Continued improvement in the development of the SARS-CoV-2 whole genome sequencing proficiency testing program.

Application of whole genome sequencing (WGS) has allowed monitoring of the emergence of variants of concern (VOC) of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) globally. Genomic investigation of emerging variants and surveillance of clinical progress has reduced the public health impact of infection during the COVID-19 pandemic. These steps required developing and implementing a proficiency testing program (PTP), as WGS has been incorporated into routine reference laboratory practice. In this study, we describe how the PTP evaluated the capacity and capability of one New Zealand and 14 Australian public health laboratories to perform WGS of SARS-CoV-2 in 2022. The participants' performances in characterising a specimen panel of known SARS-CoV-2 isolates in the PTP were assessed based on: (1) genome coverage, (2) Pango lineage, and (3) sequence quality, with the choice of assessment metrics refined based on a previously reported assessment conducted in 2021. The participants' performances in 2021 and 2022 were also compared after reassessing the 2021 results using the more stringent metrics adopted in 2022. We found that more participants would have failed the 2021 assessment for all survey samples and a significantly higher fail rate per sample in 2021 compared to 2022. This study highlights the importance of choosing appropriate performance metrics to reflect better the laboratories' capacity to perform SARS-CoV-2 WGS, as was done in the 2022 PTP. It also displays the need for a PTP for WGS of SARS-CoV-2 to be available to public health laboratories ongoing, with continuous refinements in the design and provision of the PTP to account for the dynamic nature of the COVID-19 pandemic as SARS-CoV-2 continues to evolve.

Correlative Light and Electron Cryo-Microscopy Workflow Combining Micropatterning, Ice Shield, and an In-Chamber Fluorescence Light Microscope.

In situ cryo-electron tomography (cryo-ET) is the most current, state-of-the-art technique to study cell machinery in its hydrated near-native state. The method provides ultrastructural details at sub-nanometer resolution for many components within the cellular context. Making use of recent advances in sample preparation techniques and combining this method with correlative light and electron microscopy (CLEM) approaches have enabled targeted molecular visualization. Nevertheless, the implementation has also added to the complexity of the workflow and introduced new obstacles in the way of streamlining and achieving high throughput, sample yield, and sample quality. Here, we report a detailed protocol by combining multiple newly available technologies to establish an integrated, high-throughput, optimized, and streamlined cryo-CLEM workflow for improved sample yield. Key features • PRIMO micropatterning allows precise cell positioning and maximum number of cell targets amenable to thinning with cryo focused-ion-beam-scanning electron microscopy. • CERES ice shield ensures that the lamellae remain free of ice contamination during the batch milling process. • METEOR in-chamber fluorescence microscope facilitates the targeted cryo focused-ion-beam (cryo FIB) milling of these targets. • Combining the three technologies into one cryo-CLEM workflow maximizes sample yield, throughput, and efficiency. Graphical overview.

Prediction of adverse outcome by ophthalmic artery Doppler and angiogenic markers in pregnancies with new onset hypertension.

OBJECTIVES: To compare the ophthalmic artery Doppler peak systolic velocity ratio (OA PSV-ratio) and soluble fms-like tyrosine kinase-1/placental growth factor ratio (sFlt-1/PlGF ratio) in predicting adverse maternal and perinatal outcomes in women presenting with new onset hypertension. STUDY DESIGN: Prospective cohort study in a specialist hypertension clinic, within a tertiary referral centre. MAIN OUTCOME MEASURES: Comparison between the OA PSV-ratio and sFlt-1/PlGF ratio in predicting delivery within one week from presentation and adverse maternal and perinatal outcomes e.g. severe hypertension, neonatal unit admission, small for gestational age. RESULTS: Women who delivered within one week, compared to those who did not, had a higher OA PSV-ratio (0.82 vs 0.71, p < 0.01) and sFlt-1/PlGF ratio (93.3 vs 40.5, p = 0.08). Independent predictors of the OA PSV-ratio included mean arterial pressure and maternal weight and predictors of the sFlt-1/PlGF ratio included diastolic blood pressure and use of antihypertensive medications. Prediction of adverse outcomes with both ratios were similar and only modest e.g. AUROC for predicting delivery within one week for OA PSV-ratio was 0.57 (95% CI 0.47-0.67) and for sFlt-1/PlGF ratio was 0.61 (95% CI 0.52-0.70) (p = 0.53). CONCLUSIONS: In women presenting with new onset hypertension, the OA PSV-ratio and sFlt-1/PlGF ratio have similar and modest performance in predicting adverse outcomes.

Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance.

The COVID-19 pandemic has necessitated the rapid development and implementation of whole-genome sequencing (WGS) and bioinformatic methods for managing the pandemic. However, variability in methods and capabilities between laboratories has posed challenges in ensuring data accuracy. A national working group comprising 18 laboratory scientists and bioinformaticians from Australia and New Zealand was formed to improve data concordance across public health laboratories (PHLs). One effort, presented in this study, sought to understand the impact of the methodology on consensus genome concordance and interpretation. SARS-CoV-2 WGS proficiency testing programme (PTP) data were retrospectively obtained from the 2021 Royal College of Pathologists of Australasia Quality Assurance Programmes (RCPAQAP), which included 11 participating Australian laboratories. The submitted consensus genomes and reads from eight contrived specimens were investigated, focusing on discordant sequence data and findings were presented to the working group to inform best practices. Despite using a variety of laboratory and bioinformatic methods for SARS-CoV-2 WGS, participants largely produced concordant genomes. Two participants returned five discordant sites in a high-Cτ replicate, which could be resolved with reasonable bioinformatic quality thresholds. We noted ten discrepancies in genome assessment that arose from nucleotide heterogeneity at three different sites in three cell-culture-derived control specimens. While these sites were ultimately accurate after considering the participants' bioinformatic parameters, it presented an interesting challenge for developing standards to account for intrahost single nucleotide variation (iSNV). Observed differences had little to no impact on key surveillance metrics, lineage assignment and phylogenetic clustering, while genome coverage <90 % affected both. We recommend PHLs bioinformatically generate two consensus genomes with and without ambiguity thresholds for quality control and downstream analysis, respectively, and adhere to a minimum 90 % genome coverage threshold for inclusion in surveillance interpretations. We also suggest additional PTP assessment criteria, including primer efficiency, detection of iSNVs and minimum genome coverage of 90 %. This study underscores the importance of multidisciplinary national working groups in informing guidelines in real time for bioinformatic quality acceptance criteria. It demonstrates the potential for enhancing public health responses through improved data concordance and quality control in SARS-CoV-2 genomic analysis during pandemic surveillance.

Diagnostic application of intraoral ultrasonography to assess furcation involvement in mandibular first molars.

OBJECTIVES: The objectives were to clarify if intraoral ultrasonography (USG) is: (1) more accurate than conventional periodontal examinations in detection of furcation involvement, and (2) comparable to conventional periodontal examinations in accurate horizontal classification of furcation involvement in comparison to cone beam computed tomography (CBCT). METHODS: The buccal furcation in 61 lower first molars were evaluated with conventional periodontal examinations, intraoral USG and CBCT. The presence and classification of the horizontal depth of furcation involvement were defined clinically by assessment with a Nabers periodontal probe and a periapical radiograph with reference to the bone loss under the fornix. The horizontal depth of furcation involvement was measured in intraoral USG and CBCT images. Based on the measurements, presence diagnosis and horizontal classification were performed. Results from conventional periodontal examinationsand intraoral USG were compared with those from CBCT. RESULTS: κ value (κ) for agreement of presence diagnosis of furcation involvement between intraoral USG and CBCT was 0.792, while agreement with conventional periodontal examinations was 0.225. Diagnostic accuracy of intraoral USG exhibited higher values (sensitivity: 98.3%, accuracy: 98.4 %) than conventional periodontal examinations (81.4% and 81.9 %). Weighted κ statistics showed substantial agreement in the classification between intraoral USG and CBCT (κ = 0.674). High agreement (ICC: 0.914) for the measurement of horizontal depth of furcation involvement was found between intraoral USG and CBCT. CONCLUSIONS: Intraoral USG may be a reliable diagnostic tool for assessment of furcation involvement of mandibular molars with a similar performance to CBCT, but without ionizing radiation.

Proficiency testing for SARS-CoV-2 whole genome sequencing.

Extensive studies and analyses into the molecular features of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) have enhanced the surveillance and investigation of its clusters and transmission worldwide. The whole genome sequencing (WGS) approach is crucial in identifying the source of infection and transmission routes by monitoring the emergence of variants over time and through communities. Varying SARS-CoV-2 genomics capacity and capability levels have been established in public health laboratories across different Australian states and territories. Therefore, laboratories performing SARS-CoV-2 WGS for public health purposes are recommended to participate in an external proficiency testing program (PTP). This study describes the development of a SARS-CoV-2 WGS PTP. The PTP assessed the performance of laboratories while providing valuable insight into the current state of SARS-CoV-2 genomics in public health across Australia. Part 1 of the PTP contained eight simulated SARS-CoV-2 positive and negative specimens to assess laboratories' wet and dry laboratory capacity. Part 2 involved the analysis of a genomic dataset that consisted of a multi-FASTA file of 70 consensus genomes of SARS-CoV-2. Participating laboratories were required to (1) submit raw data for independent bioinformatics analysis, (2) analyse the data with their processes, and (3) answer relevant questions about the data. The performance of the laboratories was commendable, despite some variation in the reported results due to the different sequencing and bioinformatics approaches used by laboratories. The overall outcome is positive and demonstrates the critical role of the PTP in supporting the implementation and validation of SARS-CoV-2 WGS processes. The data derived from this PTP will contribute to the development of SARS-CoV-2 bioinformatic quality control (QC) and performance benchmarking for accreditation.

Proficiency testing for SARS-CoV-2 in assuring the quality and overall performance in viral RNA detection in clinical and public health laboratories.

Diagnostic testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone significant changes over the duration of the pandemic. In early 2020, SARS-CoV-2 specific nucleic acid testing (NAT) protocols were predominantly in-house assays developed based on protocols published in peer reviewed journals. As the pandemic has progressed, there has been an increase in the choice of testing platforms. A proficiency testing program for the detection of SARS-CoV-2 by NAT was provided to assist laboratories in assessing and improving test capabilities in the early stages of the pandemic. This was vital in quality assuring initial in-house assays, later commercially produced assays, and informing the public health response. The Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) offered three rounds of proficiency testing for SARS-CoV-2 to Australian and New Zealand public and private laboratories in March, May, and November 2020. Each round included a panel of five specimens, consisting of positive (low, medium or high viral loads), inconclusive (technical specimen of selected SARS-CoV-2 specific genes) and negative specimens. Results were received for round 1 from 16, round 2 from 97 and round 3 from 101 participating laboratories. Improvement in the accuracy over time was shown, with the concordance of results in round 1 being 75.0%, in round 2 above 95.0% for all samples except one, and for round 3 above 95.0%. Overall, participants demonstrated high capabilities in detecting SARS-CoV-2, even in samples of low viral load, indicating excellent testing accuracy and therefore providing confidence in Australian and New Zealand public and private laboratories test results.

Impact of inter-vendor variability on evaluation of left ventricular mechanical dispersion.

PURPOSE: Left ventricular mechanical dispersion (LVMD) is a novel speckle tracking parameter for prognostic assessment of arrhythmic risk prediction. There is growing evidence to support its use in a variety of cardiomyopathic processes. There is paucity of data addressing any presence of inter-vendor discrepancies for LVMD. The aim of this study was to assess inter-vendor variability of LVMD in vendor specific software (VSS) and vendor independent software (VIS) in subjects with preserved and reduced left ventricular function. METHODS: Fifty-nine subjects (14 normal subjects and 45 subjects with cardiac disease) were recruited and 2D speckle tracking echocardiographic images were acquired on two different ultrasound machines (GE and Philips). LVMD was measured by two different VSS (EchoPac GE and QLAB Philips) and one VIS (TomTec Arena). RESULTS: There was significant bias and wide limits of agreement (LOA) in the overall cohort observed between two different VSS (17.6 ms; LOA: -29.6 to 64.8; r: .47). There was acceptable bias and narrower LOA with good agreement for LVMD between images obtained on different vendors when performed on VIS (-3.1 ms; LOA: -27.6 to 21.4; r: .75). QLAB LVMD was consistently higher than GE LVMD and TomTec LVMD in both preserved and reduced left ventricular function. LVMD measurements have high intra-vendor reproducibility with excellent inter and intra-observer agreement. CONCLUSIONS: There was acceptable bias and narrower LOA for LVMD assessment on a VIS. Inter-vendor variability exists for LVMD assessment between VSS. Serial measurements of LVMD should be performed using a single vendor for consistent and reliable results.

Absence of fetal heart rate cycling on the intrapartum cardiotocograph (CTG) is associated with intrapartum pyrexia and lower Apgar scores.

BACKGROUND: Cycling consists of alternating periods of reduced and normal fetal heart variability, reflecting changes in fetal behavioral states. Occurrence of active and quiet sleep cycles is considered to be a hallmark of fetal autonomic nervous system integrity, demonstrating healthy interaction between the parasympathetic and sympathetic nervous systems. Cycling is an overlooked feature in most international cardiotocography (CTG) guidelines. The authors tested the hypothesis that fetuses showing no cycling in the intrapartum period have poorer outcomes. AIM: To investigate whether the absence of cycling at the commencement of intrapartum fetal monitoring is associated with poorer neonatal outcomes (umbilical arterial cord pH, Apgar scores and neonatal unit admission). METHODS: Analysis of a database of sequentially acquired intrapartum CTG traces from a single center. Only cases of singleton pregnancies over 36 weeks gestation in cephalic presentation with recorded umbilical artery cord pH were considered. Neonatal outcomes were assessed based on umbilical cord artery pH, Apgar ≤7 at 5 min and unexpected admission to the neonatal unit. Intrapartum pyrexia, presence of meconium-stained amniotic fluid and mode of delivery were also recorded. RESULTS: A total of 684 cases were analyzed. Absence of cycling from the beginning of the intrapartum CTG recording was noted in 5% of cases. Cases with no cycling were more likely to have maternal pyrexia (≥37.8 °C) (p = .006) and Apgars ≤7 at 5 min (p = .04). There was an association between increasing baseline fetal heart rate and the proportion of cases with no cycling. There was no significant difference between the two groups with regard to the mode of delivery or umbilical cord arterial pH <7.05 (p = .53). CONCLUSION: Absence of cycling is associated with intrapartum maternal pyrexia and fetuses with the absence of cycling are more likely to have poorer perinatal outcomes measured by Apgar ≤ 7 at 5 min, despite no association with fetal acidosis. Results from this research were presented at the XXVI European Congress of Perinatal Medicine in September 2018.

Ophthalmic artery peak systolic velocity ratio distinguishes pre-eclampsia from chronic and gestational hypertension: A prospective cohort study.

OBJECTIVE: To examine whether the ophthalmic artery peak systolic velocity ratio (OA PSV-ratio) is higher in women with pre-eclampsia compared with gestational hypertension (GH) and chronic hypertension (CH), after controlling for confounding variables. DESIGN: Prospective cohort. SETTING: Specialist hypertension clinic in a tertiary referral centre. POPULATION: Singleton pregnancies presenting between 32+0 and 36+6  weeks of gestation with pre-eclampsia (n = 50), GH (n = 54) and CH (n = 56). METHODS: Paired measurements of maternal mean arterial pressure (MAP) and OA PSV-ratio were performed by trained sonographers. Multiple linear regression was fitted to the OA PSV-ratio, including maternal characteristics and medical history, GH, pre-eclampsia and MAP and use of antihypertensive medication. MAIN OUTCOME MEASURE: Whether pre-eclampsia is independently associated with higher OA PSV-ratio. RESULTS: MAP was significantly higher in both GH (p = 0.0015) and pre-eclampsia (p = 0.008) than in CH pregnancies. There was no significant difference between pre-eclampsia and GH (0.670). The OA PSV-ratio was significantly higher in pre-eclampsia than CH (p = 0.0008) and GH (p = 0.015). There was no significant difference between the OA PSV-ratio in CH and GH (p = 0.352). Multiple linear regression modelling showed that the OA PSV-ratio was influenced by maternal weight (p = 0.005), maternal age (p = 0.014), antihypertensive medications (p = 0.007) and MAP (p < 0.0001). After controlling for these variables, the OA PSV-ratio was still significantly higher in those with pre-eclampsia (p = 0.0002). CONCLUSIONS: The OA PSV-ratio is influenced by maternal weight, age, antihypertensive medications and MAP. Pre-eclampsia is an independent predictor of OA PSV-ratio, which therefore may be a useful point-of-care test when assessing women presenting with hypertension.

Multi-species single-cell transcriptomic analysis of ocular compartment regulons.

The retina is a widely profiled tissue in multiple species by single-cell RNA sequencing studies. However, integrative research of the retina across species is lacking. Here, we construct the first single-cell atlas of the human and porcine ocular compartments and study inter-species differences in the retina. In addition to that, we identify putative adult stem cells present in the iris tissue. We also create a disease map of genes involved in eye disorders across compartments of the eye. Furthermore, we probe the regulons of different cell populations, which include transcription factors and receptor-ligand interactions and reveal unique directional signalling between ocular cell types. In addition, we study conservation of regulons across vertebrates and zebrafish to identify common core factors. Here, we show perturbation of KLF7 gene expression during retinal ganglion cells differentiation and conclude that it plays a significant role in the maturation of retinal ganglion cells.

Proficiency testing for bacterial whole genome sequencing in assuring the quality of microbiology diagnostics in clinical and public health laboratories.

The adoption of whole genome sequencing (WGS) data over the past decade for pathogen surveillance, and decision-making for infectious diseases has rapidly transformed the landscape of clinical microbiology and public health. However, for successful transition to routine use of these techniques, it is crucial to ensure the WGS data generated meet defined quality standards for pathogen identification, typing, antimicrobial resistance detection and surveillance. Further, the ongoing development of these standards will ensure that the bioinformatic processes are capable of accurately identifying and characterising organisms of interest, and thereby facilitate the integration of WGS into routine clinical and public health laboratory setting. A pilot proficiency testing (PT) program for WGS of infectious agents was developed to facilitate widely applicable standardisation and benchmarking standards for WGS across a range of laboratories. The PT participating laboratories were required to generate WGS data from two bacterial isolates, and submit the raw data for independent bioinformatics analysis, as well as analyse the data with their own processes and answer relevant questions about the data. Overall, laboratories used a diverse range of bioinformatics tools and could generate and analyse high-quality data, either meeting or exceeding the minimum requirements. This pilot has provided valuable insight into the current state of genomics in clinical microbiology and public health laboratories across Australia. It will provide a baseline guide for the standardisation of WGS and enable the development of a PT program that allows an ongoing performance benchmark for accreditation of WGS-based test processes.

Numerical optimization of microfluidic vortex shedding for genome editing T cells with Cas9.

Microfluidic vortex shedding (µVS) can rapidly deliver mRNA to T cells with high yield and minimal perturbation of the cell state. The mechanistic underpinning of µVS intracellular delivery remains undefined and µVS-Cas9 genome editing requires further studies. Herein, we evaluated a series of µVS devices containing splitter plates to attenuate vortex shedding and understand the contribution of computed force and frequency on efficiency and viability. We then selected a µVS design to knockout the expression of the endogenous T cell receptor in primary human T cells via delivery of Cas9 ribonucleoprotein (RNP) with and without brief exposure to an electric field (eµVS). µVS alone resulted in an equivalent yield of genome-edited T cells relative to electroporation with improved cell quality. A 1.8-fold increase in editing efficiency was demonstrated with eµVS with negligible impact on cell viability. Herein, we demonstrate efficient processing of 5 × 106 cells suspend in 100 µl of cGMP OptiMEM in under 5 s, with the capacity of a single device to process between 106 to 108 in 1 to 30 s. Cumulatively, these results demonstrate the rapid and robust utility of µVS and eµVS for genome editing human primary T cells with Cas9 RNPs.

Safety and efficacy of in vitro fertilisation in patients with chronic liver disease and liver transplantation recipients.

BACKGROUND & AIMS: Chronic liver disease and liver transplantation (LT) can delay both timing and ability of women to conceive. With increased awareness and availability of in vitro fertilisation (IVF), the need for accurate counselling is paramount. To date, minimal data exist on outcomes of IVF in patients with chronic liver disease, cirrhosis, or post-LT. We report the largest experience of IVF in women with liver-related subfertility (LRSF). METHODS: A retrospective analysis was performed on 42 women with LRSF who had undergone 57 IVF cycles between 1990 and 2019. RESULTS: Forty-two women with LRSF received IVF; 9 cycles in 6 women with cirrhosis, 14 cycles in 11 women post-LT, and 34 cycles in 25 women without cirrhosis. The main aetiologies of liver disease included HBV, HCV, and autoimmune hepatitis (AIH). Of 57 IVF cycles evaluated, 43 (75%) resulted in successful implantation. Eight (2 post-LT, 3 with cirrhosis, 4 without cirrhosis) resulted in miscarriage. The live birth rate (LBR) was 74% (32/43). Two of 9 (22%) patients with cirrhosis, 4/14 (29%) patients who were post-LT, and 6/34 (18%) patients without cirrhosis had unsuccessful IVF attempts. Nine of 57 (16%) IVF cycles resulted in new liver enzyme derangement during therapy, which improved after treatment completion. Six pregnancies (2 in patients who were post-LT, 4 without cirrhosis) were complicated by obstetric cholestasis (OC). Ovarian hyperstimulation syndrome (OHSS) was rare (n = 3, 7%). One patient with AIH-related cirrhosis decompensated after initiating IVF, warranting discontinuation of therapy. There were no maternal deaths. Three women developed a hypertensive disorder of pregnancy. Half the pregnancies resulted in premature deliveries (range 27-36 weeks). CONCLUSIONS: In selected cases, IVF in women with LRSF can be successful. However, patients should be counselled on the potential increased risks of OHSS, OC, and prematurity. LAY SUMMARY: Women with liver disease or those who have had a liver transplant can experience difficulties getting pregnant. In this study, we look at whether alternative approaches to achieve pregnancy are harmful in these women. Overall, there were no significant issues with the use of in vitro fertilisation in women with liver disease, but they need to be aware of potential risks, such as early delivery of the baby.

Closed-Incision Negative Pressure Wound management Following Midline Laparotomy in Gynecological Oncology Operations: A Feasibility Pilot Study.

Introduction Surgical site infections (SSIs) are a cause of considerable morbidity and mortality in healthcare. Increasingly, closed-incision negative pressure wound therapy (ciNPWT) is being studied as a potential method of reducing incidence of SSI with conflicting results in the literature. Few studies however have looked at its use in the field of gynecological oncology. Objectives We aimed to compare the incidence of SSI when using ciNPWT dressings versus conventional dressings in gynecological oncology patients undergoing midline laparotomies. Methods This was a pilot study involving 14 patients receiving the ciNPWT dressing and 26 control patients. All patients were followed up for a period of 30 days. We used the American College of Surgeons (ACS) risk calculator to estimate each patient's risk of SSI in order to risk stratify the groups. Results The incidence of wound infection was 21% (3/14) in the ciNPWT group and 23% (6/26) in the control group (p=0.886). The ciNPWT group was found to be at significantly higher risk for SSI as calculated by the ACS tool (8.8% ciNPWT, 6% control, p=0.004). After stratifying for this difference in risk, still no significant difference in incidence of SSI was found between the two groups (27% (3/11) ciNPWT, 29% (2/7) control p=0.929). Conclusion The incidence of SSI does not appear to decrease by the prophylactic use of the closed-incision negative pressure wound dressing.