Pathogenic Bacteriology Exam 1

Taken from lecture slides and the textbook (Medical Microbiology 10th Ed).

What gene sequencing methods did the human microbiome project use?

16S rRNA gene sequencing and Shotgun metagenomics

What is functional redundancy?

Multiple bacterial species perform similar or identical roles in the microbiome. If one species is lost, another can fulfill its role. Individuals can have different bacterial taxa that perform the same function.

How does the host benefit from the microbiome?

important metabolic functions, stimulates immunity, prevents pathogen colonization.

What are the environmental factors of colonization of a specific body site?

Tolerance to oxygen (or lackof it), pH, salt, bioavailability of minerals like iron, and nutrients. Most colonizers are anaerobic or facultative anaerobic.

What host behaviors contribute to colonization?

Hygiene, Diet (fiber rich vs sugar rich), Water source (contaminated versus clean), antibiotics, and environmental toxins

Which two phyla are most common of the gut microbiota?

Bacteroidetes and Firmicutes

What number is an important proxy for overall community health?

Firmicutes : Bacteroidetes ratio

What kinds of chemicals do bacteria produce to fight competitors and establish a niche in the microbiome?

bacteriocins, antibacterial proteins, and metabolites

What do gut microbiota produce when they break down complex carbohydrates? How does this help the host?

Short-chain fatty acids (SCFAs): Acetate, Propionate, and Butyrate. SCFAs play a role in metabolism and immunologic functions.

What is microbiome dysbiosis? What causes it?

A state in which the normal microbiome is altered or disrupted. Dysbiosis can be caused by antibiotics.

What is the main idea of the Koch postulates? How did this change over time?

Traditional view of disease. One organism: one disease. The Microbiome view of disease reveals that communities of organisms can be responsible for disease and disorders like IBD, Obesity, Type 2 diabetes, and Celiac.

What causes a Clostridium difficile infection?

Depletion of normal intestinal microbiota (usually due to exposure to antibiotics) can allow C. difficile spores to colonize the colon, causing inflammation.

What is ulcerative colitis? What causes it?

An IBD caused by an increase in the abundance of bacteria that produce mucin-degrading sulfatases. Degrades mucosal lining and leads to inflammatory response.

How can different microbiomes contribute to obesity?

Some individuals have gut microbiomes with higher efficiency to degrade complex carbohydrates, making them more susceptible to obesity and diabetes.

What is celiac disease? How does the microbiome play a role in its effects?

Chronic autoimmune disease triggered by exposure to gluten proteins. Most people house bacteria capable of degrading glutens. In the absence of these microbes, disease can occur.

What treatment has been used to prevent recurring C. difficile infections?

Fecal microbiota transplants (FMT)

What causes bacterial vaginosis?

Loss of lactobacillus and overgrowth of harmful bacteria in the vaginal region, causing raised pH, degradation of mucosal layer (discharge), irritation, and odor (amines).

What is IBD? What are two types of IBD?

Long term condition causing swelling and sores in the digestive tract. Includes Chron’s disease and Ulcerative Colitis

What causes IBD?

Genetic predisposition and environmental triggers lead to disruption of the epithelial barrier, which in turn affects the gut microbiome. Gut microbiome disruption further intensifies symptoms – chronic inflammation

What are probiotics and prebiotics?

Probiotics: Mixture of gram-positive bacteria or yeast that promote healthy metabolic function when ingested. Prebiotics: metabolic supplements, such as fibers, which promote the growth of gut microbiota.

What is 16s rRNA gene sequencing?

16S rRNA gene encodes for the RNA component of the small subunit of prokaryotic ribosomes. This nucleotide base sequence acts as a “molecular clock” that allows us to track species divergence. Acts as a “bar code” for bacterial species. One or several hypervariable regions are amplified using PCR.

How is 16S rRNA data analyzed?

Alpha diversity: A measure of community richness/diversity within each microbiome sample. Beta Diversity: a measure of community diversity between samples in
a study.

What is metagenomics?

Study all the genetic material from bacteria in a microbiome. Collection of genomes and genes from the members of a microbiota.

What are some important steps in processing metagenomic samples?

Important to collect sufficient biomass of microbial cells and minimize contamination of sample

What is shotgun metagenomics?

A sequencing method used to determine an organism’s genome. Microbial samples are extracted, cells are lysed to get DNA samples, and the DNA is cut into smaller pieces. The DNA fragments are then sequenced and translated to a file.

What are some limitations of 16S rRNA sequencing?

Drawbacks: Sequencing and computational costs, Biases/limitations of reference databases, Contamination from host DNA sequences, and DNA sequencing does not inform us of microbial activity.

What are HAIs?

Hospital acquired infections

What is an Infection Prevention Program?

Multidisciplinary team that performs several tasks with the goal to prevent and control
HAIs.

What are Standard Precautions (SPs)?

Hand hygiene, PPE, respiratory/cough hygiene, sharps safety, and care bundles.

What is IPP Surveillance?

Monitors the frequency and type of HAIs, investigates outbreaks, monitor compliance, effectiveness of IPPs.

What is targeted surveillance?

Most common, active type of surveillance that focuses on specific: patient-care areas, infections sites, certain organisms, and processes in infections

What types of PPE are commonly used?

Protective clothing, helmets, gloves, face shields, face masks,
respirators. Proposal disposal of PPE is important.

What is an AMS (Antimicrobial and Diagnostic Stewardship) program?

Programs designed to improve antibiotic prescribing. Limits selection pressures that drive antimicrobial resistance development.

Define sterilization.

Destruction of all microbes, including the bacterial spores, fungi, and viruses.

What is an autoclave?

Sterilization method. Uses saturated steam under pressure: inexpensive, non-toxic, reliable.

What are some other sterilization methods?

Ethylene oxide gas: flammable, explosive, and carcinogenic. Hydrogen peroxide vapors: Oxidizing nature of gas, used on instruments.

Define disinfection

Disinfection is not sterilization. Method of destroying microbes, but more resilient organisms can survive (example: spores). Can be categorized in high, medium, and low levels.

Provide examples of high-level disinfectants

Moist heat, glutaraldehyde, hydrogen peroxide, and chlorine compounds

Provide examples of intermediate-level disinfectants

alcohols, iodophor compounds, phenolic compounds

Provide examples of low-level disinfectants

Quaternary ammonium compounds

Define Antisepsis and give examples of antisepsis agents.

inhibiting/eliminating microbes on skin or other living tissue. Alcohols, Triclosan (in soaps and toothpaste), and Chlorohexidine.

What do Clinical Microbiology Labs do?

Aid in infection prevention via providing data for HAI surveillance, emerging pathogen detection, antimicrobial stewardship, develop organism banks, culturing, and genotyping.