NCTC3000: a century of bacterial strain collecting leads to a rich genomic data resource

The National Collection of Type Cultures (NCTC) was founded on 1 January 1920 in order to fulfil a recognized need for a centralized repository for bacterial and fungal strains within the UK. It is among the longest-established collections of its kind anywhere in the world and today holds approximately 6000 type and reference bacterial strains - many of medical, scientific and veterinary importance - available to academic, health, food and veterinary institutions worldwide. Recently, a collaboration between NCTC, Pacific Biosciences and the Wellcome Sanger Institute established the NCTC3000 project to long-read sequence and assemble the genomes of up to 3000 NCTC strains. Here, at the beginning of the collection's second century, we introduce the resulting NCTC3000 sequence read datasets, genome assemblies and annotations as a unique, historically and scientifically relevant resource for the benefit of the international bacterial research community.

Occupational (In)visibility: The emerging role of the Remote Education Tutor as an educational conduit

Remote Education Tutors (RETs) are central to the delivery of distance schooling in Australia and are accountable for the face-to face supervision and educational support of students. They act as the government mandated adult supervisors of Australian primary and secondary school students enrolled in distance education, including geographically isolated learners. This paper draws on statistical data from a national survey (N = 575) that was designed to map the perceptions of Australian RETs. These data confirmed that RETs act as a conduit between the distance schooling teacher and student, and that their role requires complex capabilities to be performed within a structured framework. Time restrictions with competing demands present a constant challenge to the RETs' work satisfaction. Constraining this occupation is the reality that there is no formal qualification available for RETs. Without specific credentialling, it appears that the RETs' (in)visible role risks being overlooked as a substantive educational occupation.

How much is that doodle in the window? Exploring motivations and behaviours of UK owners acquiring designer crossbreed dogs (2019-2020)

Background

Demand for intentional crosses of purebred dog breeds, often labelled ‘designer crossbreeds’ (e.g., Labrador Retriever X Poodle, the ‘Labradoodle’), has recently increased in the UK. This study aimed to explore this phenomenon by comparing pre-purchase motivations, pre-purchase and purchase behaviours of UK owners of designer crossbred puppies purchased during 2019-2020 with those of owners of purebred puppies purchased during the same period.

Results

Data were collected in an online cross-sectional survey between November-December 2020. Responses from n = 6293 puppies (designer crossbred puppies: n = 1575; purebred puppies: n = 4718) were analysed. Perceived hypoallergenicity was cited as a motivator for breed/crossbreed choice by almost half of designer crossbreed owners (47.1%), six times more than purebred dog owners (7.86%; odds ratio [OR]: 9.12, 95% CI: 7.70-10.8). Designer crossbred puppies were more likely to have been acquired via a general selling website (e.g., Gumtree; 13.8%) compared to purebred puppies (7.67%; OR: 2.19, 95% CI: 1.77-2.71), or an animal-specific selling websites (e.g., Pets4Homes; 55.7%) compared to purebred puppies (37.4%; OR: 1.89, 95% CI: 1.65-2.17). Designer crossbreed owners were less likely to see their puppy in person prior to purchase than purebred owners (60.4% vs. 67.0%, respectively; OR: 0.74, 95% CI: 0.64-0.85), and at purchase, designer crossbred puppies were less likely to be seen with their mother (73.1% vs. 79.8%, respectively; OR: 0.82, 95% CI: 0.70-0.95), and littermates (67.7% vs. 78.1%, respectively; OR: 0.63, 95% CI: 0.55-0.73). Designer crossbreeds had a significantly higher purchase price, with 25.7% of designer crossbreed puppies costing £2000-£2999 compared to 15.1% of purebred puppies (X² = 207.31, p <  0.001).

Conclusions

The recent boom in designer crossbreeds in the UK has been fuelled by a desire for perceived hypoallergenic and generally healthy dogs that fit the lifestyles of households with children and limited experience with dogs. Some sought-after traits in designer crossbreeds are misconceptions that risk canine welfare, including relinquishment risk, if owner expectations are not met. Purchasing practices fuelling this boom support irresponsible breeding and selling practices, which combined with reduced pressure for health testing from buyers, may result in a higher disease burden and poorer future welfare for this growing designer dog population.

Investigation of the utility of the 1.1B4 cell as a model human beta cell line for study of persistent enteroviral infection

The generation of a human pancreatic beta cell line which reproduces the responses seen in primary beta cells, but is amenable to propagation in culture, has long been an important goal in diabetes research. This is particularly true for studies focussing on the role of enteroviral infection as a potential cause of beta-cell autoimmunity in type 1 diabetes. In the present work we made use of a clonal beta cell line (1.1B4) available from the European Collection of Authenticated Cell Cultures, which had been generated by the fusion of primary human beta-cells with a pancreatic ductal carcinoma cell, PANC-1. Our goal was to study the factors allowing the development and persistence of a chronic enteroviral infection in human beta-cells. Since PANC-1 cells have been reported to support persistent enteroviral infection, the hybrid 1.1B4 cells appeared to offer an ideal vehicle for our studies. In support of this, infection of the cells with a Coxsackie virus isolated originally from the pancreas of a child with type 1 diabetes, CVB4.E2, at a low multiplicity of infection, resulted in the development of a state of persistent infection. Investigation of the molecular mechanisms suggested that this response was facilitated by a number of unexpected outcomes including an apparent failure of the cells to up-regulate certain anti-viral response gene products in response to interferons. However, more detailed exploration revealed that this lack of response was restricted to molecular targets that were either activated by, or detected with, human-selective reagents. By contrast, and to our surprise, the cells were much more responsive to rodent-selective reagents. Using multiple approaches, we then established that populations of 1.1B4 cells are not homogeneous but that they contain a mixture of rodent and human cells. This was true both of our own cell stocks and those held by the European Collection of Authenticated Cell Cultures. In view of this unexpected finding, we developed a strategy to harvest, isolate and expand single cell clones from the heterogeneous population, which allowed us to establish colonies of 1.1B4 cells that were uniquely human (h1.1.B4). However, extensive analysis of the gene expression profiles, immunoreactive insulin content, regulated secretory pathways and the electrophysiological properties of these cells demonstrated that they did not retain the principal characteristics expected of human beta cells. Our data suggest that stocks of 1.1B4 cells should be evaluated carefully prior to their use as a model human beta-cell since they may not retain the phenotype expected of human beta-cells.

Impact of rotavirus vaccine on all-cause diarrhea and rotavirus hospitalizations in Madagascar

BACKGROUND

Rotavirus vaccine was introduced into the Extended Program on Immunization in Madagascar in May 2014. We analyzed trends in prevalence of all cause diarrhea and rotavirus hospitalization in children <5years of age before and after vaccine introduction and assessed trend of circulating rotavirus genotypes at Centre Hospitalier Universitaire Mère Enfant Tsaralalàna (CHU MET).

METHODS

From January 2010 to December 2016, we reviewed the admission logbook to observe the rate of hospitalization caused by gastroenteritis among 19619 children <5years of age admitted at the hospital. In June 2013-December 2016, active rotavirus surveillance was also conducted at CHUMET with support from WHO. Rotavirus antigen was detected by EIA from stool specimen of children who are eligible for rotavirus gastroenteritis surveillance at sentinel site laboratory and rotavirus positive specimens were further genotyped at Regional Reference Laboratory by RT-PCR.

RESULTS

Diarrhea hospitalizations decreased after rotavirus vaccine introduction. The median proportion of annual hospitalizations due to diarrhea was 26% (range: 31-22%) before vaccine introduction; the proportion was 25% the year of vaccine introduction, 17% in 2015 and 16% in 2016. Rotavirus positivity paralleled patterns observed in diarrhea. Before vaccine introduction, 56% of stool specimens tested positive for rotavirus; the percent positive was 13% in 2015, 12% in 2016. Diverse genotypes were detected in the pre-vaccine period; the most common were G3P[8] (n=53; 66%), G2P[4] (n=12; 15%), and G1P[8] (n=11; 14%). 6 distinct genotypes were found in 2015; the most common genotype was G2P[4] (n=10; 67%), the remaining, 5, G12[P8], G3[P8], G1G3[P4], G3G12[P4][P8] and G1G3[NT] had one positive specimen each.

CONCLUSIONS

Following rotavirus vaccine introduction all-cause diarrhea and rotavirus-specific hospitalizations declined dramatically. The most common genotypes detected in the pre-vaccine period were G3P[8] and G2P[4] in 2015, the post vaccine period.

The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that predate the widespread clinical use of antimicrobials. The Murray collection of several hundred bacterial strains of pre-antibiotic era Enterobacteriaceae is an invaluable resource of historical strains from important pathogen groups. Studies performed on the Collection to date merely exemplify its potential, which will only be realised through the continued effort of many scientific groups. To enable that aim, we announce the public availability of the Murray collection through the National Collection of Type Cultures, and present associated metadata with whole genome sequence data for over half of the strains. Using this information we verify the metadata for the collection with regard to subgroup designations, equivalence groupings and plasmid content. We also present genomic analyses of population structure and determinants of mobilisable antimicrobial resistance to aid strain selection in future studies. This represents an invaluable public resource for the study of these important pathogen groups and the emergence and evolution of antimicrobial resistance.

The outcome competency framework for practitioners in infection prevention and control: use of the outcome logic model for evaluation

Healthcare is delivered in a dynamic environment with frequent changes in populations, methods, equipment and settings. Infection prevention and control practitioners (IPCPs) must ensure that they are competent in addressing the challenges they face and are equipped to develop infection prevention and control (IPC) services in line with a changing world of healthcare provision. A multifaceted Framework was developed to assist IPCPs to enhance competence at an individual, team and organisational level to enable quality performance and improved quality of care. However, if these aspirations are to be met, it is vital that competency frameworks are fit for purpose or they risk being ignored. The aim of this unique study was to evaluate short and medium term outcomes as set out in the Outcome Logic Model to assist with the evaluation of the impact and success of the Framework. This study found that while the Framework is being used effectively in some areas, it is not being used as much or in the ways that were anticipated. The findings will enable future work on revision, communication and dissemination, and will provide intelligence to those initiating education and training in the utilisation of the competences.

Hand hygiene knowledge and attitudes: comparisons between student nurses

It is recognised that early intervention in healthcare workers’ education is important in terms of embedding effective infection prevention and control knowledge into practice. One of the most important aspects of this education is hand hygiene compliance and technique expectations. This small study was undertaken in collaboration with the University of Dundee, School of Nursing and Midwifery and NHS Tayside. It explored the differences in knowledge, attitudes and practice towards hand hygiene among second and third year student nurses with the aim of reviewing and informing the development of future educational material at undergraduate level in order to continually enhance knowledge and skills and bridge the theory–practice gap. This study concluded that third year student nurses did have a slightly better knowledge base than the second years and that although knowledge, attitudes and practice were reported to be of a good standard overall, there were still some important issues that must be addressed.

Immunoglobulin isotypes and functional anti-FVIII antibodies in response to FVIII treatment in Balb/c and C57BL/6 haemophilia A mice

Previous studies have demonstrated that genetic factors play an important role in determining the likelihood of formation of anti-factor VIII (FVIII) antibodies in haemophilia A patients. We were interested in characterizing the spectrum of FVIII antibody formation and the primary and secondary immune responses after FVIII administration in two different exon 16-disrupted haemophilia A mouse strains, Balb/c and C57BL/6. Balb/c and C57BL/6 E16 haemophilia A mice were used in all experiments. Total FVIII antibodies and FVIII inhibitors were measured using ELISA and Bethesda assays respectively. T- and B-cell cytokines were quantified using ELISA and flow cytometry. FVIII antibodies, but not functional inhibitors were detectable 1 week after the first FVIII treatment in both strains. These antibodies mainly belonged to the IgM and IgA isotypes. After the fourth FVIII treatment, neutralizing anti-FVIII antibodies were detected in both mouse strains: Balb/c (mean inhibitory titer 58 BU) and C57BL/6 (mean inhibitory titer 82 BU). IgG1 levels were similar in both strains but the IgG2A and IgG2B subclasses were higher in C57BL/6 mice. The results of intracellular cytokine staining of T cells indicated that the FVIII-treated C57BL/6 mice produced more IL10 and Th1 cytokines than the FVIII-treated Balb/c mice. These studies show that C57BL/6 mice develop a stronger immune response towards FVIII than Balb/c mice. We propose that the enhanced Th1 and IL10 cytokine micro-environment induced in C57BL/6 mice is responsible for this difference. Therefore, genetic strain-dependent differences must be considered when evaluating immunological outcomes in mouse models of haemophilia A.

Innovative infection prevention and control teaching for nursing students: a personal reflection

A crucial part of our role as Infection Prevention and Control Practitioners is to develop, facilitate and evaluate the teaching and learning of students and healthcare workers. However, creating an environment for participation, interaction and socialisation whilst effectively stimulating reflective and critical thinking in order to promote good practice can be challenging. This paper is a critical reflection, based on Gibb’s model of reflection to demonstrate the development, facilitation, support and evaluation of learning using an innovative, interactive method.

From theory to practice in learning about healthcare associated infections: reliable assessment of final year medical students' ability to reflect

BACKGROUND

Healthcare associated infection affects 9% of patients admitted to hospital. One of the greatest challenges in addressing this problem is transferring theory to practice in relation to hand hygiene. Developing the ability to reflect can promote this transfer. This study illustrates how an instrument to assess the reflective ability of final year medical students was applied to the context of hand hygiene within the infection control cleanliness champion programme (CCP) and demonstrated inter-rater reliability at all three levels of reflection. The results suggest behaviour change in relation to practice.

METHODS

One hundred and thirty two reflective accounts were used for this study, provided by 44 5th year medical students. Each student had written three reflective accounts for each part of the hand hygiene unit. Results show that the inter-rater agreement was consistently high for all three levels of reflection. However, the least consistent was at reflective level three.

CONCLUSIONS

These results suggest that the students were able to link theory to practice following the completion of the CCP. It could also indicate that assessors might require more skills and knowledge to enable effective and consistent examination of all areas of reflection.

A genome-wide association study of global gene expression

We have created a global map of the effects of polymorphism on gene expression in 400 children from families recruited through a proband with asthma. We genotyped 408,273 SNPs and identified expression quantitative trait loci from measurements of 54,675 transcripts representing 20,599 genes in Epstein-Barr virus-transformed lymphoblastoid cell lines. We found that 15,084 transcripts (28%) representing 6,660 genes had narrow-sense heritabilities (H2) > 0.3. We executed genome-wide association scans for these traits and found peak lod scores between 3.68 and 59.1. The most highly heritable traits were markedly enriched in Gene Ontology descriptors for response to unfolded protein (chaperonins and heat shock proteins), regulation of progression through the cell cycle, RNA processing, DNA repair, immune responses and apoptosis. SNPs that regulate expression of these genes are candidates in the study of degenerative diseases, malignancy, infection and inflammation. We have created a downloadable database to facilitate use of our findings in the mapping of complex disease loci.

A consensus DNA recognition motif for two KDWK transcription factors identifies flexible-length, CpG-methylation sensitive cognate binding sites in the majority of human promoters

Parvovirus initiation factor (PIF), identified in HeLa cells as a host factor essential for parvoviral DNA replication, is a ubiquitous heterodimeric cellular transcription factor. This protein complex was simultaneously identified as glucocorticoid modulatory element binding protein (GMEB) by its ability to bind to the glucocorticoid modulating element (GME) upstream of the tyrosine transaminase promoter. Here, we show that the two PIF/GMEB subunits form site-specific DNA-binding heterodimers when co-expressed from recombinant baculoviruses and homodimers when expressed separately. Degenerate oligonucleotide selection experiments, combined with analysis of dissociation rates, established that the three complexes bind to flexibly spaced tetranucleotide half-sites that conform to the consensus ACGPy N(1-9) PuCGPy, with an optimum of N=6. Binding of all three complexes is extremely sensitive to methylation of the cytosine residues in the invariant CpG half-site core, suggesting a means by which PIF/GMEB binding could be regulated in vivo. Because CpG dinucleotides are suppressed in eukaryotic genomes, such binding sites would be expected to be very rare. However, analysis of 100 human promoters showed that over half of them contained at least one site conforming to the consensus, a significant deviation from the expected random distribution. In many of these, the binding site is within 100 nucleotides of the transcriptional start site, indicating that PIF/GMEB may be involved in regulation of these genes. Oligonucleotides corresponding to five of these sequences, chosen to represent the range of half-site separations identified by the consensus, were tested for PIF/GMEB binding by mobility shift assay. All five probes bound the heterodimer efficiently and, in each case, binding was completely abrogated by 5-methylation of the C residues in the CpGs of the putative half-sites.

Activation of EphA receptor tyrosine kinase inhibits the Ras/MAPK pathway

Interactions between Eph receptor tyrosine kinases (RTKs) and membrane-anchored ephrin ligands critically regulate axon pathfinding and development of the cardiovascular system, as well as migration of neural cells. Similar to other RTKs, ligand-activated Eph kinases recruit multiple signalling and adaptor proteins, several of which are involved in growth regulation. However, in contrast to other RTKs, activation of Eph receptors fails to promote cell proliferation or to transform rodent fibroblasts, indicating that Eph kinases may initiate signalling pathways that are distinct from those transmitted by other RTKs. Here we show that stimulation of endogenous EphA kinases with ephrin-A1 potently inhibits the Ras/MAPK cascade in a range of cell types, and attenuates activation of mitogen-activated protein kinase (MAPK) by receptors for platelet-derived growth factor (PDGF), epidermal growth factor (EGF) and vascular endothelial growth factor (VEGF). In prostatic epithelial cells and endothelial cells, but not fibroblasts, treatment with ephrin-A1 inhibits cell proliferation. Our results identify EphA kinases as negative regulators of the Ras/MAPK pathway that exert anti-mitogenic functions in a cell-type-specific manner.

Activation of EphA2 kinase suppresses integrin function and causes focal-adhesion-kinase dephosphorylation

Interactions between receptor tyrosine kinases of the Eph family and their ligands, ephrins, are implicated in establishment of organ boundaries and repulsive guidance of cell migration during development, but the mechanisms by which this is achieved are unclear. Here we show that activation of endogenous EphA2 kinase induces an inactive conformation of integrins and inhibits cell spreading, migration and integrin-mediated adhesion. Moreover, EphA2 is constitutively associated with focal-adhesion kinase (FAK) in resting cells. Within one minute after stimulation of EphA2 with its ligand, ephrin-A1, the protein tyrosine phosphatase SHP2 is recruited to EphA2; this is followed by dephosphorylation of FAK and paxillin, and dissociation of the FAK-EphA2 complex. We conclude that Eph kinases mediate some of their functions by negatively regulating integrins and FAK.

A case report: special needs of hospitalized elders

A case report is used to discuss common problems and complications of hospitalized elders. The report also illustrates the need for proactive hospital staff who are knowledgeable about the special needs of the aging population if this group is to be cared for successfully. The geriatric resource nurse model involves informal unit-based education aimed at expanding staff nurses' geriatric knowledge and is one of several models sponsored by the Hartford Foundation to improve care of the hospitalized elderly. Teaching rounds between geriatric resource nurses and advanced practice nurses are a primary feature of this model.

Targeting speech processing strengths to facilitate pronunciation change

This paper reports investigation and intervention with a 5 year old boy (AG) with unintelligible speech. Phonological analysis and psycholinguistic investigation allowed exploration of his speech processing strengths and difficulties as a basis for planning intervention. It was hypothesised that intervention which exploited his strengths, without focusing directly on his difficulties, would enable him to discover how to modify his pronunciation patterns. Significant positive changes had occurred by age 6 years.