J. Swann

Giardia Antagonizes Beneficial Functions of Indigenous and Therapeutic Intestinal Bacteria during Malnutrition

This study shows Giardia reduces the beneficial effects of Lactobacillus in malnourished mice, altering microbial balance and increasing intestinal damage.

Amino acid availability acts as a metabolic rheostat to determine the magnitude of ILC2 responses

This study shows that amino acid availability regulates ILC2 responses by affecting mTOR activation and expansion, highlighting nutritional cues in innate immunity.

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

The paper identifies amino acid substitutions in penicillin binding proteins (PBPs) PBP1 and PBP3 as a mechanism of cephalosporin resistance in C. difficile, which co-occurs with fluoroquinolone resistance in epidemic lineages.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

This study evaluates four AMR gene typing methods using simulated and real E. coli data, revealing significant discrepancies and highlighting issues with current bioinformatic approaches.

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

The paper analyzes the pangenome dynamics of Enterobacteriaceae from environmental sources, finding that plasmids carry more AMR genes and are influenced by niche and geography rather than phylogeny.

Enteropathogenic Escherichia coli (EPEC) Infection Induces Diarrhea, Intestinal Damage, Metabolic Alterations and Increased Intestinal Permeability in a Murine Model

This study uses a murine model to show that EPEC infection causes diarrhea, intestinal damage, metabolic changes, and increased permeability, with the T3SS playing a key role in virulence.

High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

This study develops a workflow for high-precision variant and antimicrobial resistance calling from metagenomic Nanopore sequencing of Neisseria gonorrhoeae.

Reconciling the potentially irreconcilable? Genotypic and phenotypic amoxicillin-clavulanate resistance in Escherichia coli

This study shows that amoxicillin-clavulanate resistance in E. coli is quantitative, not binary, and that WGS-based predictions outperform traditional phenotyping methods.

Global post-translational modification profiling of HIV-1-infected cells reveals mechanisms of host cellular pathway remodeling

The paper uses proteomics to analyze PTM changes in HIV-1-infected cells, identifying mechanisms of host pathway remodeling through Aurora kinase A and PP2A modulation.

Microbiota supplementation with Bifidobacterium and Lactobacillus modifies the preterm infant gut microbiota and metabolome

This study shows that supplementing preterm infants with Bifidobacterium and Lactobacillus changes their gut microbiota and increases fecal acetate and lactate levels, resembling a full-term infant's gut environment.

Gut microbiome communication with bone marrow regulates susceptibility to amebiasis

The paper shows that introducing Clostridium scindens into the gut microbiota epigenetically alters bone marrow and provides protection against Entamoeba histolytica infection.

The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

This study evaluates how sequencing depth affects taxonomic composition and AMR gene detection in metagenomic samples, finding that higher depth is needed for AMR gene richness.

Real-time analysis of nanopore-based metagenomic sequencing from orthopaedic device infection

This paper compares metagenomic sequencing using Illumina MiSeq and Oxford Nanopore MinION platforms for diagnosing prosthetic joint infections, demonstrating a real-time analysis pipeline for rapid bacterial detection.