Rayane Rafei
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View article: Shifting respiratory pathogens: Post-COVID-19 trends in community-acquired infections in underserved communities
Shifting respiratory pathogens: Post-COVID-19 trends in community-acquired infections in underserved communities Open
Respiratory tract infections, caused by various bacteria and viruses, pose a significant global health burden. In Lebanon, post-COVID-19 epidemiological data on respiratory infections remain scarce. To address this gap, this multicenter st…
View article: Knowledge, attitudes, and self-reported practices regarding cholera among six MENA countries following cholera outbreaks in the region
Knowledge, attitudes, and self-reported practices regarding cholera among six MENA countries following cholera outbreaks in the region Open
Background Cholera persists as a global public health threat, endangering the lives of vulnerable societies including the MENA region where many countries are facing recent cholera outbreaks. The present study aimed to characterize the kno…
View article: Nasopharyngeal Carriage, Antimicrobial Resistance, and Serotype Distribution of Streptococcus pneumoniae in Children Under Five in Lebanon: Baseline Data Prior to PCV13 Introduction
Nasopharyngeal Carriage, Antimicrobial Resistance, and Serotype Distribution of Streptococcus pneumoniae in Children Under Five in Lebanon: Baseline Data Prior to PCV13 Introduction Open
Background: The nasopharyngeal carriage of Streptococcus pneumoniae can be the source of transmission between humans and the starting step towards invasive pneumococcal diseases. Data on the carriage of pneumococci in children before and a…
View article: A Cross-Sectional Study Revealed a Low Prevalence of SARS-CoV-2 Infection among Asymptomatic University Students in Tripoli, North Lebanon
A Cross-Sectional Study Revealed a Low Prevalence of SARS-CoV-2 Infection among Asymptomatic University Students in Tripoli, North Lebanon Open
This study aimed to investigate the SARS-CoV-2 infection prevalence among >18-year-old students in the Faculty of Public Health and Faculty of Sciences at the Lebanese University in Tripoli, Northern Lebanon, in June 2023 and to characteri…
View article: Spotlight on the epidemiology and antimicrobial susceptibility profiles of <i>Vibrio</i> species in the MENA region, 2000–2023
Spotlight on the epidemiology and antimicrobial susceptibility profiles of <i>Vibrio</i> species in the MENA region, 2000–2023 Open
Recent cholera outbreaks in many countries in the Middle East and North Africa (MENA) region have raised public health concerns and focused attention on the genus Vibrio. However, the epidemiology of Vibrio species in humans, water, and se…
View article: Evaluation of SARS-CoV-2 anti-Spike antibody levels and breakthrough infection risk among vaccinated adults in North Lebanon
Evaluation of SARS-CoV-2 anti-Spike antibody levels and breakthrough infection risk among vaccinated adults in North Lebanon Open
Since March 2020, the COVID-19 pandemic has swiftly propagated, triggering a competitive race among medical firms to forge vaccines that thwart the infection. Lebanon initiated its vaccination campaign on February 14, 2021. Despite numerou…
View article: Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance
Genomic analysis of Shigella isolates from Lebanon reveals marked genetic diversity and antimicrobial resistance Open
In this study, we characterized 54 clinical isolates of Shigella collected in North Lebanon between 2009 and 2017 through phenotypic and genomic analyses. The most prevalent serogroup was S. sonnei, accounting for 46.3 % (25/54) of the iso…
View article: An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study
An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study Open
Background Cholera is a bacterial infection caused by the ingestion of contaminated water or food. It principally affects the gastrointestinal system and spreads easily, causing outbreaks. The first case of cholera in this outbreak was det…
View article: Emergence of<i>Acinetobacter baumannii</i>International Clone 10 predominantly found in the Middle East
Emergence of<i>Acinetobacter baumannii</i>International Clone 10 predominantly found in the Middle East Open
Acinetobacter baumannii is a globally distributed human pathogen. Infections caused by carbapenem-resistant isolates of A. baumannii (CRAB) are of great concern, as treatment options are very limited. Despite having among the highest rates…
View article: Genomic analysis of Neisseria meningitidis ST23 serogroup Y isolated from the semen
Genomic analysis of Neisseria meningitidis ST23 serogroup Y isolated from the semen Open
International audience
View article: ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies Open
Shigella is one of the commonest causes of diarrhoea worldwide and a major public health problem. Shigella serotyping is based on a standardized scheme that splits Shigella strains into four serogroups and 60 serotypes on the basis of bioc…
View article: Zoonotic Tuberculosis: A Neglected Disease in the Middle East and North Africa (MENA) Region
Zoonotic Tuberculosis: A Neglected Disease in the Middle East and North Africa (MENA) Region Open
Mycobacterium bovis is the etiologic agent of bovine tuberculosis (BTB), a serious infectious disease in both humans and animals. BTB is a zoonotic disease primarily affecting cattle and occasionally humans infected through close contact w…
View article: Initial data on Helicobacter pylori resistance in Lebanon
Initial data on Helicobacter pylori resistance in Lebanon Open
There is a lack of data regarding the prevalence of antimicrobial-resistant Helicobacter pylori isolates in Lebanon. Here, we aimed to estimate the prevalence of H. pylori infection and clarithromycin resistance in symptomatic patients wit…
View article: The <i>Acinetobacter baumannii</i> website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace
The <i>Acinetobacter baumannii</i> website (Ab-web): a multidisciplinary knowledge hub, communication platform, and workspace Open
Acinetobacter baumannii is a Gram-negative bacterium increasingly implicated in hospital-acquired infections and outbreaks. Effective prevention and control of such infections are commonly challenged by the frequent emergence of multidrug-…
View article: Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity
Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity Open
Genome sequencing facilitates the study of bacterial taxonomy and allows the re-evaluation of the taxonomic relationships between species. Here, we aimed to analyze the draft genomes of four commensal Neisseria clinical isolates from the s…
View article: The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example
The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example Open
In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in d…
View article: A global snapshot on the prevalent macrolide-resistant emm types of Group A Streptococcus worldwide, their phenotypes and their resistance marker genotypes during the last two decades: A systematic review
A global snapshot on the prevalent macrolide-resistant emm types of Group A Streptococcus worldwide, their phenotypes and their resistance marker genotypes during the last two decades: A systematic review Open
Watchful epidemiological surveillance of macrolide-resistant Group A Streptococcus (MRGAS) clones is important owing to the evolutionary and epidemiological dynamic of GAS. Meanwhile, data on the global distribution of MRGAS emm types acco…
View article: Variants of Tn <i>6924</i> , a Novel Tn <i>7</i> Family Transposon Carrying the <i>bla</i> <sub>NDM</sub> Metallo-β-Lactamase and 14 Copies of the <i>aphA6</i> Amikacin Resistance Genes Found in Acinetobacter baumannii
Variants of Tn <i>6924</i> , a Novel Tn <i>7</i> Family Transposon Carrying the <i>bla</i> <sub>NDM</sub> Metallo-β-Lactamase and 14 Copies of the <i>aphA6</i> Amikacin Resistance Genes Found in Acinetobacter baumannii Open
To date, efforts to study the resistance mechanisms of carbapenem-resistant Acinetobacter baumannii have been largely focused on the two major globally distributed clones (GC1 and GC2). ST85 is an emerging sequence type, and unlike other c…
View article: Analysis of pCl107 a large plasmid carried by an ST25<i>Acinetobacter baumannii</i>strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways
Analysis of pCl107 a large plasmid carried by an ST25<i>Acinetobacter baumannii</i>strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways Open
Acinetobacter baumannii has successfully spread during the last decades as one of the main critically important pathogens. However, many aspects including plasmids, are still under-investigated. Here, we report the complete sequence of an …
View article: Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1 Open
Acinetobacter baumannii is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global l…
View article: Teleclinical Microbiology: An Innovative Approach to Providing Web-Enabled Diagnostic Laboratory Services in Syria
Teleclinical Microbiology: An Innovative Approach to Providing Web-Enabled Diagnostic Laboratory Services in Syria Open
Objectives Telemedicine can compensate for the lack of health care specialists in response to protracted humanitarian crises. We sought to assess the usability of a teleclinical microbiology (TCM) program to provide diagnostic services in …
View article: Antimicrobial Resistance in the Protracted Syrian Conflict: Halting a War in the War
Antimicrobial Resistance in the Protracted Syrian Conflict: Halting a War in the War Open
The Syrian conflict has damaged key infrastructure and indirectly affected almost all parts of the Middle East and Europe, with no end in sight. Exhausting conditions created by the Syrian crisis and related massive displacement promote th…
View article: Population structure analysis and laboratory monitoring of <i>Shigella</i> with a standardised core-genome multilocus sequence typing scheme
Population structure analysis and laboratory monitoring of <i>Shigella</i> with a standardised core-genome multilocus sequence typing scheme Open
The laboratory surveillance of bacillary dysentery is based on a standardised Shigella typing scheme that classifies Shigella strains into four serogroups and more than 50 serotypes on the basis of biochemical tests and lipopolysaccharide …
View article: Guideline for Urine Culture and Biochemical Identification of Bacterial Urinary Pathogens in Low-Resource Settings
Guideline for Urine Culture and Biochemical Identification of Bacterial Urinary Pathogens in Low-Resource Settings Open
Medical diagnosis in low-resource settings is confronted by the lack of suitable guidelines, protocols and checklists. Online-accessible procedural documents are difficult to find, might be mistranslated or interpreted and usually do not a…