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Article ; Online: A reversible mutation in a genomic hotspot saves bacterial swarms from extinction.

Hefetz, Idan / Israeli, Ofir / Bilinsky, Gal / Plaschkes, Inbar / Hazkani-Covo, Einat / Hayouka, Zvi / Lampert, Adam / Helman, Yael

iScience

2023 Volume 26, Issue 2, Page(s) 106043

Abstract: Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit ... ...

Abstract	Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit of
Language	English
Publishing date	2023-01-25
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.106043
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Article: Insights from genomic analysis of a novel

Cohen-Gihon, Inbar / Israeli, Ofir / Bilinsky, Gal / Vasker, Barak / Lazar, Shirley / Beth-Din, Adi / Zvi, Anat / Ghanem-Zoubi, Nesrin / Atiya-Nasagi, Yafit

New microbes and new infections

2024 Volume 59, Page(s) 101242

Abstract: The diagnosis of Q fever is challenging due to nonspecific symptoms and negative standard blood culture results. Serological testing through immunofluorescence assay (IFA) is the most commonly used method for diagnosing this disease. Polymerase chain ... ...

Abstract	The diagnosis of Q fever is challenging due to nonspecific symptoms and negative standard blood culture results. Serological testing through immunofluorescence assay (IFA) is the most commonly used method for diagnosing this disease. Polymerase chain reaction (PCR) tests can also be used to detect bacterial DNA if taken at an appropriate time. Once the presence of bacteria is confirmed in a sample, an enrichment step is required before characterizing it through sequencing. Cultivating
Language	English
Publishing date	2024-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2750179-6
ISSN	2052-2975
ISSN	2052-2975
DOI	10.1016/j.nmni.2024.101242
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Article ; Online: Clinical and echocardiographic trends in percutaneous balloon mitral valvuloplasty.

Koren, Ofir / Israeli, Asaf / Rozner, Ehud / Darawshy, Nassem / Turgeman, Yoav

Journal of cardiothoracic surgery

2021 Volume 16, Issue 1, Page(s) 68

Abstract: Background: The prevalence of Rheumatic Mitral Stenosis (MS) has significantly changed over the last decades. We intend to examine patient demographics, Echocardiographic characteristics, procedural success rates, and complications throughout 30-years.!# ...

Abstract	Background: The prevalence of Rheumatic Mitral Stenosis (MS) has significantly changed over the last decades. We intend to examine patient demographics, Echocardiographic characteristics, procedural success rates, and complications throughout 30-years. Methods: We conducted a single-center descriptive observational study. The study population consists of patients undergone percutaneous balloon mitral valvuloplasty (PBMV) at Emek Medical Center in Israel from January 1990 to May 2019. Results: Four hundred seventeen patients underwent PBMV during the study period and were eligible for the study. Age did not change significantly over time (p = 0.09). The prevalence of Male and patients who were smoking and had multiple comorbidities such as hypertension, dyslipidemia, ischemic heart disease, and chronic kidney disease became increases over time (p = 0.02, p = 0.02, p = 0.001, p = 0.01, p = 0.02, and p = 0.001, respectively). Wilkins score and all its components increased over time, and the total score was higher in females (p = 0.01). Seventy-nine (18.9%) patients had complications. The rate of complications did not change over decades. Patients with Wilkins score > 8, post-procedural MR of ≥2, and post-procedural MVA < 1.5 had the highest risk for the need of Mitral valve replacement (MVR) surgery in 2 years following PBMV (3.64, 4.03, 2.44, respectively, CI 95%, p < .0001 for all). The median time in these patients was 630 days compared to 4-5 years in the entire population. Patients with Post-procedural MR of ≥2 and post-procedural MVA < 1.5 had ten times risk for developing heart failure (HR 9.07 and 10.06, respectively, CI 95%, P < .0001). Conclusion: Our research reveals trends over time in patients' characteristics and echocardiographic features. Our study population consists of more male patients with multiple comorbidities and more complex and calcified valvular structures in the last decade. Wilkins score > 8, post-procedural MR of ≥2, and post-procedural MVA < 1.5 cm
MeSH term(s)	Balloon Valvuloplasty/methods ; Echocardiography/methods ; Female ; Humans ; Male ; Middle Aged ; Mitral Valve/diagnostic imaging ; Mitral Valve/surgery ; Mitral Valve Stenosis/diagnosis ; Mitral Valve Stenosis/surgery
Language	English
Publishing date	2021-04-01
Publishing country	England
Document type	Journal Article ; Observational Study
ISSN	1749-8090
ISSN (online)	1749-8090
DOI	10.1186/s13019-021-01442-w
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Article ; Online: A reversible mutation in a genomic hotspot saves bacterial swarms from extinction

Idan Hefetz / Ofir Israeli / Gal Bilinsky / Inbar Plaschkes / Einat Hazkani-Covo / Zvi Hayouka / Adam Lampert / Yael Helman

iScience, Vol 26, Iss 2, Pp 106043- (2023)

2023

Abstract: Summary: Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit of Paenibacillus glucanolyticus generated ... ...

Abstract	Summary: Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit of Paenibacillus glucanolyticus generated spontaneous non-swarming mutants with increased stress resistance. These mutants, which survived conditions that eliminated wild-type cultures, could be carried by their swarming siblings when the colony spread, consequently increasing their numbers at the spreading edge. Of interest, the hypermutable nature of the aforementioned sequence enabled the non-swarming mutants to serve as “seeds” for a new generation of wild-type cells through reversion of the mutation.Using a mathematical model, we examined the survival dynamics of P. glucanolyticus colonies under fluctuating environments. Our experimental and theoretical results suggest that the non-swarming, stress-resistant mutants can save the colony from extinction. Notably, we identified this hypermutable sequence in flagellar genes of additional Paenibacillus species, suggesting that this phenomenon could be wide-spread and ecologically important.
Keywords	Biological sciences ; Genetics ; Microbiology ; Mathematical biosciences ; Science ; Q
Subject code	612
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Antiviral activity of glucosylceramide synthase inhibitors in alphavirus infection of the central nervous system.

Avraham, Roy / Melamed, Sharon / Achdout, Hagit / Erez, Noam / Israeli, Ofir / Barlev-Gross, Moria / Pasmanik-Chor, Metsada / Paran, Nir / Israely, Tomer / Vitner, Einat B

Brain communications

2023 Volume 5, Issue 3, Page(s) fcad086

Abstract: Virus-induced CNS diseases impose a considerable human health burden worldwide. For many viral CNS infections, neither antiviral drugs nor vaccines are available. In this study, we examined whether the synthesis of glycosphingolipids, major membrane ... ...

Abstract	Virus-induced CNS diseases impose a considerable human health burden worldwide. For many viral CNS infections, neither antiviral drugs nor vaccines are available. In this study, we examined whether the synthesis of glycosphingolipids, major membrane lipid constituents, could be used to establish an antiviral therapeutic target. We found that neuroinvasive Sindbis virus altered the sphingolipid levels early after infection
Language	English
Publishing date	2023-03-25
Publishing country	England
Document type	Journal Article
ISSN	2632-1297
ISSN (online)	2632-1297
DOI	10.1093/braincomms/fcad086
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Article ; Online: Transcriptome Sequencing Data Sets of Human Lung Epithelial Cells in the Course of Francisella tularensis Infection.

Bercovich-Kinori, Adi / Israeli, Ma'ayan / Chitlaru, Theodor / Cohen-Gihon, Inbar / Israeli, Ofir / Cohen, Ofer

Microbiology resource announcements

2020 Volume 9, Issue 42

Abstract: Francisella ... ...

Abstract	Francisella tularensis
Language	English
Publishing date	2020-10-15
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00991-20
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Article: Beating the Bio-Terror Threat with Rapid Antimicrobial Susceptibility Testing.

Rotem, Shahar / Steinberger-Levy, Ida / Israeli, Ofir / Zahavy, Eran / Aloni-Grinstein, Ronit

Microorganisms

2021 Volume 9, Issue 7

Abstract: A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may ... ...

Abstract	A bioterror event using an infectious bacterium may lead to catastrophic outcomes involving morbidity and mortality as well as social and psychological stress. Moreover, a bioterror event using an antibiotic resistance engineered bacterial agent may raise additional concerns. Thus, preparedness is essential to preclude and control the dissemination of the bacterial agent as well as to appropriately and promptly treat potentially exposed individuals or patients. Rates of morbidity, death, and social anxiety can be drastically reduced if the rapid delivery of antimicrobial agents for post-exposure prophylaxis and treatment is initiated as soon as possible. Availability of rapid antibiotic susceptibility tests that may provide key recommendations to targeted antibiotic treatment is mandatory, yet, such tests are only at the development stage. In this review, we describe the recently published rapid antibiotic susceptibility tests implemented on bioterror bacterial agents and discuss their assimilation in clinical and environmental samples.
Language	English
Publishing date	2021-07-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms9071535
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Article: Postoperative New-Onset Atrial Fibrillation following Noncardiac Operations: Prevalence, Complication, and Long-Term MACE.

Koren, Ofir / Hakim, Rony / Israeli, Asaf / Rozner, Ehud / Turgeman, Yoav

Cardiology research and practice

2020 Volume 2020, Page(s) 8156786

Abstract: Background: Postoperative new-onset atrial fibrillation (POAF) is a common complication following cardiothoracic surgery, but little is known regarding its occurrence and outcome following noncardiothoracic surgery. This study was intended to examine ... ...

Abstract	Background: Postoperative new-onset atrial fibrillation (POAF) is a common complication following cardiothoracic surgery, but little is known regarding its occurrence and outcome following noncardiothoracic surgery. This study was intended to examine the incidence of POAF in noncardiothoracic surgeries performed under general anesthesia and its effects on the length of hospitalization stay, short-term and long-term morbidity, and mortality. Results: A total of 24,125 general anesthesia operations were performed at 7 surgical wards. About two-fifth of the operations (40%) were operated electively, and the rest underwent emergency surgery. The mean age was 63.78 ± 11.50, and more than half (56.9%) of the participants were female. The prevalence of POAF was 2.69 per 1000 adult patients (95% CI: 2.11-3.43) and vary significantly among wards. The highest prevalence was observed after hip fixation and laparotomy surgeries (54.9 and 26.7 per 1000 patients, respectively). The median length of hospitalization was significantly higher in POAF patients (21.0 vs. 4.8 days, Conclusion: New-onset AF following noncardiac surgery is rare, yet poses significant clinical implications, both immediate and long-term. POAF is associated with a longer length of hospitalization and a significantly higher mortality rate, both in short- and long-term.
Language	English
Publishing date	2020-10-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2506187-2
ISSN	2090-0597 ; 2090-8016
ISSN (online)	2090-0597
ISSN	2090-8016
DOI	10.1155/2020/8156786
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Article ; Online: Rapid Amplicon Nanopore Sequencing (RANS) for the Differential Diagnosis of Monkeypox Virus and Other Vesicle-Forming Pathogens.

Israeli, Ofir / Guedj-Dana, Yehoudit / Shifman, Ohad / Lazar, Shirley / Cohen-Gihon, Inbar / Amit, Sharon / Ben-Ami, Ronen / Paran, Nir / Schuster, Ofir / Weiss, Shay / Zvi, Anat / Beth-Din, Adi

Viruses

2022 Volume 14, Issue 8

Abstract: As of July 2022, more than 16,000 laboratory-confirmed monkeypox (MPX) cases have been reported worldwide. Until recently, MPX was a rare viral disease seldom detected outside Africa. MPX virus (MPXV) belongs to the Orthopoxvirus (OPV) genus and is a ... ...

Abstract	As of July 2022, more than 16,000 laboratory-confirmed monkeypox (MPX) cases have been reported worldwide. Until recently, MPX was a rare viral disease seldom detected outside Africa. MPX virus (MPXV) belongs to the Orthopoxvirus (OPV) genus and is a genetically close relative of the Variola virus (the causative agent of smallpox). Following the eradication of smallpox, there was a significant decrease in smallpox-related morbidity and the population's immunity to other OPV-related diseases such as MPX. In parallel, there was a need for differential diagnosis between the different OPVs' clinical manifestations and diseases with similar symptoms (i.e., chickenpox, herpes simplex). The current study aimed to provide a rapid genetic-based diagnostic tool for accurate and specific identification of MPXV and additional related vesicle-forming pathogens. We initially assembled a list of 14 relevant viral pathogens, causing infectious diseases associated with vesicles, prone to be misdiagnosed as MPX. Next, we developed an approach that we termed rapid amplicon nanopore sequencing (RANS). The RANS approach uses diagnostic regions that harbor high homology in their boundaries and internal diagnostic SNPs that, when sequenced, aid the discrimination of each pathogen within a group. During a multiplex PCR amplification, a dA tail and a 5'-phosphonate were simultaneously added, thus making the PCR product ligation ready for nanopore sequencing. Following rapid sequencing (a few minutes), the reads were compared to a reference database and the nearest strain was identified. We first tested our approach using samples of known viruses cultured in cell lines. All the samples were identified correctly and swiftly. Next, we examined a variety of clinical samples from the 2022 MPX outbreak. Our RANS approach identified correctly all the PCR-positive MPXV samples and mapped them to strains that were sequenced during the 2022 outbreak. For the subset of samples that were negative for MPXV by PCR, we obtained definite results, identifying other vesicle-forming viruses: Human herpesvirus 3, Human herpesvirus 2, and Molluscum contagiosum virus. This work was a proof-of-concept study, demonstrating the potential of the RANS approach for rapid and discriminatory identification of a panel of closely related pathogens. The simplicity and affordability of our approach makes it straightforward to implement in any genetics lab. Moreover, other differential diagnostics panels might benefit from the implementation of the RANS approach into their diagnostics pipelines.
MeSH term(s)	Diagnosis, Differential ; Humans ; Mpox (monkeypox)/epidemiology ; Monkeypox virus/genetics ; Nanopore Sequencing ; Orthopoxvirus ; Smallpox/diagnosis ; Variola virus/genetics
Language	English
Publishing date	2022-08-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14081817
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Article ; Online: Whole genome sequencing and taxonomic profiling of two Pantoea sp. isolated from environmental samples in Israel.

Guedj-Dana, Yehoudit / Cohen-Gihon, Inbar / Israeli, Ofir / Shifman, Ohad / Aminov, Tamar / Rotem, Shahar / Ber, Raphael / Zvi, Anat

BMC genomic data

2022 Volume 23, Issue 1, Page(s) 31

Abstract: Objective: As part of a research aiming at the isolation of bacteria secreting growth inhibiting compounds, cultures of Francisella tularensis were implanted in environmental samples and monitored for inhibition zones on agar. Two antibiotic-like ... ...

Abstract	Objective: As part of a research aiming at the isolation of bacteria secreting growth inhibiting compounds, cultures of Francisella tularensis were implanted in environmental samples and monitored for inhibition zones on agar. Two antibiotic-like secreting bacteria were isolated, their genomic sequence was deciphered and taxonomic profiling analysis classified them as belonging to the Pantoea genus. Data description: Two bacterial isolates exhibiting growth inhibition zones to F. tularensis (LVS) were analyzed using the Oxford Nanopore Technology (ONT). Preliminary de novo assembly of the reads was performed, followed by taxonomic profiling based on Multi Locus Sequence Analysis (MLSA) and implementation of the Average Nucleotide Identity (ANI) measure. The genomic sequences resulted in the identification of two different Pantoea species, denoted EnvD and EnvH. Subsequent de novo genome assembly generated 5 and 10 contigs for EnvD and EnvH, respectively. The largest contig (4,008,183 bps and 3,740,753 bps for EnvD and EnvH, respectively), overlaps to a major extent to the chromosome of closely related Pantoea species. ANI values calculated for both isolates revealed two apparently new species of the Pantoea genus. Our study deciphered the identity of two bacteria producing antibiotic-like compounds, and the genomic sequence revealed they represent distinct Pantoea species.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Israel ; Pantoea/genetics ; Phylogeny ; Sequence Analysis, DNA ; Whole Genome Sequencing
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2022-04-21
Publishing country	England
Document type	Journal Article
ISSN	2730-6844
ISSN (online)	2730-6844
DOI	10.1186/s12863-022-01049-7
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