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Shiga toxin-producing Escherichia coli (STEC) is a significant cause of gastrointestinal infection and the haemolytic-uremic syndrome (HUS). STEC outbreaks are commonly associated with food but animal contact is increasingly being implicated in its transmission. We report an outbreak of STEC affecting young infants at a nursery in a rural community (three HUS cases, one definite case, one probable case, three possible cases and five carriers, based on the combination of clinical, epidemiological and laboratory data) identified using culture-based and molecular techniques. The investigation identified repeated animal contact (animal farming and petting) as a likely source of STEC introduction followed by horizontal transmission. Whole genome sequencing (WGS) was used for real-time investigation of the incident and revealed a unique strain of STEC O26:H11 carrying stx2a and intimin. Following a public health intervention, no additional cases have occurred. This is the first STEC outbreak reported from Israel. WGS proved as a useful tool for rapid laboratory characterization and typing of the outbreak strain and informed the public health response at an early stage of this unusual outbreak. [ABSTRACT FROM AUTHOR]

The aim of this study was to diagnose lipid storage diseases in embryos at the preimplantation stage. Two parallel approaches were employed. Firstly, activities of several sphingolipid hydrolases were determined in extracts of murine embryos and also human oocytes and polyspermic embryos. Sensitive fluorescent or fluorogenic procedures provided indications that Tay — Sachs, Gaucher and Krabbe diseases might be diagnosed in one human blastomere, while for Niemann — Pick disease two might be required. Secondly, pyrene lipids were administered into murine embryos and their fluorescence was quantified by computerized imaging microscopy. As a model of Gaucher disease, the fluorescent substrate pyrene glucosylceramide was administered into murine embryos in the presence or absence of an inhibitor of the enzyme β-glucosidase. Because of decreased degradation of the substrate in enzyme-inhibited cells, the fluorescence per blastomere was considerably greater relative to those which received no inhibitor. The results indicated that lipid storage diseases might be diagnosed in single human blastomeres at the preimplantation stage, obviating the need for pre-natal diagnosis and abortion of affected foetuses. [ABSTRACT FROM PUBLISHER]

Background: Vibrio vulnificus is a gram-negative bacterium that causes septicaemia and wound infection. Cases occur sporadically, and no previous outbreaks due to a common source or a clonal strain have been reported. In the summer and autumn of 1996 and 1997, an outbreak of invasive V. vulnificus infection occurred in Israel in people who had recently handled fresh, whole fish purchased from artificial fish-ponds.Methods: We reviewed clinical and epidemiological information, and undertook an environmental investigation to assess disease characteristics, modes of transmission, phenotypic characteristics of the bacterium, and fish-marketing policy. The clonal nature of 19 isolates was studied by biotyping, pulsed-field gel electrophoresis, and restriction-fragment length polymorphism (RFLP) analysis of a PCR fragment.Findings: During 1996-97, 62 cases of wound infection and bacteraemia occurred. 57 patients developed cellulitis, four had necrotising fasciitis, and one developed osteomyelitis. In all cases, the fish were cultivated in inland fish-ponds. In the summer of 1996, fish-pond managers initiated a new marketing policy, in which fish were sold alive instead of being packed in ice. Phenotypically, the isolates had five atypical biochemical test results. The isolates were non-typeable by pulsed-field gel electrophoresis, and all had the same PCR-RFLP pattern which had not been seen previously.Interpretation: The cause of the outbreak was a new strain of V. vulnificus, classified as biogroup 3. A new fish-marketing policy that began in 1996 may have exposed susceptible people to the organism. [ABSTRACT FROM AUTHOR]

Rapid developments in the field of whole genome sequencing (WGS) make in silico antimicrobial resistance (AMR) a target within reach. Campylobacter jejuni is a leading cause of foodborne infections in Israel with increasing rates of resistance. We applied WGS analysis to study the prevalence and genetic basis of AMR in 263 C. jejuni human and veterinary representative isolates retrieved from a national collection during 2003-2012. We evaluated the prediction of phenotypic AMR from genomic data. Genomes were screened by the NCBI AMRFinderPlus and the BioNumerics tools for acquired AMR genes and point mutations. The results were compared to phenotypic resistance determined by broth microdilution. The most prevalent resistant determinants were the multi-drug efflux transporter gene cmeABC (100%), the tetracycline resistance tet(O) gene (82.1%), the quinolone resistance g yrA T861 point mutation (75.7%), and the aadE streptomycin resistance gene. A variety of 12 known β lactam resistance genes ( bla OXA variants) were detected in 241 (92%) isolates, the most prevalent being bla OXA-193 , bla OXA-461 , and bla OXA-580 (56, 16, and 7%, respectively). Other aminoglycoside resistance genes and the macrolide resistance point mutation were rare (<1%). The overall correlation rate between WGS-based genotypic prediction and phenotypic resistance was 98.8%, sensitivity, specificity, positive, and negative predictive values being 98.0, 99.3, 99.1, and 98.5%, respectively. wgMLST-based phylogeny indicated a high level of clonality and clustering among the studied isolates. Closely related isolates that were part of a genetic cluster (single linkage distance ≤ 15 alleles) based on wgMLST phylogeny mostly shared a homogenous AMR determinant profile. This was observed in 18 of 20 (90.0%) clusters within clonal complex-21, suggesting clonal expansion of resistant isolates. Strong association to lineage was noted for the aadE gene and the various bla OXA genes. High resistance rates to tetracycline and quinolones and a low resistance rate to macrolides were detected among the Israeli C. jejuni isolates. While a high genotypic-phenotypic correlation was found, some resistance phenotypes could not be predicted by the presence of AMR determinants, and particularly not the level of resistance. WGS-based prediction of antimicrobial resistance in C. jejuni requires further optimization in order to integrate this approach in the routine workflow of public health laboratories for foodborne surveillance., (Copyright © 2020 Rokney, Valinsky, Vranckx, Feldman, Agmon, Moran-Gilad and Weinberger.)

Exposure to Legionella spp. contaminated aerosols in hotel settings confers risk for travel-associated Legionnaire's disease (TALD). In this study, we investigated the prevalence of Legionella contamination and its molecular diversity in hotels and resorts across Israel. The study was comprised of a convenience sample of water systems from 168 hotels and resorts countrywide, routinely inspected between March 2015 and February 2017. Isolation and quantitation of Legionella were performed in a water laboratory using the ISO 11731 method. The distribution of Legionella isolates was analyzed according to geography and source. The genetic diversity of a subset of isolates was analyzed by sequence-based typing (SBT) at the National Reference Laboratory for Legionella and compared to the national database. Out of 2830 samples tested, 470 (17%) obtained from 102 different premises (60% of hotels) were positive for Legionella spp. In 230 samples (49% of all positive, 8% of total samples), accounting for 37% of hotels, Legionella spp. counts exceeded the regulatory threshold of 1000 CFU/L. The most frequently contaminated water sources were cooling towers (38%), followed by faucets, hot tubs, water lines, and storage tanks (14%-17% each). Furthermore, 32% and 17% of samples obtained from cooling towers and hot tubs, respectively, exceeded the regulatory thresholds. SBT was performed on 78 strains and revealed 27 different sequence types (STs), including two novel STs. The most prevalent STs found were ST1 (26%), ST87 (10%), ST93 (6%), and ST461 and ST1516 (5% each). Several L. pneumophila STs were found to be limited to certain geographical regions. This is the first study to investigate the prevalence and diversity of Legionella in hotels and resorts in Israel during non-outbreak environmental inspections. These findings will inform risk assessment, surveillance, and control measures of TALD., Competing Interests: The authors declare no conflict of interest.

Shigella species remains a major diarrhoeagenic agent, affecting mostly children, with global high incidence and high mortality rate specially in developing areas. Although azithromycin is recommended for treatment of shigellosis, there are currently no CLSI susceptibility breakpoints, accordingly no routine antimicrobial susceptibility test is performed in the clinical laboratory. The purpose of this study was to estimate the prevalence, resistance profile and molecular epidemiology of azithromycin non-susceptible Shigella strains in Israel during a three year period. Shigella isolates (n = 1,170) referred to the National Reference Center during 2014-2016, were included in this study. Serotyping was performed by slide agglutination. Resistance genes, mph(A) and erm(B), were identified by PCR and the phenotype profile was determined by broth microdilution (BMD). Genetic relatedness was assessed by wgMLST. Decreased susceptibility to azithromycin (DSA) phenotype and genotype were detected in various Shigella species and serotypes related to diverse genetic backgrounds and antimicrobial profiles: 6% (26/423) of Shigella flexneri and 2% (16/747) of Shigella sonnei displayed DSA (MIC16 mg/L). Correlation of this phenotype with the presence of mph(A) and erm(B) genes was confirmed. All DSA-strains displayed resistance to ≥3 different antimicrobial classes. Among DSA-strains, 14% were resistant to quinolones and 5% displayed resistance to ceftriaxone. Most of these strains (32/42) were isolated from children in the southern and central regions of Israel. Clonality and significant relatedness was confirmed by PFGE and wgMLST. The presence of macrolide resistance genes among the different species and lineages reflects the transmissible nature of these genes. The emergence of DSA-Shigella reinforces the necessity to establish clinical breakpoints that would warrant routine testing, reporting and surveillance for this drug of choice., Competing Interests: The authors have declared that no competing interests exist.

Cryptosporidium is a protozoan parasite associated with gastrointestinal illness. In immune-compromised individuals, the infection may become life-threatening. Cryptosporidiosis is a mandatory-reported disease but little was known about its prevalence and associated morbidity in Israel. Currently, laboratory diagnosis is based on microscopy or copro-antigen tests and the disease is underreported. Molecular assays, which are more sensitive and specific, are now increasingly used for identification and screening. Here, the molecular epidemiology of cryptosporidiosis is explored for the first time. Samples from 33 patients infected during an outbreak of 146 laboratory confirmed cases that occurred in Haifa and Western Galilee in 2015 were genotyped, as well as samples from 36 patients sporadically infected during 2014-2018 in different regions. The results suggest that Cryptosporidium subtypes found in Israel are more similar to those reported in the neighboring countries Jordan and Egypt than in European countries. C. hominis was the predominant species in the center and the north of Israel, implicating human-to-human transmission. C. hominis IeA11G3T3 was the most prevalent subtype contributing to morbidity., Competing Interests: The authors have declared that no competing interests exist.

Introduction: Pediatric community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are emerging worldwide. High CA-MRSA carriage rates were previously described in healthy Bedouin children. We assessed demographic, clinical and molecular characteristics of pediatric MRSA infections in southern Israel., Methods: The Soroka University Medical Center laboratory serves the entire population of southern Israel, divided into 2 ethnic groups, Bedouins and Jews. All in-hospital MRSA clinical isolates from children 0 to 18 years old obtained in 2016 were included. Health care-associated and community-associated infections were defined according to the Centers for Disease Control and Prevention case definition. All isolates were evaluated for staphylococcal cassette chromosome, Panton-Valentine leukocidin, S. aureus protein A type, pulsed field gel electrophoresis and antimicrobial susceptibility testing., Results: Overall, 95 MRSA isolates (18% of all S. aureus), with 25 different MRSA strains, were identified. Twenty-eight isolates (29.5% of MRSA) belonged to the pediatric clone, rarely observed in Israel, staphylococcal cassette chromosome IV, Panton-Valentine leukocidin positive, S. aureus protein A type 002. All isolates demonstrated identical pulsed-field-gel-electrophoresis fingerprints. Eighty-two percent of infections caused by this clone were community-acquired, mainly observed in young Bedouin children, causing skin and soft-tissue infections. The new clone infection characteristics were similar to those of other CA-MRSA. All isolates of the pediatric clone were susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, gentamicin, tetracycline, rifampicin and vancomycin; 17.8% were nonsusceptible to erythromycin and clindamycin., Conclusion: The pediatric CA-MRSA clone, previously described only in sporadic cases in Israel, is emerging among healthy, young Bedouin children, typically causing skin and soft-tissue infections. Isolates are susceptible to a variety of non-beta-lactam antibiotics.

Objectives: Campylobacter jejuni is responsible for 80% of Campylobacter infections in Israel, a country with a high incidence reaching 91/100,000 population. We studied the phylogeny, diversity and prevalence of virulence factors using whole genome sequencing (WGS) of a national sample of C. jejuni clinical, food, and animal isolates collected over a 10-year period (2003-2012). Methods: C. jejuni isolates ( n = 263) were subject to WGS using Illumina sequencing (PE 250bpx2). Raw reads and de novo assemblies were analyzed with the BioNumerics whole genome MLST (wgMLST) pipeline. Reads were screened for 71 virulence genes by the SRST2 script. Allelic profiles were analyzed to create minimum spanning trees and allelic core distances were investigated to determine a reliable cutoff for strain determination. Results: wgMLST analysis of 263 C. jejuni isolates indicated significant diversity among the prevalent clonal complexes (CCs) with CC-21 and CC-353 being the most diverse, and CC-574 the most clonal. Within CC-21, sequence type (ST)-1359 created a separate clade. Human, poultry and bovine isolates clustered together across the different STs. Forty four percent of studied isolates were assigned to 29 genetic clusters. Temporal and geographical relatedness were found among the minority of clusters, while most phylogenetically associated cases appeared diffuse and unassociated epidemiologically. The majority of virulence factors were highly prevalent across the dataset and not associated with genotype, source of isolation or invasiveness. Conversely, all 13 genes associated with type VI secretion system (T6SS) were lineage-related and identified in only 18% of the isolates. T6SS was detected in 95.2% of ST-1359, a common type in Israel. Conclusions: wgMLST supported the assessment that poultry and cattle are likely food sources of infection in Israel. Substantial genetic clustering among C. jejuni isolates suggested multiple point source and diffuse outbreaks that were previously unreported in Israel. The high prevalence of T6SS among ST-1359 isolates is unique to Israel, and requires further investigation. This study exemplifies the importance of studying foodborne pathogens using advanced genomic approaches across the entire spectrum of One Health.

Background: Campylobacter spp. are the leading cause of foodborne infection worldwide, with a seasonal disease peak that might be affected by temperature increase. We studied the relationship between ambient temperature and weekly notified Campylobacter spp.infections., Methods: Data on 29,762 laboratory-confirmed cases of Campylobacter infection for the period, January, 1999 to December, 2010 were retrieved from the Ministry of Health registry. To estimate the association between the number of weekly cases of Campylobacter infection and the national average temperature at lags 0-3 weeks, firstly, we used GAM models, and secondly two-segment piecewise linear Poisson regressions. The effect of temperature was adjusted for seasonality, long-term trends and holidays., Results: We found a J-shaped relationship between ambient temperature and notified Campylobacter spp., Cases: For C. jejuni in all ages, the curve below the threshold was constant and the percent increase in cases for 1 °C above a threshold of 27 °C was 15.4% (95%CI: 6.7-24.1%). For ages 3-10 yr and > =26 yr the curve was constant below the threshold and positive above it; the percent increase in cases for 1 °C was 17.7%(95%CI: 6.0-29.4%) and 23.7%(95%CI: 11.6-35.8%), respectively. For ages 0-2 yr the curve was linear with no threshold and the percent increase for 1 °C was 5.1%(95%CI: 2.1-8.1%). For ages 11-25 yr the curve was always constant. Results for C. coli were similar., Conclusion: Our findings indicate that higher temperatures throughout the year affect Campylobacter spp. morbidity, especially in younger children. This should be taken into consideration in public education and health system preparedness for temperature increases as a result of climate change., (Copyright © 2018. Published by Elsevier Inc.)

Israel implemented use of 7- and 13-valent pneumococcal vaccine in 2009 and 2010, respectively. We describe results of prospective, population-based, nationwide active surveillance of Streptococcus pneumoniae serotype 12F (Sp12F) invasive pneumococcal disease (IPD) dynamics in the 7 years after vaccine introduction. Of 4,573 IPD episodes during July 2009-June 2016, a total of 434 (9.5%) were caused by Sp12F. Sp12F IPD rates (cases/100,000 population) increased in children <5 years of age, from 1.44 in 2009-2010 to >3.9 since 2011-2012, followed by an increase in all ages. During 2011-2016, Sp12F was the most prevalent IPD serotype. Sp12F isolates were mostly penicillin nonsusceptible (MIC >0.06 µg/mL; MIC 50  = 0.12) and predominantly of sequence type 3774), a clone exclusively found in Israel (constituting ≈90% of isolates in 2000-2009). The sharp increase, long duration, and predominance of Sp12F IPD after vaccine implementation reflect a single clone expansion and may represent more than a transient outbreak.

The objective of this study was to examine the recent trends in the epidemiology of campylobacteriosis in Israel. A Sentinel Laboratory-Based Surveillance Network for Bacterial Enteric Diseases was established in Israel by the Israel Center for Disease Control (ICDC). This network generated data on subjects from whom Campylobacter spp. was isolated in community and hospital laboratories. Further characterization of the isolates was done at the Campylobacter National Reference Laboratory. Data from these two sources were integrated and analyzed at the ICDC. Between 1999 and 2012, 40,978 Campylobacter stool isolates were reported to the ICDC by the sentinel laboratories. The incidence rate of campylobacteriosis increased from 65.7 per 100,000 in 1999 to 101.7 per 100,000 in 2012. This increase resulted from a significant rise in the incidence of campylobacteriosis in the Jewish population which, since 2009, surpassed the consistent higher incidence of the disease in Israeli Arabs. The peak morbidity in Israel consistently occurred in late spring, with a risk excess in males compared with females, in younger age groups and earlier in the life span among Arabs than among Jews and others. These results suggest that further analytical studies should be carried out to identify risk factors responsible for the increased incidence of campylobacteriosis and better direct prevention and control of the disease in Israel.

Objectives: To enhance timely surveillance of bacterial enteric pathogens, space-time cluster analysis was introduced in Israel in May 2013., Methods: Stool isolation data of Salmonella, Shigella, and Campylobacter from patients of a large Health Maintenance Organization were analyzed weekly by ArcGIS and SaTScan, and cluster results were sent promptly to local departments of health (LDOHs)., Results: During eighteen months, we identified 52 Shigella sonnei clusters, two Salmonella clusters, and no Campylobacter clusters. S. sonnei clusters lasted from one to 33 days and included three to 30 individuals. Thirty-one (60%) of the S. sonnei clusters were known to LDOHs prior to cluster analysis. Clusters not previously known by the LDOHs prompted epidemiologic investigations. In 31 of the 37 (84%) confirmed clusters, educational institutes (nursery schools, kindergartens, and a primary school) were involved., Conclusions: Cluster analysis demonstrated capability to complement enteric disease surveillance. Scaling up the system can further enhance timely detection and control of outbreaks., (Copyright © 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.)

Water shortage around the world enhanced the search for alternative sources. Greywater (GW) can serve as a solution for water demands especially in arid and semi-arid zones. However, issues considered which include acceptability of GW segregation as a separate water treated stream, allowing its use onsite. Consequently, it is the one of next forthcoming water resources that will be used, primarily in the growing mega-cities. It will be even more rentable when combined with the roof runoff water harvesting and condensing water from air-conditioning systems. Reuse of GW is as well beneficial in the mega-cities subject to the high expenses associated with wastewater and fresh water conveyance in the opposite direction. The main problem associated with GW reuse is the quality of the water and the targeted reuse options. At least two main options can be identified: the public sector that is ready to reuse the GW and the private sector which raises extra issues related to the reuse risks. These risk stems from the on yard use of GW, relatively close to the household location. The main focus of the Israeli guidelines for GW use is on the private and single house. The problem is less rigorous in public facilities, where the amounts are relatively large and the raw GW is relatively diluted. The two main principles adopted for reuse are: (i) greywater can be minimally treated since it differs from the black wastes, and; (ii) no contact exists with the resident around. The aggravated standards are an indication of the sensitivity issues related to the problem., (Copyright © 2014. Published by Elsevier Ltd.)

Salmonella enterica is the leading etiologic agent of bacterial food-borne outbreaks worldwide. This ubiquitous species contains more than 2,600 serovars that may differ in their host specificity, clinical manifestations, and epidemiology. To characterize salmonellosis epidemiology in Israel and to study the association of nontyphoidal Salmonella (NTS) serovars with invasive infections, 48,345 Salmonella cases reported and serotyped at the National Salmonella Reference Center between 1995 and 2012 were analyzed. A quasi-Poisson regression was used to identify irregular clusters of illness, and pulsed-field gel electrophoresis in conjunction with whole-genome sequencing was applied to molecularly characterize strains of interest. Three hundred twenty-nine human salmonellosis clusters were identified, representing an annual average of 23 (95% confidence interval [CI], 20 to 26) potential outbreaks. We show that the previously unsequenced S. enterica serovar 9,12:l,v:- belongs to the B clade of Salmonella enterica subspecies enterica, and we show its frequent association with extraintestinal infections, compared to other NTS serovars. Furthermore, we identified the dissemination of two prevalent Salmonella enterica serovar Typhimurium DT104 clones in Israel, which are genetically distinct from other global DT104 isolates. Accumulatively, these findings indicate a severe underreporting of Salmonella outbreaks in Israel and provide insights into the epidemiology and genomics of prevalent serovars, responsible for recurring illness., (Copyright © 2014, American Society for Microbiology. All Rights Reserved.)

During 1999-2010, the annual incidence of Campylobacter spp. infection in Israel increased from 31.04 to 90.99 cases/100,000 population, a yearly increase of 10.24%. Children <2 years of age were disproportionally affected; incidence in this age group (356.12 cases/100,000 population) was >26-fold higher than for the 30-<50 age group.

Human infection with non-typhoidal Salmonella serovars (NTS) infrequently causes invasive systemic disease and bacteremia. To understand better the nature of invasive NTS (iNTS), we studied the gene content and the pathogenicity of bacteremic strains from twelve serovars (Typhimurium, Enteritidis, Choleraesuis, Dublin, Virchow, Newport, Bredeney, Heidelberg, Montevideo, Schwarzengrund, 9,12:l,v:- and Hadar). Comparative genomic hybridization using a Salmonella enterica microarray revealed a core of 3233 genes present in all of the iNTS strains, which include the Salmonella pathogenicity islands 1-5, 9, 13, 14; five fimbrial operons (bcf, csg, stb, sth, sti); three colonization factors (misL, bapA, sinH); and the invasion gene, pagN. In the iNTS variable genome, we identified 16 novel genomic islets; various NTS virulence factors; and six typhoid-associated virulence genes (tcfA, cdtB, hlyE, taiA, STY1413, STY1360), displaying a wider distribution among NTS than was previously known. Characterization of the bacteremic strains in C3H/HeN mice showed clear differences in disease manifestation. Previously unreported characterization of serovars Schwarzengrund, 9,12:l,v:-, Bredeney and Virchow in the mouse model showed low ability to elicit systemic disease, but a profound and elongated shedding of serovars Schwarzengrund and 9,12:l,v:- (as well as Enteritidis and Heidelberg) due to chronic infection of the mouse. Phenotypic comparison in macrophages and epithelial cell lines demonstrated a remarkable intra-serovar variation, but also showed that S. Typhimurium bacteremic strains tend to present lower intracellular growth than gastroenteritis isolates. Collectively, our data demonstrated a common core of virulence genes, which might be required for invasive salmonellosis, but also an impressive degree of genetic and phenotypic heterogeneity, highlighting that bacteremia is a complex phenotype, which cannot be attributed merely to an enhanced invasion or intracellular growth of a particular strain.