Design, development, and validation of a strand-specific RT-qPCR assay for GI and GII human Noroviruses.

Human noroviruses (HuNoV) are the major cause of viral gastroenteritis worldwide. Similar to other positive-sense single-stranded RNA viruses, norovirus RNA replication requires the formation of a negative strand RNA intermediate. Methods for detecting and quantifying the viral positive or negative sense RNA in infected cells and tissues can be used as important tools in dissecting virus replication. In this study, we have established a sensitive and strand-specific Taqman-based quantitative polymerase chain reaction (qPCR) assay for both genogroups GI and GII HuNoV. This assay shows good reproducibility, has a broad dynamic range and is able to detect a diverse range of isolates. We used tagged primers containing a non-viral sequence for the reverse transcription (RT) reaction and targeted this tag in the succeeding qPCR reaction to achieve strand specificity. The specificity of the assay was confirmed by the detection of specific viral RNA strands in the presence of high levels of the opposing strands, in both RT and qPCR reactions. Finally, we further validated the assay in norovirus replicon-bearing cell lines and norovirus-infected human small intestinal organoids, in the presence or absence of small-molecule inhibitors. Overall, we have established a strand-specific qPCR assay that can be used as a reliable method to understand the molecular details of the human norovirus life cycle

Norovirus Replication in Human Intestinal Epithelial Cells Is Restricted by the Interferon-Induced JAK/STAT Signaling Pathway and RNA Polymerase II-Mediated Transcriptional Responses.

Human noroviruses (HuNoV) are a leading cause of viral gastroenteritis worldwide and a significant cause of morbidity and mortality in all age groups. The recent finding that HuNoV can be propagated in B cells and mucosa-derived intestinal epithelial organoids (IEOs) has transformed our ability to dissect the life cycle of noroviruses. Using transcriptome sequencing (RNA-Seq) of HuNoV-infected intestinal epithelial cells (IECs), we have found that replication of HuNoV in IECs results in interferon (IFN)-induced transcriptional responses and that HuNoV replication in IECs is sensitive to IFN. This contrasts with previous studies that suggested that the innate immune response may play no role in the restriction of HuNoV replication in immortalized cells. We demonstrated that inhibition of Janus kinase 1 (JAK1)/JAK2 enhanced HuNoV replication in IECs. Surprisingly, targeted inhibition of cellular RNA polymerase II-mediated transcription was not detrimental to HuNoV replication but instead enhanced replication to a greater degree than blocking of JAK signaling directly. Furthermore, we demonstrated for the first time that IECs generated from genetically modified intestinal organoids, engineered to be deficient in the interferon response, were more permissive to HuNoV infection. Taking the results together, our work revealed that IFN-induced transcriptional responses restrict HuNoV replication in IECs and demonstrated that inhibition of these responses mediated by modifications of the culture conditions can greatly enhance the robustness of the norovirus culture system.IMPORTANCE Noroviruses are a major cause of gastroenteritis worldwide, and yet the challenges associated with their growth in culture have greatly hampered the development of therapeutic approaches and have limited our understanding of the cellular pathways that control infection. Here, we show that human intestinal epithelial cells, which represent the first point of entry of human noroviruses into the host, limit virus replication by induction of innate responses. Furthermore, we show that modulating the ability of intestinal epithelial cells to induce transcriptional responses to HuNoV infection can significantly enhance human norovirus replication in culture. Collectively, our findings provide new insights into the biological pathways that control norovirus infection but also identify mechanisms that enhance the robustness of norovirus culture

Mapping Antimicrobial Stewardship in Undergraduate Medical, Dental, Pharmacy, Nursing and Veterinary Education in the United Kingdom.

OBJECTIVES: To investigate the teaching of antimicrobial stewardship (AS) in undergraduate healthcare educational degree programmes in the United Kingdom (UK). PARTICIPANTS AND METHODS: Cross-sectional survey of undergraduate programmes in human and veterinary medicine, dentistry, pharmacy and nursing in the UK. The main outcome measures included prevalence of AS teaching; stewardship principles taught; estimated hours apportioned; mode of content delivery and teaching strategies; evaluation methodologies; and frequency of multidisciplinary learning. RESULTS: 80% (112/140) of programmes responded adequately. The majority of programmes teach AS principles (88/109, 80.7%). 'Adopting necessary infection prevention and control precautions' was the most frequently taught principle (83/88, 94.3%), followed by 'timely collection of microbiological samples for microscopy, culture and sensitivity' (73/88, 82.9%) and 'minimisation of unnecessary antimicrobial prescribing' (72/88, 81.8%). The 'use of intravenous administration only to patients who are severely ill, or unable to tolerate oral treatment' was reported in ~50% of courses. Only 32/88 (36.3%) programmes included all recommended principles. DISCUSSION: Antimicrobial stewardship principles are included in most undergraduate healthcare and veterinary degree programmes in the UK. However, future professionals responsible for using antimicrobials receive disparate education. Education may be boosted by standardisation and strengthening of less frequently discussed principles

The role of venues in structuring HIV, sexually transmitted infections, and risk networks among men who have sex with men.

Background Venues form part of the sampling frame for time-location sampling, an approach often used for HIV surveillance. While sampling location is often regarded as a nuisance factor, venues may play a central role in structuring risk networks. We investigated individual reports of risk behaviors and infections among men who have sex with men (MSM) attending different venues to examine structuring of HIV risk behaviors. However, teasing apart ‘risky people’ from ‘risky places’ is difficult, as individuals cannot be randomized to attend different venues. However, we can emulate this statistically using marginal structural models, which inversely weight individuals according to their estimated probability of attending the venue. Methods We conducted a cross-sectional survey of 609 MSM patrons of 14 bars in San Diego, California, recruited using the Priorities for Local AIDS Control Efforts (PLACE) methodology, which consists of a multi-level identification and assessment of venues for HIV risk through population surveys. Results and Discussion Venues differed by many factors, including participants’ reported age, ethnicity, number of lifetime male partners, past sexually transmitted infection (STI), and HIV status. In multivariable marginal structural models, venues demonstrated structuring of HIV+ status, past STI, and methamphetamine use, independently of individual-level characteristics. Conclusions Studies using time-location sampling should consider venue as an important covariate, and the use of marginal structural models may help to identify risky venues. This may assist in widespread, economically feasible and sustainable targeted surveillance and prevention. A more mechanistic understanding of how 'risky venues' emerge and structure risk is needed

Fragmentation of care threatens patient safety in peripheral vascular catheter management in acute care--a qualitative study.

BACKGROUND: The use of peripheral vascular catheters (PVCs) is an extremely common and necessary clinical intervention, but inappropriate PVC care poses a major patient safety risk in terms of infection. Quality improvement initiatives have been proposed to reduce the likelihood of adverse events, but a lack of understanding about factors that influence behaviours of healthcare professionals limits the efficacy of such interventions. We undertook qualitative interviews with clinical staff from a large group of hospitals in order to understand influences on PVC care behaviors and subsequent patient safety. METHODS: Ten doctors, ten clinical pharmacists, 18 nurses and one midwife at a National Health Service hospital group in London (United Kingdom) were interviewed between December 2010 and July 2011 using qualitative methods. Responses were analysed using a thematic framework. RESULTS: FOUR KEY THEMES EMERGED: 1) Fragmentation of management and care, demonstrated with a lack of general overview and insufficient knowledge about expected standards of care or responsibility of different professionals; 2) feelings of resentment and frustration as a result of tensions in the workplace, due to the ambiguity about professional responsibilities; 3) disregard for existing hospital policy due to perceptions of flaws in the evidence used to support it; and 4) low-risk perception for the impact of PVC use on patient safety. CONCLUSION: Fragmentation of practice resulted in ill-defined responsibilities and interdisciplinary resentment, which coupled with a generally low perception of risk of catheter use, appeared to result in lack of maintaining policy PVC standards which could reduced patient safety. Resolution of these issues through clearly defining handover practice, teaching interdisciplinary duties and increasing awareness of PVC risks could result in preventing thousands of BSIs and other PVC-related infections annually

A needs assessment study for optimising prescribing practice in secondary care junior doctors: the Antibiotic Prescribing Education among Doctors (APED).

BACKGROUND: Appropriate antimicrobial prescribing is essential for patient care, yet up to half of antimicrobial prescriptions written in the UK are sub-optimal. Improving prescriber education has recently been promoted as a mechanism to optimise antimicrobial use, but identification of key learning objectives to facilitate this is so far lacking. Using qualitative methods we investigated junior doctor knowledge, attitudes, and behaviours around antimicrobial prescribing to identify key areas to address in future educational programmes. METHODS: A cross-sectional survey of qualified doctors in training in West London was undertaken exploring antimicrobial prescribing practices and educational needs. RESULTS: Among 140 junior doctors from 5 London hospitals, a third (34 %) reported prescribing primarily unsupervised, and two thirds (67 %) reported difficulties obtaining prescribing support outside of hours. 20 % stated not feeling confident in writing an antimicrobial prescription, but confidence was increased through having confirmatory diagnostic results (24) and obtaining advice from a senior doctor (26 %); whether this senior was from their own specialty, or an infection-specialist, varied significantly (p < 0.01) by experience. Only a small percentage (5-13 %; depending on number of years post-qualification) of participants stated their previous antimicrobial education was effective. 60 % of those in their first year post qualification reported wanting further education in antimicrobial prescribing, rising to 74 % among more experienced junior doctors. Specific areas of educational need identified were (i) principles of antimicrobial prescribing, (ii) diagnosis of infections, (iii) clinical review of patients with infections, (iv) prescribing in the context of antimicrobial resistance, and (v) laboratory testing and test results. CONCLUSIONS: A significant proportion of junior doctors report lone prescribing of antimicrobials in the context of low self-perceived confidence and knowledge in this field, and frequent difficulty in accessing help when necessary. Innovative training, targeting five specific areas identified through this needs assessment, is urgently needed by junior doctors practising in secondary care

Analysis of TaqMan Array Cards Data by an Assumption-Free Improvement of the maxRatio Algorithm Is More Accurate than the Cycle-Threshold Method

<div><p>Quantitative PCR diagnostic platforms are moving towards increased sample throughput, with instruments capable of carrying out thousands of reactions at once already in use. The need for a computational tool to reliably assist in the validation of the results is therefore compelling. In the present study, 328 residual clinical samples provided by the Public Health England at Addenbrooke's Hospital (Cambridge, UK) were processed by TaqMan Array Card assay, generating 15 744 reactions from 54 targets. The amplification data were analysed by the conventional cycle-threshold (CT) method and an improvement of the <i>maxRatio</i> (MR) algorithm developed to filter out the reactions with irregular amplification profiles. The reactions were also independently validated by three raters and a consensus was generated from their classification. The inter-rater agreement by Fleiss' kappa was 0.885; the agreement between either CT or MR with the raters gave Fleiss' kappa 0.884 and 0.902, respectively. Based on the consensus classification, the CT and MR methods achieved an assay accuracy of 0.979 and 0.987, respectively. These results suggested that the assumption-free MR algorithm was more reliable than the CT method, with clear advantages for the diagnostic settings.</p></div

Illicit substance use and risk of HIV transmission among men who have sex with men

Human immunodeficiency virus type 1 (HIV) continues to disproportionately affect men who have sex with men (MSM). Recent concern has focused on the use of 'club' drugs among MSM as a risk factor for HIV acquisition and transmission. To determine the extent to which the current literature demonstrates a causal association between use of individual 'club' drugs and risk for HIV among MSM, Hill's criteria for causation was applied to existing studies. A theoretical framework that demonstrates potential pathways through which these drugs could be associated with HIV acquisition is proposed, and definitions of what constitutes a 'club' drug discussed. Building upon this review, and addressing the Centers for Disease Control and Prevention's call for research addressing prevention among HIV positive individuals, substance use as a risk factor for unprotected anal intercourse (UAI) was investigated among MSM with recent HIV infection. All MSM were interviewed using a computer assisted survey instrument (CASI) on average 5 weeks after HIV diagnosis and 13 weeks after estimated date of infection. Associations between substance use and UAI in within-subjects analyses were modeled using conditional logistic regression (CLR). Associations between substance use and UAI in the entire sample were examined using generalized estimating equations (GEE). GEE models that included interactions between timing of sexual activity (before versus after diagnosis) and substance use were used to examine change in associations between UAI and substance use before and after HIV diagnosis. Among participants, 16% reported no UAI with any of their last three partners; 60% (n=116) reported UAI with some, but not all, of their last three partners; and 24% reported UAI with all of their last three partners. In multivariate CLR (n=116) and GEE (n=194) models, UAI was associated with use of methamphetamine (OR: 4.9 and 2.7 respectively), marijuana (OR: 4.0 and 1.9 respectively) and erectile dysfunction medications when used with a main partner (OR: 26.0 and 17.1 respectively). In GEE models (n=207) that examined interactions between UAI and substance use before and after HIV diagnosis, UAI was associated with methamphetamine use alone (OR=4.80, 95% CI: 1.4, 16.1) and a combination of methamphetamine and other substances (OR=4.11, 95% CI: 1.9, 8.8) before diagnosis. After HIV diagnosis, UAI was associated with use of substances other than methamphetamine (OR=1.96, 95% CI: 1.3, 5.3) and a combination of methamphetamine and other substances (OR=5.08, 95% CI: 2.3, 11.2), but not methamphetamine alone. These analyses indicate that a direct association may exist between use of methamphetamine and may be differentially associated with UAI based on knowledge of HIV status. These findings have implications for both prevention of high risk sexual behavior and substance use among recently HIV infected MS

Critical risk and success factors for sustainability of an electronic health data capture, processing and dissemination platform for Uganda.

Peer reviewed: TrueSeveral studies have investigated challenges that have marred success or even caused the failure of eHealth implementations in Uganda; however, none has focused on the risks and success factors of their sustainability. This study explored critical risk and success factors for the sustainability of an electronic health data capture, processing and dissemination platform for Uganda. A mixed-method research design was followed involving collecting empirical data from all four regions of Uganda. A purposive sampling strategy was used to select the study districts per region, health facilities per district, and respondents/participants per facility or district. Findings revealed several risks and success factors for sustainability, including; bad leadership, corruption, lack of sustainable maintenance programs, lack of suitable sustainability plans, lack of ICT infrastructure investment, poor management systems, funds, stakeholder buy-ins, data sharing and access rights. The success factors included reinvestments as a partial sustainability plan for ICT infrastructure. These factors can be leveraged to ensure the continued operation of eHealth implementations in Uganda. Every electronic health project aiming at success should always make due consideration/sustainability plan at the onset of project conceptualisation; as lack of such a plan has often resulted in failed projects after the initial funds have been withdrawn