Real-Time, Multiplexed SHERLOCK for in Vitro Diagnostics

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for simple, low-cost, and scalable diagnostics that can be widely deployed for rapid testing. Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have emerged as a promising technology, but its implementation in clinical laboratories has been limited by the requirement of a separate amplification step prior to CRISPR-associated (Cas) enzyme-based detection. This article reports the discovery of two novel Cas12 enzymes (SLK9 and SLK5-2) that exhibit enzymatic activity at 60°C, which, when combined with loop-mediated isothermal amplification (LAMP), enable a real-time, single-step nucleic acid detection method [real-time SHERLOCK (real-time SLK)]. Real-time SLK was demonstrated to provide accurate results comparable to those from real-time quantitative RT-PCR in clinical samples, with 100% positive and 100% negative percent agreement. The method is further demonstrated to be compatible with direct testing (real-time SLK Direct) of samples from anterior nasal swabs, without the need for standard nucleic acid extraction. Lastly, SLK9 was combined with either Alicyclobacillus acidoterrestris AacCas12b or with SLK5-2 to generate a real-time, multiplexed CRISPR-based diagnostic assay for the simultaneous detection of SARS-CoV-2 and a human-based control in a single reaction, with sensitivity down to 5 copies/μL and a time to result of under 30 minutes.

High-Throughput CRISPR-Cas13 SARS-CoV-2 Test

BACKGROUND

The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions.

METHODS

: We developed a diagnostic method based on CRISPR that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in less than one hour.

RESULTS

Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously identified as positive using Food and Drug Administration emergency use authorized assays and re-tested with a modified version of the Centers for Disease Control and Prevention (CDC) RT-qPCR assay. When combined with magnetic bead-based extraction, the high throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percent agreements were 100% (15/15, 95% CI : 81.8-100%) and 88% (15/17, 95% CI : 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory.

CONCLUSIONS

This high throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.

O42: THE ROLE OF TOURNIQUETS IN TRANSTIBIAL AMPUTATION FOR PERIPHERAL VASCULAR DISEASE: A SYSTEMATIC REVIEW & META-ANALYSIS

Introduction

The use of lower limb tourniquets is traditionally discouraged in severe atherosclerotic disease. However, blood loss and increased transfusion requirements are associated with post-operative morbidity in patients undergoing major lower limb amputation. The aim of this systematic review is to summarise and pool the available data to determine the impact of tourniquet application when performing trans-tibial amputation for peripheral vascular disease.

Method

This systematic review was conducted according to PRISMA guidelines. A systematic search of Medline, Embase and Cochrane Library was undertaken for articles which compared the use of a tourniquet versus no tourniquet in patients undergoing trans-tibial amputation for peripheral vascular disease. The main outcomes included intra-operative blood loss, post-operative transfusion requirement, need for revision surgery and 30-day mortality.

Result

Four studies met the inclusion criteria for quantitative analysis with a total of 267 patients. A tourniquet was used in 130 patients. Both groups were matched for age, gender, co-morbidities and pre-operative haemoglobin. In patients undergoing trans-tibial amputation, tourniquets were associated with significantly lower intra-operative blood loss (Mean difference= -147.6mls; P=0.03) and lower transfusion requirements (pooled odds ratio (OR), 0.12, p=0.03). The need for stump revision (OR, 0.7; p=0.48), proceeding to transfemoral amputation within 30 days (OR, 0.67; p=0.25) and 30-day mortality (OR, 0.65; p=0.41) all favoured tourniquet use but the differences were not found to be significant.

Conclusion

Tourniquets can reduce intra-operative blood loss and transfusion requirements in patients undergoing trans-tibial amputation without increasing ischaemic complications and need for revision surgery.

Take-home message

Tourniquets are safe to use in trans-tibial amputation for severe peripheral vascular disease and can reduce intra-operative blood loss without increasing ischaemic complications.

Critical Airway Compromise due to a Massive Vagal Schwannoma

We describe the case of a 37-year-old man with a slowly enlarging neck lump and compressive symptoms. He presented to a separate institution 10 years prior where an observational approach was advocated. Following preoperative investigations and embolization, an 11cm vagal schwannoma was excised and vagus nerve was sacrificed. Although conservative management is appropriate for a select patient population, surgical excision is treatment of choice for cervical neurogenic tumours and paraganglionomas and must be considered in young patients or rapidly expanding tumours to avoid compressive symptoms, as in this case.

Outcomes in achalasia from a surgical unit where pneumatic dilatation is first-line therapy

The management of achalasia remains controversial, with little consensus on the optimal patient treatment pathway. In our own esophageal unit, we offer pneumatic dilatation as the initial therapy in most patients as first-line therapy. In this study, we aimed to examine the safety and efficacy of our own approach to the management of patients with a diagnosis of achalasia, examining symptomatic outcomes, patient satisfaction, and need for further intervention, as well as examining patient factors associated with treatment failure. Sixty-seven consecutive patients underwent pneumatic dilatation as first-line therapy (53% male, mean age 46 years). All attended regular outpatient follow-up (mean 37, range 3-132 months). Twenty-five percent of patients required a second intervention because of symptom recurrence, at a median period of 4.5 months. Symptomatic outcomes were excellent or good in 80%. Significant predictors of treatment failure and poor symptom score included a younger age at the time of diagnosis and increased esophageal diameter on barium swallow. This study suggests that pneumatic dilatation is a safe and effective approach as first-line therapy in patients with newly diagnosed achalasia.

A Prospective Feasibility Study of Duplex Ultrasound Arterial Mapping, Digital-Subtraction Angiography, and Magnetic Resonance Angiography in Management of Critical Lower Limb Ischemia by Endovascular Revascularization

Duplex ultrasound arterial mapping (DUAM) allows precise evaluation of peripheral vascular disease (PVD). However, magnetic resonance angiography (MRA) and digital-subtraction angiography (DSA) are the diagnostic tools used most frequently prior to intervention. Our aim was to compare clinical pragmatism, hemodynamic outcomes, and cost-effectiveness when using DUAM alone compared to DSA or MRA as preoperative assessment tools for endovascular revascularization (EvR) in critical lower limb ischemia (CLI). From 2002 through 2005, 465 patients were referred with PVD. Of these, 199 had CLI and 137 required EvR. Preoperative diagnostic evaluation included DUAM (n = 41), DSA (n = 50), or MRA (n = 46). EvR was aortoiliac in 27% of cases and infrainguinal in 73%. Patients were assessed at day 1, 6 weeks, 3 months, and 6 months. Composite end points were relief of rest pain, ulcer/gangrene healing, and increase in perfusion pressure, as measured by ankle-brachial index (ABI) and digital pressures. Patency by DUAM, limb salvage, morbidity, mortality, length of stay, and cost-effectiveness were compared between groups using nonparametric t-test, analysis of variance, and Kaplan-Meier analysis. The three groups were comparable in terms of age, sex, comorbidity, and Society for Vascular Surgery/International Society of Cardiovascular Surgery clinical classification. Six-month mean improvement in ABI in the DUAM group was comparable to that in the DSA group (P = 0.25) and significantly better than that in the MRA group (P < 0.05). Six-month patency rates for the DUAM group were comparable to those in the DSA group (P = 0.68, relative risk [RR] = 0.74, 95% confidence interval [CI] 0.18-2.99) and superior to that in the MRA group (P = 0.022, RR = 0.255, 95% CI 0.09-0.71). Length of hospital stay was lower in the DUAM group compared with the DSA group (P < 0.0001) and the MRA group (P = 0.0003). The cost of DUAM is lower than that of both DSA and MRA. DUAM accurately identified the total number of target lesions for revascularization; however, MRA overestimated it. Our results indicate that DUAM is outstanding when compared with other available modalities as a preoperative imaging tool in a successful EvR program. DUAM is a minimally invasive preoperative evaluation for EvR and offers precise consecutive data with patency and limb salvage rates comparable to EvR based on DSA and superior to MRA. We believe that our feasibility study has established DUAM as an economically proficient primary modality for investigating patients with CLI that significantly shortens length of hospital stay.

Laparoscopic Nissen fundoplication: predicting outcome from peri-operative evaluation

BACKGROUND

Although laparoscopic Nissen fundoplicaton is a safe, effective treatment for gastrooesophageal reflux (GOR), questions remain about the durability of the procedure and patient selection criteria.

AIMS

To review a single surgeon's experience of laparoscopic Nissen fundoplicaton and to determine which factors, if any are likely to influence long term outcome.

METHODS

Data were collected on all 124 patients who underwent laparoscopic Nissen fundoplication over a five-year period, and a detailed questionnaire was used to evaluate outcome.

RESULTS

Eighty-nine per cent of patients were satisfied with the results of surgery whilst 8.8% of patients had significant recurrence of symptoms. Time since surgery was longer in those patients with symptom recurrence who were also more likely to be female. Pre-operative age, body mass index (BMI),Visick Score, endoscopic findings or pH analysis scores were not predictive of outcome, nor were intra-operative findings or post-operative complications.

CONCLUSION

Although laparoscopic Nissen fundoplication is a safe and effective treatment for GOR, it is difficult to predict the small but significant group of patients with poor longterm outcome based on pre-operative assessment and peri-operative parameters alone.

Recombinant Factor VIIa in the Treatment of Intractable Bleeding in Vascular Surgery

Intractable bleeding unresponsive to conventional haemostatic measures is an uncommon but potentially life threatening surgical complication. Several studies have suggested that recombinant factor VIIa (rVIIa), a genetically engineered substitute for endogenous factor VIIa may have therapeutic application in patients with uncontrollable haemorrhage not previously diagnosed with coagulopathy. We report our experience of rVIIa use in eight such vascular surgery patients who developed life-threatening non-surgical haemorrhage either intra-operative or post-operatively. In all but one patient a marked clinical improvement was noted following treatment with rVIIa with significantly less transfusion, and obvious haemostasis associated with haemodynamic stability without adverse thrombotic complications.

Iodinated contrast media induce neutrophil apoptosis through a mitochondrial and caspase mediated pathway

Iodinated contrast media (ICM) can induce apoptosis (programmed cell death) in renal, myocardial and endothelial cells. Following intravascular injection, circulating immune cells are exposed to high concentrations of ICM. As neutrophils constitutively undergo apoptosis we hypothesized that ICM may adversely affect neutrophil survival. Our aim was to investigate the effect of ICM on neutrophil apoptosis. Neutrophils were isolated from healthy subjects and cultured in vitro with ionic (diatrizoate and ioxaglate) and non-ionic (iohexol and iotrolan) ICM. The effect of ICM on neutrophil apoptosis in both unstimulated and lipopolysaccharide-stimulated neutrophils was determined by annexin V flow cytometry. The influence of physicochemical properties of the different ICM on apoptosis of neutrophils was also studied. We further investigated the effects of ICM on key intracellular signal pathways, including p38 mitogen-activated protein kinase (MAPK) by Western blotting, and mitochondrial depolarization and caspase activity by flow cytometry. Isoiodine concentrations (20 mg ml(-1)) of ionic (diatrizoate 69.6+/-2.9%; ioxaglate 58.9+/-2.0%) and non-ionic (iohexol 57.3+/-2.9%; iotrolan 57.1+/-2.6%) ICM significantly induced neutrophil apoptosis over control levels (47.7+/-1.4%). The apoptotic effect of ICM was influenced by their chemical structure, with ionic ICM having a more significant (p<0.01) apoptotic effect than non-ionic ICM (p<0.05). Furthermore, ICM reversed the anti-apoptotic effect of lipopolysaccharide (1000 ng ml(-1)) treated neutrophils to control levels (23.0+/-3.5% to 61.2+/-5.3%; n=4; p<0.05). These agents induce apoptosis through a p38 MAPK independent pathway that results in mitochondrial depolarization, and is dependent on caspase activation. As neutrophils play a central role in host response to infection and injury, ICM, through induction of neutrophil apoptosis, could have a significant deleterious effect on host immune defence and resolution of an inflammatory response.

Nasogastric intubation causes gastroesophageal reflux in patients undergoing elective laparotomy

BACKGROUND

The routine use of nasogastric tubes in patients undergoing elective abdominal operation is associated with an increased incidence of postoperative fever, atelectasis, and pneumonia. Previous studies have shown that nasogastric tubes have no significant effect on the incidence of gastroesophageal reflux or on lower esophageal sphincter pressure in healthy volunteers. We hypothesized that nasogastric intubation in patients undergoing laparotomy reduces lower esophageal sphincter pressure and promotes gastroesophageal reflux in the perioperative period.

METHODS

A prospective randomized case-control study was undertaken in which 15 consenting patients, admitted electively for bowel surgery, were randomized into 2 groups. Group 1 underwent nasogastric intubation after induction of anesthesia, and Group 2 did not. All patients had manometry and pH probes placed with the aid of endoscopic vision at the lower esophageal sphincter and distal esophagus, respectively. Nasogastric tubes, where present, were left on free drainage, and sphincter pressures and pH were recorded continuously during a 24-hour period. Data were analyzed with 1-way analysis of variance.

RESULTS

The mean number of reflux episodes (defined as pH < 4) in the nasogastric tube group was 137 compared with a median of 8 episodes in the group managed without nasogastric tubes (P =.006). The median duration of the longest episode of reflux was 132 minutes in Group 1 and 1 minute in Group 2 (P =.001). A mean of 13.3 episodes of reflux lasted longer than 5 minutes in Group 1, with pH less than 4 for 37.4% of the 24 hours. This was in contrast to Group 2 where a mean of 0.13 episodes lasted longer than 5 minutes (P =.001) and pH less than 4 for 0.2% of total time (P =.001). The mean lower esophageal sphincter pressures were lower in Group 1. CONCLUSIONS. These findings demonstrate that patients undergoing elective laparotomy with routine nasogastric tube placement have significant gastroesophageal reflux in the perioperative period and a reduced ability to clear refluxed acid from the distal esophagus. Due to the associated risk of postoperative pulmonary complications, we recommend that nasogastric intubation be performed on a selective rather than routine basis.

A prospective comparison of pedal ergometry with conventional treadmill testing in the investigation of lower extremity pain

BACKGROUND

Investigation of lower extremity pain is compromised by comorbid disorders that may interfere with conventional testing.

AIMS

To compare pedal ergometry with conventional treadmill testing.

METHODS

A prospective study was performed where patients presenting with a diagnosis of intermittent claudication were assessed by both methods of testing.

RESULTS

Of 78 patients studied with both tests, no exercise-induced ankle pressure changes occurred in 26, two were unable to complete either test despite normal pressure measurements, while 24 had exercise-induced pressure drop detected by both tests. Of patients who completed pedal ergometry, 21 were unable to complete the treadmill test, 14 of whom had negative ergometry, while seven had a pressure drop detected by pedal ergometry. Three had pressure changes with pedal ergometry, but not with treadmill testing and two had pressure changes on the treadmill not reproduced by pedal ergometry.

CONCLUSIONS

Pedal ergometer is more sensitive than treadmill testing in detecting arterial insufficiency, as indicated by a 20% or greater fall in ankle pressure, and more suitable in a subgroup of patients unable to tolerate conventional treadmill testing.