Ashlee M. Earl
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View article: Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network
Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network Open
Antimicrobial resistance (AMR) is a global public health threat that disproportionately affects vulnerable populations, including nursing home (NH) residents. Surveillance and control in NHs are resource-limited and typically restricted to…
View article: Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species
Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species Open
The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing…
View article: Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis
Single-nucleus transcriptomics illuminates sex differences during murine Escherichia coli pyelonephritis Open
There are profound sex differences in the prevalence and outcomes of urinary tract infections (UTI). While females comprise the majority of infections, males exhibit higher morbidity and mortality with upper-tract UTI. Correspondingly, pre…
View article: The carbapenem inoculum effect provides insights into the molecular mechanisms underlying carbapenem resistance in the Enterobacterales
The carbapenem inoculum effect provides insights into the molecular mechanisms underlying carbapenem resistance in the Enterobacterales Open
Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveil…
View article: Insights Into Global Antimicrobial Resistance Dynamics Through the Sequencing of Enteric Bacteria From US International Travelers
Insights Into Global Antimicrobial Resistance Dynamics Through the Sequencing of Enteric Bacteria From US International Travelers Open
Background Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers freque…
View article: Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children
Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children Open
Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early …
View article: Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species
Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species Open
The ability to detect and reconstruct plasmids from genome assemblies is crucial for studying the evolution and spread of antimicrobial resistance and virulence in bacteria. Though long-read sequencing technologies have made reconstructing…
View article: Rapid emergence of resistance to broad-spectrum direct antimicrobial activity of avibactam
Rapid emergence of resistance to broad-spectrum direct antimicrobial activity of avibactam Open
Avibactam (AVI) is a diazabicyclooctane (DBO) β-lactamase inhibitor used clinically in combination with ceftazidime. At concentrations higher than those typically achieved in vivo , it also has broad-spectrum direct antibacterial activity …
View article: An Anaerobic Pathogen Rewires Host Metabolism to Fuel Oxidative Growth in the Inflamed Gut
An Anaerobic Pathogen Rewires Host Metabolism to Fuel Oxidative Growth in the Inflamed Gut Open
To colonize their host and cause disease, enteric pathogens must deploy their virulence factors to establish distinct nutrient niches. How obligate anaerobic pathogens construct nutrient niches in the densely populated large intestine rema…
View article: Author Correction: Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain
Author Correction: Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain Open
View article: Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain Open
View article: Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements
Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements Open
Identifying bacterial transmission pathways is crucial to inform strategies that limit the spread of pathogenic and antibiotic-resistant bacteria. Here we assessed Escherichia coli strain-sharing and overlap of antibiotic resistance genes …
View article: Genetic diversity of <i>Salmonella enterica</i> during acute human infections
Genetic diversity of <i>Salmonella enterica</i> during acute human infections Open
The ubiquitous bacterial pathogen Salmonella enterica is the causative agent of both enteric fever and gastroenteritis. Despite its significant global health burden, we lack an understanding of its genetic diversity during acute inf…
View article: Mechanisms of uropathogenic <i>E. coli</i> mucosal association in the gastrointestinal tract
Mechanisms of uropathogenic <i>E. coli</i> mucosal association in the gastrointestinal tract Open
Urinary tract infections (UTIs) are highly recurrent and frequently caused by Uropathogenic Escherichia coli (UPEC) strains that can be found in patient intestines. Seeding of the urinary tract from this intestinal reservoir likely contrib…
View article: Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of <i>Borrelia burgdorferi</i>
Complex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of <i>Borrelia burgdorferi</i> Open
Background In the United States, Borrelia burgdorferi ( Bb ) is the principal etiologic agent of Lyme disease. The complex structure of Bb genomes has posed challenges for genomic studies because homology among the bacterium’s many plasmid…
View article: Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers
Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers Open
Antimicrobial resistance (AMR) is an urgent threat to public health, but gaps in surveillance limit the detection of emergent novel threats and knowledge about the global distribution of AMR genes. International travelers frequently acquir…
View article: zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters
zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters Open
Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic el…
View article: Fast and exact gap-affine partial order alignment with POASTA
Fast and exact gap-affine partial order alignment with POASTA Open
Motivation Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial o…
View article: Clinical and genomic characterization of Klebsiella pneumoniae infections in Dhaka, Bangladesh
Clinical and genomic characterization of Klebsiella pneumoniae infections in Dhaka, Bangladesh Open
Our findings suggest alarming levels of AMR among Kpn isolates in Bangladesh and a critical need for improved treatment modalities and vaccine development.
View article: Effects of commonly used antibiotics on children’s developing gut microbiomes and resistomes in peri-urban Lima, Peru
Effects of commonly used antibiotics on children’s developing gut microbiomes and resistomes in peri-urban Lima, Peru Open
Synopsis Background The effects of antibiotic use on children’s gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effe…
View article: Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children
Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children Open
Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low and middle-income countries. Some children nevertheless remain never or rarely colonized during early l…
View article: Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection Open
Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. W…
View article: High Prevalence of Carbapenem-resistant <i>Klebsiella Pneumoniae</i> in Fecal and Water Samples in Dhaka, Bangladesh
High Prevalence of Carbapenem-resistant <i>Klebsiella Pneumoniae</i> in Fecal and Water Samples in Dhaka, Bangladesh Open
We evaluated Klebsiella pneumoniae (Kp) gut carriage in healthy, unrelated adults and children living in separate households in Dhaka, Bangladesh. Average Kp prevalence in stool samples ranged from 61% in young children (15/25) to 81% in a…
View article: Rapid Emergence of Resistance to Broad-Spectrum Direct Antimicrobial Activity of Avibactam
Rapid Emergence of Resistance to Broad-Spectrum Direct Antimicrobial Activity of Avibactam Open
Avibactam (AVI) is a diazabicyclooctane (DBO) β-lactamase inhibitor used clinically in combination with ceftazidime. At concentrations higher than those typically achieved in vivo , it also has broad-spectrum direct antibacterial activity …
View article: Bacterial strain sharing between humans, animals, and the environment among urban households
Bacterial strain sharing between humans, animals, and the environment among urban households Open
Identifying bacterial transmission pathways is crucial to inform strategies aimed at curbing the spread of pathogenic and antibiotic-resistant bacteria, especially in rapidly urbanizing low– and middle-income countries. In this study, we a…
View article: Dynamics of microbiome and resistome in a poultry burger processing line
Dynamics of microbiome and resistome in a poultry burger processing line Open
Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted moni…
View article: Fast and exact gap-affine partial order alignment with POASTA
Fast and exact gap-affine partial order alignment with POASTA Open
Motivation Partial order alignment is a widely used method for computing multiple sequence alignments, with applications in genome assembly and pangenomics, among many others. Current algorithms to compute the optimal, gap-affine partial o…
View article: SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings
SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings Open
Motivation Today, we know the function of only a small fraction of the protein sequences predicted from genomic data. This problem is even more salient for bacteria, which represent some of the most phylogenetically and metabolically diver…
View article: Distinct<i>Escherichia coli</i>transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection
Distinct<i>Escherichia coli</i>transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection Open
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli , a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urin…
View article: Global diversity of enterococci and description of 18 previously unknown species
Global diversity of enterococci and description of 18 previously unknown species Open
Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococca…