Derek Fleming

Derek Fleming
Mayo Clinic - Rochester · Department of Laboratory Medicine & Pathology

PhD

About

24
Publications
4,234
Reads
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626
Citations
Introduction
I am currently investigating post-operative hyperammonemia syndrome secondary to respiratory Ureaplasma infection in lung transplant recipients. Previously, I researched enzymatic biofilm dispersal in chronic wound infections.
Additional affiliations
June 2020 - present
Mayo Clinic
Position
  • PostDoc Position
July 2018 - May 2020
Texas Tech University Health Sciences Center
Position
  • PostDoc Position
Description
  • Conduct translational research and clinical studies for the Department of Surgery and the Burn Center of Research Excellence.
August 2014 - July 2018
Texas Tech University Health Sciences Center
Position
  • PhD Student
Description
  • Investigated variable methods of chronic wound biofilm dispersal and bacterial eradication by selectively targeting essential biofilm components.
Education
August 2014 - August 2018
Texas Tech University Health Sciences Center
Field of study
  • Immunology and Molecular Microbiology

Publications

Publications (24)
Article
Full-text available
A new technique was used to measure the viscoelasticity of in vivo Pseudomonas aeruginosa biofilms. This was done through ex vivo microrheology measurements of in vivo biofilms excised from mouse wound beds. To our knowledge, this is the first time that the mechanics of in vivo biofilms have been measured. In vivo results are then compared to typic...
Article
Full-text available
Biofilms are the cause of most chronic bacterial infections. Living within the biofilm matrix, which is made of extracellular substances, including polysaccharides, proteins, eDNA, lipids and other molecules, provides microorganisms protection from antimicrobials and the host immune response. Exopolysaccharides are major structural components of ba...
Article
Full-text available
Lung transplant recipients (LTRs) are vulnerable to hyperammonemia syndrome (HS) in the early postoperative period, a condition typically unresponsive to nonantibiotic interventions. HS in LTRs is strongly correlated with Ureaplasma infection of the respiratory tract, although it is not well understood what makes LTRs preferentially susceptible to...
Preprint
Full-text available
Lung transplant recipients (LTRs) are vulnerable to unexplained hyperammonemia syndrome (HS) in the early post-operative period, a condition typically unresponsive to non-antibiotic interventions. Recently, we showed that HS in LTRs is strongly correlated with Ureaplasma infection of the respiratory tract. It is not well-understood what makes LTRs...
Article
Full-text available
Pseudomonas aeruginosa is an opportunistic pathogen that causes thousands of deaths every year in part due to its ability to form biofilms composed of bacteria embedded in a matrix of self-secreted extracellular polysaccharides (EPS), e-DNA, and proteins. In chronic wounds, biofilms are exposed to the host extracellular matrix, of which collagen is...
Article
Full-text available
Wound biofilms must be identified to target disruption and bacterial eradication but are challenging to detect with standard clinical assessment. This study tested whether bacterial fluorescence imaging could detect porphyrin-producing bacteria within a biofilm using well-established in vivo models. Mouse wounds were inoculated on Day 0 with plankt...
Article
Ureaplasma species, including Ureaplasma parvum and Ureaplasma urealyticum, are challenging to culture and maintain. Here, we describe a novel bioreactor for growing high-titer liquid Ureaplasma cultures in a stable manner.
Article
Full-text available
Opportunistic pathogens are associated with a number of chronic human infections, yet the evolution of virulence in these organisms during chronic infection remains poorly understood. Here, we tested the evolution of virulence in the human opportunistic pathogen Pseudomonas aeruginosa in a murine chronic wound model using a two-part serial passage...
Article
Full-text available
The complexity of microbial biofilms offers several challenges to the use of traditional means of microbial research. In particular, it can be difficult to calculate accurate numbers of biofilm bacteria, because even after thorough homogenization or sonication, small pieces of the biofilm remain, which contain numerous bacterial cells and result in...
Article
Infection is responsible for up to 60% of deaths in burn patients and Pseudomonas aeruginosa (PA) has the highest mortality rate among all causes of bacteremia. These aggressive and virulent infections are often not detected until there is a positive blood culture for PA, meaning the patient already has bacteremia. An assay that rapidly detects PA...
Article
Full-text available
The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were...
Preprint
Full-text available
Opportunistic pathogens are associated with a number of widespread, treatment-resistant chronic infections in humans. As the pipeline for new antibiotics thins, virulence management presents an alternative solution to the rising antimicrobial resistance crisis in treating chronic infections. However, the nature of virulence in opportunists is not f...
Article
Full-text available
The opportunistic pathogen Pseudomonas aeruginosa is a leading cause of morbidity and mortality worldwide. To survive in both the environment and in the host, P. aeruginosa must cope with redox stress. In P. aeruginosa , a primary mechanism for protection from redox stress is the antioxidant glutathione (GSH). GSH is a low molecular weight thiol-co...
Article
Biofilms are communities of bacteria embedded in a polymeric matrix which are found in infections and in environments outside the body. Breaking down the matrix renders biofilms more susceptible to physical disruption and to treatments such as antibiotics. Different species of bacteria, and different strains within the same species, produce differe...
Chapter
There is no question that new antibiotics are sorely needed as bacteria become more and more resistant. However, another important cause of antibiotic failure is the tolerance bacteria exhibit to treatment when they are present within a biofilm. In contrast to the heritable changes bacteria undergo when acquiring new resistance determinants, tolera...
Article
Background: Probiotics are often used in critically ill patients to prevent antibiotic-associated complications, including Clostridium difficile colitis. However, clinical evidence of their efficacy is lacking. Objective: To assess the impact of prophylactic probiotic administration on bowel function, gut microbial diversity, and nutritional mar...
Preprint
Full-text available
Biofilms are communities of bacteria embedded in a matrix of polymeric substances. This polymer matrix lends the bacteria protection against a wide array of chemical and mechanical stresses. Breaking down the matrix network renders biofilms more susceptible to physical disruption and to treatments. Different species of bacteria, and different strai...
Article
Full-text available
Chronic infections are often associated with the presence of a biofilm, a community of microorganisms coexisting within a protective matrix of extracellular polymeric substance. Living within a biofilm can make resident microbes significantly more tolerant to antibiotics in comparison to planktonic, free-floating cells. Thus, agents that can degrad...
Article
Identifying genes required by pathogens during infection is critical for antimicrobial development. Here, we use a Monte Carlo simulation-based method to analyse high-throughput transposon sequencing data to determine the role of infection site and co-infecting microorganisms on the in vivo ‘essential’ genome of Staphylococcus aureus. We discovered...
Article
Full-text available
Biofilm-associated infections pose a complex problem to the medical community, in that residence within the protection of a biofilm affords pathogens greatly increased tolerances to antibiotics and antimicrobials, as well as protection from the host immune response. This results in highly recalcitrant, chronic infections and high rates of morbidity...
Article
Full-text available
The persistent nature of chronic wounds leaves them highly susceptible to invasion by a variety of pathogens that have the ability to construct an Extracellular Polymeric Substance (EPS). This EPS makes the bacterial population, or biofilm, up to one-thousand-fold more antibiotic tolerant than planktonic cells, and makes wound healing extremely dif...
Article
Background: Probiotics are widely used in healthy and nonhealthy individuals to maintain a favorable gut microbiome and inhibit pathogen takeover. Currently, there are many varieties of probiotic delivery vehicles on the market, with no real research indicating which is the most effective at allowing for colon colonization. In this study, we sough...
Article
Full-text available
Unlabelled: Bacteria rarely inhabit infection sites alone, instead residing in diverse, multispecies communities. Despite this fact, bacterial pathogenesis studies primarily focus on monoculture infections, overlooking how community interactions influence the course of disease. In this study, we used global mutant fitness profiling (transposon seq...
Chapter
From birth to death the human host immune system interacts with bacterial cells. Biofilms are communities of microbes embedded in matrices composed of extracellular polymeric substance (EPS), and have been implicated in both the healthy microbiome and disease states. The immune system recognizes many different bacterial patterns, molecules, and ant...

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Project (1)
Project
In-vitro and ex-vivo viscoelastic characterization of biofilms