Timothy D. Read
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Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections Open
Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis ( Ct ) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that…
Staphylococcus aureus induces Gasdermin A-dependent keratinocyte pyroptosis Open
Staphylococcus aureus is a common colonizer of human skin, which, despite its ubiquitous nature, has a high virulence potential. Tolerating microbes in health but responding effectively to pathogens presents a challenge to the barrier tiss…
Using wastewater surveillance to investigate community-level differences in antibacterial resistance in a major urban center, USA Open
Wastewater surveillance could be a low-cost strategy for assessing patterns of antibiotic resistance across urban populations. We quantified fluoroquinolone-resistant (FQ-R) Enterobacterales, third-generation cephalosporin-resistant (3GC-R…
Transition of <i>Staphylococcus aureus</i> tetracycline resistance plasmid pT181 from independent multicopy replicon to predominantly integrated chromosomal element over 65 years Open
Mobile genetic elements (MGEs), including plasmids, phages and genome islands, are major sources of bacterial genetic diversity. The small plasmid pT181 confers tetracycline resistance in bacterial pathogen Staphylococcus aureus via an eff…
Host and antibiotic jointly select for greater virulence in Staphylococcus aureus Open
Widespread antibiotic usage has resulted in the rapid evolution of drug-resistant bacterial pathogens and poses significant threats to public health. Resolving how pathogens respond to antibiotics under different contexts is critical for u…
Host and antibiotic jointly select for greater virulence in Staphylococcus aureus Open
Widespread antibiotic usage has resulted in the rapid evolution of drug-resistant bacterial pathogens and poses significant threats to public health. Resolving how pathogens respond to antibiotics under different contexts is critical for u…
Methicillin-Resistant <i>Staphylococcus aureus</i> Bacteremia Relapses Show Diverse Genomic Profiles but Convergence in Bacteremia-Associated Genes Open
Background Recurrence of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is a high risk complication for patients. Distinguishing persistent lineages from new infections is not standardized across clinical studies. Methods We…
A fluorescence-based protocol to monitor bacterial antagonism Open
Bacteria are often found in polymicrobial communities where competition for limited space and resources drives antagonistic interactions. Therefore, bacteria have evolved various antibacterial weapons to outcompete their neighbors. These a…
Effect of Azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal microbiomes of women in Fiji with <i>Chlamydia trachomatis</i> infection Open
Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes with Chlamydia trachomatis ( Ct ) infection remain poorly understood. Some data exist on vaginal microbiomes pre- and post-treatment, but none are available …
Genomic investigation of MRSA bacteremia relapse reveals diverse genomic profiles but convergence in bacteremia-associated genes Open
Background Recurrence of methicillin-resistant Staphylococcus aureus (MRSA) bacteremia is a high risk complication for patients. Distinguishing persistent lineages from new infections is not standardized across clinical studies. Methods We…
Comparative genomic analysis of emerging non-typeable <i>Haemophilus influenzae</i> (NTHi) causing emerging septic arthritis in Atlanta Open
Background Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have h…
Whole-genome automated assembly pipeline for <i>Chlamydia trachomatis</i> strains from reference, <i>in vitro</i> and clinical samples using the integrated CtGAP pipeline Open
Whole genome sequencing (WGS) is pivotal for the molecular characterization of Chlamydia trachomatis (Ct)—the leading bacterial cause of sexually transmitted infections and infectious blindness worldwide. Ct WGS can inform epidemiologic, p…
Intraspecific Diversity of <i>Staphylococcus aureus</i> Populations Isolated from Cystic Fibrosis Respiratory Infections Open
Chronic bacterial infections are often polymicrobial, comprising multiple bacterial species or variants of the same species. Because chronic infections may last for decades, they have the potential to generate high levels of intraspecific …
Metagenome-wide characterization of shared antimicrobial resistance genes in sympatric people and lemurs in rural Madagascar Open
Background Tracking the spread of antibiotic resistant bacteria is critical to reduce global morbidity and mortality associated with human and animal infections. There is a need to understand the role that wild animals in maintenance and t…
Chlamydia suis undergoes interclade recombination promoting Tet-island exchange Open
Background The obligate intracellular bacterial family Chlamydiaceae comprises a number of different species that cause disease in various vertebrate hosts including humans. Chlamydia suis , primarily found in the gastrointestinal tract of…
Average nucleotide identity-based <i>Staphylococcus aureus</i> strain grouping allows identification of strain-specific genes in the pangenome Open
Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding re…
Corrigendum: Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis Open
[This corrects the article DOI: 10.3389/fmicb.2023.1154664.].
Genomic insights into the evolution of secondary metabolism of <i>Escovopsis</i> and its allies, specialized fungal symbionts of fungus-farming ants Open
The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteri…
Strain Differences in Bloodstream and Skin Infection: Methicillin-Resistant <i>Staphylococcus aureus</i> Isolated in 2018–2021 in a Single Health System Open
Staphylococcus aureus is a common cause of skin and soft-tissue infections (SSTIs) and has become the most common cause of bloodstream infections (BSIs) in recent years, but whether the strains causing these two clinical syndromes overlap …
A laboratory-based predictive pathway for the development of <i>Neisseria gonorrhoeae</i> high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase Open
The continued emergence of Neisseria gonorrhoeae strains that express resistance to multiple antibiotics, including the last drug for empiric monotherapy (ceftriaxone), necessitates the development of new treatment options to cure gonorrhe…
Experimentally evolved Staphylococcus aureus shows increased survival in the presence of Pseudomonas aeruginosa by acquiring mutations in the amino acid transporter, GltT Open
When cultured together under standard laboratory conditions Pseudomonas aeruginosa has been shown to be an effective inhibitor of Staphylococcus aureus . However, P. aeruginosa and S. aureus are commonly observed in coinfections of individ…
Factors associated with foreign body infection in methicillin-resistant Staphylococcus aureus bacteremia Open
Background We aimed to compare patient characteristics, MRSA sequence types, and biofilm production of MRSA strains that did and did not cause a foreign body infection in patients with MRSA bloodstream infections (BSI) Methods All adult pa…
View article: The Burden and Impact of Early Post-transplant Multidrug-Resistant Organism Detection Among Renal Transplant Recipients, 2005–2021
The Burden and Impact of Early Post-transplant Multidrug-Resistant Organism Detection Among Renal Transplant Recipients, 2005–2021 Open
Background Reducing the burden of multidrug-resistant organism (MDRO) colonization and infection among renal transplant recipients (RTRs) may improve patient outcomes. We aimed to assess whether the detection of an MDRO or a comparable ant…
Average Nucleotide Identity based <i>Staphylococcus aureus</i> strain grouping allows identification of strain-specific genes in the pangenome Open
Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding reso…