Main projects @MAGICAL group

Legionella and Legionnaires’ disease
We have been working on Legionella in collaboration a wide range of stakeholders and partners for several years now. Together with the Central Laboratories of the Ministry of Health, we have studied the epidemiology and molecular epidemiology of legionellosis in Israel [26864322, 24118162]. Our recent studies (in writing) focus on specific settings such as defense establishments and hotels and resorts. We have also investigated the emergence of cold water humidifiers as the cause of paediatric Legionnaires’ disease [23078810].
 In a recent study looking at the largest legionellosis outbreak in Germany, we demonstrated the importance of combining epidemiological and genomic data in interpreting findings of epidemiological investigations [29162202]. Another recent study exploring the occurrence of legionellosis in the City of Basel, Switzerland revealed surprising findings with respect to the spread of this organism in an urban environment [30696527]. Currently we are working on the development of unique markers for the detection of specific Lp lineages and deep genomic characterisation of L. pneumophila ST1. We are also engaged in an ESCMID-funded study led by ESGLI regarding the water microbiome in the context of Legionella.  
 Prof. Moran-Gilad has led the development of the core genome MLST scheme for Legionella, which was among the first organisms to have such a scheme [26212142]. In a later study, in collaboration with the Israeli MOH and the NIBN at BGU, a computational solution for in silico typing of the organism has been developed which is now used globally by most players in the field [28082190]. Prof. Moran-Gilad is chairing the International Working Group on Next-generation sequencing for Legionella, on behalf of ESGLI. This WG is devising a new cgMLST scheme that would be widely adopted across public health institutions worldwide. Preliminary results have been presented at the 5th ESGLI meeting in Lyon, 2018. The scheme is expected to be launched by the end of 2019, and it will be using a recent allele calling pipeline to which we have also contributed [29543149].

Global antimicrobial resistance
The MAGICAL group is involved in a range of studies focusing on different aspects of AMR on a global scale. We are active partners in four recent JPI-AMR-funded consortia. The first deals with rapid diagnostic testing (RDT) for AMR which has been funded by the 4th call and gave rise to two exciting publications concerning behavioural change and RDT implementation [30710202] and a roadmap for RDT development, published in Nature Reviews in Microbiology [30333569]. This project has now led to another consortium, AMR Dx Global, which has recently been funded by the 8th call under the JPI-AMR Virtual Research Institute led by Till Bachman (UK). We are a collaborator for the OPENStewardship consortium funded by the 5th call, looking at innovative ways of performing antimicrobial stewardship led by David Fisman. Another of our collaborations is the SOLIDNESS – Surveillance Of mobiLome meDiated aNtibiotic rEsiStance Spread consortium, funded by the 7th call ( led by John Rossen (NL). We also collaborate with the DTU-led Global Sewage Surveillance consortium which has recently published its first scientific output in Nature Communications [30850636].

Local antimicrobial resistance
We have been studying resistant local pathogens, with special emphasis on Gram-negative pathogens, for a long time. Some of our recent studies involve WGS of pathogens such as Pseudomonas aeruginosa [29337862], Acinetobacter baumannii [28287300] and isolates producing ESBLs [24084536]. We constantly work on these pathogens and have recently implemented rapid WGS protocols for nosocomial cluster investigation. A current focus of study in collaboration with Avi Peretz is analysis of the resistome of Israeli Helicobacter pylori isolates.
 One of our flagship projects involves the surveillance of AMR in the Negev desert, especially among indigenous populations (collaborators: Zeev Ronen, Michael Gdalevich, Nadav Davidovitch). We are currently conducting several studies in this context, such as looking at the epidemiology of resistance and risk factors for its spread using mixed qualitative and quantitative methods, detecting resistant GNR in the environment (especially greywater) involved in the domestic spread of resistance in Bedouin villages, studying the resistome of environmental and clinical multi-resistant isolates and the relationship between the microbiome and spread of resistance.

Policy-making and tool development in public health microbiology
Our group contributes to policy making in this field on a national and international scale. Prof. Moran-Gilad has recently guest-edited a special issue for Eurosurveillance concerning advanced diagnostics for public health, which is summarised in his Editorial [30696524]. Together with Panayotis Tassios, he has guest-edited a special issue in Clinical Microbiology and Infection concerning whole genome sequencing of bacterial pathogens [29548687]. Two of the review papers in this thematic series, focusing on practical aspects of implementing WGS [29117578] and on bioinformatics tools [29309933] are highly accessed and cited. We have also contributed recently to the ongoing discussion concerning the importance of diagnostics for antimicrobial stewardship [30594652].
 The MAGICAL Group is actively participating in several initiatives for external quality assurance and proficiency testing for genomics and metagenomics. We have taken part in designing the EQA launched by the Global Microbial Identifier initiative (GMI) [25887164], and we are currently involved in promoting this topic under ESGMD. Another focus of the group is capacity building for advanced methods under the framework of ESGMD [29555344, 28669790]. Some of our recent projects involve the development of new tools that inform public health microbiology policy. This includes decision-support tools for implementation of WGS with Tzahit Simon-Tuval, exploring cyber defense implications of microbial genomics with Lior Rokach and Yossi Oren and development of new and improved metagenomics tools for simulation and analysis [28811246].

Genomics and epidemiology of foodborne and zoonotic pathogens
Over recent years we have been involved in studies focusing on a range of pathogens implicated in foodborne and zoonotic transmission. In a range of studies led by Prof. Miri Weinberger and funded by ISF we have shown the rapidly changing epidemiology of campylobacteriosis which has become the leading bacterial cause of gastroenteritis in Israel. This has involved traditional [24188185], molecular [27615719] and genomic epidemiology tools [30386311]. We are also involved in the investigation of recent regional and national outbreaks of salmonellosis and listeriosis, together with the Central Laboratories and Public Health Services of the Israeli Ministry of Health. We have investigated the recent explosive outbreak of leptospirosis in Israel [30255835] and the first reported outbreak of shiga-toxin producing Escherichia coli (STEC) in Israel [28925349]. There are further described in an editorial on the topic from Prof Moran-Gilad [28661389].
 We are very interested in Brucella melitensis which is the cause of endemic brucellosis in our region. We are currently studying this organism by looking into the genomic epidemiology of the organism in the Negev, in collaboration with the Veterinary Services at the Ministry of Agriculture (Svetlana Bardenstein), the Ministry of Health (Michael Gdalevich), University of Washington (Peter Rabinowitz) and BGU/SUMC collaborators (Nadav Davidovitch, Lior Nesher, Shalom Ben Shimol). We are also looking at the genotype-phenotype correlation and trying to link genomic signatures with clinical disease. We support the investigation of brucellosis incidents (e.g. transmission by camel milk) and seek to devise optimised typing schemes for this organism.

Research funding