Gautam Dantas
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View article: Molecular methods to diagnose pertussis: a case of confusion with <i>Bordetella bronchiseptica</i>
Molecular methods to diagnose pertussis: a case of confusion with <i>Bordetella bronchiseptica</i> Open
Background Prompt identification of clinically relevant Bordetella (e.g., B. pertussis and B. parapertussis ) is critical for both treatment and isolation decisions to mitigate transmission among close contacts. Due to the organisms’ fasti…
View article: The effects of a prospective sink environmental hygiene intervention on Pseudomonas aeruginosa and Stenotrophomonas maltophilia burden in hospital sinks
The effects of a prospective sink environmental hygiene intervention on Pseudomonas aeruginosa and Stenotrophomonas maltophilia burden in hospital sinks Open
View article: Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome
Metagenomic signatures of extraintestinal bacterial infection in the febrile term infant gut microbiome Open
The intestine plausibly serves as a reservoir for EBI pathogens in a subset of febrile term infants, prompting consideration of new opportunities for surveillance and EBI prevention among colonized, pre-symptomatic infants. Video Abstract.
View article: Engineering genetic tools to control individual microbes and microbiota without antibiotic resistance genes at a single strain level
Engineering genetic tools to control individual microbes and microbiota without antibiotic resistance genes at a single strain level Open
View article: C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity
C10-Benzoate Esters of Anhydrotetracycline Inhibit Tetracycline Destructases and Recover Tetracycline Antibacterial Activity Open
Tetracyclines (TCs) are an important class of antibiotics threatened by enzymatic inactivation. These tetracycline-inactivating enzymes, also known as tetracycline destructases (TDases), are a subfamily of class A flavin monooxygenases (FM…
View article: Comparison of sampling and culture methods for the recovery of yeast from hospital surfaces
Comparison of sampling and culture methods for the recovery of yeast from hospital surfaces Open
Objective: To compare the recovery of yeast from hospital surfaces from two different collection methods: Eswab moistened with molecular water, and premoistened stick-mounted sponge. Design: Comparison of collection methods for the recover…
View article: Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization
Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization Open
Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why …
View article: Improving Differentiation of Crohn’s Disease and Ulcerative Colitis Proteomes through Protein-Wide Association Study Feature Selection in Machine Learning
Improving Differentiation of Crohn’s Disease and Ulcerative Colitis Proteomes through Protein-Wide Association Study Feature Selection in Machine Learning Open
Background and Aims Diagnostic differentiation between Crohn’s disease (CD) and ulcerative colitis (UC) is crucial for timely and suitable therapeutic measures. The current gold standard for differentiating between CD and UC involves endos…
View article: Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants
Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants Open
View article: Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants
Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants Open
Aberrant preterm infant gut microbiota assembly predisposes to early-life disorders and persistent health problems. Here, we characterize gut microbiome dynamics over the first 3 months of life in 236 preterm infants hospitalized in three …
View article: Commensal-pathogen dynamics structure disease outcomes during<i>Clostridioides difficile</i>colonization
Commensal-pathogen dynamics structure disease outcomes during<i>Clostridioides difficile</i>colonization Open
Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in clinical presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investi…
View article: Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators
Increased triacylglycerol production in Rhodococcus opacus by overexpressing transcriptional regulators Open
Lignocellulosic biomass is currently underutilized, but it offers promise as a resource for the generation of commercial end-products, such as biofuels, detergents, and other oleochemicals. Rhodococcus opacus PD630 is an oleaginous, Gram-p…
View article: Quantifying the genomic determinants of fitness in<i>E. coli</i>ST131 using phylodynamics
Quantifying the genomic determinants of fitness in<i>E. coli</i>ST131 using phylodynamics Open
Antimicrobial resistant pathogens such as Escherichia coli sequence type 131 (ST131) pose a serious threat to public health globally. In the United States, ST131 acquired multiple antimicrobial resistance (AMR) genes and rapidly grew to it…
View article: Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study
Gut microbiome correlates of recurrent urinary tract infection: a longitudinal, multi-center study Open
This work was supported in part by awards from the U.S. Centers for Disease Control and Prevention Epicenter Prevention Program (grant U54CK000482; principal investigator, V.J.F.); to J.H.K. from the Longer Life Foundation (an RGA/Washingt…
View article: Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes
Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes Open
View article: Genomic surveillance of <i>Clostridioides difficile</i> transmission and virulence in a healthcare setting
Genomic surveillance of <i>Clostridioides difficile</i> transmission and virulence in a healthcare setting Open
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital settin…
View article: Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of <i>Staphylococcus saprophyticus</i>
Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of <i>Staphylococcus saprophyticus</i> Open
Staphylococcus saprophyticus is the leading Gram-positive cause of uncomplicated urinary tract infections. Recent reports of increasing antimicrobial resistance (AMR) in S. saprophyticus warrant investigation of its understudied resistance…
View article: The gut microbiome as an early biomarker of preclinical Alzheimer disease
The gut microbiome as an early biomarker of preclinical Alzheimer disease Open
Background The current paradigm of Alzheimer disease (AD) pathology teaches that people progress from cognitive normality, to cognitive normality with biomarker evidence of disease (preclinical AD), and ultimately to symptomatic AD with co…
View article: 691. Association between <i>Clostridioides difficile</i> Colonization, Rectal Swab NAAT Positivity, and Environmental Contamination
691. Association between <i>Clostridioides difficile</i> Colonization, Rectal Swab NAAT Positivity, and Environmental Contamination Open
Background Clostridioides difficile (CD) colonization is common among hospitalized patients. Screening for toxigenic CD (TCD) colonization with rectal swab nucleic acid amplification tests (NAAT) may identify people at risk for CDI and hel…
View article: 981. Sink drain environmental hygiene intervention successfully reduces burden of AROs
981. Sink drain environmental hygiene intervention successfully reduces burden of AROs Open
Background Healthcare associated infections (HAIs) and outbreaks due to hospital sinks have been noted for many years, however, there remains no standardized environmental hygiene protocol to combat these HAIs. The goal of this study was t…
View article: Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms
Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms Open
View article: Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial
Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial Open
Bill & Melinda Gates Foundation; Médecins sans Frontières Operational Center Paris; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; Eunice Kennedy Shriver National Institute of Child H…
View article: Genomic surveillance of<i>Clostridioides difficile</i>transmission and virulence in a healthcare setting
Genomic surveillance of<i>Clostridioides difficile</i>transmission and virulence in a healthcare setting Open
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital settin…
View article: A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan
A novel immune modulator IM33 mediates a glia-gut-neuronal axis that controls lifespan Open
View article: Antibiotic perturbations to the gut microbiome
Antibiotic perturbations to the gut microbiome Open
View article: Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids
Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids Open
Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization pa…
View article: Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose
Systems Engineering of Rhodococcus opacus to Enable Production of Drop-in Fuels from Lignocellulose Open
Production of drop-in fuels from lignocellulose using Rhodococcus opacus PD630 (hereafter R. opacus) is a challenging goal. During the grant period we have pushed the field forward significantly in several areas of research. Towards the en…
View article: Microbiome-targeting therapies in the neonatal intensive care unit: safety and efficacy
Microbiome-targeting therapies in the neonatal intensive care unit: safety and efficacy Open
Microbiome-targeting therapies have received great attention as approaches to prevent disease in infants born preterm, but their safety and efficacy remain uncertain. Here we summarize the existing literature, focusing on recent meta-analy…
View article: Uncharacterized and lineage-specific accessory genes within the <i>Proteus mirabilis</i> pan-genome landscape
Uncharacterized and lineage-specific accessory genes within the <i>Proteus mirabilis</i> pan-genome landscape Open
Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibi…
View article: Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease
Gut microbiome composition may be an indicator of preclinical Alzheimer’s disease Open
Alzheimer’s disease (AD) pathology is thought to progress from normal cognition through preclinical disease and ultimately to symptomatic AD with cognitive impairment. Recent work suggests that the gut microbiome of symptomatic patients wi…