Biofilm Formation by Hospital-Acquired Resistant Bacteria Isolated from Respiratory Samples

BACKGROUND

Hospital-acquired resistant infections (HARI) are infections, which develop 48 h or more after admission to a healthcare facility. HARI pose a considerably acute challenge, due to limited treatment options. These infections are associated bacterial biofilms, which act as a physical barrier to diverse external stresses, such as desiccation, antimicrobials and biocides. We assessed the influence of multiple factors on biofilm production by HARI -associated bacteria.

METHODS

Bacteria were isolated from samples of patients with respiratory HARI who were hospitalized during 2020-2022 in north Israel. Following antibiotic susceptibility testing by disc diffusion or broth microdilution, biofilm formation capacities of resistant bacteria (methicillin-resistant staphylococcus aureus, extended spectrum beta-lactamase-producing Escherichia coli and Klebsiela pneumonia, and multidrug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii) was assessed using the crystalline violet staining method. Data regarding season, time to infection, bacterial species, patient age and gender, year, and medical department were collected from the patient medical records.

RESULTS

Among the 226 study isolates, K. pneumonia was the most prevalent (35.4%) bacteria, followed by P. aeruginosa (23.5%), and methicillin-resistant staphylococcus aureus (MRSA) (21.7%). A significantly higher rate of HARI was documented in 2022 compared to 2020-2021. The majority of isolates (63.3%) were strong biofilm producers, with K. pneumonia (50.3%) being most dominant, followed by P. aeruginosa (29.4%). Biofilm production strength was significantly affected by seasonality and hospitalization length, with strong biofilm production in autumn and in cases where hospitalization length exceeded 30 days.

CONCLUSION

Biofilm production by HARI bacteria is influenced by bacterial species, season and hospitalization length.

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.

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.

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.

Characterization of community-acquired Clostridioides difficile strains in Israel, 2020-2022

Background

The prevalence of community-acquired Clostridioides difficile infection (CA-CDI) has been rising, due to changes in antibiotics prescribing practices, emergence of hypervirulent strains and improved diagnostics. This study explored CA-CDI epidemiology by examining strain diversity and virulence factors of CA-CDI isolates collected across several geographical regions in Israel.

Methods

Stool samples of 126 CA-CDI patients were subjected to PCR and an immunoassay to identify toxin genes and proteins, respectively. Toxin loci PaLoc and PaCdt were detected by whole-genome sequencing (WGS). Biofilm production was assessed by crystal violet-based assay. Minimum inhibitory concentration was determined using the Etest technique or agar dilution. WGS and multi-locus sequence typing (MLST) were used to classify strains and investigate genetic diversity.

Results

Sequence types (ST) 2 (17, 13.5%), ST42 (13, 10.3%), ST104 (10, 8%) and ST11 (9, 7.1%) were the most common. All (117, 92.8%) but ST11 belonged to Clade 1. No associations were found between ST and gender, geographic area or antibiotic susceptibility. Although all strains harbored toxins genes, 34 (27%) produced toxin A only, and 54 (42.9%) strains produced toxin B only; 38 (30.2%) produced both toxins. Most isolates were biofilm-producers (118, 93.6%), primarily weak producers (83/118, 70.3%). ST was significantly associated with both biofilm and toxin production.

Conclusion

C. difficile isolates in Israel community exhibit high ST diversity, with no dominant strain. Other factors may influence the clinical outcomes of CDI such as toxin production, antibiotic resistance and biofilm production. Further studies are needed to better understand the dynamics and influence of these factors on CA-CDI.

A Multi-Laboratory Evaluation of Commercial Monkeypox Virus Molecular Tests

In this report, we describe the first national scale multi-laboratory evaluation of monkeypox virus (MPXV) DNA commercial PCR kits. The objective of this study was to evaluate 2 kits by different diagnostic laboratories across Israel. Ten standardized samples were tested simultaneously using the Novaplex (15 laboratories) and Bio-Speedy (seven laboratories) kits. An in-house assay based on previously published reactions was used as reference. Comparison of the results showed high intra-assay agreement between laboratories, with small variations for most samples. The in-house assay had an analytical detection limit of less than 10 copies per reaction. While the 2 commercial kits were able to detect specimens with low viral loads similarly to the in-house assay, significant differences were observed, in the Cq values and relative fluorescence (RF), between the assays. The RF signal of the in-house and Bio-Speedy assays ranged between 5,000 and 10,000 RFU, while the signal in the Novaplex assay was less than 600 RFU. Due to the kit measurement protocol, the Cq values of the Bio-Speedy kit were 5 to 7.5 cycles lower than those of the in-house assay. On the contrary, the Cq values of the Novaplex kit were significantly higher than those of the in-house assay, with differences of 3 to 5 cycles per sample. Our results suggest that while all assays were similar in their overall sensitivity, direct comparison of Cq values between them may be misleading. To our knowledge, this is the first methodical evaluation of commercial MPX test kits. We therefore anticipate that this study would help diagnostic laboratories in choosing a specific MPX detection assay. IMPORTANCE To the best of our knowledge, this study is the first methodical evaluation of commercial kits designed for Monkeypox virus detection. This was done by performing the same tests using the same sample set in multiple laboratories, simultaneously, on a national scale. It therefore provides important and unique information on the performance of such kits and provides a guideline for choosing the assay of choice for monkeypox virus diagnosis in a standard diagnostic laboratory. It also demonstrates potential complications when trying to compare the results of different assays, even when testing exactly the same samples, under identical conditions.

The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes

The gold standard diagnostic method for gastrointestinal infections is stool culture, which has limited sensitivity and long turnaround time. Infection diagnosis recently shifted to syndrome-based panel assays. This study employed the FilmArray® Gastrointestinal Panel, which detects 22 pathogens simultaneously, to investigate gastrointestinal infection and pathogen distribution in 91 stool samples of patients hospitalized at the Tzafon Medical Center, Israel, during 2020, and to compare the clinical and demographic data of negative vs. positive samples. Among the 61 positive samples (67%), the most common pathogen was Campylobacter (34.4%). Positive test results were associated with a slightly younger patient age (p = 0.012), significantly higher post-diagnosis use of antibiotics (63.9% vs. 36.7%; p = 0.014), and shorter length of stay and time to discharge (p = 0.035, p = 0.003, respectively) than negative test results. To conclude, the FilmArray® Gastrointestinal Panel enabled the early identification of causative infectious agents and enhanced clinical management and outcomes.

Different bile acids have versatile effects on sporulation, toxin levels and biofilm formation of different Clostridioides difficile strains

Clostridioides difficile infection develops following ingestion of virulent stains by a susceptible host. Once germinated, toxins TcdA and TcdB, and in some of the strains binary toxin, are secreted, eliciting disease. Bile acids play a significant role in the process of spore germination and outgrowth, with cholate and its derivative enhancing colony formation, while chenodeoxycholate inhibit germination and outgrowth. This work investigated bile acids' impact on spore germination, toxin levels and biofilm formation in various strain types (STs). Thirty C. difficile isolates (A⁺ B⁺ CDT^-\+) of different STs were exposed to increasing concentrations of the bile acids, cholic acid (CA), taurocholic acid (TCA) and chenodeoxycholic acid (CDCA). Following treatments, spore germination was determined. Toxin concentrations were semi-quantified using the C. Diff Tox A/B II™ kit. Biofilm formation was detected by the microplate assay with crystal violet. SYTO® 9 and propidium iodide staining were used for live and dead cell detection, respectively, inside the biofilm. Toxins levels were increased by 1.5-28-fold in response to CA and by 1.5-20-fold in response to TCA, and decreased by 1-37-fold due to CDCA exposure. CA had a concentration-dependent effect on biofilm formation, with the low concentration (0.1%) inducing- and the higher concentrations inhibiting biofilm formation, while CDCA significantly reduced biofilm production at all concentrations. There were no differences in the bile acids effects on different STs. Further investigation might identify a specific bile acids' combination with inhibitory effects on C. difficile toxin and biofilm production, which could modulate toxin formation to reduce the likelihood of developing CDI.

The effect of different C. difficile MLST strains on viability and activity of macrophages

Objectives

Clostridioides difficile is the most common infectious agent of nosocomial diarrhea. C. difficile infection (CDI) pathogenesis and disease severity depend on its toxins (toxins A, B and binary) and on the host's immune response, especially the innate immune system. The current study examined the efficacy of macrophage activity, macrophages viability and cytokine secretion levelsin response to different sequence type (ST) strains of C. difficile.

Methods

RAW 264.7 macrophages were exposed to six different strains of C. difficile as well as to both toxins A and B and macrophage viability was measured. The levels of four secreted cytokines were determined by RT-PCR and ELISA. Morphological changes to the macrophages were investigated by fluorescent microscopy.

Results

Strains ST37 and ST42 affected macrophages' vitality the most. Toxins A and B led to a significant reduction in macrophages' vitality at most time points. In addition, starting at 30-min post-exposure to 5 ng/μl of both toxins led to significant differences in macrophage viability versus at lower concentrations. Furthermore, cytokine secretion levels, including IL-12, IL-6 and TNF-α, increased dramatically when macrophages were exposed to strains ST42 or ST104. Finally, gene expression surveys point to increases in IL-12 gene expression in response to both ST42 and ST104.

Conclusions

C. difficile strains with higher toxins levels induced an increased activation of the innate immune system and may activate macrophages more profoundly resulting in secretion of higher levels of pro-inflammatory cytokines. However, higher toxin levels may also damage macrophages' normal skeletal structure, reducing macrophage viability.

Trend of Changes in Chloramphenicol Resistance during the Years 2017-2020: A Retrospective Report from Israel

Resistant bacteria limit treatment options. This challenge has awakened interest in antibiotics that are no longer in use due to side effects, such as chloramphenicol. This work investigated trends in chloramphenicol resistance rates during 2017-2020 in bacteria isolated from diverse clinical samples at the Baruch Padeh Medical Center, Poriya, Israel. Bacteria were isolated from 3873 samples and identified using routine methods, including matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology. Chloramphenicol susceptibility was tested using a VITEK II instrument or by the Kirby-Bauer disk-diffusion test. The average chloramphenicol resistance rate was 24%, with no significant differences between study years. Chloramphenicol resistance was associated with sample origin (p < 0.001); isolates originating from sputum samples showed 49.8% resistance rate, compared to 2.3% of the body fluid isolates, 10.4% of the ear/eye isolates and 22.5% of the blood isolates. Furthermore, there was a significant decrease in chloramphenicol resistance among blood and ear/eye isolates during the study period (p = 0.01, p < 0.001, respectively). The highest resistance rate was among Pseudomonas aeruginosa isolates (50.5%). In conclusion, since chloramphenicol susceptibility seems to be retained, its comeback to the clinical world should be considered.

Impact of Helicobacter pylori virulence markers on clinical outcomes in adult populations

BACKGROUND

In recent years, associations between specific virulence markers of Helicobacter pylori (H. pylori) and gastrointestinal disorders have been suggested.

AIM

To investigate the presence of virulence factors including vacuolating cytotoxin A genotypes (s1m1, s1m2, s2m1, and s2m2), cytotoxin-associated gene A (CagA), and urease activity in H. pylori strains isolated from Arab and Jewish populations in northern Israel and to assess associations between these factors and patients’ demographics and clinical outcomes.

METHODS

Patients (n = 108) who underwent gastroscopy at the Baruch Padeh Medical Center, Poriya due to symptomatic gastroduodenal pathologies as part of H. pylori diagnosis were enrolled in the study. Gastric biopsy specimens were collected from the antrum of the stomach. Clinical condition was assessed by clinical pathology tests. Bacteria were isolated on modified BD Helicobacter Agar (BD Diagnostics, Sparks, MD, United States). Bacterial DNA was extracted, and PCR was performed to detect CagA and vacuolating cytotoxin A genes. Urease activity was assessed using a rapid urease test.

RESULTS

A significant correlation was found between disease severity and patient ethnicity (P = 0.002). A significant correlation was found between CagA presence and the s1m1 genotype (P = 0.02), which is considered the most virulent genotype. Further, a higher level of urease activity was associated with isolates originating from the Jewish population. Moreover, higher urease activity levels were measured among CagA-/s1m1 and CagA-/s2m2 isolates.

CONCLUSION

Our study highlights the importance of incorporating molecular methods for detection of virulence markers of H. pylori in order to tailor optimal treatments for each patient. Further investigation should be performed regarding associations between H. pylori virulence factors and ethnicity.

Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity

Introduction

The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance.

Methods

We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls.

Results

In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients.

Discussion

These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges.

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.

Should pregnant women be screened for SARS-CoV-2 infection? A prospective multicenter cohort study

OBJECTIVE

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), ranges from asymptomatic to severe infection. We aimed to compare the prevalence of COVID-19 in asymptomatic pregnant versus nonpregnant women in order to establish recommendations for a COVID-19 screening strategy.

METHODS

A prospective multicenter cohort study was conducted. Asymptomatic pregnant or nonpregnant women after March 2020 (the time when COVID-19 was first detected in north Israel) were tested for SARS-CoV-2 using nasopharyngeal reverse transcription polymerase chain reaction test, anti-nucleocapsid IgG, and anti-spike IgG. Diagnosis was made if at least one test result was positive. Pregnant women were tested between 34 and 42 weeks, mostly at birth.

RESULTS

Among the 297 participating women, 152 were pregnant and 145 were nonpregnant. The prevalence of asymptomatic COVID-19 was similar between the groups (4 [2.6%] and 8 [5.5%], respectively; P = 0.2). All women with COVID-19 delivered healthy appropriate-for-gestational-age babies without malformations, at term.

CONCLUSIONS

The rate of asymptomatic COVID-19 in pregnant women is low and comparable to the rate among nonpregnant women. Pregnancy outcomes are favorable. Future screening programs should consider that one of 25 screened asymptomatic women will be positive.

Rapid SARS-CoV-2 Detection Using the Lucira™ Check It COVID-19 Test Kit

The need for the early identification of SARS-CoV-2 has let to a quest for reliable tests that meet the standards of polymerase chain reaction (PCR) tests, on the one hand, and are low-cost, easy-to-use, and fast, on the other hand. One such test is the Lucira™ Check It COVID-19 Test kit (“Lucira”) (Lucira Health, Inc., Emeryville, CA, USA), which utilizes real-time loop-mediated isothermal amplification technology, developed for at-home use. This study evaluated the clinical sensitivity and specificity of Lucira in identifying the virus in 190 nasopharyngeal samples collected between January and October 2021. Each sample was also subjected to RT-PCR. All negative RT-PCR results were paralleled by a negative Lucira result. Out of 90 participants who had a positive RT-PCR result, 82 (91.1%) tested positive by Lucira. Among the 72 symptomatic participants, 67 (93%) tested positive by Lucira. All samples with a positive RT-PCR result with a threshold cycle (Ct) > 36, yielded a negative Lucira result. In addition, a significant positive correlation was found between Ct and time-to-positivity with Lucira (R = 0.8612, p < 0.0001). The implementation of such a portable and affordable assay may aid in breaking the COVID-19 transmission chain.

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.

High throughput optical modulation biosensing for highly sensitive and rapid detection of biomarkers

Rapid, highly sensitive, and high-throughput detection of biomarkers at low concentrations is invaluable for early diagnosis of various diseases. In many highly sensitive immunoassays, magnetic beads are used to capture fluorescently labeled target molecules. The target molecules are then quantified by detecting the fluorescent signal from individual beads, which is time consuming and requires a complicated and expensive detection system. Here, we demonstrate a high-throughput optical modulation biosensing (ht-OMB) system, which uses a small permanent magnet to aggregate the beads into a small detection volume and eliminates background noise by steering a laser beam in and out of the cluster of beads. Shortening the aggregation, acquisition, and well-to-well scanning transition times enables reading a 96-well plate within 10 min. Using the ht-OMB system to detect human Interleukin-8, we demonstrated a limit of detection of 0.14 ng/L and a 4-log dynamic range. Testing 94 RNA extracts from 36 confirmed RT-qPCR SARS-CoV-2-positive patients (C_t≤40) and 58 confirmed RT-qPCR SARS-CoV-2-negative individuals resulted in 100% sensitivity and 100% specificity.

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.

Evaluation of Factors that Affect the Performance of COVID-19 Molecular Assays Including Presence of Symptoms, Number of Detected Genes and RNA Extraction Type

BACKGROUND AND AIMS

Rapid and accurate detection of COVID-19 is crucial for mitigation of the pandemic. We evaluated the performance of six molecular kits and the effect of several factors on the performance of the kits.

MATERIALS AND METHODS

Two hundred and four nasopharyngeal samples were collected from participants aged ≥18 years at the Baruch Padeh Medical Center Poriya, Israel, between June and August 2020. Samples were tested by: Allplex 2019-nCOV Assay (Seegene), Real-Time Fluorescent RT-PCR Kit for Detecting SARS-2019-nCoV (BGI Genomics), Xpert^® Xpress SARS-CoV-2 test (Cepheid), Simplexa^® COVID-19 Direct Kit (Focus Diagnostics), BD SARS-CoV-2 Reagents for BD MAX™ System (BD), and Logix Smart™ Coronavirus Disease 2019 (COVID-19) Test kit (CO-DIAGNOSTICS).

RESULTS

Xpert^® Xpress SARS-CoV-2 test and Logix Smart™ COVID-19 Kit had the highest (91.2%) and the lowest (74.5%) sensitivity, respectively. Symptoms were a predictor of a positive result. Traditional assays had a higher minimum cycle threshold (min Ct), i.e. detected lower viral load, compared to rapid assays (p = 0.012). Samples of symptomatic participants had lower min Ct, than samples of asymptomatic participants (p < 0.001). Additionally, the more genes were detected, the lower the min Ct (p < 0.001), indicating that a greater percentage of the viral genome was amplified.

CONCLUSIONS

Taken together, most assays had overall good performance. Since several factors affect the performance of kits, each laboratory must be familiar with its kit's limitations in order to produce the most reliable results.

COVID-19 Vaccination Compliance and Associated Factors among Medical Students during an Early Phase of Vaccination Rollout-A Survey from Israel

COVID-19 is "a once-in-a-century" pandemic, bringing with it unparalleled health, social, and economic ramifications. As part of the world's efforts to restrain the pandemic, vaccine development has been expedited. This population-representative survey in Israel aimed to investigate whether the knowledge, attitudes, and vaccination status of medical students affect their intention to recommend COVID-19 vaccination (as well as reasons for refusal and acceptance of the vaccine). The questionnaire was anonymous, via Google Forms app in December 2021. One-hundred and four medical students completed the survey. Overwhelmingly, (91.3%) COVID-19 vaccination status and intention to receive the vaccine were positively associated with intention to recommend. Twenty-five percent of the students replied that they lacked knowledge regarding the vaccine. A statistically significant association was found between experiencing quarantine and the intention to be vaccinated (p = 0.034). There was a significant positive relationship between the number of symptoms from previous vaccines and the fear of COVID-19 (rs = 0.272, p < 0.01). Prior vaccination did not have an effect on COVID-19 vaccine hesitancy. This first study evaluating COVID-19 vaccine hesitancy among Israeli medical students highlighted the need for medical programs to emphasize the benefits of COVID-19 vaccination in the protection of healthcare workers and patient safety. Education, awareness campaigns, and regulation of vaccine trials could further decrease COVID-19 vaccine hesitancy and increase vaccine rates among medical students.

The Cytopathic Effect of Different Toxin Concentrations From Different Clostridioides difficile Sequence Types Strains in Vero Cells

Clostridioides difficile is one of the leading causes of healthcare-associated diarrhea, with severity ranging from mild, self-limiting disease, to life-threatening toxic megacolon. C. difficile infection (CDI) pathogenesis is mediated by the TcdA and TcdB toxins. This work aimed to draw correlations between toxin levels, bacterial strains, and disease severity in 63 CDI patients. C. difficile typing was performed by multi-locus sequence types (MLST). Toxin concentrations were measured using the TOX A/B test. In addition, cell cytotoxicity assay was performed following Vero cell exposure to stool extracts (24 h). The most prevalent sequence types (ST) were ST2, ST4, ST6, ST13, ST37, ST42, and ST104, with highest toxin levels produced by ST42 and ST104 (302.5 and 297.1 ng/ml, respectively). These strains had a stronger cytopathic effect (CPE) on Vero cells as compared to strains with lower toxin concentrations (p < 0.001), as manifested by lower cell counts and higher percentages of cell rounding and adhesion loss. Although no association was found between ST, toxin concentrations, and disease severity, a diverse in vitro effect of different STs on the viability and activity of Vero cells was observed. These findings suggest that disease severity is affected by both host immune responses and by bacterial characteristics.

Characterization of reduced susceptibility to chlorhexidine among Gram-negative bacteria

Chlorhexidine gluconate (CHG) is one of the most commonly used antiseptic, acting against Gram-negative, Gram-positive bacteria, yeast and fungi. However, over use may lead to reduced susceptibility of different bacteria to CHG. This study aimed to characterize the CHG susceptibility among Gram-negative strains in Israel, to evaluate factors that may affect this susceptibility, and to compare CHG susceptibility between ESBLs bacteria to strains without these enzymes. P. aeruginosa, P. mirabilis, K. spp, E. coli, and A. baumannii were isolated from clinical samples of 193 patients hospitalized at Padeh-Poriya Medical Center. Phenotypic CHG susceptibility was assessed by determining minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The highest CHG MIC was found among P. mirabilis. The differences between the CHG MIC values among the different strains were statistically significant (p <0.001). ESBL-positive strains had higher MIC values as compared to ESBL-negative strains (p =0.030). A significant association was found between CHG susceptibility and sample source (p =0.015). In conclusion, the information gathered here significantly improves our knowledge on the reduced susceptibility to CHG among Gram-negative bacteria in Israel. Moreover, ESBL-positive bacteria are less susceptible to CHG and finally, bacteria in sputum, wounds, and body fluids are less CHG-susceptible.

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.

Antibiotic Resistance and Biofilm Production Capacity in Clostridioides difficile

Background

Clostridioides difficile (C. difficile) is one of the primary pathogens responsible for infectious diarrhea. Antibiotic treatment failure, occurring in about 30% of patients, and elevated rates of antibiotic resistance pose a major challenge for therapy. Reinfection often occurs by isolates that produce biofilm, a protective barrier impermeable to antibiotics. We explored the association between antibiotic resistance (in planktonic form) and biofilm-production in 123 C. difficile clinical isolates.

Results

Overall, 66 (53.6%) out of 123 isolates produced a biofilm, with most of them being either a strong (44%) or moderate (34.8%) biofilm producers. When compared to susceptible isolates, a statistically higher percentage of isolates with reduced susceptibility to metronidazole or vancomycin were biofilm producers (p < 0.0001, for both antibiotics). Biofilm production intensity was higher among tolerant isolates; 53.1% of the metronidazole-susceptible isolates were not able to produce biofilms, and only 12.5% were strong biofilm-producers. In contrast, 63% of the isolates with reduced susceptibility had a strong biofilm-production capability, while 22.2% were non-producers. Among the vancomycin-susceptible isolates, 51% were unable to produce biofilms, while all the isolates with reduced vancomycin susceptibility were biofilm-producers. Additionally, strong biofilm production capacity was more common among the isolates with reduced vancomycin susceptibility, compared to susceptible isolates (72.7% vs. 18.8%, respectively). The distribution of biofilm capacity groups was statistically different between different Sequence-types (ST) strains (p =0.001). For example, while most of ST2 (66.7%), ST13 (60%), ST42 (80%) isolates were non-producers, most (75%) ST6 isolates were moderate producers and most of ST104 (57.1%) were strong producers.

Conclusions

Our results suggest an association between reduced antibiotic susceptibility and biofilm production capacity. This finding reinforces the importance of antibiotic susceptibility testing, mainly in recurrence infections that may be induced by a strain that is both antibiotic tolerant and biofilm producer. Better adjustment of treatment in such cases may reduce recurrences rates and complications. The link of biofilm production and ST should be further validated; if ST can indicate on isolate virulence, then in the future, when strain typing methods will be more available to laboratories, ST determination may aid in indecision between supportive vs. aggressive treatment.

Dynamics of Invasive Pneumococcal Disease in Israel in Children and Adults in the 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 >65 years was ~75%. For pre-PCV episodes with missing serotype, extrapolations were applied. Overall, PCV13 serotypes (VT13) and non-VT13 (NVT) incidence rates 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, 8,614 IPD cases were recorded. IPD rates declined by 67% in children <5 and 5-17 years, comparing late-PCV13 vs. pre-PCV periods (IRR=0.33; CI: 0.27-0.40; and IRR=0.33; CI: 0.21-0.50, respectively). For adults, comparing late-PCV13 vs. early-PCV periods, rates significantly declined by 53% in 18-44 years, 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 years age groups. In late-PCV13 period, serotypes 3, 14 and 19A remained the predominant VT13, while serotypes 8 and 12F emerged as the predominant NVT.

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.

Serum Albumin to Creatinine Ratio as Predictor for 30-Day All-Cause Mortality in Patients with Clostridium Di!cile-Associated Diarrhea

BACKGROUND

Clostridium difficile-associated diarrhea (CDAD) is a significant cause of mortality and morbidity in hospitalized patients. Several scores have developed in order to assess the severity of CDAD.

OBJECTIVE

To determine the role of the serum albumin to creatinine ratio (sACR) in predicting the 30-day all-cause mortality of patients with CDAD in comparison with other known severity scores of CDAD.

METHODS

A retrospective study was conducted at Baruch-Padeh Medical Center from January 2014 to December 2019. Patients with CDAD were recruited from Internal Medicine Departments, Intensive Care Units, and Surgical Departments. Data on demographic characteristics, clinical signs, underlying conditions, and several risk factors for CD infection were collected. We compared between severity scores of CDAD, such as ATLAS, the CDAD severity score, and the sACR in predicting the 30-day all-cause mortality in hospitalized patients with CDAD.

RESULTS

116 patients with CDAD were included. The ATLAS, CDAD scores, and sACR were calculated for all patients. The mean age of the participants was 71.4±16.4 years. 57.7% were of female gender. Fifty-two (44.8%) died within 30 days. An ATLAS score of ≥8 points had a 3.6-fold higher risk of 30-day all-cause mortality in hospitalized patients with CDAD (HR 3.6, 95% CI 3.28-3.99, p=0.001), a CDAD score of ≥5 points (HR 1.1, 95% CI 0.91-1.42, p=0.05), and a sACR≤3.4 (HR 1.5, 95%CI 1.25-1.82, p=0.04).

CONCLUSION

In this study, it was found that a sACR≤3.4 could predict the 30-day all-cause mortality in patients with CDAD.

Mother-to-Neonate Transmission of Antibiotic-Resistant Bacteria: A Cross-Sectional Study

We evaluated carriage rates of extended spectrum β-lactam-producing Enterobacterales (ESBL-E), Carbapeneme-resistant Enterobacterales (CRE), vancomycin-resistant Enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA) among pregnant women and determined the maternal-to-neonate transmission rates of these antibiotic-resistant bacteria (ARB). Pregnant women provided rectal and vaginal samples, proximal to delivery. Stool samples were collected from newborns within 48 h of birth. All samples were cultured on selective media for ARB identification. Clinical and demographic data were collected from the participants' medical files. We performed molecular and phenotypic characterization of the different resistance mechanisms, and determined the isolates' antibiotic susceptibility and biofilm-forming ability. The prevalence of ESBL-E, MRSA and VRE among pregnant women were 16%, 6% and 1%, respectively. The prevalence of ESBL-E and MRSA among neonates were 7.6% and 1.6%, respectively. Maternal-to-neonate transmission rates of ESBL-E and MRSA were 48% and 27.8%, respectively. Maternal and neonatal isolates shared similar characteristics. Maternal-to-neonate transmission of ARB plays an important role in bacterial colonization in newborns. Future studies should investigate the outcomes of the high ESBL-E transmission rate. The biofilm-forming ability of ARB was found to affect transmission. Additional factors should be investigated in order to understand the differences between transmitted and non-transmitted bacteria.

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.

IL-16 and BCA-1 Serum Levels Are Associated with Disease Severity of C. difficile Infection

Clostridioides difficile infection (CDI) is associated with a high risk for complications and death, which requires identifying severe patients and treating them accordingly. We examined the serum level of six cytokines and chemokines (IL-16, IL-21, IL-23, IL-33, BCA-1, TRAIL) and investigated the association between them and patients’ disease severity. Concentrations of six cytokines and chemokines were measured using the MILLIPLEX^®MAP kit (Billerica, MA, USA) in serum samples attained from CDI patients within 24–48 h after laboratory confirmation of C. difficile presence. Demographic and clinical data were collected from medical records. The disease severity score was determined according to guidelines of the “Society for Healthcare Epidemiology of America and the Infectious Diseases Society of America” (SHEA-IDSA). Out of 54 patients, 20 (37%) had mild to moderate disease and 34 (63%) had severe disease. IL-16 (p = 0.005) and BCA-1 (p = 0.012) were associated with a more severe disease. In conclusion, IL-16 and BCA-1, along with other cytokines and chemokines, may serve as biomarkers for the early prediction of CDI severity in the future. An improved and more accessible assessment of CDI severity will contribute to the adjustment of the medical treatment, which will lead to a better patient outcome.

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.

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.

Reduced Susceptibility to Chlorhexidine among Staphylococcus aureus Isolates in Israel: Phenotypic and Genotypic Tolerance

Antiseptic use for body decolonization is the main activity applied to prevent healthcare-associated infections, including those caused by S. aureus. Consequentially, tolerance to several antiseptics such as chlorhexidine gluconate (CHG) has developed. This study aimed to estimate the prevalence of CHG tolerance among S. aureus strains in Israel and to evaluate factors that may affect this tolerance. Furthermore, it tested the associations between phenotypic and genotypic CHG tolerance. S. aureus strains (n = 190) were isolated from clinical samples of patients admitted to various medical institutions in Israel. Phenotypic susceptibility to CHG was assessed by determining minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Genotypic tolerance was detected using real-time PCR for detection of qac A/B genes. MIC for the antibiotic mupirocin was determined using the Etest method. Presence of the Panton-Valentine Leucocidin (pvl) toxin, mecA and mecC genes was detected using an eazyplex^® MRSAplus kit (AmplexDiagnostics GmbH, Gars, Germany). CHG tolerance was observed in 13.15% of the isolates. An association between phenotypic and genotypic tolerance to CHG was observed. Phenotypic tolerance to CHG was associated with methicillin resistance but not with mupirocin resistance. Additionally, most of the CHG-tolerant strains were isolated from blood cultures. In conclusion, this work shed light on the prevalence of reduced susceptibility to CHG among S. aureus strains in Israel and on the characteristics of tolerant strains. CHG-tolerant strains were more common than methicillin-resistant ones in samples from invasive infections. Further research should be performed to evaluate risk factors for the development of CHG tolerance.

Detection of Carbapenem-Resistant Enterobacterales in Simulated Blood Culture in 15 Minutes

Bacteremia leading to sepsis and organ dysfunction is a life-threatening situation, leading to death of up to one fourth of the infected individuals around the world. One major challenge in the treatment of sepsis is the rising prevalence of antibiotic resistant bacteria, such as carbapenem-resistant Enterobacterales (CRE). In recent years, several molecular assays have been developed for the detection of CRE mechanisms, enabling rapid results reporting. We evaluated the performance of the NG-Test CARBA 5 (NG Biotech) kit in detection of CRE in simulated blood cultures. Carbapenemase-producing (CP) CRE isolates (n = 38) and non-carbapenemase CRE (Non-CP) isolates (n = 10), previously identified using the routine methods practiced at the clinical microbiology laboratory of the Baruch Padeh Medical Center, Israel, were used in this analysis. Variable concentrations of the bacterial isolates were added to a suspension composed of human blood and saline, simulating the composition of a blood culture. Samples were then transferred to an anaerobic blood culture bottle and later tested with the NG-Test CARBA 5 (NG Biotech) kit, that identifies the CRE mechanism within 15 min. The NG-Test CARBA 5 kit correctly identified 43 samples (89.5%). The sensitivity and specificity of the kits were 86.8% and 100%, respectively. In conclusion, the NG-Test CARBA 5 kit is a reliable and accessible tool for the rapid diagnosis of CRE bloodstream infections.

Clinical and Demographic Characteristics of Patients With a New Diagnosis of Carriage or Clinical Infection With Carbapenemase-Producing Enterobacterales: A Retrospective Study

Background: To examine the clinical, demographic, and microbiologic characteristics of new rectal carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE) carriers vs. those with a clinical infection, hospitalized at Padeh-Poriya Medical Center between 2014 and 2017 and to examine the susceptibility profiles of isolates from clinical infections.

Methods: In this retrospective, chart analysis, demographic and clinical data were collected from medical charts of 175 adult patients with either new- onset carbapenemase-producing Enterobacterales (CPE) carriage or clinical CPE infection. Collected data included age, ethnic group, place of residence, hospitalizations in the past 90 days, and 30-day mortality. Microbiological analyses considered bacterial genus, molecular resistance mechanism and antibiotic susceptibility.

Results: A significantly higher percentage (42.4%) of CPE carriers were long-term care facility residents, and had been recently hospitalized (56.3%), as compared to patients with clinical CPE infection (29.2 and 45.9%, respectively). Additionally, we noted a high (58.3%) acquision of CPE in our hospital. The most common bacterial isolate was K. pneumoniae and the most common resistance mechanism was Klebsiella pneumoniae (K. pneumoniae) carbapenemases (KPC). High susceptibility rates to amikacin and chloramphenicol were also noted.

Conclusions: This study reaffirmed the importance of CPE screening and infection control measures. The observed antibiotic susceptibility profile suggests amikacin and chloramphenicol as potential treatments for CPE infection.

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori

Antimicrobial resistance (AMR) in Helicobacter pylori is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the H. pylori resistome and phylogeny in order to characterize Israeli H. pylori. Israeli H. pylori isolates (n = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis. Literature review identified 111 mutations reported to correlate with phenotypic resistance to these antimicrobials. Analysis was conducted via our in-house bioinformatics pipeline targeting point mutations in the relevant genes (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) in order to assess genotype-to-phenotype correlation. Resistance rates of study isolates were as follows: clarithromycin 54%, metronidazole 31%, amoxicillin 10%, rifampicin 4%, and levofloxacin 2%. Genotype-to-phenotype correlation was inconsistent; for every analyzed gene at least one phenotypically susceptible isolate was found to have a mutation previously associated with resistance. This was also observed regarding mutations commonly used in commercial kits to diagnose AMR in H. pylori cases. Furthermore, 11 novel point mutations associated with a resistant phenotype were detected. Analysis of a unique set of H. pylori isolates demonstrates that inferring resistance phenotypes from WGS in H. pylori remains challenging and should be optimized further.

Characterization of Clostridioides difficile Strains, the Disease Severity, and the Microbial Changes They Induce

BACKGROUND

Clostridioides difficile infection (CDI) is a major nosocomial disease. The characteristics of different strains, the disease severity they cause, their susceptibility to antibiotics, and the changes they inflict on gut microbiome, have not been comprehensively studied in Israel.

METHODS

A severity score was calculated for 70 patients. Stool samples were tested for toxins presence using a special kit. Bacteria were isolated, identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and antibiotic susceptibility tests were performed for several antibiotics. Strains were classified by Multi-locus sequence typing (MLST), and changes in gut microbiome were tested.

RESULTS

ST04 (22.5%) and ST37 (12.7%) were the most frequent strains. Clade (phylogenetic lineage) 1 was the most (81.4%) prevalent. We found significant associations between ST and age (p = 0.024) and between ST and moxifloxacin susceptibility (p = 0.001). At the clade level, we found significant associations with binary toxin gene occurrence (p = 0.002), and with susceptibility to both metronidazole and vancomycin (p = 0.024, 0.035, respectively). Differences in intestine microbiome were affected by age, clades' distribution and STs.

CONCLUSIONS

By defining the characteristics of the different strains and clades, clinicians can choose medical interventions based on the predicted response or disease severity associated with each strain, enabling new advances in the field of personalized medicine.

Evaluation of the NG-Test CARBA 5 Kit for Rapid Detection of Carbapenemase Resistant Enterobacteriaceae

OBJECTIVE

We evaluated NG-Test CARBA 5, a new phenotypic carbapenemase detection assay, and compared it to the routine Xpert CARBA-R polymerase chain reaction assay. Furthermore, we tested the kit's performance after bacterial growth on 4 different solid media.

METHODS

Seventy carbapenem resistant Enterobacteriaceae (CRE) isolates (60 were carbapenemase producers) were collected at the Poriya Baruch Padeh Medical Center. All isolates were grown on 4 types of agar media-BD BBL CHROMagar carbapenem resistant Enterobacteriaceae, BD CHROMagar Orientation, BD MacConkey II agar, and BD Trypticase Soy Agar II with 5% sheep blood-and were then subjected to NG-Test CARBA 5 kit analysis.

RESULTS

The NG-Test CARBA 5 specificity was 100% for all 4 media. However, the sensitivity was higher when bacteria were grown on TSA with 5% sheep blood (98.3%) as compared with the Orientation medium (88.3%), the CPE medium (84.7%), and the MacConkey medium (83.6%). In addition, some of the carbapenemase mechanisms such as Verona Integron-Mediated Metallo-β-lactamase were detected with low agreement levels in specific media but higher agreement levels in the other media.

CONCLUSION

NG-Test CARBA 5 may enable faster detection of carbapenemase producing CRE, which will be of value for treatment adjustment and prevention control. However, the medium type on which the bacteria are grown affects kit sensitivity.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel

Full genome sequences are increasingly used to track the geographic spread and transmission dynamics of viral pathogens. Here, with a focus on Israel, we sequence 212 SARS-CoV-2 sequences and use them to perform a comprehensive analysis to trace the origins and spread of the virus. We find that travelers returning from the United States of America significantly contributed to viral spread in Israel, more than their proportion in incoming infected travelers. Using phylodynamic analysis, we estimate that the basic reproduction number of the virus was initially around 2.5, dropping by more than two-thirds following the implementation of social distancing measures. We further report high levels of transmission heterogeneity in SARS-CoV-2 spread, with between 2-10% of infected individuals resulting in 80% of secondary infections. Overall, our findings demonstrate the effectiveness of social distancing measures for reducing viral spread.

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.

Performance of the Influ a + B K-SeT® assay as compared to two RT-PCR assays for detection of influenza virus

OBJECTIVES

To evaluate the performance of Influ A + B K-SeT®, a rapid influenza antigen detection kit, in order to determine whether its implementation as a point-of-care test in the emergency room (ER) is justified.

METHODS

Nasopharyngeal swabs (n = 170) were collected in triplicates from patients with suspected influenza infection. One sample was tested by the Influ A + B K-SeT® kit and the other two samples were analyzed with Simplexa™ Flu A/B & RSV Direct Kit and Xpert® Flu, two RT-PCR-based assays routinely used in the ER.

RESULTS

The sensitivity and specificity of the Influ A + B K-SeT® kit were 91.2%-94.5% and 98.2%, respectively, compared to the Xpert® Flu assay and the Simplexa™ Flu A/B & RSV Direct Kit, respectively.

CONCLUSIONS

Considering the satisfactory diagnostic performance of the Influ A + B K-SeT® test, its implementation as a point-of-care is expected to aid in decision-making, minimize time-to-result and reduce healthcare costs.

Nonalcoholic fatty liver disease as a risk factor for Clostridium difficile-associated diarrhea

AIMS

Clostridium difficile is the most common cause of infectious nosocomial diarrhea among adults in developed countries. Nonalcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease and it is associated with bacterial infections. Our goal was to assess whether NAFLD considered a risk factor for C. difficile-associated diarrhea (CDAD).

METHODS

We conducted a retrospective study of patients admitted with CDAD at Baruch Padeh Medical Center, Poria, Israel during a period of four years. Data on demographic characteristics, clinical signs, underlying conditions, presence of fatty liver based on computed tomography/ultrasonography imaging and several risk factors for CDI were collected. The control group included patients with diarrhea who were negative for CDT and had been hospitalized during the same period. The controls were matched for age (±5 years) and gender.

RESULTS

Totally, 115/164 patients with CDAD met the inclusion criteria. The control group was consisted of 115 hospitalized patients with non-CDAD. The mean age of all the participants (230) was 69.57 ± 18 years. NAFLD was found in 76/115 (66%) patients with CDAD vs. 35/115 (30.4%) in the control group, P < 0.001. Moreover, we found significant associations between CDAD group and metabolic syndrome, prior use of antibiotic in the last 3 months, NAFLD and high serum levels of C-reactive protein. Multivariate analysis showed that NAFLD, odds ratio 1.51, 95% confidence interval 1.2-1.95, P = 0.05 was significantly associated with CDAD.

CONCLUSIONS

This retrospective study showed that NAFLD is a risk factor for CDAD. Moreover, metabolic syndrome and high serum levels of C-reactive protein were significantly associated with the risk of CDAD.

Maternal and neonatal outcome of asymptomatic bacteriuria at term pregnancy

OBJECTIVES

Guidelines recommend antibiotic treatment for every episode of asymptomatic bacteriuria throughout pregnancy in order to reduce maternal and fetal complications. We evaluated intra- and post-partum, as well as puerperal maternal and neonatal outcomes of an untreated group of pregnant women with asymptomatic bacteriuria at term.

METHODS

This was a single center prospective cohort study. We enrolled women who came for labor or checkups, 37-42 weeks gestation, with singleton, vertex presentation. On admission, women gave a urine sample; we compared maternal, obstetric and neonatal data from the positive culture group to the negative culture.

RESULTS

Among 248 pregnant women recruited, 205 negative and 32 positive urine cultures were collected. None of the women that participated in this study developed pyelonephritis during hospitalization or during the puerperium. No significant differences were detected between the two groups in terms of age, nulliparity, gestational age at delivery, length of hospitalization, birth type, intra- or post-partum fever, antibiotic treatment during labor or post-partum.

CONCLUSIONS

No increased maternal or neonatal adverse effects were observed in women with untreated ASB detected at term.