Impact of molecular ciprofloxacin resistance testing in management of gonorrhoea in a large urban clinic.

OBJECTIVES: Antibiotic resistance in gonorrhoea is of significant public health concern with the emergence of resistance to last-line therapies such as ceftriaxone. Despite around half of Neisseria gonorrhoeae isolates tested in the UK being susceptible to ciprofloxacin, very little ciprofloxacin is used in clinical practice. Testing for the S91F mutation associated with ciprofloxacin resistance is now available in CE-marked assays and may reduce the requirement for ceftriaxone, but many patients are treated empirically, or as sexual contacts, which may limit any benefit. We describe the real-world impact of such testing on antimicrobial use and clinical outcomes in people found to have gonorrhoea in a large urban UK sexual health clinic. METHODS: Molecular ciprofloxacin resistance testing (ResistancePlus GC assay (SpeeDx)) was undertaken as an additional test after initial diagnosis (m2000 Realtime CT/NG assay (Abbott Molecular)) in those not already known to have had antimicrobial treatment. Data from a 6-month period (from March to September 2022) were analysed to determine treatment choice and treatment outcome. RESULTS: A total of 998 clinical samples tested positive for N. gonorrhoeae in 682 episodes of infection. Of the 560 (56%) samples eligible for resistance testing, 269 (48.0%) were reported as wild-type, 180 (32.1%) were predicted to be resistant, 63 (11.3%) had an indeterminate resistance profile, and in 48 (8.6%) samples, N. gonorrhoeae was not detected. Ciprofloxacin was prescribed in 172 (75%) of 228 episodes in which the wild-type strain was detected. Four (2%) of those treated with ciprofloxacin had a positive test-of-cure sample by NAAT, with no reinfection risk. All four had ciprofloxacin-susceptible infection by phenotypic antimicrobial susceptibility testing. CONCLUSIONS: In routine practice in a large UK clinic, molecular ciprofloxacin resistance testing led to a significant shift in antibiotic use, reducing use of ceftriaxone. Testing can be targeted to reduce unnecessary additional testing. Longer term impact on antimicrobial resistance requires ongoing surveillance.

Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent.

OBJECTIVES: To determine how the intrinsic severity of successively dominant SARS-CoV-2 variants changed over the course of the pandemic. METHODS: A retrospective cohort analysis in the NHS Greater Glasgow and Clyde (NHS GGC) Health Board. All sequenced non-nosocomial adult COVID-19 cases in NHS GGC with relevant SARS-CoV-2 lineages (B.1.177/Alpha, Alpha/Delta, AY.4.2 Delta/non-AY.4.2 Delta, non-AY.4.2 Delta/Omicron, and BA.1 Omicron/BA.2 Omicron) during analysis periods were included. Outcome measures were hospital admission, ICU admission, or death within 28 days of positive COVID-19 test. We report the cumulative odds ratio; the ratio of the odds that an individual experiences a severity event of a given level vs all lower severity levels for the resident and the replacement variant after adjustment. RESULTS: After adjustment for covariates, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177, 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha, 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta, 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta, and 0.86 (95% CI: 0.68-1.09) for BA.2 Omicron versus BA.1 Omicron. CONCLUSIONS: The direction of change in intrinsic severity between successively emerging SARS-CoV-2 variants was inconsistent, reminding us that the intrinsic severity of future SARS-CoV-2 variants remains uncertain.

The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis.

OBJECTIVES: The SARS-CoV-2 Alpha variant was associated with increased transmission relative to other variants present at the time of its emergence and several studies have shown an association between Alpha variant infection and increased hospitalisation and 28-day mortality. However, none have addressed the impact on maximum severity of illness in the general population classified by the level of respiratory support required, or death. We aimed to do this. METHODS: In this retrospective multi-centre clinical cohort sub-study of the COG-UK consortium, 1475 samples from Scottish hospitalised and community cases collected between 1st November 2020 and 30th January 2021 were sequenced. We matched sequence data to clinical outcomes as the Alpha variant became dominant in Scotland and modelled the association between Alpha variant infection and severe disease using a 4-point scale of maximum severity by 28 days: 1. no respiratory support, 2. supplemental oxygen, 3. ventilation and 4. death. RESULTS: Our cumulative generalised linear mixed model analyses found evidence (cumulative odds ratio: 1.40, 95% CI: 1.02, 1.93) of a positive association between increased clinical severity and lineage (Alpha variant versus pre-Alpha variants). CONCLUSIONS: The Alpha variant was associated with more severe clinical disease in the Scottish population than co-circulating lineages.

Exploring the implementation of child life services with facility dogs.

Many children's hospitals around the United States have programs in which a trained facility dog goes to work daily with a psychosocial healthcare worker, typically a Certified Child Life Specialist (CCLS). CCLSs help children and their families cope with the stress of a healthcare experience by utilizing evidence-based, developmentally appropriate interventions. The purpose of this study was to explore how CCLSs incorporate facility dogs into their treatments and gain their perspectives on handling a facility dog. Participants, four CCLSs, completed a checklist, which assessed patients seen by facility dogs for 10 workdays, and a semi-structured interview. Participants primarily saw patients of ages three to five years and aided with general anxiety and coping support. Findings indicated the dog's specific training, therapeutic value, and ability to bond with patients allowed these interactions to be successful and impactful. This study provides information about the benefits of facility dogs for child life programs and presents data for programs that are considering incorporating this therapeutic modality into their services offered.

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning.

Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.

Performance characteristics of the SpeeDx PlexPCR VHS assay for the molecular detection of herpes simplex virus, varicella zoster virus, and Treponema pallidum in lesion swabs.

This study compares the performance of a commercial polymerase chain reaction (PCR) assay for detection of herpes simplex virus (HSV) 1 and 2, varicella zoster virus (VZV), and Treponema pallidum with laboratory-developed assays. A panel of 250 samples, previously tested using in-house assays, was tested on the PlexPCR® VHS assay. The panel consisted of 202 positive specimens [HSV-1 (n=51); HSV-2 (n=51); VZV (n=51); T. pallidum (n=49)] and 48 negative specimens. Genital samples had been previously tested for HSV-1/2 and T. pallidum and nongenital or unspecified samples for HSV-1/2 and VZV. The overall agreement between the PlexPCR® VHS and in-house assays was 97%. Negative agreement was ≥99%, and positive agreement for individual targets was 96% (47/49) for T. pallidum, 98% for HSV-1 and HSV-2 (50/51), and 100% (51/51) for VZV. Adoption of this assay would allow greater availability of molecular syphilis detection and enhance the diagnostic yield of samples collected from cutaneous/mucocutaneous lesions.

Investigating utilising the Alinity m platform to detect hepatitis C virus RNA in dried blood spot samples.

BACKGROUND: Elimination of Hepatitis C virus (HCV) relies on increasing HCV diagnostic rates in hard to reach populations. Dried blood spot (DBS) samples are a convenient sample type for HCV testing, as they can be collected in non-traditional settings such as drug services and prison settings, increasing access to HCV testing. OBJECTIVES: Herein we investigate an off-label DBS protocol for use on the Abbott Alinity m platform. STUDY DESIGN: A dilution series of HCV RNA positive blood was used to determine the analytical sensitivity of the test. We assess the sensitivity and specificity of HCV RNA detection in 50 mock DBS specimens compared to associated plasma viral load, and re-test 66 clinical DBS, previously tested on the m2000 to determine the clinical sensitivity and specificity of the assay. RESULTS: The dilution panel suggested that the Alinity m DBS assay is one log more sensitive than our current DBS HCV RNA assay. Mock DBS demonstrated 100% specificity, and 100% sensitivity for samples with plasma HCV RNA viral loads > 2.7 log10 IU/mL, however four samples with viral loads between 1.3 and 2.4 log10 IU/mL were not detected. The clinical sensitivity and specificity of previously tested DBS was 94% and 100% respectively, with two samples reported as low level RNA positive on the m2000 testing negative on Alinty m. CONCLUSIONS: The data suggests that DBS can be used as an off-label specimen type on the Alinity m HCV assay. Allowing continuous, random access testing of DBS simultaneously alongside other Alintiy m assays, potentially improving test turn-around times.

Multicenter clinical evaluation of alinity m HBV assay performance.

BACKGROUND: Accurate molecular methods to detect and quantify hepatitis B virus (HBV) DNA are essential to diagnose chronic infections, guide treatment decisions, assess response to treatment, and determine risk of HBV-related complications. New generations of real-time HBV DNA assay platforms provide results in less than 2-3 h, with continuous loading of specimens and true random-access capability. OBJECTIVES: We examined the clinical performance of the new Alinity m HBV assay, run on the fully automated, continuous, random-access Alinity m platform, to accurately detect and quantify HBV DNA in a large series of patient samples infected with different HBV genotypes frequently encountered in clinical practice. STUDY DESIGN: This international, multisite study assessed the precision and reproducibility of the Alinity m HBV assay and compared its performance to four HBV assays currently in clinical use. RESULTS: The Alinity m HBV assay demonstrated linear quantitation of HBV DNA in plasma samples, with high precision (coefficient of variation 4.1 %-8.8 %) and reproducibility. The Alinity m HBV assay showed excellent correlation (correlation coefficients ≥0.947) with comparator HBV assays, with an overall observed bias ranging from -0.07 to 0.17 Log10 IU/mL. 97 % of quantifiable patient results were <1 Log10 IU/mL different than the respective comparator assays, with comparable results across HBV genotypes. CONCLUSIONS: The newly developed real-time PCR-based Alinity m HBV assay is sensitive, reproducible, and accurately quantifies HBV DNA levels from HBsAg-positive patients across the full dynamic range of quantification.

Multicenter clinical evaluation of alinity m HCV assay performance.

BACKGROUND: Nucleic acid testing is essential for the detection and quantification of HCV RNA in the diagnosis of HCV infection and treatment monitoring. The Alinity m HCV assay was recently developed by Abbott Molecular for rapid detection and quantification of HCV RNA on the fully automated, continuous, random-access Alinity m analyzer. OBJECTIVES: Our study assessed the performance of the new Alinity m HCV assay for detection and quantification of HCV RNA in a large series of patient samples of various genotypes. This international, multicentric study evaluated the linearity, precision, and reproducibility of the Alinity m HCV assay and its performance in comparison to three other HCV assays currently used in clinical practice. RESULTS: The Alinity m HCV assay demonstrated high linearity (correlation coefficient r = 1.00), precision (coefficients of variation [CV] 6.6-13.5 %) and reproducibility (CV 1.7-4.3 % across three control lots). At a concentration near the lower limit of detection, the Alinity m HCV assay exhibited >98 % detectability. The Alinity m HCV assay showed excellent correlation with comparator HCV assays in serum (n = 406) and plasma (n = 1401) samples (correlation coefficients ≥0.96, bias 0.01 to 0.14 Log10 IU/mL). More than 95 % of the quantified results with the Alinity m HCV assay were less than mean bias ± 1.96 SD different from those of the comparator assays. CONCLUSIONS: The newly developed Alinity m HCV assay is sensitive, reproducible, and accurately quantifies HCV RNA levels in serum and plasma samples from patients with chronic HCV infection, with no impact of HCV genotype on assay performance.

Multicenter clinical comparative evaluation of Alinity m HIV-1 assay performance.

BACKGROUND: Accurate, rapid detection of HIV-1 RNA is critical for early diagnosis, treatment decision making, and long-term management of HIV-1 infection. OBJECTIVE: We evaluated the diagnostic performance of the Alinity m HIV-1 assay, which uses a dual target/dual probe design against highly conserved target regions of the HIV-1 genome and is run on the fully automated Alinity m platform. STUDY DESIGN: This was an international, multisite study that compared the diagnostic performance of the Alinity m HIV-1 assay to four commercially available HIV-1 assays routinely used in nine independent clinical laboratories. Alinity m HIV-1 assay precision, detectability, and reproducibility was compared across four study sites. RESULTS: The Alinity m HIV-1 assay produced comparable results to currently available HIV-1 assays (correlation coefficient >0.995), with an overall bias of -0.1 to 0.10 Log10 copies/mL. The Alinity m HIV-1 assay and its predecessor m2000 HIV-1 assay demonstrated comparable detection of 16 different HIV-1 subtypes (R2 = 0.956). A high level of agreement (>88 %) between all HIV-1 assays was seen near clinical decision points of 1.7 Log10 copies/mL (50 copies/mL) and 2.0 Log10 copies/mL (200 copies/mL). Alinity m HIV-1 assay precision was 0.08 and 0.21 Log10 copies/mL at VLs of 1000 and 50 copies/mL, respectively, with a high level of detectability (≥97 % hit rate) and reproducibility across sites. CONCLUSIONS: The Alinity m HIV-1 assay provides comparable diagnostic accuracy to current HIV-1 assays, and when run on the Alinity m system, has the capacity to shorten the time between diagnosis and treatment.

The Influence of Microaffirmations on Undergraduate Persistence in Science Career Pathways.

The present studies aimed to advance the measurement and understanding of microaffirmation kindness cues and assessed how they related to historically underrepresented (HU) and historically overrepresented (HO) undergraduate student persistence in science-related career pathways. Study 1 developed and tested the dimensionality of a new Microaffirmations Scale. Study 2 confirmed the two-factor structure of the Microaffirmations Scale and demonstrated that the scale possessed measurement invariance across HU and HO students. Further, the scale was administered as part of a longitudinal design spanning 9 months, with results showing that students' reported microaffirmations did not directly predict higher intentions to persist in science-related career pathways 9 months later. However, scientific self-efficacy and identity, measures of student integration into the science community, mediated this relationship. Overall, our results demonstrated that microaffirmations can be measured in an academic context and that these experiences have predictive value when they increase students' integration into their science communities, ultimately resulting in greater intentions to persist 9 months later. Researchers and practitioners can use the Microaffirmations Scale for future investigations to increase understanding of the positive contextual factors that can ultimately help reduce persistence gaps in science, technology, engineering, and mathematics degree attainment.

Yellow fever vaccine-associated neurological disease: it is not just the silver generation at risk.

A 35-year-old man presented to his optician with sudden onset diplopia and a 1-week history of headaches. He was noted to have sixth nerve palsy. The following day he was admitted to hospital with confusion and expressive dysphasia. He had been due to travel to Ghana on business and had received yellow fever (YF) vaccination 18 days prior to onset of headaches. His initial cerebrospinal fluid (CSF) revealed elevated protein, increased white cell count but was PCR negative for standard viral pathogens. Herpes simplex virus (HSV)-1 was detected by PCR in CSF at a very low level from a second lumbar puncture performed 6 days later, and the patient was treated for HSV meningoencephalitis. However, retrospective investigation for yellow fever vaccine-associated neurological disease revealed increasing titres of YF IgG in three serial CSF samples, and no evidence of HSV antibodies in CSF or plasma, ruling out HSV encephalitis.

Prevalence of pre-treatment hepatitis C virus NS5A resistance associated amino-acid substitutions in genotype 1A infected patients in Scotland.

BACKGROUND: Hepatitis C (HCV) NS5A resistance associated amino-acid substitutions (RAS) can exist at baseline in treatment naïve individuals and have been shown to be associated with lower rates of sustained virological response (SVR) for patients infected with HCV genotype 1A (G1A) following treatment with NS5A inhibitors. OBJECTIVES: The aim of this study was to measure the prevalence of baseline NS5A resistance in Scotland. STUDY DESIGN: The study population consisted of 531 treatment naïve, G1A infected patients. The patient samples were collected between March and September 2017. The NS5A region was amplified and sequenced. RESULTS: Baseline NS5A resistance in Scotland is high (16.8%) and is comparable to rates reported by a number of previously published studies. The high rate of baseline RAS, together with the high cost of direct-acting antivirals (DAAs), supports resistance testing to guide current patient treatment. However, given the rate at which new DAAs are currently being licensed with ever broader genotype efficacy and higher SVR rates, baseline resistance testing may not be required in the near future. CONCLUSIONS: Baseline NS5A inhibitor resistance is high. The results of the present study support performing resistance testing at baseline for current regimens.

Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses.

Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.

'Speaking Truth' Protects Underrepresented Minorities' Intellectual Performance and Safety in STEM.

We offer and test a brief psychosocial intervention, Speaking Truth to EmPower (STEP), designed to protect underrepresented minorities' (URMs) intellectual performance and safety in science, technology, engineering, and math (STEM). STEP takes a 'knowledge as power' approach by: (a) providing a tutorial on stereotype threat (i.e., a social contextual phenomenon, implicated in underperformance and early exit) and (b) encouraging URMs to use lived experiences for generating be-prepared coping strategies. Participants were 670 STEM undergraduates [URMs (Black/African American and Latina/o) and non-URMs (White/European American and Asian/Asian American)]. STEP protected URMs' abstract reasoning and class grades (adjusted for grade point average [GPA]) as well as decreased URMs' worries about confirming ethnic/racial stereotypes. STEP's two-pronged approach-explicating the effects of structural 'isms' while harnessing URMs' existing assets-shows promise in increasing diversification and equity in STEM.