Zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) provide powerful platforms for genome editing in plants and animals. Typically, a single nuclease is ...sufficient to disrupt the function of protein-coding genes through the introduction of microdeletions or insertions that cause frameshifts within an early coding exon. However, interrogating the function of cis-regulatory modules or noncoding RNAs in many instances requires the excision of this element from the genome. In human cell lines and invertebrates, two nucleases targeting the same chromosome can promote the deletion of intervening genomic segments with modest efficiencies. We have examined the feasibility of using this approach to delete chromosomal segments within the zebrafish genome, which would facilitate the functional study of large noncoding sequences in a vertebrate model of development. Herein, we demonstrate that segmental deletions within the zebrafish genome can be generated at multiple loci and are efficiently transmitted through the germline. Using two nucleases, we have successfully generated deletions of up to 69 kb at rates sufficient for germline transmission (1%-15%) and have excised an entire lincRNA gene and enhancer element. Larger deletions (5.5 Mb) can be generated in somatic cells, but at lower frequency (0.7%). Segmental inversions have also been generated, but the efficiency of these events is lower than the corresponding deletions. The ability to efficiently delete genomic segments in a vertebrate developmental system will facilitate the study of functional noncoding elements on an organismic level.
Summary
Background
Most patients are prescribed Helicobacter pylori treatment without culture and antibiotic susceptibility testing, as current guidance recommends that patients with recurrent ...dyspepsia should be tested for H. pylori using a non‐invasive breath or faecal antigen test.
Aims
To determine the prevalence of H. pylori antibiotic resistance in patients attending endoscopy in England and Wales, and the feasibility of an antibiotic resistance surveillance programme testing.
Methods
We tested the antibiotic susceptibility of H. pylori isolates from biopsy specimens from 2063 of 7791 (26%) patients attending for endoscopy in Gloucester and Bangor, and 339 biopsy specimens sent to the Helicobacter Reference Unit (HRU) in London. Culture and susceptibility testing was undertaken in line with National and European methods.
Results
Helicobacter pylori were cultured in 6.4% of 2063 patients attending Gloucester and Bangor hospitals. Resistance to amoxicillin, tetracycline and rifampicin/rifabutin was below 3% at all centres. Clarithromycin, metronidazole and quinolone resistance was significantly higher in HRU (68%, 88%, 17%) and Bangor isolates (18%, 43%, 13%) than Gloucester (3%, 22%, 1%). Each previous course of these antibiotics is associated with an increase in the risk of antibiotic resistance to that agent clarithromycin: RR = 1.5 (P = 0.12); metronidazole RR = 1.6 (P = 0.002); quinolone RR = 1.8 (P = 0.01).
Conclusions
Helicobacter pylori infection is now uncommon in dyspeptic patients at endoscopy. A surveillance system is feasible and necessary to inform dyspepsia management guidance. Clinicians should take a thorough antibiotic history before prescribing metronidazole, clarithromycin or levofloxacin for H. pylori.
Since the onset of the COVID-19 pandemic, it has been unclear how vulnerable people with HIV (PwH) are to SARS-CoV-2 infection. We sought to determine if PwH are more likely to test positive for ...SARS-CoV-2 than people without HIV, and to identify risk factors associated with SARS-CoV-2 positivity among PwH. We conducted a cross-sectional study in which we collected electronic medical record data for all patients who underwent SARS-CoV-2 PCR testing at an academic medical center. Presence of HIV and other chronic diseases were based on the presence of ICD-10 diagnosis codes. We calculated the percent positivity for SARS-CoV-2 among PwH and among people without HIV. Among PwH, we compared demographic factors, comorbidities, HIV viral load, CD4 T-cell count, and antiretroviral therapy (ART) regimens between those who tested positive for SARS-CoV-2 and those who tested negative. Comparisons were made using chi squared tests or Wilcoxon rank sum tests. Multivariate models were created using logistic regression. Among 69,763 people tested for SARS-CoV-2, 0.6% (431) were PwH. PwH were not significantly more likely to test positive for SARS-CoV-2 than people without HIV (7.2% (31/431) vs 8.4% (5820/69763), p = 0.35), but were more likely to be younger, Black, and male (p-values < .0001). There were no significant differences in HIV clinical factors, chronic diseases, or ART regimens among PwH testing positive for SARS-CoV-2 versus those testing negative. In our sample, PwH were not more likely to contract SARS-CoV-2, despite being more likely to be members of demographic groups known to be at higher risk for infection. Differences between PwH who tested positive for SARS-CoV-2 and those who tested negative were only seen in Hispanic/Latino ethnicity (non-Hispanic or Latino vs unknown Hispanic or Latino ethnicity (OR 0.2 95% CI (0.6, 0.9)) and site of testing(inpatient vs outpatient OR 3.1 95% CI (1.3, 7.4)).
Escherichia coli bacteraemia rates in the UK have risen; rates are highest among older adults. Previous urinary tract infections (UTIs) and catheterization are risk factors.
To examine effectiveness ...of behavioural interventions to reduce E. coli bacteraemia and/or symptomatic UTIs for older adults.
Sixteen databases, grey literature, and reference lists were searched. Titles and/or abstracts were scanned and selected papers were read fully to confirm suitability. Quality was assessed using Critical Appraisal Skills Programme guidelines and Scottish Intercollegiate Guidelines Network grading.
Twenty-one studies were reviewed, and all lacked methodological quality. Six multi-faceted hospital interventions including education, with audit and feedback or reminders reduced UTIs but only three supplied statements of significance. One study reported decreasing catheter-associated UTI (CAUTI) by 88% (F (1,20) = 7.25). Another study reported reductions in CAUTI from 11.17 to 10.53 during Phase I and by 0.39 during Phase II (χ2 = 254). A third study reported fewer UTIs per patient week (risk ratio = 0.39). Two hospital studies of online training and catheter insertion and care simulations decreased CAUTIs from 33 to 14 and from 10.40 to 0. Increasing nursing staff, community continence nurses, and catheter removal reminder stickers reduced infection. There were no studies examining prevention of E. coli bacteraemias.
The heterogeneity of studies means that one effective intervention cannot be recommended. We suggest that feedback should be considered because it facilitated reductions in UTI when used alone or in multi-faceted interventions including education, audit or catheter removal protocols. Multi-faceted education is likely to be effective. Catheter removal protocols, increased staffing, and patient education require further evaluation.
The COVID-19 and HIV epidemics have exacerbated existing inequities among vulnerable groups and severely impacted communities of color. People living with HIV (PLWH), who may already face stigma or ...discrimination, are at risk of experiencing further stigma as a result of COVID-19, which can result in medical mistrust.
We performed qualitative interviews between June and August 2020 among 32 PLWH, including 10 individuals diagnosed with COVID-19. A majority of participants perceived themselves as having an increased risk of contracting COVID-19 due to their HIV status.
Of those who tested positive for COVID-19, the majority regarded their HIV diagnosis as having a more profound impact on their lives but found similarities between COVID-19 stigma and HIV-related stigma. Many participants also expressed mistrust.
These results can be used to better understand the perspectives of PLWH during the COVID-19 pandemic and have important implications for potential COVID-19 vaccine hesitancy and future health crises.
Environmental RNAi (eRNAi) is a sequence-specific regulation of endogenous gene expression in a receptive organism by exogenous double-stranded RNA (dsRNA). Although demonstrated under artificial ...dietary conditions and via transgenic plant presentations in several herbivorous insects, the magnitude and consequence of exogenous dsRNA uptake and the role of eRNAi remains unknown under natural insect living conditions. Our analysis of coleopteran insects sensitive to eRNAi fed on wild-type plants revealed uptake of plant endogenous long dsRNAs, but not small RNAs. Subsequently, the dsRNAs were processed into 21 nt siRNAs by insects and accumulated in high quantities in insect cells. No accumulation of host plant-derived siRNAs was observed in lepidopteran larvae that are recalcitrant to eRNAi. Stability of ingested dsRNA in coleopteran larval gut followed by uptake and transport from the gut to distal tissues appeared to be enabling factors for eRNAi. Although a relatively large number of distinct coleopteran insect-processed plant-derived siRNAs had sequence complementarity to insect transcripts, the vast majority of the siRNAs were present in relatively low abundance, and RNA-seq analysis did not detect a significant effect of plant-derived siRNAs on insect transcriptome. In summary, we observed a broad genome-wide uptake of plant endogenous dsRNA and subsequent processing of ingested dsRNA into 21 nt siRNAs in eRNAi-sensitive insects under natural feeding conditions. In addition to dsRNA stability in gut lumen and uptake, dosage of siRNAs targeting a given insect transcript is likely an important factor in order to achieve measurable eRNAi-based regulation in eRNAi-competent insects that lack an apparent silencing amplification mechanism.
Objectives: To determine whether patients with an uncomplicated community-acquired urinary tract infection (UTI) and an isolate resistant to trimethoprim had worse clinical outcomes following ...empirical treatment with trimethoprim 200 mg twice daily for 3 days than did those with a susceptible isolate. Patients and methods: This was a prospective cohort study of clinical outcome. We enrolled 497 women (≥18–70 years) presenting to general practitioner surgeries in Norwich and Gloucester with at least two symptoms of acute (<7 days) uncomplicated UTI. Significant bacteriuria was defined as ≥104 cfu/mL from a mid-stream urine (MSU). Results: Of enrolled patients 75% (334/448) had significant bacteriuria, and trimethoprim resistance was present in 13.9% (44/317) of isolates. Patients with resistant isolates had a longer median time to symptom resolution (7 versus 4 days, P = 0.0002), greater reconsultation to the practice (39% versus 6% in first week, P < 0.0001), more subsequent antibiotics (36% versus 4% in first week, P < 0.0001) and higher rates of significant bacteriuria at 1 month (42% versus 20% with susceptible isolate, P = 0.04). Half of patients reconsulting in the first week had a resistant organism. Conclusions: Patients with uncomplicated UTI caused by trimethoprim-resistant organisms had significantly worse clinical outcomes than those with trimethoprim-susceptible organisms. Nevertheless, trimethoprim resistance was rarer than predicted from routine laboratory submissions and we calculate that 23 women require microbiological investigation to prevent one reconsultation arising from resistance-based treatment failure. We therefore suggest empirical antibiotic treatment in acute, uncomplicated UTIs. If patients reconsult in the first week, we suggest a change of antibiotic treatment with urine culture and susceptibility testing then done. More generally, laboratory resources should concentrate on resistance surveillance to inform empirical antibiotic choice.
The survey included demographic details, esports experience, the International Physical Activity Questionnaire-Long Form (IPAQ-LF), and the Behavioural Regulations towards Exercise Questionnaire ...(BREQ-3). The median physical activity time reported through the IPAQ-LF was 2916 (4400) MET.mins/week, comprising 120 (161) minutes of moderate to vigorous physical activity (MVPA) and 60 (90) minutes of light intensity activity (LIA) per day. ...e-athletes over-report levels of physical activity, which could underrepresent the actual physical activity behaviours in this population.
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