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Article: Rapid Phenotypic Antibiotic Susceptibility Profiling of Clinical

Hefetz, Idan / Bardenstein, Rita / Rotem, Shahar / Zaide, Galia / Bilinsky, Gal / Shifman, Ohad / Zimhony, Oren / Aloni-Grinstein, Ronit

Antibiotics (Basel, Switzerland)

2024 Volume 13, Issue 3

Abstract: Bloodstream infections (BSI) are defined by the presence of viable bacteria or fungi, accompanied by systemic signs of infection. Choosing empirical therapy based solely on patient risk factors and prior antibiotic susceptibility test (AST) may lead to ... ...

Abstract	Bloodstream infections (BSI) are defined by the presence of viable bacteria or fungi, accompanied by systemic signs of infection. Choosing empirical therapy based solely on patient risk factors and prior antibiotic susceptibility test (AST) may lead to either ineffective treatment or unnecessarily broad-spectrum antibiotic exposure. In general, Clinical & Laboratory Standards Institute guideline-approved ASTs have a turnaround time of 48-72 h from sample to answer, a period that may result in a critical delay in the appropriate selection of therapy. Therefore, reducing the time required for AST is highly advantageous. We have previously shown that our novel rapid AST method, MAPt (Micro-Agar-PCR-test), accurately identifies susceptibility profiles for spiked bioterrorism agents like
Language	English
Publishing date	2024-02-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2681345-2
ISSN	2079-6382
ISSN	2079-6382
DOI	10.3390/antibiotics13030231
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Global transcriptomic analysis of Francisella tularensis SchuS4 differentially expressed genes in response to doxycycline or ciprofloxacin exposure.

Zaide, Galia / Cohen-Gihon, Inbar / Shifman, Ohad / Israeli, Ofir / Aftalion, Moshe / Maoz, Sharon / Chitlaru, Theodor / Ber, Raphael / Zvi, Anat / Steinberger-Levy, Ida

BMC genomic data

2023 Volume 24, Issue 1, Page(s) 23

Abstract: Objective: As part of a research aiming at presenting an alternative approach for rapid determination of antimicrobial susceptibility by quantification of changes in expression levels of specific marker genes and gene sets, cultures of the virulent ... ...

Abstract	Objective: As part of a research aiming at presenting an alternative approach for rapid determination of antimicrobial susceptibility by quantification of changes in expression levels of specific marker genes and gene sets, cultures of the virulent bacterial strain Francisella tularensis SchuS4 were grown in the presence of inhibitory/sub-inhibitory concentrations of either ciprofloxacin or doxycycline and their transcriptomic profiles were elucidated using differential expression analysis followed by functional annotation. Data description: RNA sequencing was performed to identify differentially expressed genes (DEGs) in response to exposure of F. tularensis SchuS4 to either ciprofloxacin or doxycycline, the antibiotics of choice for Tularemia therapy. Accordingly, RNA samples were collected 2 h post antibiotic exposure and subjected to RNA sequence analysis. Transcriptomic quantification of RNA representing duplicated samples generated highly similar gene expression data. Exposure to sub-inhibitory concentration [0.5 x MIC (minimal inhibitory concentration)] of doxycycline or ciprofloxacin modulated the expression of 237 or 8 genes, respectively, while exposure to an inhibitory concentration (1 x MIC) resulted in the modulation of 583 or 234 genes, respectively. Amongst the genes modulated upon doxycycline exposure upregulation of 31 genes encoding for translation-functions could be distinguished, as well as downregulation of 14 genes encoding for functions involved in DNA transcription and repair. Ciprofloxacin exposure impacted differently the RNA sequence profile of the pathogen, resulting in upregulation of 27 genes encoding mainly DNA replication and repair functions, transmembrane transporters and molecular chaperons. In addition, 15 downregulated genes were involved in translation processes.
MeSH term(s)	Doxycycline/pharmacology ; Francisella tularensis/genetics ; Ciprofloxacin/pharmacology ; Transcriptome/genetics ; Anti-Bacterial Agents/pharmacology ; RNA
Chemical Substances	Doxycycline (N12000U13O) ; Ciprofloxacin (5E8K9I0O4U) ; Anti-Bacterial Agents ; RNA (63231-63-0)
Language	English
Publishing date	2023-04-19
Publishing country	England
Document type	Journal Article
ISSN	2730-6844
ISSN (online)	2730-6844
DOI	10.1186/s12863-023-01125-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates.

Zaide, Galia / Cohen-Gihon, Inbar / Israeli, Ofir / Stein, Dana / Shifman, Ohad / Weiss, Shay / Simon, Irit / Laskar, Orly / Beth-Din, Adi / Zvi, Anat

Microbiology resource announcements

2021 Volume 10, Issue 1

Abstract: We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic ... ...

Abstract	We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.01387-20
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of

Zaide, Galia / Elia, Uri / Cohen-Gihon, Inbar / Israeli, Ma'ayan / Rotem, Shahar / Israeli, Ofir / Ehrlich, Sharon / Cohen, Hila / Lazar, Shirley / Beth-Din, Adi / Shafferman, Avigdor / Zvi, Anat / Cohen, Ofer / Chitlaru, Theodor

Microorganisms

2020 Volume 8, Issue 12

Abstract: We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant ... ...

Abstract	We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of
Language	English
Publishing date	2020-11-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms8121896
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Article ; Online: Transcriptome Sequencing Data of Bacillus anthracis Vollum Δ

Chitlaru, Theodor / Cohen-Gihon, Inbar / Israeli, Ofir / Elia, Uri / Zaide, Galia / Israeli, Ma'ayan / Beth-Din, Adi / Lazar, Shirley / Ehrlich, Sharon / Zvi, Anat / Cohen, Ofer

Microbiology resource announcements

2020 Volume 9, Issue 35

Abstract: The high-temperature requirement chaperone/protease (HtrA) is involved in the stress response of the anthrax-causing ... ...

Abstract	The high-temperature requirement chaperone/protease (HtrA) is involved in the stress response of the anthrax-causing pathogen
Language	English
Publishing date	2020-08-27
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00618-20
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Article ; Online: Spotted Fever Group Rickettsioses in Israel, 2010-2019.

Cohen, Regev / Finn, Talya / Babushkin, Frida / Paran, Yael / Ben Ami, Ronen / Atamna, Alaa / Reisfeld, Sharon / Weber, Gabriel / Petersiel, Neta / Zayyad, Hiba / Leshem, Eyal / Weinberger, Miriam / Maor, Yasmin / Makhoul, Nicola / Nesher, Lior / Zaide, Galia / Klein, Dar / Beth-Din, Adi / Atiya-Nasagi, Yafit

Emerging infectious diseases

2022 Volume 27, Issue 8, Page(s) 2117–2126

Abstract: In a multicenter, nationwide, retrospective study of patients hospitalized with spotted fever group rickettsiosis in Israel during 2010-2019, we identified 42 cases, of which 36 were autochthonous. The most prevalent species was the Rickettsia conorii ... ...

Abstract	In a multicenter, nationwide, retrospective study of patients hospitalized with spotted fever group rickettsiosis in Israel during 2010-2019, we identified 42 cases, of which 36 were autochthonous. The most prevalent species was the Rickettsia conorii Israeli tick typhus strain (n = 33, 79%); infection with this species necessitated intensive care for 52% of patients and was associated with a 30% fatality rate. A history of tick bite was rare, found for only 5% of patients; eschar was found in 12%; and leukocytosis was more common than leukopenia. Most (72%) patients resided along the Mediterranean shoreline. For 3 patients, a new Rickettsia variant was identified and had been acquired in eastern, mountainous parts of Israel. One patient had prolonged fever before admission and clinical signs resembling tickborne lymphadenopathy. Our findings suggest that a broad range of Rickettsia species cause spotted fever group rickettsiosis in Israel.
MeSH term(s)	Humans ; Israel/epidemiology ; Retrospective Studies ; Rickettsia/genetics ; Rickettsia conorii ; Spotted Fever Group Rickettsiosis/diagnosis ; Spotted Fever Group Rickettsiosis/epidemiology
Language	English
Publishing date	2022-01-26
Publishing country	United States
Document type	Journal Article ; Multicenter Study
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2708.203661
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Article: Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracishtrA-Disrupted and Parental Wild Type Strains

Zaide, Galia / Elia, Uri / Cohen-Gihon, Inbar / Israeli, Ma’ayan / Rotem, Shahar / Israeli, Ofir / Ehrlich, Sharon / Cohen, Hila / Lazar, Shirley / Beth-Din, Adi / Shafferman, Avigdor / Zvi, Anat / Cohen, Ofer / Chitlaru, Theodor

Microorganisms. 2020 Nov. 30, v. 8, no. 12

2020

Abstract	We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis. Virulence attenuation of htrA-disrupted Bacillus anthracis strains was attributed to susceptibility of ΔhtrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracis htrA-disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the ΔhtrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the ΔhtrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the ΔhtrA strain resulted in partial alleviation of the H₂O₂-sensitive phenotype.
Keywords	Bacillus anthracis ; bacteria ; databases ; genes ; nucleosides ; oxidative stress ; phenotype ; protein synthesis ; proteinases ; quality control ; sequence analysis ; strains ; stress response ; temperature ; transcription factors ; transcriptomics ; virulence
Language	English
Dates of publication	2020-1130
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-light
ZDB-ID	2720891-6
ISSN	2076-2607
ISSN	2076-2607
DOI	10.3390/microorganisms8121896
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Spotted Fever Group Rickettsioses in Israel, 2010–2019

Regev Cohen / Talya Finn / Frida Babushkin / Yael Paran / Ronen Ben Ami / Alaa Atamna / Sharon Reisfeld / Gabriel Weber / Neta Petersiel / Hiba Zayyad / Eyal Leshem / Miriam Weinberger / Yasmin Maor / Nicola Makhoul / Lior Nesher / Galia Zaide / Dar Klein / Adi Beth-Din / Yafit Atiya-Nasagi

Emerging Infectious Diseases, Vol 27, Iss 8, Pp 2117-

2021 Volume 2126

Abstract: In a multicenter, nationwide, retrospective study of patients hospitalized with spotted fever group rickettsiosis in Israel during 2010–2019, we identified 42 cases, of which 36 were autochthonous. The most prevalent species was the Rickettsia conorii ... ...

Abstract	In a multicenter, nationwide, retrospective study of patients hospitalized with spotted fever group rickettsiosis in Israel during 2010–2019, we identified 42 cases, of which 36 were autochthonous. The most prevalent species was the Rickettsia conorii Israeli tick typhus strain (n = 33, 79%); infection with this species necessitated intensive care for 52% of patients and was associated with a 30% fatality rate. A history of tick bite was rare, found for only 5% of patients; eschar was found in 12%; and leukocytosis was more common than leukopenia. Most (72%) patients resided along the Mediterranean shoreline. For 3 patients, a new Rickettsia variant was identified and had been acquired in eastern, mountainous parts of Israel. One patient had prolonged fever before admission and clinical signs resembling tickborne lymphadenopathy. Our findings suggest that a broad range of Rickettsia species cause spotted fever group rickettsiosis in Israel.
Keywords	R. conorii Israeli tick typhus strain ; Rickettsia conorii israelensis ; R. conorii Malish strain ; Rickettsia conorii conorii ; Rickettsia africae ; spotted fever group rickettsiosis ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Subject code	610
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA -Disrupted and Parental Wild Type Strains

Galia Zaide / Uri Elia / Inbar Cohen-Gihon / Ma’ayan Israeli / Shahar Rotem / Ofir Israeli / Sharon Ehrlich / Hila Cohen / Shirley Lazar / Adi Beth-Din / Avigdor Shafferman / Anat Zvi / Ofer Cohen / Theodor Chitlaru

Microorganisms, Vol 8, Iss 1896, p

2020 Volume 1896

Abstract	We previously demonstrated that the HtrA (High Temperature Requirement A) protease/chaperone active in the quality control of protein synthesis, represents an important virulence determinant of Bacillus anthracis . Virulence attenuation of htrA -disrupted Bacillus anthracis strains was attributed to susceptibility of Δ htrA strains to stress insults, as evidenced by affected growth under various stress conditions. Here, we report a comparative RNA-seq transcriptomic study generating a database of differentially expressed genes in the B. anthracis htrA -disrupted and wild type parental strains under oxidative stress. The study demonstrates that, apart from protease and chaperone activities, HtrA exerts a regulatory role influencing expression of more than 1000 genes under stress. Functional analysis of groups or individual genes exhibiting strain-specific modulation, evidenced (i) massive downregulation in the Δ htrA and upregulation in the WT strains of various transcriptional regulators, (ii) downregulation of translation processes in the WT strain, and (iii) downregulation of metal ion binding functions and upregulation of sporulation-associated functions in the Δ htrA strain. These modulated functions are extensively discussed. Fifteen genes uniquely upregulated in the wild type strain were further interrogated for their modulation in response to other stress regimens. Overexpression of one of these genes, encoding for MazG (a nucleoside triphosphate pyrophosphohydrolase involved in various stress responses in other bacteria), in the Δ htrA strain resulted in partial alleviation of the H 2 O 2 -sensitive phenotype.
Keywords	Bacillus anthracis ; anthrax ; oxidative stress ; HtrA ; transcriptomics ; RNA-seq ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2020-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Differential Response Following Infection of Mouse CNS with Virulent and Attenuated Vaccinia Virus Strains.

Israely, Tomer / Paran, Nir / Erez, Noam / Cherry, Lilach / Tamir, Hadas / Achdout, Hagit / Politi, Boaz / Israeli, Ofir / Zaide, Galia / Cohen-Gihon, Inbar / Vitner, Einat B / Lustig, Shlomo / Melamed, Sharon

Vaccines

2019 Volume 7, Issue 1

Abstract: Viral infections of the central nervous system (CNS) lead to a broad range of pathologies. CNS infections with Orthopox viruses have been mainly documented as an adverse reaction to smallpox vaccination with vaccinia virus. To date, there is insufficient ...

Abstract	Viral infections of the central nervous system (CNS) lead to a broad range of pathologies. CNS infections with Orthopox viruses have been mainly documented as an adverse reaction to smallpox vaccination with vaccinia virus. To date, there is insufficient data regarding the mechanisms underlying pathological viral replication or viral clearance. Therefore, informed risk assessment of vaccine adverse reactions or outcome prediction is limited. This work applied a model of viral infection of the CNS, comparing neurovirulent with attenuated strains. We followed various parameters along the disease and correlated viral load, morbidity, and mortality with tissue integrity, innate and adaptive immune response and functionality of the blood⁻brain barrier. Combining these data with whole brain RNA-seq analysis performed at different time points indicated that neurovirulence is associated with host immune silencing followed by induction of tissue damage-specific pathways. In contrast, brain infection with attenuated strains resulted in rapid and robust induction of innate and adaptive protective immunity, followed by viral clearance and recovery. This study significantly improves our understanding of the mechanisms and processes determining the consequence of viral CNS infection and highlights potential biomarkers associated with such outcomes.
Language	English
Publishing date	2019-02-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2703319-3
ISSN	2076-393X
ISSN	2076-393X
DOI	10.3390/vaccines7010019
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