Large-scale implementation of pooled RNA extraction and RT-PCR for SARS-CoV-2 detection

INTRODUCTION

Testing for active SARS-CoV-2 infection is a fundamental tool in the public health measures taken to control the COVID-19 pandemic. Because of the overwhelming use of SARS-CoV-2 reverse transcription (RT)-PCR tests worldwide, the availability of test kits has become a major bottleneck and the need to increase testing throughput is rising. We aim to overcome these challenges by pooling samples together, and performing RNA extraction and RT-PCR in pools.

METHODS

We tested the efficiency and sensitivity of pooling strategies for RNA extraction and RT-PCR detection of SARS-CoV-2. We tested 184 samples both individually and in pools to estimate the effects of pooling. We further implemented Dorfman pooling with a pool size of eight samples in large-scale clinical tests.

RESULTS

We demonstrated pooling strategies that increase testing throughput while maintaining high sensitivity. A comparison of 184 samples tested individually and in pools of eight samples showed that test results were not significantly affected. Implementing the eight-sample Dorfman pooling to test 26 576 samples from asymptomatic individuals, we identified 31 (0.12%) SARS-CoV-2 positive samples, achieving a 7.3-fold increase in throughput.

DISCUSSION

Pooling approaches for SARS-CoV-2 testing allow a drastic increase in throughput while maintaining clinical sensitivity. We report the successful large-scale pooled screening of asymptomatic populations.

Quadrivalent versus trivalent influenza vaccine: clinical outcomes in two influenza seasons, historical cohort study

OBJECTIVES

The quadrivalent influenza vaccine (QIV) contains two influenza B antigens (one of each B lineage), while the trivalent vaccine (TIV) contains solely one. As a result, a mismatch between the circulating B lineage and the lineage in the TIV occurs frequently. We aimed to compare the frequency of clinically significant outcomes in a large cohort of vaccinees receiving either TIV or QIV.

METHODS

Historical cohort study of all inactivated influenza vaccinees (aged 3 years and older) in a Health Maintenance Organization insuring 1.2 million individuals, over two influenza seasons in which both vaccines were provided non-selectively. Primary outcome was hospital admissions during the influenza season. Multivariate analysis was performed using logistic regression to adjust for relevant covariates.

RESULTS

Our cohort included 150 518 and 168 296 vaccinees in the first (S1) and second season (S2), respectively. The two influenza seasons were characterized by high Influenza B activity. Of those vaccinated with QIV, 2074 of 49 726 (4.2%) and 6563 of 121 741 (5.4%) were hospitalized compared with 7378 of 100 792 (7.3%) and 3372 of 46 555 (7.2%) of those vaccinated with TIV (S1 and S2, respectively). After multivariate analysis adjusting for several covariates (gender, age, socioeconomic status, chronic morbidity, timing of vaccination), compared with TIV recipients, QIV vaccinees had lower odds for hospitalization (OR = 0.92, 95% CI 0.87-0.98 and OR = 0.89, 95% CI 0.85-0.93) or emergency department visit (OR = 0.91, 95% CI 0.87-0.95 and OR = 0.84, 95% CI 0.81-0.87) in S1 and S2, respectively (p < 0.001). Lower odds of mortality and influenza-like illness were also observed in S2 (OR = 0.61, 95% CI 0.50-0.75 and OR = 0.92, 95% CI 0.90-0.95, respectively).

CONCLUSIONS

In seasons with relatively high influenza B activity, QIV appeared more protective than TIV in Israel.

Successful control of a large outbreak of HIV infection associated with injection of cathinone derivatives in Tel Aviv, Israel

OBJECTIVES

Outbreaks of HIV infection have been linked to injectable drug abuse, but specific triggers often remain obscure. We report on an outbreak of primary HIV infection among people who inject drugs (PWID) in Tel Aviv, associated with a local shift in drug-use practices.

METHODS

A cluster of primary HIV infection cases in PWID was detected in May 2012. Retrospective and prospective multi-hospital case finding was initiated. PWID were interviewed and risk factors for primary HIV infection were identified. Starting in December 2012, a multifaceted intervention was implemented, including educational activities, increasing syringe exchange supplies, active screening, early initiation of antiretroviral therapy, and referral to drug withdrawal programmes.

RESULTS

Forty-two PWID with primary HIV infection were detected between May 2012 and April 2013. Compared with the corresponding pre-outbreak period, the annual incidence of primary HIV infection in PWID increased from 0 to 20 cases/1000 population (p <0.0001). Sixty-nine per cent were hospitalized because of concomitant bacterial infections and sepsis. Phylogenetic analysis of HIV isolates from case patients showed tight clustering suggesting a single common source of infection. The outbreak was temporally related to a widespread shift from heroin to injectable cathinone-derivatives and buprenorphine, which entailed high-risk injection practices. Targeted intervention resulted in a dramatic and sustained reduction in HIV infection in the PWID population.

CONCLUSIONS

Injectable amphetamines are gaining momentum among PWID worldwide. Tracing of this outbreak to cathinone use and implementing a targeted intervention programme effectively terminated the outbreak.

Differential association of fluconazole dose and dose/MIC ratio with mortality in patients with Candida albicans and non-albicans bloodstream infection

Targeting fluconazole therapy to achieve predefined pharmacodynamic goals has been suggested as a means of optimizing the treatment of patients with candidaemia. However, data regarding species-specific dosing targets are inconclusive. We retrospectively analysed a cohort of 75 adult patients with Candida bloodstream infection (BSI) who received initial treatment with fluconazole for ≥48 h (36 Candida albicans and 39 non-albicans Candida (NAC)). Fluconazole dose, the dose/MIC ratio and the 24-h area under the concentration-time curve (AUC24)/MIC ratio were determined for each patient, and classification and regression tree analysis was used to determine breakpoints for significant interactions with 30-day survival. Both fluconazole exposure parameters and patient-related and disease-related variables were assessed in univariable and multivariable survival models. The crude 30-day mortality rate was 32% (44% and 21% for C. albicans and NAC, respectively). An average fluconazole dose of >200 mg/day, a dose/MIC ratio of >400 and an AUC24/MIC ratio of >400 were associated with a higher 30-day survival rate and better microbiological response in patients with C. albicans BSI but not in those with NAC BSI. Baseline chronic kidney disease was a risk factor for fluconazole underdosing and mortality. Severity of sepsis (Sequential Organ Failure Assessment score) was the only significant predictor of death in patients with NAC BSI. We conclude that, although pharmacodynamic target-directed fluconazole dosing may help to optimize outcomes for patients with C. albicans BSI, additional studies are needed to define the role of fluconazole in the treatment of NAC BSI.

Does pre-exposure of Aspergillus fumigatus to voriconazole or posaconazole in vitro affect its virulence and the in vivo activity of subsequent posaconazole or voriconazole, respectively? A study in a fly model of aspergillosis

OBJECTIVES

Voriconazole and posaconazole are effective as both prophylaxis and treatment for invasive aspergillosis (IA) in immunocompromised patients. Hence, it is important to determine whether Aspergillus pre-exposure to voriconazole or posaconazole diminishes subsequent posaconazole or voriconazole activity, respectively.

METHODS

We used Aspergillus fumigatus (AF) 293 conidia with or without prior exposure to voriconazole or posaconazole [three serial passages on plates containing regular yeast extract-glucose (YAG) media, YAG+0.0625 mg/L voriconazole or YAG+0.025 mg/L posaconazole]. Toll-deficient Drosophila melanogaster flies were infected by injection, and 8 day survival was monitored. Following infection, flies were fed either regular food, food containing 1000 mg/L voriconazole (posaconazole-exposed conidia) or 1000 mg/L posaconazole (voriconazole-exposed conidia). Voriconazole and posaconazole concentrations in flies were confirmed by HPLC.

RESULTS

AF inoculation resulted in 71% mortality 8 days post-infection (median survival 4 days). Prior conidial exposure to voriconazole or posaconazole did not affect mortality (73%, P = 0.8 for voriconazole pre-exposed and 76%, P = 0.49 for posaconazole pre-exposed). Voriconazole treatment post-infection had a protective effect, reducing mortality to 42% (P = 0.0002), while prior conidial exposure to posaconazole did not alter the protective effect of voriconazole (34% 8 day mortality, P = 0.35). Likewise, posaconazole treatment post-infection reduced mortality to 36%, while prior conidial exposure to voriconazole did not alter the protective effect of posaconazole (39% mortality, P = 0.92). Median fly homogenate concentrations of voriconazole and posaconazole were 0.44 and 2.05 mg/L, respectively.

CONCLUSIONS

Prior exposure of AF to voriconazole or posaconazole did not affect the virulence of AF nor the subsequent activity of the alternate triazole in a Drosophila model of IA.

Increased red blood cell aggregation in patients with Gaucher disease is non-inflammatory

Red blood cell (RBC) aggregation is enhanced in the presence of ongoing inflammation, because of plasma protein effects, especially fibrinogen. Large RBC aggregates, in addition to being a marker of systemic inflammation, may hinder tissue perfusion and oxygenation. Gaucher disease, the most common lysosomal storage disorder, evinces many of the hallmarks of chronic inflammation. Manifestations of Gaucher disease which may be related to microvascular occlusion include avascular necrosis (AVN), bone crisis, and pulmonary hypertension. This study aims to determine whether increased RBC aggregation in non-splenectomized patients with Gaucher disease is due to Gaucher-related inflammation. The Cell Flow Properties Analyzer (CFA) monitors blood under conditions of different shear stress by creating varying pressure gradients. Blood from non-splenectomized patients with Gaucher disease showed only a slight correlation between aggregation parameters and fibrinogen levels, whereas blood from non-splenectomized patients treated with enzyme replacement therapy (ERT) showed marked correlation between aggregation parameters and fibrinogen, as in the control group. These results underscore the hypothesis that RBC aggregation in Gaucher disease is increased by (at least) two mechanisms: a fibrinogen-mediated inflammatory process and another non-inflammatory process that may be induced by elevated glucocerebroside levels in the RBC and/or inhibited by elevated plasma cerebroside levels.

Influx of extended-spectrum beta-lactamase-producing enterobacteriaceae into the hospital

BACKGROUND

The prevalence of infections caused by extended-spectrum beta -lactamase (ESBL)-producing Enterobacteriaceae is increasing worldwide. The influx of these bacteria into hospitals has major implications for infection-control and empirical treatment strategies.

METHODS

Isolates from 2 patient cohorts--patients with gram-negative bacteremia within 2 days after admission and patients screened for fecal colonization at admission--were assessed for ESBL production. ESBL phenotype was confirmed according to Clinical and Laboratory Standards Institute guidelines. Predictors of ESBL phenotype were examined by univariate and multivariate analyses.

RESULTS

Of 80 Enterobacteriaceae isolates from blood samples obtained at admission to the hospital, 13.7% produced ESBL. Thirty-eight patients with ESBL-positive isolates and 72 with ESBL-negative isolates were included in a case-control study. Predictors of ESBL production were male sex and nursing home residence (area under receiver operator characteristic curve, 0.7). Of 241 persons screened at admission, 26 (10.8%) had fecal carriage of ESBL-producing Enterobacteriaceae. Predictors of fecal carriage were poor functional status, antibiotic use, chronic renal insufficiency, liver disease, and use of histamine2 blockers (area under receiver operator characteristic curve, 0.8). Four (15.4%) of the 26 individuals with fecal carriage had subsequent bacteremia with ceftazidime-resistant Enterobacteriaceae, compared with 1 (0.5%) noncarrier (odds ratio, 38.9; P<.001). Of 80 ESBL-producing Enterobacteriaceae isolates obtained at admission, 65 were health care associated, and 15 were community acquired. The 15 community-acquired ESBL-producing Enterobacteriaceae belonged to diverse clones. The most prevalent ESBL gene among these isolates was CTX-M-2 (found in 53.3% of the isolates).

CONCLUSIONS

We report high rates of bacteremia and colonization with ESBL-producing Enterobacteriaceae at admission to our institution, which may undermine infection-control measures and complicate the selection of empirical treatment.

Erroneous reporting of coagulase-negative Staphylococci as Kocuria spp. by the Vitek 2 system

Misidentification of coagulase-negative staphylococci (CoNS) may delay appropriate treatment. We investigated 20 clinical isolates identified as Kocuria spp. by the Vitek 2 system. All were identified as CoNS by 16S rRNA gene sequencing (18 Staphylococcus epidermidis, 1 Staphylococcus haemolyticus). Four Kocuria isolates were shown to be identical to CoNS from the same patient by pulsed-field gel electrophoresis. Isolates identified by Vitek 2 as Kocuria most likely represent misidentified CoNS, and if clinically indicated, should be investigated further by genomic methods.

Liver failure and transplantation after itraconazole treatment for toenail onychomycosis

Three weeks after completing a 4-pulse course of itraconazole for toenail onychomycosis, a 25-year-old woman patient developed severe liver crisis and required an emergency liver transplant. We report the case and discuss the use of itraconazole in onychomycosis and dermatomycoses.

Flow-resistant red blood cell aggregation in morbid obesity

OBJECTIVE

Enhanced red blood cell (RBC) aggregation has an adverse effect on microcirculatory blood flow and tissue oxygenation. It has been previously shown that obesity is associated with increased RBC aggregation. The objectives of the present study were to further characterize obesity-related RBC aggregation and to examine whether the enhanced aggregation is a plasma- or cellular-dependent process.

METHODS

Obese (body mass index (BMI)=40+/-6.3 kg/m2, n=22) and nonobese (BMI=24+/-3.4 kg/m2, n=18) individuals were evaluated for inflammation markers and aggregation parameters. Aggregation parameters were derived from the distribution of RBC population into aggregate sizes, and from the variation of the distribution as a function of flow-derived shear stress, using a cell flow properties analyzer. To differentiate plasmatic from cellular factors, we determined the aggregation in the presence of autologous plasma or dextran-500 kDa and calculated the plasma factor (PF) in the obese group. PF ranges from 0 to 1. When the PF=1, the aggregation is all due to plasmatic factors, when PF=0, the altered aggregation depends entirely on cellular factors, whereas 0<PF<1 reflects the joint contribution of cellular and plasmatic factors.

RESULTS

Obese subjects had relatively larger aggregates that were more resistant to dispersion by flow. The calculated PF in the obese group was 0.9, indicating a pronounced contribution of plasma to RBC aggregation in obesity.

DISCUSSION

Our results suggest that obese individuals present pathological plasma-dependent RBC aggregation, which is probably triggered by plasma macromolecules associated with the inflammatory response. These findings impact the future attempts to develop strategies aimed at attenuation of the enhanced RBC aggregation in obese individuals.

Protocol for the Accelerated Detection of Extended-Spectrum �-Lactamase-Producing Escherichia coli and Klebsiella pneumoniae Strains from Blood Cultures

The study presented here was performed to evaluate an accelerated protocol for the early detection of organisms producing extended-spectrum beta-lactamase (ESBL). The procedure involved testing isolates directly from positive blood-culture bottles, and a total of 40 clinical isolates (10 ESBL-producing and 10 non-ESBL-producing isolates of both Escherichia coli and Klebsiella pneumoniae) were used. The isolates were inoculated into blood cultures bottles and, upon growth signal, fluid from the bottle was cultured directly onto plates with combination discs containing cefotaxime or ceftazidime with and without clavulanate. Results were compared with those of standard methods for the detection of ESBL. High concordance between the two methods was found, and the direct test showed high sensitivity (95%) and specificity (100%). Use of this accelerated protocol may speed detection of the ESBL phenotype and thereby facilitate the early administration of appropriate antimicrobial therapy.

Cutaneous involvement in a rare case of adult visceral leishmaniasis acquired in Israel

Skin lesions are rare in visceral leishmaniasis, especially in Mediterranean countries. We describe an unusual case of visceral leishmaniasis in a 41-year-old man that began with a skin lesion. The parasites isolated from both the skin lesion and the bone marrow were typed as Leishmania donovani sensu stricto. This pathogen is not endemic in Israel or neighboring countries; its contribution to adult visceral leishmaniasis in Israel is summarized.

Thrombolytic therapy reduces red blood cell aggregation in plasma without affecting intrinsic aggregability

Red blood cell (RBC) aggregation may contribute to occlusion of the coronary microcirculation during myocardial infarction. We studied the effect of thrombolytic therapy on RBC aggregation in patients with acute myocardial infarction (AMI). Compared with patients with myocardial infarction who did not receive thrombolytic therapy, those treated with systemic thrombolysis exhibited significantly reduced RBC aggregation, reduced plasma fibrinogen levels and increased plasma D-dimer levels. Using measurement of RBC aggregation in a standardized dextran-500 solution, reduction in RBC aggregation after thrombolysis was shown to be plasma dependent. Thrombolytic therapy had no direct effect on intrinsic RBC aggregability in patients with AMI. We conclude that thrombolytic therapy has rheologic consequences that may contribute to its overall efficacy. Inhibition of RBC aggregation by thrombolytic therapy may result from the degradation of fibrinogen, a key factor in the formation of RBC aggregates, and from the generation of fibrinogen degradation products capable of disaggregating RBCs.

Retinal artery occlusion in a patient with factor V Leiden and prothrombin G20210A mutations

Retinal artery occlusion is rare in young adults, and may be associated with hereditary thrombophilia. We present a 19-year-old male who was evaluated for central retinal artery occlusion and found to be homozygous for the factor V Leiden mutation and heterozygous for the prothrombin G20210A mutation. Anterior chamber paracenthesis resulted in dramatic improvement, but recurring loss of vision necessitated repeated paracenthesis and the addition of aspirin to standard anticoagulation treatment. The literature concerning hereditary thrombophilia and retinal artery occlusion is reviewed, and the synergistic effect of multiple risk factors is emphasized. Screening for hereditary thrombophilia should be considered for young people presenting with unexplained retinal artery occlusion.

The Mount Sinai Hospital clinicalpathological conference: a 45-year-old man with Pompe's disease and dilated cardiomyopathy

This is an unusual case of a 45-year-old man, born in Ecuador, with evidence of profound left ventricular dysfunction, dilated cardiomyopathy and marked myocardial hypertrophy. Preceding events were advanced atrioventricular block (necessitating pacemaker implantation) and atrial flutter. The diagnosis of Pompe's disease was established by endomyocardial biopsy and appropriate staining, which indicated abnormal glycogen storage.