Comparing the yield of Staphylococcus aureus recovery with static versus agitated broth incubation

Given the lack of standardization of methodologies for microbial recovery from built environments, we sought to compare the yield of Staphylococcus aureus with a broth enrichment method when incubated in agitated versus static conditions. Five unique strains of S. aureus at five different concentrations were cultured to compare direct plating, agitated broth enrichment, and static broth enrichment culture methods. All samples were incubated at 35° in ambient air. The lowest concentration recovered across three replicates and five strains did not differ between culture methods (Fisher’s exact test, p=0.50); notably, recovery of S. aureus was equivalent between static and agitated broth incubation. When broth enrichment was used (both static and agitated), the burden of S. aureus growth was higher (by semiquantitative assessment of 4-quadrant streaking) compared to the direct plating culture method. Optimizing strategies for microbial recovery is essential, particularly in areas of lower biomass, given the paucity of research concerning microbial communities of built environments. The results of this study, in conjunction with other experiments investigating microbiomes of built environments, can help inform protocols for standardizing culturing methods within built environments

Antimicrobial susceptibility profiles of Staphylococcus aureus isolates recovered from humans, environmental surfaces, and companion animals in households of children with community-onset methicillin-resistant S. aureus infections

Our objective was to determine the antibiotic susceptibility profiles of Staphylococcus aureus isolates recovered from 110 households of children with community-onset methicillin-resistant S. aureus (MRSA) infections. Cultures were obtained from household members, household objects, and dogs and cats, yielding 1,633 S. aureus isolates. The S. aureus isolates were heterogeneous, although more than half were methicillin resistant. The highest proportion of MRSA was found in bathrooms. The majority of isolates were susceptible to antibiotics prescribed in outpatient settings

Epidemiology of plasmid lineages mediating the spread of extended-spectrum beta-lactamases among clinical Escherichia coli

The prevalence of extended-spectrum beta-lactamases (ESBLs) among clinical isolates of Escherichia coli has been increasing, with this spread driven by ESBL-encoding plasmids. However, the epidemiology of ESBL-disseminating plasmids remains understudied, obscuring the roles of individual plasmid lineages in ESBL spread. To address this, we performed an in-depth genomic investigation of 149 clinical ESBL-like E. coli isolates from a tertiary care hospital. We obtained high-quality assemblies for 446 plasmids, revealing an extensive map of plasmid sharing that crosses time, space, and bacterial sequence type boundaries. Through a sequence-based network, we identified specific plasmid lineages that are responsible for the dissemination of major ESBLs. Notably, we demonstrate that IncF plasmids separate into 2 distinct lineages that are enriched for different ESBLs and occupy distinct host ranges. Our work provides a detailed picture of plasmid-mediated spread of ESBLs, demonstrating the extensive sequence diversity within identified lineages, while highlighting the genetic elements that underlie the persistence of these plasmids within the clinical E. coli population

Longitudinal dynamics of skin bacterial communities in the context of Staphylococcus aureus decolonization

Decolonization with topical antimicrobials is frequently prescribed in health care and community settings to prevent Staphylococcus aureus infection. However, effects on commensal skin microbial communities remains largely unexplored. Within a household affected by recurrent methicillin-resistant S. aureus skin and soft tissue infections (SSTI), skin swabs were collected from the anterior nares, axillae, and inguinal folds of 14 participants at 1- to 3-month intervals over 24 months. Four household members experienced SSTI during the first 12-months (observational period) and were prescribed a 5-day decolonization regimen with intranasal mupirocin and bleach water baths at the 12-month study visit. We sequenced the 16S rRNA gene V1-V2 region and compared bacterial community characteristics between the pre- and post-intervention periods and between younger and older subjects. The median Shannon diversity index was stable during the 12-month observational period at all three body sites. Bacterial community characteristics (diversity, stability, and taxonomic composition) varied with age. Among all household members, not exclusively among the four performing decolonization, diversity was unstable throughout the year post-intervention. In the month after decolonization, bacterial communities were changed. Although communities largely returned to their baseline states, relative abundance of some taxa remained changed throughout the year following decolonization (e.g., more abundan

Change in First Graders’ Science-Related Competence Beliefs During Digitally Intensive Science Workshops

The aim of this research was to examine if a set of three science and technology workshops would promote first-grade pupils’ science-related competence beliefs. The first workshop dealt with electric circuits and related handicraft tasks. The second workshop involved programming with Lego Mindstorms robots. The third workshop was related to computer-based data logging. Fifty-nine Finnish first graders (age 7–8 years) participated in the digitally intensive science workshops, and 38 pupils served as a control group. The data were analysed using a paired samples t-test. The analysis results reveal that the set of three workshops increased the pupils’ science and technology-related competence beliefs.Peer reviewe

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9–2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.</p