in Mbeya, Tanzania. Sputum samples were collected at baseline and thereafter at week 2, month 2, 5 and 6 of treatment. Samples were analysed for M. tuberculosis (M.tb) by MBLA and compared to SM, culture and clinical monitoring.

Results
59 TB patients were enrolled for the study. Median age, 37 (18-65) years, 62.7 % (37/59) male, 45.6 % (27/59) HIV positive and 8.47 % (5/59) were re-treatment. Mean BL (± SD) at baseline was 5.48 ± 1.3 declining to 3.42 ± 0.7  at month 2 and 3.51 ± 0.62 log10CFU/ml at month 6 of treatment. This corresponds MBLA positivity of 92.98, 65.5 and 7.84 % at baseline, month 2 and 6 respectively. In contrast, positivity of SM and culture were 78.95, 9.62 and 0 %, and 85.96, 25 and 3.39 % at baseline, month 2 and 6 respectively. Decline in test positivity reflected resolution of clinical signs. While night sweat, and chest pain resolved earlier on in treatment, resolution of cough was slow and consistent with MBLA. Furthermore, the turn-around-time for MBLA results was 24  h compared to median (range) of 14.83 (4.33–42)  days for liquid culture.

Conclusion
MBLA exhibited higher sensitivity and shorter turn-around-time than standard tests and clinical signs. This demonstrates the potential of MBLA to offer real-time results for clinical decision making.
Different oral niches give rise to varying levels of genetic diversity in Streptococcus mitis
Authors: Davison Charlotte , Beleza Sandra 
Published: April 2019

Background
The commensal bacterium, Streptococcus mitis is a major coloniser of the oral cavity. This close cousin of Streptococcus pneumoniae has been identified to occupy a range of oral niches independent of pH, epithelial surface and redox state. We have previously observed a high level of genetic diversity in S. mitis with an open pan-genome and only 46 % of the genome identified as core.

Aim
We aim to identify the driving force behind the high levels of genetic diversity identified in S. mitis and determine if this diversity can be attributed to oral location.

Methods
Samples were collected from the buccal mucosa and tongue dorsum. A total of 75 S. mitis isolates were whole genome and Ion Torrent sequenced and subject to bioinformatic analysis.

Results
In contrast to S. pneumoniae, genetic diversity in S. mitis is predominantly driven by mutation with recombination playing only a minor role. It was also observed that isolates collected from the tongue dorsum were significantly more diverse than those collected from the buccal mucosa. Due to the mutational nature of S. mitis diversity, this suggests varying pressures on S. mitis in these two environments. Study is now underway to establish the genetic differences between S. mitis from these oral niches and determine how this will impact future study and study design of this significant oral microbiome component.
Whole genome analysis of the common pathogens associated with microbial keratitis
Authors: Glenn Michael , Kaye Stephen , Neal Timothy , Roberts Paul , Winstanley Craig , Fairley Derek , Simpson David 
Published: April 2019

Background
Microbial Keratitis is a serious infection of the cornea and a major cause of corneal opacity and vision loss worldwide. Whole-genome sequencing (WGS) of keratitis bacterial isolates has the ability to provide a wealth of clinically-valuable information. The potential of metagenomics has also been evaluated as current techniques for pathogen identification are laborious, time-consuming and associated with poor culture rates, making metagenomics an exciting future prospect.

Methods/Results
Samples from keratitis patients were collected and isolates grown in agar before DNA was extracted from pure-cultures and WGS data was obtained from a total of 30 isolates, including common causative agents Pseudomonas aeruginosa and Staphylococcus aureus. Libraries were prepared using a miniaturised Nextera XT protocol and sequencing was carried out on Illumina’s NextSeq platform. Genomic analysis was then based around MLST-typing, comparative genomics, and the identification of key genes inferring antibiotic resistance and virulence. Our pathogens exhibited diverse evolutionary lineages and a range of virulence-associated genes, providing insight into pathogenicity. The ability to obtain sufficient DNA quantities for metagenomics sequencing was also assessed using various host depletion and microbiome enrichment techniques.

Discussion/Conclusion
The clinical role of next-generation sequencing is currently limited due to associated costs and required computational resources, however in the future this method could replace current techniques for pathogen identification. WGS provides important insights into the genomes of the common keratitis infectious agents, improving understanding of the aetiology of corneal infections and metagenomics shows future potential to be the centre of culture-independent pathogen identification.
Characterization of Enterococcus faecium SP15, a novel isolate with probiotic and therapeutic potential
Authors: Aziz Fauzia , Khan Muhammad , Ahmed Safia , Jones Ian , Andrews Simon 
Published: April 2019

Aims
To characterise the genome and enterocin content of Enterococcus faecium SP15, a new isolate from natural spring water.

Methods and Results

Enterococcus faecium strain SP15 was isolated from natural spring water and its identity confirmed using 16S rDNA sequence. The bacterial strain produced antimicrobial compounds (enterocins) against pathogenic bacteria including Listeria monocytogenesis as determined by the agar spot method. In addition, an anti-cancer activity was observed on human cancer cell line HT-29 by cytotoxicity assay (MTT) and apoptosis study. A draft genome sequence revealed the presence of several enterocin genes capable of activity against a panel of pathogenic bacteria including L. monocytogenesis. The active production of enterocins was also supported by the presence of peptides in part purified fermentates following trypsin digest and mass spectrometry. The genome showed no classical virulence factors or hemolysins and was free of antibiotic resistance genes. To confirm enterocin related killing, select enterocin genes were cloned and expressed as His-tagged proteins in E. coli. Purified enterocin retained activity in L. monocytogenes overlay assay.

Conclusion

E. faecium SP15 is a promising strain for probiotic use and/or food preservation. Purified enterocins retain their activity suggesting them a template for structure-function studies and future improvements as antimicrobial and cancer cell therapeutics. Significance and Impact of the Study: New antibacterial and anticancer agents are required to combat antibiotic resistance and a limited drug repertoire. Enterocins from Enterococcus faecium SP15 could fulfil these goals in addition to use of the strain as a whole organism probiotic.
Film-forming agents as potential barriers to fungal skin infections
Authors: Ho Kaho , Delgado-Charro Begona , Bolhuis Albert 
Published: April 2019

Background
Superficial fungal infections are one of the most common causes of human disease caused by dermatophytes or yeasts. Dermatophyte infections are caused by fungi that can digest keratin, infecting the keratinised tissues e.g. skin, hair and nails. It has a higher prevalence than the other superficial mycoses, and its incidence has increased continuously over the last few decades, probably because of the change in lifestyle and frequent usage of antibiotics. Therefore, the aim of the project is to develop a physical barrier that can prevent the early stages of infection to the skin, to avoid development of antifungal resistance and cross-contamination.

Materials/methods
We developed an ex vivo model using porcine skin to study the potential of film-forming agents in prevention and treatment of dermatophytosis caused by Trichophyton rubrum. We used cell viability assays, confocal and electron microscopy to study the effects of film-forming agents on T. rubrum, followed by using QTOF-LCMS and NMR to analyse the carbohydrates binding and chelation to study its mechanism of action.

Results
A cationic polymer used in pharmaceutical and cosmetic products inhibited growth of T. rubrum on porcine skin. Viability assays indicated that the polymer has a fungistatic activity and microscopy imaging indicated it formed a coating on top of T. rubrum. The QTOF-LCMS and NMR indicated the polymer inhibits fungal growth by removing the carbohydrate content and chelation.

Conclusions
The present study suggests this cationic polymer has considerable antifungal activity against Trichophyton rubrum by preventing the supply of nutrients to the fungi.
Epidemiological characteristics of the Manchurian plague pandemic of 1910-1911
Authors: Dou Xiangfeng , Chen Meng , Li Shuang , Chen Yanwei , Pang Xinghuo , Wang Quanyi 
Published: April 2019

Objective
To investigate the epidemiological characteristics of the Manchurian plague pandemic of 1910–1911 with descriptive epidemiological methods.

Methods
The epidemiological data were distracted from Report of Manchurian Plague, which is a summary of local official reports about plague in 1910–1911. The time distribution by day, and the space distribution by country was recorded, and also the source of infection.

Results
The pandemic of plague continued from October 25th, 1910 to April 18th, 1911. There were 46 747 dead cases on record in the three provinces of Manchuria. There were 24 867 dead cases and 7068 dead cases were reported, and the average mortality rates were 41.21 and 10.25 per ten thousands in Jilin and Liaoning province, respectively. In Heilongjiang province, 14 812 dead cases of plague were reported. The huge difference was found in different epidemic regions, the highest mortality rate was 4121 per ten thousands in Binjiang country of Jilin province. Patient zero of pneumonic plague had been infected in Russia and got sick and died in Manzhouli, a northern country in Heilongjiang province. Then the pneumonic plague was mainly spread through railway to other cities.

Conclusion
The epidemiological characteristics of the Manchurian plague pandemic of 1910–1911 were first described with modern epidemiological methods.
Investigation into the physicochemical interactions of silica nanoparticles and EPS biomolecules within the biofilm matrix of Pseudomonas spp.
Authors: Hiebner Dishon , Barros Caio , Devlin Henry , Fulaz Stephanie , Quinn Laura , Vitale Stefania , Casey Eoin 
Published: April 2019

Difficulties in the removal of bacterial biofilms in the industrial and biomedical sectors have driven the development of new technologies. Although numerous studies have highlighted the use of nanoparticles (NPs) as antibiofilm agents, the fundamental physicochemical interactions between NPs and the biofilm matrix is still poorly understood 1. The development of ‘smart nanoparticles’ for biofilm removal requires an in-depth understanding of the complex interactions between NPs and biomolecules within the extracellular polymeric substances (EPS) of the biofilm matrix. These interactions are highly dependent on the physical and chemical properties of the NPs 2. In order to identify and characterize the specificity of binding and the direct interaction between silica NPs (SiNPs) and EPS matrix components of Pseudomonas spp. biofilms, a range of experiments were carried out. Biofilms were exposed to SiNPs of different sizes, charges and surface functionalization while biomolecules such as proteins, polysaccharides, and eDNA were fluorescently labelled and their distribution, relative abundance and their colocalization with SiNPs within the biofilm was quantitatively assessed using CLSM microscopy. Changes to the SiNPs size and surface-chemistry dramatically affected their interactions with biomolecules in the biofilm matrix. This includes the increased affinity (or interaction) of SiNPs to preferentially bind to proteins and beta-linked polysaccharides and also lead to changes in the degree to which aggregation of SiNPs occurs within and on the surface of the biofilm.
1. Ikuma K et al. (2015). Front. Microbiol. 6, 591
2. Bewersdorff, et al. (2017). Int. J. Nanomed. 12, 2001–2019
From Antarctic DNA to stress tolerant crop plants – exploiting the why protein domain
Authors: Mertens Jasmin , Anderson Dominique , Ferreras Eloy , Cowan Don 
Published: April 2019

Screening of an Antarctic soil functional fosmid metagenomic library identified a novel bacterial gene, homologous to known Water Hypersensitivity (WHy) domains. The WHy domain is a typical component of Late Embryogenesis Abundant (LEA) proteins which occurs widely in both prokaryotes and in plant eukaryotes and are expressed under various stress conditions [1]. A phylogenetic analysis of multiple WHy homologues from different species suggested that the ancestral origin of this protein gene lies within the ancient archaea [1]. Our previous studies have shown that this bacterial protein elicits significant protection against freeze and cold stress in recombinant E. coli [2]. Expression of the WHy gene in Arabidopsis resulted in a wide range of statistically significant stress-tolerant phenotypic properties. These included an increase of up to 6-fold higher germination efficiency of transgenic recombinant seeds compared to the WT, and a 100 % survival rate of WHy gene-expressing plants compared to 0 % survival of adult WT plants after freeze shock. Similar improvements in survival rates were observed for recombinant plants in drought stress experiments.

References
Mertens J, Aliyu H, Cowan DA (2018). Applied and environmental microbiology, AEM-00539.
Anderson D, Ferreras E, Trindade M, Cowan D (2015). FEMS Microbiology Letters, 362(15):fnv110.
Assessing metabolite biogeography of Micrococcus spp. and Pseudonocardia spp. isolated from marine environments
Authors: Parra Jonathan , Duncan Katherine R. 
Published: April 2019

The study of biogeography enables an understanding of the distribution patterns of biodiversity across space and time [1]. Therefore, byusing a trait-based approach, such as antibiotic production, it is possible to assess the evolutionary, geographic and ecological variables that affect the Actinobacteria specialized metabolism [2, 3]. This is particularly important as Actinobacteria isolated from marine ecosystems have been shown to be a promising source of new drugs [4, 5]. In this study, a comparative metabolomics approach using molecular networking was applied to understand the role of biogeography on the specialized metabolism of Micrococcus spp. and Pseudonocardia spp. isolated from Arctic and Antarctic marine sediments. The LC-MS/MS analysis showed differences in the specialized metabolism of phylogenetically related strains isolated from different geographic regions. These preliminary results suggest an influence on the microbial chemical space through assessing biogeographic impact. Future work on further marine ecosystems will expand our knowledge on the relationship between the chemistry and ecology of rare Actinobacteria.

References
1. Lomolino, M. V., Riddle, B. R. and Whittaker, R. J. Biogeography. (Sinauer, 2016).
2. Morlon, H. et al. The biogeography of putative microbial antibiotic production. PLoS One 10, 1–15 (2015).
3. Krause, S. et al. Trait-based approaches for understanding microbial biodiversity and ecosystem functioning. Front Microbiol 5, 1–10 (2014).
4. Fenical, W. and Jensen, P. R. Developing a new resource for drug discovery: Marine actinomycete bacteria. Nat Chem Biol 2, 666–673 (2006).
5. Hug, J. et al. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics 7, 44 (2018).
Understanding the pathogenic process of uropathogenic Escherichia coli ST127 using proteomics on uroepithelial co-culture samples
Authors: Saeedi Nizar , Sharma Vikram , Jackson Simon , Upton Mathew 
Published: April 2019

Background
Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). Strains of sequence type (ST) 127 exhibit the highest virulence potential of most UPEC strains, but little is known about pathogenicity during infection. We sought to investigate this using a quantitative proteomics approach.

Material/Methods
Three strains of UPEC ST127 (EC18, EC41 and SA189), in addition to non-pathogenic strain E. coli K12, were analysed in co-culture with the uroepithelial cell-line HT1197 for 5 h. We analyzed the bacterial and uroepithelial proteome along with the secreted proteins in the medium (secretome). The digested proteins and peptides from all fractions were separated on a Dionex Ultimate 3000 RSLC nano flow system and analyzed in an Orbitrap Velos Pro FTMS. Data were processed using Persues software.

Results
Label free quantitative proteomics revealed different proteomic profiles of the co-cultured strains. Gene Ontology enrichmentanalysis showed upregulation in the pentose phosphate pathway and glycolysis/glycogenesis in EC18 (an O-antigen deficient mutant). These two pathways could be important routes of carbon flux through the central metabolic pathways during growth in urine. Co-culture of SA189 with HT1197 cells leads to apparent cytotoxic effects in HT1197 cells not seen with other UPEC strains. Analysis of the SA189 secretome revealed highly abundant bacterial proteins, some of which (e.g. aromatic-amino-acid aminotransferase) were uniquely found during co-culture conditions.

Conclusion
Proteomics is crucial towards increasing our understanding of the pathogenic potential of UPEC ST127 strains and may facilitate identification of novel diagnostic or therapeutic targets to reduce UTI.
Macrolide-resistant Mycoplasma genitalium in male and female patients attending a Northern Irish Genitourinary Medicine Clinic
Authors: Cox Ciara , McKenna James , McCaughey Conall , Watt Alison 
Published: April 2019

Background

Mycoplasma genitalium (MG) can cause urethritis in men and pelvic inflammatory disease in women. Despite the increasing rate of MG resistance to first-line macrolide treatment due to 23S rRNA gene mutations, the availability of testing remains limited in UK laboratories. This study obtained preliminary data on the rate of macrolide resistant strains circulating in N. Ireland.

Methods
Clinical specimens from 1052 patients attending a Genitourinary Medicine (GUM) clinic in Belfast from April 2017 to April 2018 were screened using an in-house MG PCR assay. MG positive samples were subsequently tested using Resistance Plus™ MG assay (Speedx, Australia) to detect 23S rRNA gene mutations associated with macrolide resistance.

Results
Amongst all study samples, 3.9 % (n=41) tested positive for MG. Out of these 41.5 % (n=17) had a 23S rRNA mutation. The rate of MG was highest in rectal swabs (8.13 %) followed by vaginal swabs (4.96 %) and then male urines (2.85 %). The rate of 23 S rRNA mutations associated with macrolide resistance in positive vaginal swabs was 21.4 % whereas the rate amongst urine and rectal swabs was at least 50 %.

Conclusion
Data from this study adds to the evidence base to perform MG testing in risk groups in N. Ireland to improve patient outcomes and reduce antimicrobial resistance.