Phenotypic and genotypic analysis of antimicrobial resistance and population structure of gastroenteritis-related Aeromonas isolates.

BACKGROUND: The population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them. METHODS: This microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results. RESULTS: The study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1-2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the blaOXA genes. Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other ß-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission. CONCLUSIONS: A. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.

Twenty-five years of sentinel laboratory-based surveillance of shigellosis in a high-income country endemic for the disease, Israel, 1998 to 2022.

BackgroundShigella is a leading cause of moderate-to-severe diarrhoea worldwide and diarrhoeal deaths in children in low- and-middle-income countries.AimWe investigated trends and characteristics of shigellosis and antimicrobial resistance of Shigella sonnei in Israel.MethodsWe analysed data generated by the Sentinel Laboratory-Based Surveillance Network for Enteric Pathogens that systematically collects data on detection of Shigella at sentinel laboratories, along with the characterisation of the isolates at the Shigella National Reference Laboratory. Trends in the shigellosis incidence were assessed using Joinpoint regression and interrupted time-series analyses.ResultsThe average incidence of culture-confirmed shigellosis in Israel declined from 114 per 100,000 population (95% confidence interval (CI): 112-115) 1998-2004 to 80 per 100,000 population (95% CI: 79-82) 2005-2011. This rate remained stable 2012-2019, being 18-32 times higher than that reported from the United States or European high-income countries. After decreasing to its lowest values during the COVID-19 pandemic years (19/100,000 in 2020 and 5/100,000 in 2021), the incidence of culture-confirmed shigellosis increased to 39 per 100,000 population in 2022. Shigella sonnei is the most common serogroup, responsible for a cyclic occurrence of propagated epidemics, and the proportion of Shigella flexneri has decreased. Simultaneous resistance of S. sonnei to ceftriaxone, ampicillin and sulphamethoxazole-trimethoprim increased from 8.5% (34/402) in 2020 to 92.0% (801/876) in 2022.ConclusionsThese findings reinforce the need for continuous laboratory-based surveillance and inform the primary and secondary prevention strategies for shigellosis in Israel and other endemic high-income countries or communities.

Candida Bloodstream Infection, a Dire Complication in Hospitalized COVID-19 Patients: Three Cases from a Single Center in Northern Israel.

BACKGROUND: Patients with severe coronavirus disease-2019 (COVID-19) are susceptible to superimposed infections. OBJECTIVES: To describe COVID-19 patients who presented with complications due to Candida bloodstream co-infection (candidemia) and their outcome in a single center in northern Israel (Emek Medical Center) during the second outbreak of COVID-19 in Israel (15 June 2020 to 20 September 2020). METHODS: A retrospective study of COVID-19 patients presenting with candidemia was conducted, including clinical and laboratory data. The incidence of candidemia among hospitalized COVID-19 patients was compared to a historical cohort of non-COVID-19 controls. RESULTS: Three COVID-19 patients complicated with candidemia were documented. All three patients died shortly after the detection of candidemia. Three different Candida sp. were isolated from the blood cultures: C. albicans, C. parapsilosis, and C. glabrata. The incidence of candidemia among COVID-19 patients was 0.679 episodes per 1000 hospital days. CONCLUSIONS: Our small sample suggests a much higher incidence of candidemia among COVID-19 patients compared to a historical cohort of non-COVID-19 controls. All clinicians treating COVID-19 patients in GICU should be aware of this complication.

Evaluation of Bio-Rad® discs for antimicrobial susceptibility testing by disc diffusion and the ADAGIO™ system for the automatic reading and interpretation of results.

The disc diffusion test is used for antimicrobial susceptibility testing worldwide. In this study, the performance of both Bio-Rad® antibiotic discs (as compared with Oxoid® discs) and the ADAGIO™ automated system for the reading of disc diffusion test results was evaluated with American Type Culture Collection (ATCC) quality control (QC) and wild strains of bacteria. Inhibition zones of both disc brands were read manually and through use of the ADAGIO™ system. Categorized interpretation of the results for each strain and antibiotic combination was summarized according to the Clinical Laboratory Standards Institute MS-100 (2017 update) manual and ADAGIO™ readings. Eight ATCC QC strains and 120 different wild strains were evaluated, to give a total of 1226 antibiotic/bacteria combinations and 2486 manual readings. One major error and four minor errors (0.08% and 0.34%, respectively) were detected via manual readings of the Bio-Rad® discs as compared with the Oxoid® discs. For the same number of antibiotic/bacteria combinations, five minor errors and one major error (0.42% and 0.08%, respectively) were detected with the Bio-Rad® discs read by the ADAGIO™ system. In addition, the number of times the automatic reading needed manual edition with Bio-Rad® discs was statistically lower than it did with Oxoid® discs (3.7% vs. 5.7%, p < 0.05). These findings support the hypothesis that Bio-Rad discs are not inferior to Oxoid® discs, and the performance of the ADAGIO™ system is comparable to that of manual readings with both disc brands.

Urinary Tract Infection in Outpatient Children and Adolescents: Risk Analysis of Antimicrobial Resistance.

BACKGROUND: Urinary tract infection (UTI) is a common bacterial infection in children. ​​​​​​​Early treatment may prevent renal damage in pyelonephritis. The choice of empiric antibiotic treatment is based on knowledge of the local susceptibility of urinary bacteria to antibiotics. In Israel the recommended empiric oral antibiotic treatment are First or second generation cephalosporin, trimethoprim-sulfamethoxazole or amoxicillin-clavulanic acid. OBJECTIVES: To describe resistance rates of urine bacteria isolated from children with UTI in the community settings. Identify risk factors for resistance. METHODS: A retrospective cross-sectional study of UTI in children aged 3 months to 18 years diagnosed with UTI and treated as outpatients in a large community clinic between 7/2015 and 7/2017 with a diagnosis of UTI. RESULTS: A total of 989 urinary samples were isolated, 232 were included in the study. Resistance rates to cephalexin, cefuroxime, ampicillin/clavulanate and Trimethoprim-Sulfamethoxazole were 9.9%, 9.1%, 20.7%, and 16.5%, respectively. Urinary tract abnormalities and recurrent UTI were associated with an increase in antibiotic resistance rates. Other factors such as age, fever, and previous antibiotic treatment were not associated with resistance differences. CONCLUSIONS: Resistance rates to common oral antibiotics were low compared to previous studies performed in Israel in hospital settings. First generation cephalosporins are the preferred empiric antibiotics for febrile UTI for outpatient children. Amoxicillin/clavulanate is not favorable due to resistance of over 20% and the broad spectrum of this antibiotic. Care should be taken in children with renal abnormalities as there is a worrying degree of resistance rates to the oral first line antibiotic therapy.

Detection of Ureaplasma Species by a Semi-Quantitative PCR Test in Urine Samples: Can It Predict Clinical Significance?

BACKGROUND: Ureaplasma species (Usp) are the most prevalent genital Mycoplasma isolated from the urogenital tract of both men and women. Usp may be commensals in the genital tract but may also be contributors to a number of pathological conditions of the genital tract. Because they can also just colonize the genital tract of healthy people, their pathogenic role can be difficult to prove. OBJECTIVES: The aim of the study was to evaluate the efficacy of a quantitative polymerase chain reaction (qPCR) method for the discrimination between infection and colonization by measuring prevalence of Usp in asymptomatic versus symptomatic patients. METHODS: Urine samples were tested for U. parvum and U. urealyticum using a semi-quantitative multiplex PCR technique for sexually transmitted diseases (Anyplex™ STI-7 Detection Kit, Seegene, South Korea). A total of 250 symptomatic and 250 asymptomatic controls were included. RESULTS: A strong positive result for U. parvum was significantly more prevalent in symptomatic compared to asymptomatic patients. This finding was observed especially in women and in the young group (15-35 years of age). No significant differences were observed between the prevalence in symptomatic and asymptomatic patients of U. parvum with low strength of positivity and for U. urealyticum in all groups by age, gender, and strength of positivity. CONCLUSIONS: The significant difference between the symptomatic and asymptomatic group in the highest positivity group for U. parvum using the Anyplex™ STI-7 detection kit in urine may indicate a high probability of infection rather than colonization, especially in women and young patients.

Seasonal Influenza Vaccination Effectiveness and Compliance among Hospital Health Care Workers.

BACKGROUND: Recent studies show that vaccination of health care workers (HCW) might reduce influenza transmission and mortality among hospitalized patients. No studies have compared the incidence of laboratory-proven influenza in vaccinated versus unvaccinated hospital HCW. OBJECTIVES: To evaluate the effectiveness of influenza vaccination among hospital HCW and to examine the attitudes of this population towards influenza vaccination. METHODS: We performed a prospective cohort study between 1 January and 30 April 2014 of 1641 HCW at our medical center; 733 were vaccinated and 908 were not. A random sample of 199 subjects was obtained: 97 vaccinated and 102 non-vaccinated. Participating individuals were contacted on a weekly basis during the flu season and were asked to report any respiratory or flu symptoms and, if positive, to undergo a polymerase chain reaction (PCR) test for influenza. Results: In the general HCW population vaccination was more frequent among physicians (298/498, 58%) than among nurses (324/862, 38%) and among males than females. Flu symptoms were reported by 20 of 199 participants, 13 in the non-vaccinated group (12.7%) and 7 in the vaccinated group (7.2%). A positive PCR test for influenza A virus was present in 4 of 20 people tested (20%). All positive cases were from the non-vaccinated group (P = 0.0953). CONCLUSIONS: Non-vaccinated HCW showed a higher, although not statistically significant, tendency for contracting laboratory-proven influenza than the vaccinated population. The main reasons for vaccination and non-vaccination were personal beliefs and habits. Education efforts are needed to improve compliance. Larger studies could further clarify this issue.

The effect of the transition to molecular diagnosis on the epidemiology and the clinical characteristics of bacterial gastroenteritis in Northern Israel.

BACKGROUND: The transition to PCR-based diagnosis of bacterial gastroenteritis (BGE) can increase the sensitivity but might reduce the clinical specificity. The aims of this study were (1) to compare the effect of the change from culture to PCR-based diagnostics on the reported incidence and positivity rates of BGE due to Salmonella, Shigella and Campylobacter species and (2) to compare the demographics, medical background, clinical characteristics and pre-analytic variables between cases with PCR-positive, culture-negative samples to cases with PCR-positive, culture-positive samples. METHODS: The study was performed at the Emek Medical Centre that serves a population of 0.5 million people in Northern Israel. The study included two parts: (1) a retrospective cohort study, comparing the incidence and positivity rates of laboratory-diagnosed BGE from January 2016 until December 22nd, 2019 when culture was the sole method to January 2020 until April 2023 when PCR was used; (2) a prospective cohort study, conducted between November 2020 until April 2023 that compared the demographics and clinical characteristics of BGE cases that were diagnosed by PCR alone versus cases that were diagnosed by both PCR and culture. RESULTS: The incidence rate between-periods comparability ratio was only 113% since the incidence rate did not increase during 2020, the first year of the COVID-19 pandemic. The sample positivity rate increased since 2020, with between-periods comparability ratio of 159%. In the second period, the sample positivity rates of culture vs. PCR alone differed between the pathogens and were 90.2%, 63.8% and 54.2% for Salmonella, Campylobacter and Shigella species, respectively (p < 0.001). The following variables were identified as independent predictors of culture positivity: (1) Salmonella infection (O.R. = 10.6, 95% C.I. 3.6-31.1, p < 0.001); (2) Shigella infection (O.R. = 0.46, 95% C.I.0.23-0.93, p = 0.032); (3) time from sample submission to culture (O.R.=0.73, 95% C.I. 0.58-0.92, p = 0.008); (4) the presence of abdominal pain (O.R. = 1.98, 95% C.I. 1.04-3.79, p = 0.038) and the PCR mean Ct value (O.R. = 0.89, 95% C.I.0.85-0.94, p < 0.001). CONCLUSIONS: The use of PCR had led to improved sensitivity, without noticeable decrease in the clinical specificity. This was especially important in the case of the more fastidious organisms.

Epidemiology and clinical characteristics of Aeromonas-associated gastroenteritis in Northern Israel: Insights and implications for public health.

The role of Aeromonas spp. in gastroenteritis is controversial due to varied clinical presentations and variable prevalence in asymptomatic. This study, conducted in Northern Israel, aimed to compare positivity rate and demographic characteristics of patients with Aeromonas-associated gastroenteritis (AAG) to asymptomatic, and examine the role of Aeromonas in AAG by comparing clinical and epidemiological characteristics between AAG and Campylobacter-associated gastroenteritis (CAG) patients. Results showed that 4.24%-4.81% of AAG patients had Aeromonas spp. in stools as a sole pathogen in 2020-2022, compared to 4.9% of asymptomatic. Analysis of 243 CAG patients versus 70 AAG patients revealed significantly less diarrhea, fever, abdominal pain, and muscle pain in AAG patients. Multivariate analysis identified higher Ct values, recent restaurant dining, and prolonged diarrhea as predictive factors for AAG versus CAG. In conclusion, similar positivity rates of Aeromonas spp. in symptomatic and asymptomatic making the distinction between true pathogen versus commensal bacteria difficult, unlike CAG.

A comparative study of a rapid phenotypic antimicrobial susceptibility testing system directly from positive blood cultures to the disk diffusion and VITEK 2 methods.

BACKGROUND: Sepsis is a life-threatening condition that impacts 49 million people annually and causes 11 million deaths worldwide. Surviving bloodstream infections (BSIs) depends on the rapid administration of effective antimicrobial treatment, underscoring a need for rapid antimicrobial susceptibility testing (AST). AIM: To evaluate the performance of Quantamatrix's dRAST v2.5 system (Seoul, South Korea) for AST directly from positive blood cultures as compared to the Disk-Diffusion (DD) and VITEK 2 methods. METHODS: The study included 191 positive blood cultures from clinical samples and spiked blood culture bottles. Following Gram staining and species-level identification, AST was performed by VITEK 2 and standard DD methods using CLSI (2021) interpretation. RESULTS: dRAST demonstrated very good AST performance for a Gram-negative isolate, and good performance for Gram-positive isolates, meeting CLSI criteria for the acceptance of a new method. Antimicrobials that were not considered verified compared to VITEK 2 and DD were cefazolin, ceftazidime, meropenem, and trimethoprim/sulfamethoxazole for Gram-negatives and clindamycin, erythromycin, penicillin, and oxacillin for Gram-positives. dRAST ESBL detection results were strongly correlated with the ESBL phenotypes obtained with other methods. Additional resistance mechanisms were in concordance with traditional tests. CONCLUSIONS: dRAST demonstrated good AST performance, meeting CLSI criteria for most relevant antibiotics. dRAST was associated with a significant reduction in time-to-results, labor, and the subjectivity of result analyses, making it a valuable addition to efforts supporting the treatment of patients with bacteremia. AST (antimicrobial susceptibility test), blood culture, dRAST, rapid methods, sepsis, turnaround time (TAT).

The Epidemiology of PCR-Confirmed Cutaneous Leishmaniasis in Israel: A Nationwide Study.

BACKGROUND: Leishmaniasis, mainly cutaneous leishmaniasis (CL), is endemic in Israel. In recent years, the diagnosis of leishmaniasis has transitioned to a molecular diagnosis. OBJECTIVE: To summarize all cases of leishmaniasis and the identified species seen in Israel based on molecular diagnosis. METHODS: A retrospective study was performed of patients diagnosed with leishmaniasis between January 2017 and December 2022. All five medical centers in Israel in which Leishmania diagnosis is performed were included: Soroka, HaEmek, Hadassah, Rambam, and Sheba, all utilized molecular diagnostic methods. Data on the annual number of cases, species, age, and gender were retrieved. RESULTS: During the years 2017-2022, a total of 4168 cases of leishmaniasis were diagnosed, which corresponds with ~7/100,000 inhabitants. L. (L.) major and L. (L.) tropica accounted for 84% and 14%, respectively. During the years 2020-2021, L. (L.) infantum emerged as a new form of cutaneous disease [2.7% of cases during this period]. Visceral L. (L.) infantum was found in five cases. Imported New World leishmaniasis accounted for 1% of the cases. L. (L.) major affected more males (67%) while L. (L.) tropica commonly affected more children and caused more facial lesions. CONCLUSIONS: The mean annual number of cases during these years is ~700. The dominant species is L. (L.) major. Since 2020, cutaneous L. (L.) infantum is an emerging infection in Israel.

The epidemiology of intestinal protozoa in the Israeli population based on molecular stool test: a nationwide study.

Stool examination using microscopy was the traditional method for the diagnosis of intestinal parasites. Recently, the use of molecular tests to identify stool protozoa has become the main tool used in most clinical laboratories in Israel. This study aimed to evaluate the prevalence of intestinal parasites in Israel and to compare this prevalence in laboratories that use molecular tests vs a laboratory that uses microscopy. Samples collected from January to October 2021 at seven laboratories were analyzed by real-time PCR (RT-PCR) or by microscopy. The multiplex panel included the following pathogens: Giardia lamblia, Entamoeba histolytica, Cryptosporidium spp., Cyclospora, Dientamoeba fragilis, and Blastocystis spp. Overall, 138,415 stool samples were tested by RT-PCR and 6,444 by microscopy. At least one protozoa species was identified in 28.4% of the PCR-tested samples compared to 4.6% of the microscopy-tested samples. D. fragilis was the most common PCR-identified species (29%). D. fragilis, G. lamblia, and Cryptosporidium spp. were mainly found in pediatric population, while Blastocystis spp. was most prevalent among adults (P < 0.001). In a sub-cohort of 21,480 samples, co-infection was found in 4,113 (19.15%) samples, with Blastocystis spp. and D. fragilis being the most common (14.9%) pair. Molecular stool testing proved more sensitive compared to microscopy. D. fragilis was the most commonly detected pathogen. The above profile was identified during the COVID pandemic when traveling was highly restricted and most likely represents the locally circulating protozoa. IMPORTANCE: This study sheds light on the prevalence of stool parasites in Israel. Additionally, this study indicates that the shift from microscope analysis to molecular tests improved protozoa diagnosis.

Accurate Prediction of Antimicrobial Susceptibility for Point-of-Care Testing of Urine in Less than 90 Minutes via iPRISM Cassettes.

The extensive and improper use of antibiotics has led to a dramatic increase in the frequency of antibiotic resistance among human pathogens, complicating infectious disease treatments. In this work, a method for rapid antimicrobial susceptibility testing (AST) is presented using microstructured silicon diffraction gratings integrated into prototype devices, which enhance bacteria-surface interactions and promote bacterial colonization. The silicon microstructures act also as optical sensors for monitoring bacterial growth upon exposure to antibiotics in a real-time and label-free manner via intensity-based phase-shift reflectometric interference spectroscopic measurements (iPRISM). Rapid AST using clinical isolates of Escherichia coli (E. coli) from urine is established and the assay is applied directly on unprocessed urine samples from urinary tract infection patients. When coupled with a machine learning algorithm trained on clinical samples, the iPRISM AST is able to predict the resistance or susceptibility of a new clinical sample with an Area Under the Receiver Operating Characteristic curve (AUC) of ∼ 0.85 in 1 h, and AUC > 0.9 in 90 min, when compared to state-of-the-art automated AST methods used in the clinic while being an order of magnitude faster.

Trends in the Epidemiology of Non-Typhoidal Salmonellosis in Israel between 2010 and 2021.

Non-typhoidal salmonellosis (NTS) is one of the most common foodborne diseases worldwide. In this study, we aimed to analyze trends in the epidemiology of NTS in the last decade in Israel. Laboratory-confirmed cases of NTS at eight sentinel laboratories were reported to the Israel Sentinel Laboratory-Based Surveillance Network, integrated with the serotype identification performed at the Salmonella National Reference Laboratory of the Ministry of Health. The decrease in NTS incidence since 1999 continued between 2010 and 2014 (16.1 per 100,000 in 2014) and was interrupted by a rise between 2015 and 2017 (39.1 per 100,000 in 2017) associated with outbreaks of Salmonella Enteritidis. The incidence of NTS dropped again thereafter (21.4 per 100,000 in 2021). The 0-4 age group was the most affected by NTS (55.5% of the cases) throughout the surveillance period. The age-adjusted incidence rates were consistently high in the summer months (June-September) and low in the winter months (December-February). The overall decrease in the incidence of NTS in Israel since 1999 was temporarily interrupted in the last decade by country-wide outbreaks involving emerging or re-emerging Salmonella serotypes. Control measures should be enhanced for all risk points of food chain transmission of Salmonella spp. to further reduce the NTS morbidity in Israel.

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.

High throughput SARS-CoV-2 variant analysis using molecular barcodes coupled with next generation sequencing.

The identification of SARS-CoV-2 variants across the globe and their implications on the outspread of the pandemic, infection potential and resistance to vaccination, requires modification of the current diagnostic methods to map out viral mutations rapidly and reliably. Here, we demonstrate that integrating DNA barcoding technology, sample pooling and Next Generation Sequencing (NGS) provide an applicable solution for large-population viral screening combined with specific variant analysis. Our solution allows high throughput testing by barcoding each sample, followed by pooling of test samples using a multi-step procedure. First, patient-specific barcodes are added to the primers used in a one-step RT-PCR reaction, amplifying three different viral genes and one human housekeeping gene (as internal control). Then, samples are pooled, purified and finally, the generated sequences are read using an Illumina NGS system to identify the positive samples with a sensitivity of 82.5% and a specificity of 97.3%. Using this solution, we were able to identify six known and one unknown SARS-CoV-2 variants in a screen of 960 samples out of which 258 (27%) were positive for the virus. Thus, our diagnostic solution integrates the benefits of large population and epidemiological screening together with sensitive and specific identification of positive samples including variant analysis at a single nucleotide resolution.

Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals.

The BNT162b2 mRNA vaccine is highly effective against SARS-CoV-2. However, apprehension exists that variants of concern (VOCs) may evade vaccine protection, due to evidence of reduced neutralization of the VOCs B.1.1.7 and B.1.351 by vaccine sera in laboratory assays. We performed a matched cohort study to examine the distribution of VOCs in infections of BNT162b2 mRNA vaccinees from Clalit Health Services (Israel) using viral genomic sequencing, and hypothesized that if vaccine effectiveness against a VOC is reduced, its proportion among breakthrough cases would be higher than in unvaccinated controls. Analyzing 813 viral genome sequences from nasopharyngeal swabs, we showed that vaccinees who tested positive at least 7 days after the second dose were disproportionally infected with B.1.351, compared with controls. Those who tested positive between 2 weeks after the first dose and 6 days after the second dose were disproportionally infected by B.1.1.7. These findings suggest reduced vaccine effectiveness against both VOCs within particular time windows. Our results emphasize the importance of rigorously tracking viral variants, and of increasing vaccination to prevent the spread of VOCs.

A Randomized Controlled Open Label Crossover Trial to Study Vaginal Colonization of Orally Administered Lactobacillus Reuteri RC-14 and Rhamnosus GR-1 in Pregnant Women at High Risk for Preterm Labor.

Lactobacilli administration has been suggested for the treatment and prevention of bacterial vaginosis, which increases the risk for preterm birth. We aimed to evaluate the vaginal colonization of lactobacilli orally administered to pregnant women at risk for preterm birth. We performed a randomized and controlled crossover study between January 2016 and May 2017. Forty pregnant women at high risk for preterm birth with normal vaginal flora (Nugent score ≤ 3) were randomized to either receive two oral capsules/day each containing 5 × 109 Lactobacilli (L.) rhamnosus GR-1 and L. reuteri RC-14 (n = 20) or no treatment (n = 20) for 2 months. Treatments were then crossed over for an additional two months. A vaginal examination and swabbing were performed for assessment of bacterial vaginosis at baseline and every month until study completion. At the same time points, vaginal samples were cultured and subjected to matrix-assisted-laser-desorption/ionization-time-of-flight-mass-spectrometry (MALDI TOF-MS) for the detection of the specific bacterial strains contained in the capsules. The primary endpoint was the presence of the administered lactobacilli strains in the vagina during the first two months of follow-up. Thirty-eight women completed the study. During the first two months of treatment, L. rhamnosus GR-1 was detected in one (5%) woman on the probiotic treatment and 2 (11%) women receiving no treatment (p = 0.6). L. rhamnosus GR-1 was detected in vaginal samples of 4 (11%) women during probiotic treatment (of both groups) and L. reuteri RC-14 was not detected in any samples. The rest of the endpoints were not different between the groups. Altogether, vaginal colonization of lactobacilli following oral administration is low during pregnancy.

Downregulation of the hemoglobin scavenger receptor in individuals with diabetes and the Hp 2-2 genotype: implications for the response to intraplaque hemorrhage and plaque vulnerability.

In individuals with diabetes mellitus (DM), the haptoglobin (Hp) genotype is a major determinant of susceptibility to myocardial infarction. We have proposed that this is because of DM and Hp genotype-dependent differences in the response to intraplaque hemorrhage. The macrophage hemoglobin scavenging receptor CD163 plays an essential role in the clearance of hemoglobin released from lysed red blood cells after intraplaque hemorrhage. We sought to test the hypothesis that expression of CD163 is DM and Hp genotype-dependent. CD163 was quantified in plaques by immunohistochemistry, on peripheral blood monocytes (PBMs) by FACS, and as soluble CD163 (sCD163) in plasma by ELISA. In DM plaques, despite an increase in macrophage infiltration, CD163 immunoreactivity was lower, resulting in a dramatic reduction in the percentage of macrophages expressing CD163 (27+/-2% versus 70+/-2%, P=0.0001). In individuals with DM as compared with individuals without DM, the percentage of PBMs expressing CD163 was reduced (3.7+/-0.6% versus 7.1+/-0.9%, P<0.002) whereas soluble plasma CD163 was increased (2.6+/-1.1 microg/mL versus 1.6+/-0.8 microg/mL, P<0.0005). Among DM individuals, the Hp 2-2 genotype was associated with a decrease in the percentage of PBMs expressing CD163 (2.3+/-0.5% versus 5.6+/-1.3%, P=0.01) and an increase in plasma soluble CD163 (3.0+/-0.2 microg/mL versus 2.3+/-0.2 microg/mL, P=0.04). Taken together, these results demonstrate an impaired hemoglobin clearance capacity in Hp 2-2 DM individuals and may provide the key insight explaining the increased incidence of myocardial infarction in this population.

Haptoglobin genotype modulates the balance of Th1/Th2 cytokines produced by macrophages exposed to free hemoglobin.

The haptoglobin genotype has been demonstrated to be an independent risk factor for CVD in multiple epidemiological studies. The primary function of haptoglobin is to mitigate the deleterious effects of extracorpuscular hemoglobin. We sought to determine if the protein products of the two haptoglobin alleles differed in their ability to modulate the cytokine profile produced by macrophages in response to hemoglobin. Peripheral blood mononuclear cells were isolated from normal human volunteers and cultured in the presence of complexes formed by the protein products of the two different haptoglobin alleles with hemoglobin. The release of specific cytokines in the conditioned media of these cells was assessed by ELISA. We found that the haptoglobin 1 allele protein product-hemoglobin complex stimulated the secretion of significantly more Il-6 and Il-10 than the haptoglobin 2 allele protein product-hemoglobin complex. We demonstrate that the release of these cytokines is dependent on the liganding of the haptoglobin-hemoglobin complex to the CD163 receptor and the activity of casein kinase II. Haptoglobin genotype modulates the balance of inflammatory (Th1) and anti-inflammatory (Th2) cytokines produced by macrophages exposed to free hemoglobin. This may have implications in understanding inter-individual differences in the inflammatory response to hemorrhage.