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Related Concept Videos

Plasmids01:28

Plasmids

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Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
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Urinary Tract Infection I: Introduction01:26

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Urinary tract infections (UTIs) impact various parts of the urinary system, including the kidneys, ureters, bladder, and urethra. These infections are generally bacterial, with Escherichia coli being the most common causative agent, often originating from the gastrointestinal tract. However, other bacteria, such as Staphylococcus saprophyticus, Klebsiella pneumoniae, and Proteus mirabilis, are also known to cause UTIs. The type, location, and underlying complexity of the UTI guide both...
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Urinary Tract Infection II: Pathophysiology01:25

Urinary Tract Infection II: Pathophysiology

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The pathophysiology of urinary tract infections (UTIs) encompasses several progressive stages, beginning with bacterial colonization and culminating in potential systemic complications if untreated. UTIs are primarily initiated by bacteria, such as Escherichia coli, which often originate from the gastrointestinal tract and migrate to the urinary system through the periurethral area. This migration can occur via several routes, including improper hygiene practices, sexual activity, or...
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Genomic DNA in Prokaryotes00:46

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
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Urine Studies II: Urine Culture and Sensitivity Test01:26

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A urine culture and sensitivity test is a diagnostic procedure used to identify urinary tract bacterial infections and determine the most effective antibiotics for treatment. This test is generally preferred when a patient shows manifestations of a urinary tract infection, such as frequent or painful urination, cloudy or foul-smelling urine, or lower abdominal pain.Purpose of the TestThe primary goals of a urine culture and sensitivity test are to:Determine the specific bacteria causing the...
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Bacterial Phylum Tenericutes01:24

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The phylum Tenericutes, which includes the single class Mollicutes, comprises bacteria that lack cell walls. The term "Mollicutes" derives from the Latin word mollis, meaning "soft." These organisms are among the smallest known and are commonly referred to as mycoplasmas due to the prominence of the genus Mycoplasma, which includes well-known human pathogens. Despite their inability to stain gram-positively (a result of their lack of cell walls), mycoplasmas are phylogenetically related to the...
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Plasmids of the urinary microbiota.

Genevieve Johnson1, Seanna Bataclan2, Minerva So3

  • 1Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.

Access Microbiology
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Summary

Researchers investigated mobile genetic elements, specifically plasmids, in the urinary tract microbiome. They identified 603 high-confidence plasmids, with 70% similar to gut plasmids, highlighting potential urobiome-gut connections.

Keywords:
microbiomeplasmidplasmidomeurinary tracturobiome

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • The urinary tract harbors a diverse bacterial community, the urobiome.
  • Mobile genetic elements (MGEs) like plasmids can influence bacterial virulence and antibiotic resistance.
  • Plasmids within the urobiome are under-explored, especially in under-studied species.

Purpose of the Study:

  • To comprehensively investigate the plasmid content of urinary tract bacterial isolates.
  • To identify and characterize plasmids from diverse urobiome species.
  • To assess the similarity of urobiome plasmids to those found in other body sites.

Main Methods:

  • A two-pronged bioinformatic approach using plasmidSPAdes and Recycler for plasmid identification.
  • Manual curation of identified plasmid sequences from raw short-read data.
  • Validation of bioinformatic predictions using long-read sequencing for select isolates.

Main Results:

  • Identified 603 high-confidence plasmid sequences across 20 genera of the urobiome.
  • Found that 70% of these plasmids show sequence similarity to plasmids from the gut microbiome.
  • Confirmed 66.95% of bioinformatic predictions through long-read sequencing, indicating tool efficacy and limitations.

Conclusions:

  • Plasmids are prevalent in the urobiome and share significant similarity with gut plasmids, particularly in *E. coli*.
  • Bioinformatic tools are valuable for plasmid discovery but have limitations that long-read sequencing can address.
  • Future urobiome research should incorporate long-read sequencing to enhance plasmid cataloging, especially for under-studied bacteria.