Environmental microbiology Flashcards
What is environmental microbiology?
- Environmental microbiology is the study of the composition and physiology of microbial communities in the environment.
- The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas.
- Environmental microbiology also includes the study of microorganisms that exist in artificial environments such as bioreactors.
What is John Snow’s background?
- 1813 Born in York & at 14 was apprenticed to a surgeon.
- 1836, he moved to London to start his formal medical education.
- 1844 graduated University of London.
- 1850 admitted to the Royal College of Physicians
- Miasma theorists concluded that cholera was caused by particles in the air “miasmata”, which arose from decomposing matter/ other dirty organic sources.
- These particles were thought to travel through the air and infect individuals.
How did John Snow’s map change the world?
- He first publicised his theory in an 1849 essay On the Mode of Communication of Cholera
- Why would cholera not affect the lungs if it were an airborne disease?
- Why did it instead attack the bowels and cause dehydration and excessive diarrhoea?
- In August 1854, Soho in London was struck with a severe cholera outbreakcausing 600 deaths
- Snow talked to local residents and suspected that the source was the public water pump on Broad Street. Dot map to illustrate the cluster of cases around the pump and presented it to the council.
- The local council disabled the well pump by removing its handle (force rod).
- He showed the linkage between drinking contaminated water and spread of cholera
Accepting The Faecal Oral Route Transmission Model
- Post cholera epidemic government replaced the Broad Street pump handle.
- They only responded to the urgent threat posed to the population, and afterward they rejected Snow’s theory.
- To accept his proposal would have meant indirectly accepting the faecal-oral route
- 1866- William Farr, one of Snow’s chief opponents, realized the validity of his diagnosis when investigating another outbreak of cholera and issued immediate orders that un-boiled water was not to be drunk.
- Farr denied Snow’s explanation of how exactly the contaminated water spread cholera; he accepted that water had a role in the spread of the illness
Describe the properties of Vibrio cholera
- V.cholerae is a gram-negative curved rod
- 5-.8 μm width and 1.4-2.6 μm length
- Highly motile - flagellum
- Pili
- Non-spore-forming
- Oxidase positive - (determine production of cytochrome c oxidases)
What are the symptoms of Vibrio cholera?
Explain V. cholera Pathogenicity
- Ingestion of contaminated water or food.
- Passage through the acid barrier of the stomach.
- It colonizes the epithelium of the small intestine by means of the toxin-co-regulated pili, (haemagglutinins, accessory colonization factor, and core-encoded pilus).
- Cholera enterotoxin is secreted across the bacterial outer membrane into the extracellular environment.
- This disrupts ion transport by intestinal epithelial cells.
- Loss of water and electrolytes leads to the severe diarrhoea.
What is the laboratory diagnosis procedure for Vibrio cholerae serogroup O1 or O139?
- Fecal sample in a cup or Cary Blair medium
- Using a cotton swab, innoculate a tupe of 1% alkaline peptone water from the fecal sample
- After 6 hours of incubation, test the APW using the crystal violet VC
- If the dipstick is positive, confirm a sample of the positve samples by culturing using TCBS (Thiosulfate–Citrate–Bile Salts Agar)
- OPTIONAL- Place 2 drops onto protein saver card and allow to air dry to save DNA from APW for later confirmation using PCR
State the composition of Thiosulfate–Citrate–Bile Salts Agar (TCBS) and the purpose of each component
- Thiosulfate and sodium citrate →alkalinity of the medium & inhibit the growth of Enterobacteria.
- Ox bile and sodium cholate →Slow the growth of enterococci and inhibit the development of Gram-positive bacteria
- Bromthymol Blue & Thymol Blue →pH indicators Thiosulfate →Acts as sulfur source. production of hydrogen sulfide is visualized in the presence of ferric citrate.
- Yeast extract and peptone →Provides the nitrogen, vitamins, and amino acids
- Sodium chloride →Optimum growth and metabolic activity of halophilic Vibrio spp.
- Agar →Solidifying agent
Incubated aerobically at 35 to 37 ° C for 18 to 24 hours. If negative, incubate for an additional 24 hours.
Yemen cholera epidemic
- Scientists at Wellcome Sanger Institute & institute Pasteur used genomic sequencing, to estimate the strain of cholera causing the current outbreak in Yemen
- The worst cholera outbreak in recorded history—came from Eastern Africa and entered Yemen with the migration of people in and out of the region.
- The disease has affected over 1 million people and caused almost 2,500 deaths
Water Microbiology- Indicator Organisms
What are the properties of effective indicator organisms?
Indicators are easily detectable organisms whose presence correlates directly to one or more pathogens contaminating an environment.
- The indicator organism must be present when the pathogen is present, and the indicator organism must be absent when the pathogen is absent.
- The indicator organism’s concentration must correlate with the pathogen’s concentration. However, the indicator organism should always be found at higher numbers.
- The indicator organism should be able to survive easier & longer in the environment than the pathogen.
- Detection for the indicator organism should be easy, safe, & inexpensive.
- The indicator organism should be effective for all water types
What are coliforms
The presence of bacteria commonly found in human faeces, are called coliforms
What are the characteristics of coliforms?
- Rod-shaped
- Gram-negative
- Non-spore forming
- Motile or non-motile bacteria
- Lactose fermenters
- Production of acid & gas at 35–37°C
What are some typical indicator organisms?
- Escherichia
- Citrobacter
- Enterobacter
- Klebsiella
- Pseudomonas
- Clostridium
How is Most Probable Number (MPN) Analysis carried out?
- Add reagent to sample (sample will turn pink)
- Pour into Quanti-Tray or Quanti-Tray/2000
- Seal using a Wuanti-Tray sealer; incubate for 24 hours at 35°C
- Read under ultraviolet light; count blue fluorescent wells and refer to MPN table
What can MPN be used to estimate?
MPN is used to estimate the concentration of viable microorganisms in a sample by means of replicate liquid broth growth in ten-fold dilutions.
Few faecal coliform bacteria =water probably contains no disease-causing organisms
Presence of large numbers of faecal coliform bacteria = high probability that the water could contain organisms making the water unsafe for consumption.
Thermotolerant Coliforms can grow at 44.5°C
Describe the membrane filtration method
A busy microbiology laboratory
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What further tests can be carried out?
CATALASE TEST -when bacterial isolate is added to hydrogen peroxide catalasepositive bacteria will produce bubbles of oxygen
OXIDASE TEST- Identifies bacteria that produce cytochrome c oxidase, an enzyme of the bacterial electron transport chain.
MALDITOF
GRAM STAINING
Treatment of drinking water STEP 1: Coagulation
WHAT IS COAGULATION?
- Adding iron or aluminum salts, to the water (coagulants with a positive charge).
- The positive charge of the coagulant neutralizes the negative charge of dissolved & suspended particles in the water.
- When this reaction occurs, the particles bind together, or coagulate (flocculation).
- The larger particles, settle to the bottom of the water supply (sedimentation).
does not remove all of the viruses and bacteria
Treatment of drinking water STEP 2: Filtration
- Removes particulate matter from water by forcing the water to pass through porous media.
- The filtration system consists of filters with varying sizes of pores, and is often made up of sand, gravel and charcoal.
- Slow sand filtration removes bacteria, protozoa and viruses, and produces essentially clean water.
- Rapid sand filtration removes suspended particles, which may have bacteria attached, but in general does not remove bacteria, protozoa, or viruses.
Food contaminants: Food contaminated with microorganisms such as bacteria, yeasts, molds or viruses may pose a risk to the consumer
- Food contaminated with microorganisms such as bacteria, yeasts, molds or viruses may pose a risk to the consumer. Microorganisms can be found everywhere in the natural environment (water, soil, air, etc.)
- Microorganisms may naturally be present in foods or on the surfaces of foods (e.g. fresh vegetables) or added as contamination during the manufacturing process of food products (e.g. insufficient hygiene in meat processing). Pathogenic microorganisms are either not allowed at all to occur in the foodstuff or they are limited to a specified number of cells per gram food.
- If limits are exceeded, this might have tremendous consequences for consumer’s health.
- A zero tolerance per 25 g of food sample is predicted for most of all common pathogens (Salmonella, Campylobacter, E. coli, etc.)
Describe the detection Of Microorganisms in the food production Environment
Tests for cleaning and hygiene control detect general residues of foods on insufficient cleaned surfaces in the production environment.
These residues of nutrients are the basis for growth of microorganisms.
Colony counting in foods or on surfaces can be done using the ready-to-use Compact Dry plates.
Residues of foods on surfaces can be detected using protein tests (RIDA®CHECK) or ATP measurements (LuciPac™Pen).
What is the procedure for use of Compact Dry™ plates?
- 1ml of liquid sample to the plate and the sample will diffuse evenly throughout the media.
- Dry samples can be collected and hydrated using the Compact Dry™ Swab. (swab, mix and apply)
- Once grown, the colonies are pigmented with different colours, developed by chromogenic substrates and redox indicators.
- Bacteria is identified by its colour
