A multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.

Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved.

Temperatures above 37°C increase virulence of a convergent sequence type 307 strain.

Background: Convergence of (KP) pathotypes has been increasingly reported in recent years. These pathogens combine features of both multidrug-resistant and hypervirulent KP. However, clinically used indicators for hypervirulent KP identification, such as hypermucoviscosity, appear to be differentially expressed in convergent KP, potential outbreak clones are difficult to identify.

exhibiting a phenotypic hyper-splitting phenomenon including the formation of small colony variants.

In this study, we characterized a strain in a patient with shrapnel hip injury, which resulted in multiple phenotypic changes, including the formation of a small colony variant (SCV) phenotype. Although already described since the 1960s, there is little knowledge about SCV phenotypes in . The formation of SCVs has been recognized as a bacterial strategy to evade host immune responses and compromise the efficacy of antimicrobial therapies, leading to persistent and recurrent courses of infections.

Case Report: Hip arthroplasty after fracture-related joint infection caused by extensively drug-resistant .

This case-report focuses on a 23-year-old soldier suffering from a fracture-related hip joint infection (FRI) due to extensively drug-resistant and . The patient underwent multiple septic revision surgeries including the removal of remaining shrapnel accompanied by last-resort antimicrobial therapy with cefiderocol and colistin. Additionally, the surgeries included repeated tissue sampling for microbiological and histopathological analysis.

Evaluation of a Novel Benchtop Tool for Acceleration of Sample Preparation for MALDI-TOF Mass Spectrometry.

During the past decade, MALDI-TOF mass spectrometry (MS) has become a standard method for identification of bacteria and yeasts. Nonetheless, further optimization of the identification process is important to streamline workflows and save resources. This study evaluated the application of a multipurpose benchtop tool, MBT FAST Shuttle IVD, for accelerated drying of liquid assay components (matrix, formic acid, and/or sample) on a MALDI target.

Evaluation of an Automated System for the Counting of Microbial Colonies.

Counting of microbial colonies is a common technique employed in research and diagnostics. To simplify this tedious and time-consuming process, automated systems have been proposed. This study aimed to elucidate the reliability of automated colony counting.

Advanced Skin Antisepsis: Application of UVA-Cleavable Hydroxyethyl Starch Nanocapsules for Improved Eradication of Hair Follicle-Associated Microorganisms.

Hair follicles constitute important drug delivery targets for skin antisepsis since they contain ≈25% of the skin microbiome. Nanoparticles are known to penetrate deeply into hair follicles. By massaging the skin, the follicular penetration process is enhanced based on a ratchet effect.

Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395.

Background: Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage.

Bactericidal Activity of Sodium Bituminosulfonate against .

Antibiotic resistance is increasing worldwide making it necessary to search for alternative antimicrobials. Sodium bituminosulfonate is a long-known substance, whose antimicrobial inhibitory activity has recently been re-evaluated. However, to the best of our knowledge, the bactericidal mode of action of this substance has not been systematically characterized.

Susceptibility of Complex to Ceftazidime/Avibactam and Standard Drugs of Treatment for Cystic Fibrosis Patients.

complex (Bcc) in airways of patients with cystic fibrosis (CF) is associated with an increased morbidity and mortality. A huge range of intrinsic antimicrobial resistances challenges the treatment of Bcc infections. The aim was to assess the susceptibility of Bcc to ceftazidime/avibactam and standard drugs for the treatment for CF patients and to determine the respective genomic determinants of resistance.

Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition.

The ability of extensively drug-resistant (XDR) Klebsiella pneumoniae to rapidly acquire resistance to novel antibiotics is a global concern. Moreover, Klebsiella clonal lineages that successfully combine resistance and hypervirulence have increasingly occurred during the last years. However, the underlying mechanisms of counteracting fitness costs that accompany antibiotic resistance acquisition remain largely unexplored.

Exploration of Bacterial Re-Growth as In Vitro Phenomenon Affecting Methods for Analysis of the Antimicrobial Activity of Chimeric Bacteriophage Endolysins.

Drug alternatives to combat methicillin-resistant (MRSA) in human and animal healthcare are urgently needed. Recently, the recombinant bacteriophage endolysins, PRF-119 and its successor substance HY-133, have proven to be highly active against various clonal lineages and to exhibit a very rapid bactericidal effect when standard methods for susceptibility testing are applied. Along with subsequent growth curve experiments, a re-growth phenomenon was observed in vitro necessitating its clarification for the assessment of the agent's stability and activity as well as for methodological aspects of endolysin testing in general.

MALDI-TOF Mass Spectrometry-Based Optochin Susceptibility Testing for Differentiation of from other Group Streptococci.

Discrimination of from other group (SMG) species is still challenging but very important due to their different pathogenic potential. In this study, we aimed to develop a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based optochin susceptibility test with an objective read-out. Optimal test performance was established and evaluated by testing consecutively collected respiratory isolates.

Rapid Simultaneous Testing of Multiple Antibiotics by the MALDI-TOF MS Direct-on-Target Microdroplet Growth Assay.

Accelerating antimicrobial susceptibility testing (AST) is a priority in the development of novel microbiological methods. The MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA) has recently been described as a rapid phenotypic AST method. In this proof-of-principle study, we expanded this method to simultaneously test 24 antimicrobials.

Phenotypic Variants of Bacterial Colonies in Microbiological Diagnostics: How Often Are They Indicative of Differing Antimicrobial Susceptibility Patterns?

Phenotypic variants (PV) are colonies of the same species in the same specimen with different morphological features. It is controversial whether antimicrobial susceptibility testing (AST) should be done for all PV. The objectives of this study were to quantify the proportion of differing antimicrobial susceptibility patterns (dASP) among PV and to identify species and antimicrobial compounds that are mostly affected.

Hypervirulent Sequence Type 420 with a Chromosomally Inserted Virulence Plasmid.

Background: causes severe diseases including sepsis, pneumonia and wound infections and is differentiated into hypervirulent (hvKp) and classic (cKp) pathotypes. hvKp isolates are characterized clinically by invasive and multiple site infection and phenotypically in particular through hypermucoviscosity and increased siderophore production, enabled by the presence of the respective virulence genes, which are partly carried on plasmids.

Methods: Here, we analyzed two isolates of a human patient that caused severe multiple site infection.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Antimicrobial Susceptibility Testing.

The advent of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has dramatically improved the accuracy and speed of diagnostics. However, this progress has mainly been limited to the identification of microorganisms, whereas the practical improvement of antimicrobial susceptibility testing (AST) still lags behind. MALDI-TOF MS-based approaches include the detection of selected resistance mechanisms and the universal phenotypic AST.

Short Incubation of Positive Blood Cultures on Solid Media for Species Identification by MALDI-TOF MS: Which Agar Is the Fastest?

Short incubation of positive blood cultures on solid media is now increasingly applied to speed up species identification by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Although Columbia blood agar (CBA) and chocolate agar (Choc) are widely used, a direct comparison of standard agars is lacking. We therefore compared the time to species identification of blood cultures incubated on CBA, Choc, and MacConkey agar (MAC, for Gram-negative rods).

Antibiotic Resistant Bloodstream Infections in Pediatric Patients Receiving Chemotherapy or Hematopoietic Stem Cell Transplant: Factors Associated with Development of Resistance, Intensive Care Admission and Mortality.

Bloodstream infections (BSI) are a severe complication of antineoplastic chemotherapy or hematopoietic stem cell transplantation (HSCT), especially in the presence of antibiotic resistance (AR). A multinational, multicenter retrospective study in patients aged ≤ 18 years, treated with chemotherapy or HSCT from 2015 to 2017 was implemented to analyze AR among non-common skin commensals BSI. Risk factors associated with AR, intensive care unit (ICU) admission and mortality were analyzed by multilevel mixed effects or standard logistic regressions.

Variability of antibiograms: how often do changes in the antimicrobial susceptibility pattern occur in isolates from one patient?

Objectives: Many laboratories do not perform antimicrobial susceptibility testing (AST) for all consecutive isolates of the same species from one patient. The objective of this study was to assess how often changes in antimicrobial susceptibility patterns (cASP) occur in such isolates.

Methods: AST was performed for all isolates of defined species obtained from clinical routine (2015-2018) without restrictions for consecutive or sequential isolates of one patient.

Breakthrough Fungemia in an Immuno-Compromised Adolescent: Case Report and Review of the Literature.

is a rare cause of candidemia that is known for its unique capability to rapidly acquire resistance to amphotericin B. We report the case of an adolescent with grade IV graft-vs.-host disease after hematopoietic cell transplantation who developed catheter-associated candidemia while on therapeutic doses of liposomal amphotericin B.

Investigation of In-Vitro Adaptation toward Sodium Bituminosulfonate in .

The global increase in antimicrobial resistance has revived the interest in "old" substances with antimicrobial activity such as sodium bituminosulfonate. However, for those "old" compounds, scientific studies are still sparse and the ones available do not mostly meet the current standards. Since this compound is used for topical applications, investigation of a potential increase in minimal inhibitory concentrations (MICs) is of particular importance.

Prevention and Control of Multidrug-Resistant Bacteria in The Netherlands and Germany-The Impact of Healthcare Structures.

The Netherlands and Germany are neighbouring countries within the European Union but are differently affected by multidrug-resistant microorganisms (MDRO). In this narrative review, we summarize data about antibiotic use, the occurrence of MDRO and healthcare-associated infections in these two countries, as well as data about organizational and structural differences between the Dutch and German healthcare systems. These results are discussed with a focus on whether or how the organization of healthcare influences MDRO prevention.

Development of a MALDI-TOF MS-based screening panel for accelerated differential detection of carbapenemases in Enterobacterales using the direct-on-target microdroplet growth assay.

Carbapenemase-producing bacteria are a growing issue worldwide. Most phenotypic detection methods are culture-based, requiring long incubation times. We present a phenotypic screening panel for detection of carbapenem non-susceptibility and differentiation of carbapenemase classes and AmpC, the MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA).

Activity of Sodium Bituminosulfonate: Susceptibility Data for the Revival of an Old Antimicrobial.

Revival of old antibiotic compounds is a promising strategy to strengthen the antimicrobial armamentarium in the era of increasing resistance and limited development pipelines. To exploit their full potential, their reinvestigation using current standards is needed. We aimed to investigate the activity of the old antimicrobial agent sodium bituminosulfonate in accordance with the current recommendations for antimicrobial susceptibility testing (AST) and to generate susceptibility data reflecting the current epidemiological situation.