Epidemiological and clinical characteristics of hospitalized human metapneumovirus patients in Israel, 2015-2021: A retrospective cohort study.

This study evaluated the epidemiological and clinical characteristics of human metapneumovirus (hMPV) infection among hospitalized patients with acute respiratory infections during 2015-2021 and assessed the impact of the coronavirus disease 2019 pandemic on hMPV infection. A single-center, retrospective cohort study was performed, including pediatric and adult patients with laboratory-confirmed hMPV. Of a total of 990 patients, 253 (25.6%), 105 (10.6%), 121 (12.2%), and 511 (51.6%) belonged to age groups 0-2, 3-17, 18-59, and ≥60 years, respectively. The highest percentage (23.0%) of patients were hospitalized during 2019 and the lowest (4.7%) during 2020. Patients < 18 years experienced high rates of comorbidities (immunodeficiencies: 14.4% and malignancies: 29.9%). Here, 37/39 (94.9%) of all bronchiolitis cases were diagnosed in patients < 2 years, whereas more patients in older age groups were diagnosed with pneumonia. A greater proportion of hMPV patients diagnosed with viral coinfection (mostly respiratory syncytial virus and adenovirus) were <18 years. The highest percentages of intensive care unit admissions were recorded among patients < 18 years. Our findings demonstrate that hMPV is an important cause of morbidity in young children and a possibly underestimated cause of morbidity among older adults.

Candida lusitaniae Fungemia in Children: A multicenter case series of emerging pathogen.

Candida lusitaniae fungemia is a serious infection that is rarely reported in children. The aim of this study is to describe a case series of C. lusitaniae fungemia and review previous publications regarding this rare pathogen. This is a multicenter case series of children diagnosed with C. lusitaniae fungemia. A total of 18 cases that occurred over a 15-year period in five tertiary hospitals were included. Additionally, a review of the literature regarding C. lusitaniae fungemia in children was performed. A total of 18 cases were enrolled; 11/18 (61%) were males, with a mean age of 2.3 years. All patients had severe underlying diseases and risk factors for opportunistic infection, most commonly prematurity and malignancies. More than one-third of cases occurred during the last 2 years of the study period. All isolates were susceptible to all tested antifungals. The survival rate following the acute infection was 94%, whereas the survival rate of 14 previously published cases was 71%, with the most common underlying diseases being CGD and malignancies. Candida lusitaniae fungemia is not a common event in the pediatric population, occurring exclusively in children with severe underlying diseases and significant risk factors. This cohort revealed better clinical outcomes than previously reported. All tested isolates were susceptible to all antifungal agents; variability in susceptibility as previously reported was not found in this study. The allegedly higher rate of infection in recent years is in need of further investigation in larger prospective studies in order to conclude if a real trend is at play.

Candida lusitaniae fungemia is a serious infection rarely reported in children. This cohort revealed better clinical outcomes than previously reported. All tested isolates were susceptible to all antifungal agents. The higher rate of infection in recent years is in need of further investigation.

Early rise of West Nile fever in Israel, June 2024.

This report describes an unusual surge of West Nile fever in Israel in June 2024, during which 125 cases were diagnosed, compared with 4 cases on average during June in previous years (2014-23). Of the cases, 64 (62.1%) had neuroinvasive disease and 12 (9.6%) died; the 2024 case fatality rate was not significantly elevated vs the average rate in 2014-23. The early rise could be related to a temperature increase in spring and early summer of 2024.

Spike vs nucleocapsid SARS-CoV-2 antigen detection: application in nasopharyngeal swab specimens.

Public health experts emphasize the need for quick, point-of-care SARS-CoV-2 detection as an effective strategy for controlling virus spread. To this end, many "antigen" detection devices were developed and commercialized. These devices are mostly based on detecting SARS-CoV-2's nucleocapsid protein. Recently, alerts issued by both the FDA and the CDC raised concerns regarding the devices' tendency to exhibit false positive results. In this work, we developed a novel alternative spike-based antigen assay, comprising four high-affinity, specific monoclonal antibodies, directed against different epitopes on the spike's S1 subunit. The assay's performance was evaluated for COVID-19 detection from nasopharyngeal swabs, compared to an in-house nucleocapsid-based assay, composed of novel antibodies directed against the nucleocapsid. Detection of COVID-19 was carried out in a cohort of 284 qRT-PCR positive and negative nasopharyngeal swab samples. The time resolved fluorescence (TRF) ELISA spike assay displayed very high specificity (99%) accompanied with a somewhat lower sensitivity (66% for Ct < 25), compared to the nucleocapsid ELISA assay which was more sensitive (85% for Ct < 25) while less specific (87% specificity). Despite being outperformed by qRT-PCR, we suggest that there is room for such tests in the clinical setting, as cheap and rapid pre-screening tools. Our results further suggest that when applying antigen detection, one must consider its intended application (sensitivity vs specificity), taking into consideration that the nucleocapsid might not be the optimal target. In this regard, we propose that a combination of both antigens might contribute to the validity of the results. Schematic representation of sample collection and analysis. The figure was created using BioRender.com.

[THE EFFECT OF PNEUMOCOCCAL CONJUGATE VACCINE ON PNEUMOCOCCAL CARRIAGE AND INVASIVE DISEASE].

INTRODUCTION: Pneumococcal infections are an important cause of morbidity and mortality among children and adults worldwide. Acquisition and carriage of pneumococci are essential for the development of pneumococcal invasive (bacteremia, meningitis) and non-invasive disease. Pneumococcal conjugate vaccines (PCV) differ from the polysaccharide vaccine (PPV23) in its enhanced immunity and ability to prevent carriage of pneumococci. With the implementation of PCV to pediatric vaccination programs in different countries, we witnessed a change in the patterns of pneumococcal carriage and illness. In this review the authors present some of the changes that were observed with the implantation of PCV in Israel and other countries regarding pneumococcal carriage and invasive disease, with emphasis on the direct and indirect effect of this vaccine.

Preparing for laboratory automation and consolidation-Establishing the validity of pediatric-like low-volume urine samples in boric-acid containing tubes.

Microbiological services consolidation has increased the usage of preservative-containing urine tubes, potentially inhibiting pathogens in low-volume pediatric urine samples, yielding false-negative results. Our study demonstrates comparable growth with 1 ml versus the recommended 3 ml urine, following different shipping intervals. We advocate for regulators to consider similar large-scale validations, ensuring results' consistency.

Parvovirus B19 Outbreak in Israel: Retrospective Molecular Analysis from 2010 to 2023.

This study presents an analysis of the epidemiological trends of parvovirus B19 (B19V) in Israel from 2010 to 2023, with particular emphasis on the outbreak in 2023. The analysis utilized molecular diagnostic data from individual patients obtained at the Central Virology Laboratory. Between 2010 and 2022, 8.5% of PCR-tested samples were positive for B19V, whereas in 2023, this percentage surged to 31% of PCR-tested samples. Throughout the study period, annual cycles consistently peaked in early spring/summer, with the most recent prominent outbreak occurring in 2016. Predominantly, diagnoses were made in children and women aged 20-39. Despite the notable surge in 2023, over 80% of positive cases continued to be observed in children and young women, with a decrease in cases during winter months. Furthermore, genotype 1a of the virus remained the predominant strain circulating during the outbreak. In light of these circumstances, consideration should be given to implementing screening measures, particularly among high-risk groups such as pregnant women.

Don't rash it! The clinical significance of positive Varicella zoster virus PCR in cerebrospinal fluid of patients with neurological symptoms.

BACKGROUND: Varicella zoster virus (VZV) is among the leading pathogens causing meningitis and encephalitis. While VZV-PCR-positive CSF is considered a gold-standard for diagnosis, it is not-uncommon to detect VZV-DNA in CSF of patients with other acute or chronic illness. Our goal was to determine the clinical relevance of VZV-PCR-positive CSF when investigating patients with neurological symptoms. METHODS: In this retrospective cohort from the largest hospital in Israel, we collected demographic, clinical and laboratory data of patients with VZV-PCR-positive CSF, analyzing the significance of various parameters. RESULTS: During a 5-years study, 125 patient-unique VZV-PCR-positive CSFs were recorded, in which only 9 alternative diagnoses were noted. The commonest symptoms were headache (N = 104, 83 %) and rash (N = 96, 76 %). PCR-cycle-threshold (Ct), a surrogate of viral burden, did not significantly vary across the clinical manifestations; however, patients with rash and Ct<35 were prone to develop stroke in the following year (N = 6, 7 %). Empiric nucleoside-analogue treatment was not associated with a better outcome compared to treatment administered upon a positive-PCR result. DISCUSSION: Our findings suggest that in patients with neurological symptoms, detection of VZV-DNA in CSF renders VZV the probable culprit. Nevertheless, a systematic evaluation of treatment and follow-up algorithms of patients with suspected or proved VZV meningitis and encephalitis is needed. The benefits of a prompt treatment should be weighed against the potential complications of nucleoside-analogue. Conversely, the propensity for stroke in patients with higher viral-burden, necessitates further studies assessing VZV causal role, directing additional workup, treatment and monitoring policy.

A Systematic Review and Clinical Presentation of Central Nervous System Complications of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Pediatric Patients During the Coronavirus Disease 2019 Pandemic in Israel.

BACKGROUND: Coronavirus disease-associated central nervous system complications (CNS-C) in hospitalized children, especially during the Omicron wave, and in comparison with influenza associated CNS-C, are not well understood. METHODS: The study population included 755 children aged <18 years hospitalized with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at Sheba Medical Center, during March 2020 to July 2022. A comparative cohort consisted of 314 pediatric patients with influenza during the 2018-2019 and 2019-2020 influenza seasons. RESULTS: Overall, 5.8% (n = 44) of patients exhibited CNS-C. Seizures at presentation occurred in 33 patients with COVID-19 (4.4%), with 2.6% (n = 20) experiencing nonfebrile seizures, 1.1% (n = 8) febrile seizures, and 0.7% (n = 5) status epilepticus. More patients with CNS-C experienced seizures during the Omicron wave versus the pre-Omicron period (77.8% vs 41.2%, P = 0.03). Fewer patients were admitted to the intensive care unit in the Omicron wave (7.4%) versus prior waves (7.4% vs 41.2%, P = 0.02). Fewer patients with SARS-CoV-2 experienced CNS-C (5.8%) versus patients with influenza (9.9%), P = 0.03. More patients with SARS-CoV-2 experienced nonfebrile seizures (2.6% vs 0.6%, P = 0.06), whereas more patients with influenza experienced febrile seizures (7.3% vs 1.1%, P < 0.01). CONCLUSIONS: The Omicron wave was characterized by more seizures and fewer intensive-care-unit admissions than previous waves. Pediatric patients with SARS-CoV-2 experienced fewer CNS-C and more nonfebrile seizures compared with patients with influenza.

Optimizing the Yield of In-and-Out Urinary Catheter Cultures by Applying a "Midstream-Like" Approach in Pediatric Patients.

Despite appropriate disinfection, sample contamination during in-and-out urinary catheterization is not uncommon, yielding false-positive and "mixed-culture" interpretations. We implemented a "midstream-like" catheterization technique, and cultured both first- and second-voided urine fractions. Second-fraction cultures exhibited less contaminants and "mixed-culture" interpretations and were better aligned with pyuria, thereby enhancing diagnostic accuracy and minimizing the risk of clinical misdiagnosis and unwarranted antibiotic use.

Real-Life Experience and Diagnostic Utility of the BioFire Joint Infection PCR Panel in Bone and Joint Infections: Analysis of a Prospective Validation Study.

INTRODUCTION: Microbiological diagnosis is central for adequate treatment of bone and joint infections. Culture-based methods have a limited diagnostic sensitivity and a long turnaround time (TAT). The objective of this study was to compare the diagnostic performance of BioFire Joint Infection Panel Investigational Use Only version (hereafter BioFire)-a sample-to-result multiplex PCR panel-with culture-based methods and 16S ribosomal RNA (rRNA) PCR and sequencing, when available. METHODS: This study presents a retrospective analysis of a prospective validation study of the BioFire panel. Specimens were obtained from consecutive patients evaluated for suspected bone and joint infections and processed using culture, BioFire, and 16S rRNA PCR and sequencing. Final clinical diagnosis was used as the reference for definition of infection. RESULTS: Samples, including synovial fluid, bone and periarticular tissue, were obtained from 57 patients, 39 of whom were finally diagnosed with a bone or joint infection. Cultures were positive in 27/39 infected patients and in 3/18 uninfected patients (sensitivity 69%, specificity 83%). BioFire was positive in 22/39 infected patients and in none of the uninfected patients (sensitivity 56%, specificity 100%). Sensitivity for PCR panel organisms was 92% (22/24) and sensitivity for organisms identified by any microbiological modality was 69% (22/32). Gram stain results were positive in 13/39 infected patients and in none of the uninfected patients (sensitivity 33%, specificity 100%). 16S rRNA was positive in 20/28 infected patients and in 0/12 uninfected patients (sensitivity 71%, specificity 100%). Net machine time for BioFire-1 h-was shorter than the mean TAT for Gram stain results, which was 4 h. CONCLUSION: BioFire offered equivalent diagnostic performance with superior TAT for bone and joint infections, compared with conventional methods.

Separating the wheat from the chaff - Optimizing the diagnosis of enterovirus-associated meningitis.

BACKGROUND: Enteroviruses (EV) comprise the single most common cause of aseptic meningitis with variable geographical and temporal epidemiology. While EV-PCR in CSF is considered a gold standard for diagnosis, it is not-uncommon to use stool EV as a surrogate. Our aim was to assess the clinical significance of EV-PCR-positive CSF and stool in the investigation of patients with neurological symptoms. METHODS: In this retrospective study from Sheba Medical centre, the largest tertiary hospital in Israel, we collected demographic, clinical and laboratory data of patients with EV-PCR-positive between 2016 and 2020. A comparison between various combinations of EV-PCR-positive CSF and stool was conducted. Data regarding EV strain-type and cycle threshold (Ct) were crossed with clinical symptoms and temporal kinetics. RESULTS: Between 2016-2020, 448 CSF samples with positive EV-PCR were recorded from unique patients, the vast majority of which were diagnosed with meningitis (98%, 443/448). Unlike the diverse strain types of EV background activity, meningitis-related EV showed a clear epidemic pattern. In comparison with the EV CSF+/Stool+ group, the EV CSF-/Stool+ group had frequently more alternative pathogens detected and a higher stool Ct-value. Clinically, EV CSF-/Stool+ patients were less febrile and more lethargic and convulsive. DISCUSSION: The comparison of the EV CSF+/Stool+ and CSF-/Stool+ groups suggests that putative diagnosis of EV meningitis is prudent in the febrile, non-lethargic non-convulsive patients with an EV-PCR-positive stool. Otherwise, the detection of stool EV only, in a non-epidemic setup, especially with a high Ct-value, may be incidental and mandate a continuous diagnostic effort for an alternative culprit.

Increased detection of Echovirus 6-associated meningitis in patients hospitalized during the COVID-19 pandemic, Israel 2021-2022.

BACKGROUND: Outbreaks of enteroviral meningitis occur periodically and may lead to hospitalization and severe disease. OBJECTIVE: To analyze and describe the meningitis outbreak in patients hospitalized in Israel in 2021-2022, during the COVID-19 pandemic. RESULTS: In December 2021, before the emergence of the SARS-CoV-2 omicron variant, an off-season increase in enterovirus (EV) infections was observed among patients hospitalized with meningitis. In January 2022, enterovirus cases decreased by 66% in parallel with the peak of the Omicron wave, and then increased rapidly by 78% in March (compared with February) after a decline in Omicron cases. Sequencing of the enterovirus-positive samples showed a dominance of echovirus 6 (E-6) (29%) before and after the Omicron wave. Phylogenetic analysis found that all 29 samples were very similar and all clustered in the E-6 C1 subtype. The main E-6 symptoms observed were fever and headache, along with vomiting and neck stiffness. The median patient age was 25 years, with a broad range (0-60 years). CONCLUSION: An upsurge in enterovirus cases was observed after the decline of the SARS-CoV-2 omicron wave. The dominant subtype was E-6, which was present prior to the emergence of the omicron variant, but increased rapidly only after the omicron wave decline. We hypothesize that the omicron wave delayed the rise in E-6-associated meningitis.

An Outbreak of Coxsackievirus B Type 2 Acute Meningoencephalitis in Children, Israel, July-September 2022.

During July-September 2022, 14 children suffering from meningoencephalitis tested positive for Coxsackievirus B2 (8 cerebrospinal fluid, 9 stool samples). Mean age 22 months (range 0-60 months); 8 were males. Seven of the children presented with ataxia and 2 had imaging features of rhombencephalitis, not previously described in association with Coxsackievirus B2.

Respiratory cryptosporidiosis detected by commercial multiplex-PCR in immunosuppressed pediatric patients.

We report the off-label use of a commercial gastrointestinal protozoa multiplex-PCR panel for bronchoalveolar lavage samples, detecting respiratory cryptosporidiosis in 2 immunocompromised pediatric patients. We suggest that implying this readily available assay in cases in which systemic cryptosporidiosis is suspected, may widen our understanding regarding this rarely reported syndrome.

The emergence of a multidrug resistant Salmonella Muenchen in Israel is associated with horizontal acquisition of the epidemic pESI plasmid.

OBJECTIVES: Horizontal acquisition of mobile genetic elements is a powerful evolutionary driving force that can profoundly affect pathogens epidemiology and their interactions with the environment and host. In the last decade, the role of the epidemic megaplasmid, pESI was demonstrated in the global emergence of multi-drug resistant (MDR) Salmonella enterica serovar Infantis strains, but it was unknown if this was a one-time phenomenon, or that pESI can drive the emergence of other pathogens. METHODS: Epidemiological, molecular, whole genome sequencing, de-novo assembly, bioinformatics and genetic approaches were used to analyze the emergence of a pESI-positive Salmonella enterica serovar Muenchen strain in Israel. RESULTS: Since 2018, we report the emergence and high prevalence of S. Muenchen in Israel, which consisted at 2020, 40% (1055/2671) of all clinical Salmonella isolates. We show that the emergence of S. Muenchen is dominated by a clonal MDR strain, report its complete assembled genome sequence, and demonstrate that in contrast to preemergent strains, it harbors the epidemic megaplasmid, pESI, which can be self-mobilized into E. coli and other Salmonella serovars. Additionally, we identified bioinformatically highly similar genomes of clinical isolates that were recently collected in South Africa, UK and USA. CONCLUSIONS: This is a second documented case of a pathogen emergence associated with pESI acquisition. Considering the genetic cargo of pESI that enhances resistance, stress tolerance and virulence, and its ability to conjugate into prevalent Salmonella serovars, we provide further support that pESI facilities the emergence and spreading of new Salmonella strains.

Rapid Detection of Carbapenemase-producing Enterobacteriaceae From Blood Culture Bottles of Known CPE Carriers: Real-world Experience.

We used a rapid antigen test for the detection of carbapenemases directly from positive blood culture bottles of pediatric hemato-oncologic patients, known carriers of carbapenemase-producing enterobacteriaceae. Resistance mechanism was detected within 15 minutes of observing Gram-negative bacilli from a positive bottle, leading to treatment modification. This simple-to-use, inexpensive assay shortens the interval between empiric to tailored antimicrobial therapy.

Real World Performance of SARS-CoV-2 Antigen Rapid Diagnostic Tests in Various Clinical Settings.

OBJECTIVE: To assess the validity of Antigen rapid diagnostic tests (Ag-RDT) for SARS-CoV-2 as decision support tool in various hospital-based clinical settings. DESIGN: Retrospective cohort study among symptomatic and asymptomatic patients and Healthcare workers (HCW). SETTING: A large tertiary teaching medical center serving as a major COVID-19 hospitalizing facility. PARTICIPANTS AND METHODS: Ag-RDTs' performance was assessed in three clinical settings: 1. Symptomatic patients and HCW presenting at the Emergency Departments 2. Asymptomatic patients screened upon hospitalization 3. HCW of all sectors tested at the HCW clinic following exposure. RESULTS: We obtained 5172 samples from 4595 individuals, who had both Ag-RDT and quantitative real-time PCR (qRT-PCR) results available. Of these, 485 samples were positive by qRT-PCR. The positive percent agreement (PPA) of Ag-RDT was greater for lower cycle threshold (Ct) values, reaching 93% in cases where Ct-value was <25 and 85% where Ct-value was <30. PPA was similar between symptomatic and asymptomatic individuals. We observed a significant correlation between Ct-value and time from infection onset (p<0.001). CONCLUSIONS: Ag-RDT are highly sensitive to the infectious stage of COVID-19 manifested by either high viral load (lower Ct) or proximity to infection, whether patient is symptomatic or asymptomatic. Thus, this simple-to-use and inexpensive detection method can be used as a decision support tool in various in-hospital clinical settings, assisting patient flow and maintaining sufficient hospital staffing.

Real-World Immunogenicity and Reactogenicity of Two Doses of Pfizer-BioNTech COVID-19 Vaccination in Children Aged 5-11 Years.

There are limited data concerning the immunogenicity and reactogenicity of COVID-19 vaccines in children. A total of 110 children, 5-11 years old were vaccinated with two doses (with a 3-week interval between doses) of the Pfizer-BioNTech COVID-19 vaccine and were followed for 21, 90, and 180 days after vaccination for immunogenicity, adverse events, and breakthrough infections. Ninety days after the first vaccine dose, the GeoMean (CI 95%) of IgG ascended to 1291.0 BAU (929.6-1790.2) for uninfected children and 1670.0 BAU (1131.0-2466.0) for Infected children. One hundred and eighty days after receiving the first dose of the vaccine, the titers decreased to 535.5 BAU (288.4-993.6) for the uninfected children, while only a small decline was detected among infected children-1479.0 (878.2-2490.0). The neutralizing antibodies titer almost did not change over time in the uninfected children, and even elevated for the infected children. Of the 110 vaccinated children, 75.5% were infected, with only mild COVID-19 infection symptoms. Child vaccination was found to be safe, with mild, mostly local, and of short duration, reported AEs. No serious adverse events (SAEs) were reported after vaccination. The durability of two doses of vaccine in children is longer, thus a booster may not be needed as early as in adults.

Viral co-pathogens in COVID-19 acute respiratory syndrome - what did we learn from the first year of pandemic?

OBJECTIVE: This study aimed to describe the distribution of respiratory pathogens and the occurrence of co-pathogens during the first year of the COVID-19 pandemic. METHODS: We used a multiplex polymerase chain reaction (PCR) panel targeting 23 microorganisms to analyze the oro-pharyngeal samples of patients admitted to our hospital with acute respiratory infection (ARI) between March 1, 2020, and February 28, 2021. We matched 40 to 50 patients who were SARS-CoV-2 positive and SARS-CoV-2 negative per month for age and sex. RESULTS: A total of 939 patients with multiplex PCR test results were included in the study. Respiratory pathogens where detected in only 8/476 (1.6%) patients with COVID-19 versus 87/463 (18.7%) patients with non-COVID-19 ARI patients. Diversity and rates of pathogens vastly differed from previous years but showed seasonal variance. CONCLUSION: Patients with SARS-CoV-2 infection presenting with ARI during the first year of the COVID-19 pandemic demonstrated paucity of respiratory co-pathogens.