Evaluation of DNA extraction kits for long-read shotgun metagenomics using Oxford Nanopore sequencing for rapid taxonomic and antimicrobial resistance detection.

During a bacterial infection or colonization, the detection of antimicrobial resistance (AMR) is critical, but slow due to culture-based approaches for clinical and screening samples. Culture-based phenotypic AMR detection and confirmation require up to 72 hours (h) or even weeks for slow-growing bacteria. Direct shotgun metagenomics by long-read sequencing using Oxford Nanopore Technologies (ONT) may reduce the time for bacterial species and AMR gene identification.

Oxford Nanopore Technology-Based Identification of an Endosymbiosis in Microbial Keratitis.

(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease.

Risk Assessment and Recommended Approaches to Optimize Infection Control and Antibiotic Stewardship to Reduce External Ventricular Drain Infection: A Single-Center Study.

An external ventricular drain (EVD) is used to release elevated intracranial pressure by draining cerebrospinal fluid (CSF) from the brain's ventricles. The establishment of an EVD is one of the most commonly performed neurosurgical procedures to treat intracranial pressure in patients. Nevertheless, infections are very frequent complications.

Gram-negative bloodstream infections in six German university hospitals, 2016-2020: clinical and microbiological features.

Purpose: To analyze the longitudinal epidemiology and antimicrobial resistance (AMR) patterns of Gram-negative bloodstream infections (BSI) in Germany.

Methods: Post-hoc analysis of prospectively documented BSI due to Escherichia coli, Klebsiella spp., Enterobacter spp.

Switching Residues: A Platform for the Synthesis of Fidaxomicin Antibiotics.

Peripheral modification is often the main approach to optimize natural products for improved biological activity or desired physicochemical properties. This procedure inevitably increases molecular weight, often accompanied by undesired increased lipophilicity. Removing structural elements from natural products is not always tolerated.

An inhibitory segment within G-patch activators tunes Prp43-ATPase activity during ribosome assembly.

Mechanisms by which G-patch activators tune the processive multi-tasking ATP-dependent RNA helicase Prp43 (DHX15 in humans) to productively remodel diverse RNA:protein complexes remain elusive. Here, a comparative study between a herein and previously characterized activators, Tma23 and Pxr1, respectively, defines segments that organize Prp43 function during ribosome assembly. In addition to the activating G-patch, we discover an inhibitory segment within Tma23 and Pxr1, I-patch, that restrains Prp43 ATPase activity.

Zoonotic and other veterinary chlamydiae - an update, the role of the plasmid and plasmid-mediated transformation.

The obligate intracellular bacterial genus Chlamydia harbours species with zoonotic potential, particularly C. psittaci, causative agent of psittacosis, and C. abortus, which may lead to miscarriage in pregnant women.

LDC000067, a CDK9 inhibitor, unveils promising results in suppressing influenza virus infections and .

Influenza virus infections continue to pose a significant threat to public health. Current anti-influenza drugs target viral proteins; however, the emergence of resistant strains has hampered their effectiveness. Fortunately, as with most viruses, influenza virus depends on various host factors during its replication cycle and in pathogenicity.

In vitro activity of ceftazidime-avibactam/aztreonam combination against MBL-producing Pseudomonas aeruginosa strains.

Purpose: The emergence of multidrug-resistant P. aeruginosa isolates poses a challenge to healthcare systems worldwide. Rising numbers in deaths, duration of hospitalization as well as failing treatments prove the hazards posed by these pathogens.

Rare and risky: a unique case of concurrent chronic pulmonary aspergillosis and lemierre syndrome.

Lemierre Syndrome is a condition that appears to have been overlooked in recent decades in clinical practice, often resulting in death or long-lasting sequelae when left undetected and untreated. Typically, it occurs following an upper respiratory tract infection, often stemming from tonsillitis, leading to thrombosis of the internal jugular vein and subsequent multiple septic emboli. Here, we present a case a 46-year-old patient with the clinical presentation of pneumogenic sepsis.

Enhancing ascitic fungal infection diagnosis through next-generation sequencing: a pilot study in surgical ICU patients.

Objectives: Ascites, often associated with critical pathologies such as liver cirrhosis or bowel perforation, can be complicated by fungal infection, increasing mortality especially in intensive care settings and demanding rapid diagnosis and adequate treatment. Traditional microbiological diagnostic methods have limited sensitivity in accurately identifying fungal pathogens in ascitic fluid. Alternative diagnostic methods may offer important insights to enable guiding of antifungal therapy and refining empirical treatment strategies.

Integer programming framework for pangenome-based genome inference.

Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance.

Risk of bacterial colonization by torniquet during arthroscopy of the knee joint.

Purpose: The following study investigated the risk of transmission or spread of potentially pathogenic bacteria via surgical gloves and/or with an elastic bandage to achieve a bloodless surgical site during arthroscopy.

Methods: This was a single-center, prospective study performed at a level-1 trauma center. The included patients were between 18 and 65 years of age and underwent arthroscopy of the knee joint.

No detrimental effect on the hand microbiome of health care staff by frequent alcohol-based antisepsis.

Background: The importance of ethanol-based hand rubs (EBHRs) to prevent health care-associated infections is undisputed. However, there is a lack of meaningful data regarding the influence of EBHRs on skin microbiome.

Methods: Four nurses in a neonatal intensive care unit were included.

The first survey of endoparasite infection in the brown rat (Rattus norvegicus) from a synanthropic environment in Hungary.

Urban rats are significant reservoirs of zoonotic endoparasites, posing serious health risks to humans. This study aimed to detect common endoparasites in wild brown rats (Rattus norvegicus) in Budapest, addressing the current lack of endoparasite surveys in Hungary. Carcasses of 131 rats collected following extermination were examined.

Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections.

Objectives: The use of mouse models of complicated urinary tract infection (cUTI) has usually been limited to a single timepoint assessment of bacterial burden. Based on longitudinal in vitro and in vivo data, we developed a pharmacokinetic-pharmacodynamic (PKPD) model to assess the efficacy of apramycin, a broad-spectrum aminoglycoside antibiotic, in mouse models of cUTI.

Methods: Two Escherichia coli strains were studied (EN591 and ATCC 700336).

The T4bSS of Legionella features a two-step secretion pathway with an inner membrane intermediate for secretion of transmembrane effectors.

To promote intracellular survival and infection, Legionella spp. translocate hundreds of effector proteins into eukaryotic host cells using a type IV b protein secretion system (T4bSS). T4bSS are well known to translocate soluble as well as transmembrane domain-containing effector proteins (TMD-effectors) but the mechanisms of secretion are still poorly understood.

Antimicrobial susceptibility testing of .

Unlabelled: a short gram-positive rod, is a part of the human skin flora, but can also cause infections (e.g., skin and soft tissue infections, bone and joint infections, abscesses, peritoneal dialysis-associated peritonitis, and bacteremia).

Age-related STING suppression in macrophages contributes to increased viral load during influenza a virus infection.

Ageing is a major risk factor that contributes to increased mortality and morbidity rates during influenza A virus (IAV) infections. Macrophages are crucial players in the defense against viral infections and display impaired function during ageing. However, the impact of ageing on macrophage function in response to an IAV infection remains unclear and offers potential insight for underlying mechanisms.

Differential contributions of the gut microbiota and metabolome to pathomechanisms in ulcerative colitis: an analysis.

The gut microbiota has been implicated in onset and progression of ulcerative colitis (UC). Here, we assess potential causal involvement of the microbiota and -associated fecal water (FW) metabolome in altering key functional parameters of the colonic epithelium. Fecal samples were collected from  = 51 healthy controls (HC),  = 36 patients with active UC (UC-A), and  = 41 subjects in remission  = 41 (UC-R).