Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis.

Infectious diseases are one of the world's leading causes of morbidity. Their rapid spread emphasizes the need for accurate and fast diagnostic methods for large-scale screening. Here, we describe a robust method for the detection of pathogens based on microscale thermophoresis (MST). The method involves the hybridization of a fluorescently labeled DNA probe to a target RNA and the assessment of thermophoretic migration of the resulting complex in solution within a 2 to 30-time window. We found that the thermophoretic migration of the nucleic acid-based probes is primarily determined by the fluorescent molecule used, rather than the nucleic acid sequence of the probe. Furthermore, a panel of uniformly labeled probes that bind to the same target RNA yields a more responsive detection pattern than a single probe, and moreover, can be used for the detection of specific pathogen variants. In addition, intercalating agents (ICA) can be used to alter migration directionality to improve detection sensitivity and resolving power by several orders of magnitude. We show that this approach can rapidly diagnose viral SARS-CoV2, influenza H1N1, artificial pathogen targets, and bacterial infections. Furthermore, it can be used for anti-microbial resistance testing within 2 h, demonstrating its diagnostic potential for early pathogen detection.

Highly sensitive extraction-free saliva-based molecular assay for rapid diagnosis of SARS-CoV-2.

The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The "gold standard" molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays' sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva-based molecular assay. We blindly tested 364 paired nasopharyngeal swabs and saliva samples from suspected SARS-CoV-2 cases in Israel. Compared with the gold standard swab-based RT-qPCR assay, the sensitivity of the extraction-free saliva-based OMB assay is 90.7%, much higher than the sensitivity of extraction-free saliva-based RT-qPCR assay (77.8%) with similar specificity (95.3% and 97.6%, respectively). Moreover, out of 12 samples identified by the OMB-based assay as positive, 8 samples were collected from hospitalized patients in a COVID-19 ward and were verified to be SARS-CoV-2-positive upon admission, indicating that the actual clinical sensitivity and specificity of the OMB assay are higher. Considering its user-friendly saliva-based protocol, short and cost-effective extraction-free process, and high clinical accuracy, the OMB-based molecular assay is very suitable for high-throughput testing of large populations for respiratory viruses. IMPORTANCE: Three years after the SARS-CoV-2 outbreak, there are no molecular tests that combine low-cost and straightforward sample preparation, effective sample handling, minimal reagent and disposable requirements, high sensitivity, and high throughput required for mass screening. Existing rapid molecular techniques typically sacrifice certain requirements to meet others. Yet, localized outbreaks of novel viral diseases happen daily in different parts of the world. In this context, respiratory diseases are of specific importance, as they are frequently airborne and highly contagious, with the potential for a rapid global spread. The widely accepted opinion is that another pandemic is just a question of time. To ensure that the containment efforts for the upcoming "disease X" are successful, introducing rapid, high-throughput, and highly sensitive diagnostic methods for detecting and identifying pathogens is critical. A few months into the pandemic, saliva was suggested as a diagnostic matrix for SARS-CoV-2 detection. The collection of saliva does not require swabs and is minimally invasive. In particular, extraction-free saliva-based assays require fewer reagents and disposables, and therefore are faster and cheaper, offering an appealing alternative for low-income countries. Unfortunately, current extraction-free saliva-based detection methods, such as direct RT-qPCR or isothermal amplification, have either low sensitivity or low throughput. Therefore, we believe that the presented highly sensitive ht-OMBi platform and the extraction-free saliva-based molecular assay can become an essential tool in the infectious disease monitoring toolbox.

Associations of motility and auto-aggregation with biofilm-formation capacity levels in Clostridioidesdifficile.

Clostridioides difficile (C. difficile) is responsible for one of the most common nosocomial infections worldwide. This work assessed associations between biofilm-formation capacity levels of C. difficile and cell viability, motility, flagella, motility and auto-aggregation in 118 clinical isolates. Biofilm production was assessed by the crystal violet method. Cell viability was determined by BacTiter-Glo™ Microbial Cell Viability Assay and live-imaging microscopy. Expression levels of LuxS, Cwp84, Spo0A, PilA, and FliC were measured by real-time PCR. Motility was visually assessed in agar tubes. Auto-aggregation levels were determined by OD600 measurements. Out of 118 isolates, 66 (56 %) were biofilm producers, with most being strong or moderate producers. Cell viability, motility and auto-aggregation positively correlated with biofilm-production capacity (p = 0.0001, p = 0.036 and p < 0.0001, respectively). Positive associations were found between pilA, fliC and luxS expression levels and biofilm-production capacity (p = 0.04, p = 0.01, p = 0.036, respectively). This is the first report of associations between biofilm-formation capacity and cell viability, pilA, fliC, and luxS gene expression, auto-aggregation and motility. These correlations should be further explored to expand knowledge on the regulation of C. difficile biofilm formation, and pathogenesis, which will have notable implications on treatment options.

Clinical isolate characteristics and demographics of patients with C.jejuni and C.coli infections in Northern Israel, 2015-2021.

C.coli is a significant cause of foodborne gastroenteritis worldwide, with the majority of cases attributed to C.jejuni. Although most clinical laboratories do not typically conduct antimicrobial susceptibility testing for C.coli, the rise in resistant strains has underscored the necessity for such testing and epidemiological surveillance. The current study presents clinical isolate characteristics and demographics of 221 patients with C.coli (coli and jejuni) infections in Northern Israel, between 2015 and 2021. Clinical and demographic data were collected from patient medical records. Susceptibility to erythromycin, tetracycline, ciprofloxacin, and gentamicin was assessed using the standard E-test. No significant correlations were found between bacterial species and patient ethnicity, patient gender, or duration of hospitalization. In contrast, significant differences were found between infecting species and patient age and age subgroup (P < 0.001). Furthermore, erythromycin resistance was observed in only 0.5% of the study population, while resistance to ciprofloxacin, tetracycline, and gentamicin was observed in 95%, 93%, and 2.3% of the population, respectively. The presented study underscores the need for routine surveillance of C.coli antibiotic resistance.

Sexually Transmitted Diseases in Northern Israel: Insights From a Large Referral Laboratory.

OBJECTIVES: The aims of the study are to investigate the distribution and frequency of different sexually transmitted diseases (STDs) among a large study population of individuals undergoing STD investigation both in inpatient and STD clinic settings and to evaluate influence of test anonymity on the positivity rate of pathogens. MATERIAL AND METHODS: A retrospective study retrieved epidemiologic data from the following 3 sources: a secondary referral hospital and 2 STD clinics in Northern Israel. Positivity rate of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium , and Trichomonas vaginalis (TV) was assessed and stratified based on age, sex, site of sampling, and anonymity of test. Adjusted odds ratios (ORs) were calculated by multivariable logistic regression. RESULTS: Overall, 3,753 assays were performed on 2,407 patients who were screened for STD. Chlamydia trachomatis (4.8%) was the most frequently detected STD, followed by NG (2.1%), MG (1.9%), and TV (0.6%). Mycoplasma genitalium (OR, 4.32; 95% CI, 1.70-10.97; p = .001) and NG (OR, 6.08; 95% CI, 2.18-16.96; p < .001) were significantly associated with male sex, while TV was more frequently encountered among female individuals (OR, 4.34; 95% CI, 1.49-12.50; p = .003). Mycoplasma genitalium infection was detected most commonly by urine samples, while rectal swabs were the leading source of positive tests for CT. Compared with fully identified patients, those tested anonymously were 6-fold more likely to be tested positive for TV (adjusted OR, 6.49; 95% CI, 2.06-20.42; p = .001). CONCLUSIONS: Chlamydia trachomatis and NG are the leading non-HIV STDs in Northern Israel. Anonymous tests predict higher positivity of TV. Rectal sampling should be increasingly used because of its efficacy in detecting CT infections.

Dynamics of Invasive Pneumococcal Disease in Israel in Children and Adults in the 13-Valent Pneumococcal Conjugate Vaccine (PCV13) Era: A Nationwide Prospective Surveillance.

BACKGROUND: Following 13-valent pneumococcal conjugate vaccine (PCV13) implementation in infants worldwide, overall and vaccine-type invasive pneumococcal disease (IPD) rates declined in children, with variable indirect impact on adults. METHODS: A population-based, prospective, nationwide active surveillance of IPD in Israel, 2004-2019 (for adults ≥18 years, 2009-2019). The 7-valent PCV (PCV7)/PCV13 were implemented in Israel in July 2009/November 2010, respectively, with >90% uptake in children <2 years. The 23-valent pneumococcal polysaccharide vaccine (PPV-23) uptake among those >65 years was ~75%. For pre-PCV episodes with missing serotype, extrapolations were applied. Overall, PCV13 serotypes (VT13) and non-VT13 (NVT) incidence rate ratios (IRRs) comparing pre-PCV (2004-2008), early-PCV (2009-2011), and late-PCV13 (2016-2019) periods were calculated for different age groups. RESULTS: Overall, 8614 IPD cases were recorded. IPD rates declined by 67% in children <5 and 5-17 years, comparing late-PCV13 versus pre-PCV periods (IRR [95% CI]: .33 [.27-.40] and .33 [.21-.50], respectively). For adults, comparing late-PCV13 with early-PCV periods, rates significantly declined by 53% in those aged 18-44, while rates did not decline significantly in other age groups. VT13 rates significantly declined in all ages, with decline rates ranging between 94% in children <5 years and 60% in adults ≥85 years. NVT rates significantly increased in <5-, 50-64-, and ≥65-year age groups. In the late-PCV13 period, serotypes 3, 14, and 19A remained the predominant VT13, while serotypes 8 and 12F emerged as predominant NVTs. CONCLUSIONS: Continuous monitoring of circulating serotypes in all ages demonstrated direct and indirect PCV effects, which are essential for the development of new vaccination strategies.

Antibiotic resistance patterns of Helicobacter pylori in North Israel - A six-year study.

BACKGROUND: One main challenge in Helicobacter pylori (H. pylori) eradication is its increasing antibiotic resistance. Additionally, resistance rates vary between geographic areas and periods. However, data are limited since susceptibility testing is not routinely performed. Thus, it is valuable to gather data regarding H. pylori's resistance rates in Israel that would aid in better adjustment of treatment. MATERIALS AND METHODS: The study included 540 H. pylori isolates, recovered from gastric biopsy samples of patients who had undergone endoscopy, during 2015-2020, at the Padeh Poriya Medical Center. Antibiotic susceptibility testing to amoxicillin, clarithromycin, metronidazole, levofloxacin, rifampicin, and tetracycline was performed using the Etest technique. Data regarding participants' sex, age, and ethnic group were collected. For every antibiotic and for multi-resistance, generalized linear models were used to estimate crude and adjusted estimated differences in mean MIC and odds ratios (ORs) for every year, compared with the reference year 2015. RESULTS: The highest resistance rates were for clarithromycin and metronidazole (46.3% and 16.3%, respectively). Patients above 18 had higher resistance rate to rifampicin and multi-resistance (3.3% and 14.8%), compared with patients under 18 (0.5% and 8.4%, respectively). Resistance rates for levofloxacin, rifampicin, and multi-resistance were significantly higher among Arab patients, compared with Jewish patients. During the 6-year surveillance, a significant annual trend in MIC for metronidazole and in ORs for metronidazole, levofloxacin, and multi-resistance were observed (after adjustment). During 2020 compared with 2015, significant increased ORs were observed for levofloxacin and metronidazole [5.72 (1.03-31.84); 4.28 (1.30-14.14), respectively]. CONCLUSIONS: In light of the remarkable changes in antibiotic resistance of H. pylori during the study's period and the increasing resistance rates to various antibiotics, it is very important to continuously monitor H. pylori antibiotic susceptibly. In order to increase eradication rates of this bacterium, therapy regimes must be based on an updated antibiotic resistance data.

Incidence of biofilm formation among MRSA and MSSA clinical isolates from hospitalized patients in Israel.

AIM: To assess the biofilm-producing capacities of Staphylococcus aureus strains isolated from hospitalized patients in Israel. METHODS AND RESULTS: A total of 16 S. aureus (80 MRSA and 83 MSSA) from screening (nasal swab) and clinical samples (blood and wounds) were characterized. Biofilm-producing capacities were determined using two different biofilm detection assays: Congo Red agar (CRA) and microtiter plate (MtP). In addition, a real-time PCR analysis was performed to detect the presence of biofilm-associated genes (icaA and icaD) and mecA gene. The two assays showed similar biofilm production pattern (28.2% agreement). MRSA strains tended to be greater biofilm-producers than MSSA strains. The presence of mecA was associated with biofilm production (p = 0.030). Additionally, bacteria isolated from blood samples produced less biofilm compared to those from other sources. Finally, no association was found between icaA and icaD presence and biofilm production. CONCLUSION: This study supports earlier assumptions that biofilm formation depends strongly on environmental conditions. SIGNIFICANCE AND IMPACT OF STUDY: This study significantly improved our knowledge on the biofilm production capacity of S. aureus strains in Israel. Moreover, it revealed an association between the mecA gene and biofilm production. Finally, this study underscores the importance of further research to evaluate risk factors for biofilm production.

Unmasking Myocardial Dysfunction in Patients Hospitalized for Community-Acquired Pneumonia Using a 4-Chamber 3-Dimensional Volume/Strain Analysis.

Lower respiratory infection was reported as the most common fatal infectious disease. Community-acquired pneumonia (CAP) and myocardial injury are associated; yet, true prevalence of myocardial injury is probably underestimated. We assessed the rate and severity of myocardial dysfunction in patients with CAP. Admitted patients diagnosed with CAP were prospectively recruited. All the patients had C-reactive protein (CRP), brain natriuretic peptide (BNP), and high-sensitivity cardiac troponin (hs-cTnl) tests added to their routine workup. 2D/3D Doppler echocardiography was done on a Siemens Acuson SC2000 machine ≤ 24 h of diagnosis. 3D datasets were blindly analyzed for 4-chamber volumes/strains using EchobuildR 3D-Volume Analysis prototype software, v3.0 2019, Siemens-Medical Solutions. Volume/strain parameters were correlated with admission clinical and laboratory findings. The cohort included 34 patients, median age 60 years (95% CI 55-72). The cohort included 18 (53%) patients had hypertension, 9 (25%) had diabetes mellitus, 7 (21%) were smokers, 7 (21%) had previous myocardial infarction, 4 (12%) had chronic renal failure, and 1 (3%) was on hemodialysis treatment. 2D/Doppler echocardiography findings showed normal ventricular size/function (LVEF 63 ± 9%), mild LV hypertrophy (104 ± 36 g/m2), and LA enlargement (41 ± 6 mm). 3D volumes/strains suggested bi-atrial and right ventricular dysfunction (global longitudinal strain RVGLS = - 8 ± 4%). Left ventricular strain was normal (LVGLS = - 18 ± 5%) and correlated with BNP (r = 0.40, p = 0.024). The patients with LVGLS > - 17% had higher admission blood pressure and lower SaO2 (144 ± 33 vs. 121 ± 20, systolic, mmHg, p = 0.02, and 89 ± 4 vs. 94 ± 4%, p = 0.006, respectively). hs-cTnl and CRP were not different. Using novel 3D volume/strain software in CAP patients, we demonstrated diffuse global myocardial dysfunction involving several chambers. The patients with worse LV GLS had lower SaO2 and higher blood pressure at presentation. LV GLS correlated with maximal BNP level and did not correlate with inflammation or myocardial damage markers.

Unraveling antimicrobial resistance in Helicobacter pylori: Global resistome meets global phylogeny.

BACKGROUND: Antimicrobial resistance (AMR) in Helicobacter pylori is increasing globally and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to conduct an analysis of the H. pylori resistome and phylogeny. MATERIALS/METHODS: A total of 1040 H. pylori isolate sequences were retrieved. Analysis was conducted via an in-house bioinformatics pipeline targeting point mutations in selected genes frequently associated with AMR (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) and phylogenomic analyses using core genome multilocus sequence typing (cgMLST). RESULTS: Phylogenomic analysis revealed a notable geographical clustering of H. pylori genomes across world regions, but large distances of more than 1000 loci between isolates on individual branches were observed. Resistome analysis revealed the prevalence of common mutations which have previously been found to correlate with phenotypic antibiotic resistance; the most common point mutations for each gene were S589G (pbp1A, 48.8% of perfect aligned sequences), A2143G (23S rRNA, 27.4% of perfectly aligned sequences), N87 K\I\Y (gyrA, 14.7% of perfectly aligned sequences), R131K (rdxA, 65.7% of perfectly aligned sequences), and C193S (frxA, 62.6% of perfectly aligned sequences). CONCLUSIONS: This is the largest study to date featuring the global phylogeny of H. pylori in conjunction with a global snapshot of the H. pylori resistome based on >1000 genomes. Further analyses that combine WGS and phenotypic methods will provide further understanding of the association between the mutations and resistance.

The microbial diversity following antibiotic treatment of Clostridioides difficile infection.

BACKGROUND: Clostridioides difficile (C. difficile) is a major nosocomial pathogen that infects the human gut and can cause diarrheal disease. A dominant risk factor is antibiotic treatment that disrupts the normal gut microbiota. The aim of the study was to examine the correlation between antibiotic treatment received prior to C. difficile infection (CDI) onset and patient gut microbiota. METHODS: Stool samples were collected from patients with CDI, presenting at the Baruch Padeh Medical Center Poriya, Israel. Demographic and clinical information, including previous antibiotic treatments, was collected from patient charts, and CDI severity score was calculated. Bacteria were isolated from stool samples, and gut microbiome was analyzed by sequencing the 16S rRNA gene using the Illumina MiSeq platform and QIIME2. RESULTS: In total, 84 patients with CDI were enrolled in the study; all had received antibiotics prior to disease onset. Due to comorbidities, 46 patients (55%) had received more than one class of antibiotics. The most common class of antibiotics used was cephalosporins (n = 44 cases). The intestinal microbiota of the patients was not uniform and was mainly dominated by Proteobacteria. Differences in intestinal microbiome were influenced by the different combinations of antibiotics that the patients had received (p = 0.022) CONCLUSIONS: The number of different antibiotics administered has a major impact on the CDI patients gut microbiome, mainly on bacterial richness.

Tumor necrosis factor inhibitors are associated with a decreased risk of COVID-19-associated hospitalization in patients with psoriasis-A population-based cohort study.

The risk of coronavirus disease 2019 (COVID-19) and its complications among patients with psoriasis treated by tumor necrosis factor inhibitors (TNFis) remains to be decisively delineated. We aimed to assess the risk of COVID-19 infection, COVID-19-associated hospitalization, and mortality among Israeli patients with psoriasis treated by TNFi relative to other systemic agents. A population-based cohort study was conducted to compare psoriasis patients treated by TNFi (n = 1943), with those treated by methotrexate (n = 1929), ustekinumab (n = 348), and acitretin (n = 1892) regarding COVID-19 outcomes. Risk of investigated outcomes was assessed using uni- and multi-variate Cox regression analyses. The incidence rate of COVID-19, COVID-19-associated hospitalization, and mortality in the TNFi group was 35.8 (95% CI, 26.1-47.9), 0.8 (95% CI, 0.0-4.2), and 0.0 per 1000 person-years, respectively. Exposure to TNFi was associated with a comparable risk of COVID-19 infection [adjusted hazard ration (HR) for TNFi vs methotrexate: 1.07 (95% CI, 0.67-1.71); TNFi vs ustekinumab: 1.07 (95% CI, 0.48-2.40); TNFi vs acitretin: 0.98 (95% CI, 0.61-1.57)]. TNFi was associated with a decreased risk of COVID-19-associated hospitalization relative to methotrexate (adjusted HR, 0.10; 95% CI, 0.01-0.82) and ustekinumab (adjusted HR, 0.04; 95% CI, 0.00-0.64), but not to acitretin (adjusted HR, 1.00; 95% CI, 0.16-6.16). No significant difference in COVID-19-associated mortality was found between the four different groups. TNFi was associated with a decreased risk of admissions due to COVID-19. Our findings substantiate the continuation of TNFi treatment during the pandemic. TNFi may be positively considered in patients with moderate-to-severe psoriasis warranting systemic treatment during the pandemic.

Tinea capitis in an immigrant pediatric community; a clinical signs-based treatment approach.

BACKGROUND: Tinea capitis is a common cutaneous infection of the scalp and hair follicles, typically diagnosed by direct examination and culture. Treatment with oral antifungals is usually withheld until mycology results are available. In Israel, African refugee children demonstrate higher susceptibility to Tinea capitis and generally fail to undergo follow-up evaluations. METHODS: This study aimed to identify the clinical characteristics and treatment responses of refugee children in Israel with Tinea capitis, in order to formulate a treatment plan for primary care physicians. To this end, demographic, clinical and laboratory data were extracted from the electronic medical records of 76 refugee children presenting with Tinea capitis during 2016-2017. All measured variables and derived parameters are presented using descriptive statistics. The correlation between background clinical and demographic data and Tinea capitis diagnosis was assessed using the chi-squared and Wilcoxon tests. Correlations between demographic/clinical/laboratory characteristics and other types of fungi or other important findings were assessed using a T-test. RESULTS: Scaling was the most common clinical finding. Cultures were positive in 64 (84%) and direct examination in 65 (85%) cases, with a positive correlation between the methods in 75% of cases. The most common fungal strain was T. violaceum. Fluconazole treatment failed in 27% of cases. Griseofulvin 50 mg/kg/day was administered to 74 (97%) children, and induced clinical responses. No side effects were reported. CONCLUSIONS: The key aim of this study was to emphasize the importance of diagnosis and treatment of these immigrant children by their primary pediatric doctor since it takes, an average of 4.3 months until they visit a dermatologist. During this critical time period, the scalp can become severely and permanently damaged, and the infection can become systemic or cause an outbreak within the entire community. In conclusion, we recommend to relate to scaly scalp in high-risk populations as Tinea capitis, and to treat with griseofulvin at a dosage of up to 50 mg/kg/day, starting from the first presentation to the pediatrician.

Mycoplasma and Ureaplasma carriage in pregnant women: the prevalence of transmission from mother to newborn.

BACKGROUND: Mycoplasma and Ureaplasma have been extensively studied for their possible impact on pregnancy, and their involvement in newborn diseases. This work examined Mycoplasma and Ureaplasma carriage among gravidas women and newborns in Israel, as well as associations between carriage and demographic characteristics, risk factors, pregnancy outcomes, and newborn morbidity rates. METHODS: A total of 214 gravidas women were examined for vaginal pathogen carriage through standard culture and polymerase chain reaction assay. Pharyngeal swabs were collected from newborns of carrier mothers. Clinical and demographic data were collected and infected newborn mortality was monitored for 6 months. RESULTS: Nineteen mothers were carriers, with highest prevalence among younger women. Pathogen carriage rates were 2.32% for Mycoplasma genitalium (Mg), 4.19% for Ureaplasma parvum (Up) and 2.32% for Ureaplasma urealyticum (Uu). Arab ethnicity was a statistically significant risk factor (p = 0.002). A higher prevalence was seen among women residing in cities as compared to villages. Thirteen (68%) newborns born to carrier mothers were carriers as well, with a higher prevalence among newborns of women delivering for the first time, compared to women that had delivered before. Infection rates among newborns were 20% for Mg (p = 0.238), 100% for Up (p < 0.01), and 28.5% for Uu (p = 0.058), with more male than female newborns being infected. No association was found between maternal carriage and newborn morbidity. CONCLUSIONS: Maternal Mycoplasma or Ureaplasma carriage may be associated with ethnicity and settlement type. Further studies will be needed to identify factors underlying these associations and their implications on delivery.

Detection of group a Streptococcus in pharyngitis by two rapid tests: comparison of the BD Veritor™ and the QuikRead go® Strep A.

We compared the performance of two rapid antigen tests-QuikRead go® Strep A test (Orion Diagnostica, Espoo, Finland) and BD Veritor™ system (Becton, Dickinson and Company, Sparks, MD) with throat culture. Our aim was to evaluate each assay's performance and agreement compared to throat culture in order to choose one of the assays as a point-of-care test in the emergency room. One hundred throat samples were collected in triplicates from patients with suspected pharyngitis admitted to the emergency room. One throat swab was seeded for a throat culture. The other two throat swabs from each patient were analyzed at the emergency room by the QuikRead go® Strep A test, and by the BD Veritor™ system, according to each manufacturer's instructions. Agreement level between BD Veritor™ test and throat culture was 79%; sensitivity and specificity of this test were 80% and 78.7%, respectively. QuikRead go® Strep A test had an agreement level of 75% with throat culture; sensitivity and specificity of this test were 80% and 73.3%, respectively. Both tests have a good diagnostic performance. Other characteristics such as costs, size of instrument, and ease of implementation should be taken into consideration when choosing a point-of-care test.

Characteristics of hospitalised patients with influenza in 2015-2016 in northern Israel: three circulating strains and continued fear of 2009 A/H1N1.

This study aimed to characterise children and adults diagnosed with influenza who were admitted to three medical centres in northern Israel in the winter of 2015-2016, a unique season due to infection with three types of influenza strains: A/H1N1, A/non-H1N1 and B. Data were collected retrospectively from medical records. Influenza A/H1N1 infected mainly adults (61% vs. 16% in children, P < 0.001) while influenza B was the common type in children (54% vs. 28% in adults, P < 0.001). Adults (36% vs. 5% in children, P < 0.001) and patients infected with A/H1N1 had higher rates of pneumonia (34% vs. 16% and 14% in influenza B and A/non-H1N1, respectively, P = 0.002). Treatment with oseltamivir was prescribed to 90% of patients; adults had higher rates of treatment (96% vs. 84% in children, P = 0.002) as well as patients infected with A/H1N1 (96% vs. 86% in influenza B and A/non-H1N1, respectively, P = 0.04). Oseltamivir was given after a mean of 3.6 days of symptoms. Preferential infection of adults by A/H1N1 was evident in Israel in 2015-2016; pneumonia rates were higher in adults and in A/H1N1-infected patients. Oseltamivir was prescribed to most patients but especially to those infected with A/H1N1, and was given relatively late in the course of the disease.

Cheap and rapid in-house method for direct identification of positive blood cultures by MALDI-TOF MS technology.

BACKGROUND: Rapid and accurate pathogen identification in blood cultures is very important for septic patients and has major consequences on morbidity and mortality rates. In recent years, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based technology has become useful for highly specific and sensitive identification of bacteria and yeasts from clinical samples including sterile body fluids. Additional in-house methods enabled direct identification from blood cultures following various preparation protocols. METHODS: Blood culture (5 ml) was harvested from each positive bottle following growth identification by BACTEC™ FX system and transferred into a VACUETTE® Z Serum Sep Clot Activator tube containing an inert gel, which following centrifugation separates microorganisms from the blood cells. We used MALDI-TOF MS analysis for identification of microorganisms collected from the gel surface. RESULTS: Positive blood culture bottles (186) were collected. In comparison with the routine method, 99% (184/186) and 90% (168/186) of the isolates were correctly identified by the SepsiTyper kit and the in-house method, respectively. We found high concordance (Pearson coefficient = 0.7, p <  0.0001) between our in-house method and the SepsiTyper kit. Additionally, high correlation was found in sub-groups of identified bacteria, with Pearson coefficients of 0.77 (p <  0.0001), 0.67 (p <  0.0001), and 0.73 (p <  0.007) for Gram negative, Gram positive, and anaerobic bacteria, respectively. CONCLUSIONS: Our in-house method was found to be in good agreement with the SepsiTyper kit. Considering the low costs and the rapid and easy implementation of this procedure, we propose our in-house method for the direct identification of bacteria from blood cultures.

Pneumococcal Meningitis in Adults after Introduction of PCV7 and PCV13, Israel, July 2009-June 20151.

The indirect effect of pneumococcal conjugate vaccine on adult pneumococcal meningitis has not been thoroughly investigated. We present data from active surveillance on pneumococcal meningitis in adults in Israel occurring during July 2009-June 2015. Pneumococcal meningitis was diagnosed for 221 patients, 9.4% of all invasive pneumococcal disease (IPD) cases. Although overall IPD incidence decreased during the study period, meningitis increased nonsignificantly from 0.66 to 0.85 cases/100,000 population. Incidence of vaccine type (VT) pneumococcal meningitis (VT13) decreased by 70%, but non-VT13 pneumococcal meningitis increased from 0.32 to 0.75 cases/100,000 population (incident rate ratio 2.35, 95% CI 1.27-4.35). Pneumococcal meningitis patients were younger and healthier than nonmeningitis IPD patients, and 20.2% had a history of previous head surgery or cerebrospinal fluid leak compared with <2.0% of nonmeningitis patients (p<0.0001). Non-VT13 types that rarely cause IPD (15B/C, 6C, 23A, 23B, 24F) seem to be emerging as common causes of meningitis.

Virulence Traits of Environmental and Clinical Legionella pneumophila Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Genotypes.

Legionella pneumophila causes water-based infections resulting in severe pneumonia. Recently, we showed that different MLVA-8 (multilocus variable-number tandem-repeat analysis using 8 loci) genotypes dominated different sites of a drinking-water distribution system. Each genotype displayed a unique temperature-dependent growth behavior. Here we compared the pathogenicity potentials of different MLVA-8 genotypes of environmental and clinical strains. The virulence traits studied were hemolytic activity and cytotoxicity toward amoebae and macrophages. Clinical strains were significantly more hemolytic than environmental strains, while their cytotoxicity toward amoebae was significantly lower at 30°C. No significant differences were detected between clinical and environmental strains in cytotoxicity toward macrophages. Significant differences in virulence were observed between the environmental genotypes (Gt). Gt15 strains showed a significantly higher hemolytic activity. In contrast, Gt4 and Gt6 strains were more infective toward Acanthamoeba castellanii Moreover, Gt4 strains exhibited increased cytotoxicity toward macrophages and demonstrated a broader temperature range of amoebal lysis than Gt6 and Gt15 strains. Understanding the virulence traits of Legionella genotypes may improve the assessment of public health risks of Legionella in drinking water.IMPORTANCELegionella pneumophila is the causative agent of a severe form of pneumonia. Here we demonstrated that clinical strains were significantly more cytotoxic toward red blood cells than environmental strains, while their cytotoxicity toward macrophages was similar. Genotype 4 (Gt4) strains were highly cytotoxic toward amoebae and macrophages and lysed amoebae in a broader temperature range than to the other studied genotypes. The results can explain the relatively high success of Gt4 in the environment and in clinical samples; thus, Gt4 strains should be considered a main factor for the assessment of public health risks of Legionella in drinking water. Our findings shed light on the ecology, virulence, and pathogenicity potential of different L. pneumophila genotypes, which can be a valuable parameter for future modeling and quantitative microbial risk assessment of Legionella in drinking-water systems.