selection of carbapenem resistance during persistent sequence type 395 bloodstream infection due to OmpK36 deletion.

Non-carbapenemase-producing carbapenem-resistant (non-CP CRE) may be associated with a grave outcome. The common underlying mechanism is beta-lactamases and mutations in outer membrane porins. We report a case of a deep-seated infection caused by ST395 not amenable to source control, involving recurrent bloodstream infection, resulting in selection of carbapenem resistance under therapy.

Invasive infections caused by the recently described species Enterococcus innesii.

E. innesii is a recently described Enterococcus species which may be difficult to differentiate from the more common E. casseliflavus.

In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing bloodstream isolates from Italian hospital patients.

Bloodstream infection (BSI) caused by carbapenem-resistant (KP) poses significant challenges, particularly when the infecting isolate carries multiple antimicrobial resistance (AMR) genes/determinants. This study, employing short- and long-read whole-genome sequencing, characterizes six New Delhi metallo-β-lactamase (NDM) 1 and KP carbapenemase (KPC) 3 co-producing KP isolates, the largest cohort investigated in Europe to date. Five [sequence type (ST) 512] and one (ST11) isolates were recovered from patients who developed BSI from February to August 2022 or February 2023 at two different hospitals in Rome, Italy.

Helicobacter cinaedi Bacteremia in Children: A Case Report and Literature Review.

Helicobacter cinaedi is known to cause invasive infections in immunocompromised adults. Here we report the first case of H. cinaedi bacteremia in a child with nephrotic syndrome.

Vulnerability of pangolin SARS-CoV-2 lineage assignment to adversarial attack.

Pangolin is the most popular tool for SARS-CoV-2 lineage assignment. During COVID-19, healthcare professionals and policymakers required accurate and timely lineage assignment of SARS-CoV-2 genomes for pandemic response. Therefore, tools such as Pangolin use a machine learning model, pangoLEARN, for fast and accurate lineage assignment.

Temporal Changes in the Skin Microbiome of Epidermolysis Bullosa Patients following the Application of Wound Dressings.

Objective: Epidermolysis bullosa (EB) is a group of rare hereditary skin disorders characterized by the formation of painful blisters, erosions, and ulcers. In addition, the wounds can easily become infected with different pathogens. Therefore, the dynamics in the microbial populations across the various stages of EB can shed light on pathophysiology, the effect of treatment, and the factors involved in its recovery, but they are understudied.

Challenging diagnosis of infection: A case report and literature review.

We present the case of an immunocompromised child with infection. Our case highlights the difficulty in adequate speciation. Most isolates described in the literature were identified using 16 s- PCR, which if performed on our sample would at best be inconclusive.

Fecal microbiota of the synanthropic golden jackal (Canis aureus).

The golden jackal (Canis aureus), is a medium canid carnivore widespread throughout the Mediterranean region and expanding into Europe. This species thrives near human settlements and is implicated in zoonoses such as rabies. This study explores for the first time, the golden jackal fecal microbiota.

Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022.

BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee.

TRAF3 suppression encourages B cell recruitment and prolongs survival of microbiome-intact mice with ovarian cancer.

Background: Ovarian cancer (OC) is known for exhibiting low response rates to immune checkpoint inhibitors that activate T cells. However, immunotherapies that activate B cells have not yet been extensively explored and may be a potential target, as B cells that secrete immunoglobulins have been associated with better outcomes in OC. Although the secretion of immunoglobulins is often mediated by the microbiome, it is still unclear what role they play in limiting the progression of OC.

Public and animal health risks associated with spillover of into dairy farms.

Brucellosis is a worldwide zoonosis with important public health, animal health and economic implications. , commonly associated with small ruminants, is an emerging bovine pathogen in dairy farms. We analysed all outbreaks affecting dairy farms in Israel since 2006, combining traditional and genomic epidemiology to explore the public health implications of this One Health challenge.

LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

Background: The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community.

Findings: To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities.

Prevalence and Characteristics of Carriage of Among Young Israeli Adults.

Background: No updated data currently exist regarding carriage and genomic epidemiology among young Israeli adults.

Methods: Oropharyngeal swabs were collected from 1801 military recruits on the day of recruitment during 2019. was detected and identified by culture and quantitative polymerase chain reaction (qPCR).

Phenotypic correlates of the working dog microbiome.

Dogs have a key role in law enforcement and military work, and research with the goal of improving working dog performance is ongoing. While there have been intriguing studies from lab animal models showing a potential connection between the gut microbiome and behavior or mental health there is a dearth of studies investigating the microbiome-behavior relationship in working dogs. The overall objective of this study was to characterize the microbiota of working dogs and to determine if the composition of the microbiota is associated with behavioral and performance outcomes.

Fecal Microbiome Features Associated with Extended-Spectrum β-Lactamase-Producing Enterobacterales Carriage in Dairy Heifers.

Extended-spectrum β-lactamases (ESBLs) are a growing public health threat, and one key human exposure point is through livestock and the food supply. Understanding microbiome factors associated with fecal ESBL carriage can help detect and ideally assist with controlling and preventing ESBL dissemination among livestock. The objective of this study was to investigate the diversity and composition of the heifer fecal microbiota in ESBL-producing Enterobacterales (ESBL-PE) carriers and noncarriers.

Prevalence of Antibiotic Tolerance and Risk for Reinfection Among Escherichia coli Bloodstream Isolates: A Prospective Cohort Study.

Background: Tolerance is the ability of bacteria to survive transient exposure to high concentrations of a bactericidal antibiotic without a change in the minimal inhibitory concentration, thereby limiting the efficacy of antimicrobials. The study sought to determine the prevalence of tolerance in a prospective cohort of E. coli bloodstream infection and to explore the association of tolerance with reinfection risk.

Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Isolates.

is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of . Eighteen isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads.

Genomic Epidemiology of Clinical Isolates from Southern Israel.

Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products, is endemic in Southern Israel, mainly among the Bedouin Arab population. However, the genomic epidemiology of in this region has not yet been elucidated. A cohort of brucellosis cases ( = 118) diagnosed between 2017-2019 was studied using whole-genome sequencing (WGS).

The Effects of One Anastomosis Gastric Bypass Surgery on the Gastrointestinal Tract.

One anastomosis gastric bypass (OAGB) is an emerging bariatric procedure, yet data on its effect on the gastrointestinal tract are lacking. This study sought to evaluate the incidence of small-intestinal bacterial overgrowth (SIBO) following OAGB; explore its effect on nutritional, gastrointestinal, and weight outcomes; and assess post-OABG occurrence of pancreatic exocrine insufficiency (PEI) and altered gut microbiota composition. A prospective pilot cohort study of patients who underwent primary-OAGB surgery is here reported.

Brucellosis Outbreak Traced to Commercially Sold Camel Milk through Whole-Genome Sequencing, Israel.

Brucellosis, a neglected zoonotic disease acquired from contaminated food products, remains a public health concern worldwide. We describe an outbreak in which commercially sold camel milk containing Brucella melitensis was distributed across Israel. Whole-genome sequencing linked patients infected with B.

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.

Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance.

Unraveling antimicrobial resistance in Helicobacter pylori: Global resistome meets global phylogeny.

Background: Antimicrobial resistance (AMR) in Helicobacter pylori is increasing globally and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to conduct an analysis of the H. pylori resistome and phylogeny.

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in .

Antimicrobial resistance (AMR) in is increasing and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to comprehensively analyze the resistome and phylogeny in order to characterize Israeli . Israeli isolates ( = 48) underwent antimicrobial susceptibility testing (AST) against five antimicrobials and WGS analysis.

The Clinical and Molecular Epidemiology of Noncarbapenemase-Producing Carbapenem-Resistant : A Case-Case-Control Matched Analysis.

Background: Risk factors and outcomes associated with carbapenem-resistant (CRE) acquisitions are derived primarily from cohorts consisting of carbapenemase-producing (CP) strains. Worldwide epidemiology of non-CP-CRE is evolving, but controlled epidemiological analyses are lacking.

Methods: A matched case-case-control investigation was conducted at Shamir (Assaf Harofeh) Medical Center, Israel, on November 2014-December 2016.

minMLST: machine learning for optimization of bacterial strain typing.

Motivation: High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is based on the core genome, cgMLST, has the advantage of a high level of typeability and maximal discriminatory power. Yet, the transition from a seven loci-based scheme to cgMLST involves several challenges, that include the need by some users to maintain backward compatibility, growing difficulties in the day-to-day communication within the microbiology community with respect to nomenclature and ontology, issues with typeability, especially if a more stringent approach to loci presence is used, and computational requirements concerning laboratory data management and sharing with end-users.