Targeted decontamination of sequencing data with CLEAN.

Many biological and medical questions are answered based on the analysis of sequence data. However, we can find contamination, artificial spike-ins, and overrepresented rRNA (ribosomal RNA) sequences in various read collections and assemblies. In particular, spike-ins used as controls, as those known from Illumina or Nanopore data, are often not considered as contaminants and also not appropriately removed during analyses.

Emergence of livestock-associated MRSA in the Egyptian Nile Delta that carry the exfoliative toxin gene etA: a case for enhanced surveillance.

Background: Staphylococcus aureus is a common opportunistic pathogen. Methicillin-resistant strains, MRSA, carry SCCmec elements that include beta-lactam resistance genes mecA/mecC. One globally common lineage, Clonal Complex (CC) 15 failed to evolve MRSA until, in 2016, CC15-MRSA were described from Saudi Arabia that carried a SCCmec V element also comprising the fusidic acid resistance gene, fusC.

Staphylococcus aureus in Rwandan dogs predominantly representing human-associated lineages.

The present study aimed at examining the nasal and ear carriage of Staphylococcus aureus of Rwandan dogs and cats. Sixty-five S. aureus isolates were detected, all originating from the nostrils of dogs.

Rapid Simultaneous Detection of the Clinically Relevant Carbapenemase Resistance Genes KPC, OXA48, VIM and NDM with the Newly Developed Ready-to-Use qPCR CarbaScan LyoBead.

Antibiotic resistance, in particular the dissemination of carbapenemase-producing organisms, poses a significant threat to global healthcare. This study introduces the qPCR CarbaScan LyoBead assay, a robust, accurate, and efficient tool for detecting key carbapenemase genes, including KPC, NDM, OXA-48, and VIM. The assay utilizes lyophilized beads, a technological advancement that enhances stability, simplifies handling, and eliminates the need for refrigeration.

Characterisation of Strains and Their Prophages That Carry Horse-Specific Leukocidin Genes .

Leukocidins of (.) are bicomponent toxins that form polymeric pores in host leukocyte membranes, leading to cell death and/or triggering apoptosis. Some of these toxin genes are located on prophages and are associated with specific hosts.

Tracking Multidrug Resistance in Gram-Negative Bacteria in Alexandria, Egypt (2020-2023): An Integrated Analysis of Patient Data and Diagnostic Tools.

Background: The rise in carbapenem-resistant (CRE) in Egypt, particularly in hospital settings, poses a significant public health challenge. This study aims to develop a combined epidemiological surveillance tool utilizing the Microreact online platform (version 269) and molecular microarray technology to track and analyze carbapenem-resistant strains in Egypt. The objective is to integrate molecular diagnostics and real-time data visualization to better understand the spread and evolution of multidrug-resistant (MDR) bacteria.

Characterizing Methicillin-Resistant spp. and Extended-Spectrum Cephalosporin-Resistant in Cattle.

In the field of cattle medicine in Austria, to date, few studies have investigated the presence of methicillin-resistant and extended-spectrum β-lactamase-producing in Austria. For this reason, milk and nasal samples were examined for the presence of methicillin-resistant as well as fecal samples for extended-spectrum cephalosporin-resistant . The nasal and fecal swabs were collected during the veterinary treatment of calf pneumonia and calf diarrhea.

Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.

Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing.

Molecular characterization, virulence and antimicrobial and biocidal susceptibility of selected bacteria isolated from the cloaca of nestling ospreys (Pandion haliaetus) from Mono Lake, California, USA.

In the present study, the presence of the Enterobacterales, Staphylococcus spp., Mammaliicoccus spp., and Enterococcus spp.

Sequencing a CC239-MRSA-III with a novel composite SCC mec element from Kuwait.

Staphylococcus aureus CC239-MRSA-III is an ancient pandemic strain of hospital-associated, methicillin-resistant S. aureus that spread globally for decades and that still can be found in some parts of the world. In Kuwait, microarray-based surveillance identified from 2019 to 2022 a series of isolates of a hitherto unknown variant of this strain that carried a second set of recombinase genes, ccrA/B-2.

A Proof-of-Concept Protein Microarray-Based Approach for Serotyping of Strains.

, a bacterium causing foodborne illnesses like salmonellosis, is prevalent in Europe and globally. It is found in food, water, and soil, leading to symptoms like diarrhea and fever. Annually, it results in about 95 million cases worldwide, with increasing antibiotic resistance posing a public health challenge.

Characterisation of PVL-Positive from the United Arab Emirates.

is a recently described staphylococcal species that is related to but lacks the staphyloxanthin operon. It is able to acquire both resistance markers such as the SCC elements and mobile genetic elements carrying virulence-associated genes from . This includes those encoding the Panton-Valentine leukocidin (PVL), which is associated mainly with severe and/or recurrent staphylococcal skin and soft tissue infections.

From Shadows to Spotlight: Enhancing Bacterial DNA Detection in Blood Samples through Cutting-Edge Molecular Pre-Amplification.

One of the greatest challenges to the use of molecular methods for diagnostic purposes is the detection of target DNA that is present only in low concentrations. One major factor that negatively impacts accuracy, diagnostic sensitivity, and specificity is the sample matrix, which hinders the attainment of the required detection limit due to the presence of residual background DNA. To address this issue, various methods have been developed to enhance sensitivity through targeted pre-amplification of marker sequences.

Molecular Characterization of Chimeric Strains from Waterfowl.

is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene ; some also showed a different capsule type and a deviant type.

Diversity of Staphylococcus aureus isolated from nares of ruminants.

Aims: To examine the diversity of Staphylococcus aureus isolated from nasal swabs of ruminants in Rwanda.

Methods And Results: A total of 454 nasal swabs from 203 cows, 170 goats, and 81 sheep were examined for the presence of S. aureus, and 30 S.

Clonal Complexes Distribution of Isolates from Clinical Samples from the Caribbean Islands.

The aim of this study was to comprehensively characterise from the Caribbean Islands of Trinidad and Tobago, and Jamaica. A total of 101 / isolates were collected in 2020, mainly from patients with skin and soft tissue infections. They were characterised by DNA microarray allowing the detection of ca.

Characterisation of a Isolate Carrying Phage-Borne Enterotoxin E from a European Badger ().

() colonizes up to 30% of all humans and can occasionally cause serious infections. It is not restricted to humans as it can also often be found in livestock and wildlife. Recent studies have shown that wildlife strains of usually belong to other clonal complexes than human strains and that they might differ significantly with regard to the prevalence of genes encoding antimicrobial resistance properties and virulence factors.

Characterisation of Methicillin-Resistant from Alexandria, Egypt.

The present study aims to characterise clinical MRSA isolates from a tertiary care centre in Egypt's second-largest city, Alexandria. Thirty isolates collected in 2020 were genotypically characterised by microarray to detect their resistance and virulence genes and assign them to clonal complexes (CC) and strains. Isolates belonged to 11 different CCs and 14 different strains.

Sequence Analysis of Novel Lineages from Wild and Captive Macaques.

is a widespread and common opportunistic bacterium that can colonise or infect humans as well as a wide range of animals. There are a few studies of both methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) isolated from monkeys, apes, and lemurs, indicating a presence of a number of poorly or unknown lineages of the pathogen. In order to obtain insight into staphylococcal diversity, we sequenced strains from wild and captive individuals of three macaque species (, , and ) using Nanopore and Illumina technologies.

Occurrence and Characteristics of ESBL- and Carbapenemase- Producing from Wild and Feral Birds in Greece.

Wild and feral birds are known to be involved in the maintenance and dissemination of clinically-important antimicrobial-resistant pathogens, such as extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae. The aim of our study was to evaluate the presence of ESBL- and carbapenemase-producing among wild and feral birds from Greece and to describe their antimicrobial resistance characteristics. In this context, fecal samples of 362 birds were collected and cultured.

Cross-Sectional Survey of Antibiotic Resistance in Extended Spectrum β-Lactamase-Producing Isolated from Pigs in Greece.

This study aimed to estimate the prevalence of extended-spectrum β-lactamase-producing (ESBL) bacteria in swine. Thus, 214 fecal samples were collected from suckling and weaned piglets from 34 farms in Greece (out of an overall population of about 14,300 sows). A subset of 78 (36.

Description of Staphylococcal Strains from Straw-Coloured Fruit Bat () and Diamond Firetail () and a Review of their Phylogenetic Relationships to Other Staphylococci.

The phylogenetic tree of the complex consists of several distinct clades and the majority of human and veterinary isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named , due to the lack of the "golden" pigment staphyloxanthin.