Microbiology FAQs. Course and Journal

Microbiology (Academic Subject and Medical Department)

Meaning of Microbiology: Microbiology is one of the branches of biology. It is to study the morphological structure, growth and reproduction of various micro-organisms (bacteria, actinomycetes, fungi, viruses, Rickettsia, mycoplasma, chlamydia, spirochete protozoa and single-cell algae) at the molecular, cellular or population level. It is also a name of medical department that studies and applies the subject.

It also studies physiological metabolism, genetic variation, ecological distribution and taxonomic evolution and other basic laws of life activities, and apply it to science in the fields of industrial fermentation, medical hygiene and bioengineering. Microbiology is a science that studies the laws of life activities and biological characteristics of various tiny organisms. 

Discipline Name:    Microbiology

Subject:    Biology

Definition:    One of the branches of biology studying micro organisms

Historical origin:    Longshan Cultural Period more than 4000 years ago

Taxon:    Boundary, phylum, gang, order, family, genus, species

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Table of Content

    1 Definition

    2 Disciplines

    3 Historical origin

    ▪ Experience stage

    ▪ Morphological stage

    ▪ Physiological stage

    ▪ Biochemistry stage

    ▪ Molecular biology

    4 Types

    ▪ Overview

    ▪ Two world system

    ▪ Five World System

    ▪ Three Realms (Domain) System

    5 Features

    6 Function

    7 Research direction

    ▪ Specific application

    ▪ Pathogen diagnosis

    ▪ Participate in clinical consultation

    ▪ Participate in antibacterial drugs

    8 Naming

What is the Definition of Microbiology?

Microbiology Definition: To study the laws of life activities such as microbial morphology, physiology and biochemistry, genetic variation, ecological distribution and taxonomic evolution, and apply them to the science of practice fields such as industrial fermentation, medical hygiene, bioengineering and environmental protection. 

Microbiology as a Subject

Microbiology  is an important basic course or professional basic course that must be opened in the biology majors of colleges and universities. It is also the theoretical and technical foundation of modern high-tech biotechnology.

 Genetic engineering, cell engineering, enzyme engineering and fermentation engineering are formed and developed on the basis of microbiology principles and technologies.

Microbiology is also one of the important cornerstones for the development of biological majors and the modernization of agriculture and forestry in higher agricultural and forestry colleges. With the widespread application of biotechnology, microbiology will have a huge impact on the production activities and lives of modern and future humans.

Historical Origin

Experience stage

Since ancient times, human beings have been aware of the life activities of microorganisms and their roles in daily life and production practices. China's history of using microbes to make wine can be traced back to the Longshan Cultural Period more than 4,000 years ago.

The sauce making technology was invented 2600 years ago. The oracle bone inscriptions of the Yin and Shang Dynasties were inscribed with the word "wine". 

The Northern Wei Jia Sixie's "Qi Min Yao Shu" (533 - 544), lists the methods of cereal koji, wine, sauce, vinegar and pickles.

On the stone carvings left in ancient Greece, the operation process of wine making is recorded. 

During the Spring and Autumn period and the Warring States Period, China has used microbes to decompose organic substances to accumulate manure.

 In the 1st century AD, The Book of Pan Sheng Sheng proposed a system of cooked manure fields and intercropping of melons and adzuki beans. 

In the second century "Shen Nong's Materia Medica", there are records of white silkworm curing disease. 

In the 6th century "Zuo Zhuan", there is a record of Maiqu treating diarrhea. 

In the "Golden Book of Medical Sect" of the 10th century, there are records about the method of vaccination.

In 1796, the British Jenner invented the vaccinia vaccine, which laid the cornerstone for the development of immunology.

Morphological stage

In the 17th century, the Dutch Levin Hook observed a tartar, rainwater, well water, and plant infusion with a simple microscope (magnified 160 to 260 times)

Later, it was discovered that there were many "tiny animals" in motion, and the different forms of bacteria (spherical, rod-shaped and spiral-shaped) that were first seen by humans were scientifically recorded in words and pictures. 
Soon after, Italian botanist P. A Mikkeli also observed the morphology of the fungus with a simple microscope.

In 1838, the German zoologist C. G. in the book "Ciliates are Real Organisms", Ellenberg divided the class of ciliates into 22 families, including 3 families of bacteria (he regarded bacteria as animals), and created bacteria (bacteria).

 In 1854, the German botanist F. J. Coase discovered the spores of rod-shaped bacteria. 

He attributed the bacteria to the plant kingdom and determined the taxonomic status of the bacteria in the next hundred years.

Physiological stage

Microbiology research has entered the stage of physiology since the 1960s. 

French scientist L. Pasteur's research on microbial physiology is now showing results.

Microorganism

Modern microbiology laid the foundation. Pasteur, who was a chemist, dabbled in microorganisms to treat "wine disease" and "silkworm disease." 

He argued that the brewing of wine and vinegar and the spoilage of some substances are fermentation processes caused by certain types of microorganisms, not microorganisms produced by fermentation or spoilage.

The famous flask experiment confirmed this irrefutably. He believes that fermentation is the respiration of microorganisms in an environment without air. 
Deterioration of wine is the result of the growth of harmful microorganisms. 
He further proves that different types of microorganisms have unique metabolic functions, each requires different living conditions and causes different effects. 

He Proposed a heating sterilization method to prevent wine deterioration, which was later known as the Pasteur sterilization method. Using this method, the newly produced wine and beer can be stored for a long time.

 Koch has made great contributions to the emerging medical microbiology. Koch first demonstrated that Bacillus anthracis is the causative agent of anthrax.

He then found the causative bacteria of tuberculosis and cholera, and advocated the use of disinfection and sterilization methods to prevent the spread of these diseases.

 His students also found diphtheria, pneumonia, tetanus and plague. The pathogenic bacteria, etc., led to a high degree of attention to bacteria at that time and for decades to come.

He pioneered the method of bacterial staining, using agar as a coagulation medium to cultivate bacteria and isolate single colonies to obtain a pure culture operation process.

He stipulated the methods and steps for identifying pathogenic bacteria, and proposed the famous Koch law. In 1860, the British surgeon J. Lister applied sterilization of drugs and created a sterile surgical operation method.

 In 1901, the famous bacteriologist and zoologist H. H. Mechenikov discovered that the leukocytes engulfed the bacteria and contributed to the development of immunology.

C. Russian-born French microbiologist H. Vinograds was based on the discovery of sulfur bacteria in 1887 and nitrifying bacteria in 1890, he said it proves the microbiological process of sulfidation and nitrification in soil and the energy-energy characteristics of these bacteria.

He first discovered anaerobic autotrophic nitrogen-fixing bacteria, and used inorganic media, selective media, enrichment culture and other principles and methods to study the life activities of various physiological groups of soil bacteria, revealing the involvement of soil microorganisms in the transformation of soil materials.

This role laid the foundation for the development of soil microbiology.

In 1892, the Russian plant physiologist D. H. Ivanovsky found that tobacco mosaic pathogens are smaller than bacteria, can pass through bacterial filters, and can't be observed by optical microscopes. They are called filter viruses. 

From 1915 to 1917, F. W. Twett and F. H. De Herre observes the presence of plaque on bacterial colonies and bacteriolysis in the culture fluid, and finds the bacterial virus, bacteriophage.

The discovery of viruses has expanded people's concept of biology from cell morphology to non-cell morphology.

In this stage, the creation of microbial operating techniques and research methods is a unique symbol of the development of microbiology.

Biochemical stage

Since the 20th century, the penetration of biochemistry and biophysics into microbiology, coupled with the invention of electron microscopes and the application of isotope tracer atoms, has promoted the development of microbiology to the biochemical stage.

 German scholars in 1897 Bishner found that the cell-free extract of yeast can have the same effect of fermenting sugar liquid as ethanol to produce ethanol, thus recognizing the enzymatic process of yeast alcohol fermentation, combining the life activities of microorganisms with enzyme chemistry.

G. Neuberger et al.'S research on yeast physiology and analysis of alcohol fermentation intermediates, A. J. Kleivo's research on microbial metabolism and the research direction of comparative biochemistry he pioneered.

A series of basic physiological and metabolic pathway studies conducted by many other people using E. coli as materials have clarified the metabolic laws.

The basic principles of controlling its metabolism, and on the basis of controlling the metabolism of microorganisms, expand the use of microorganisms, develop enzymology, and promote the development of biochemistry.

Since the 1930s, people have used microorganisms for industrial production of ethanol, acetone, butanol, glycerin, various organic acids, amino acids, proteins, oils and so on.

In 1929, A. Fleming found that Penicillium can inhibit the growth of Staphylococcus, revealed the antagonistic relationship between microorganisms and discovered penicillin.

In 1949, S. A Waxman discovered streptomycin based on the accumulated data of his years of research on soil microorganisms. Since then, more and more new antibiotics have been discovered. 

In addition to medical treatment, these antibiotics are also used to prevent and control animal and plant diseases and food preservation.

What is Molecular Biology?

In 1941, G. W. Biddle and E. L. Tatum irradiates Alternaria alternata with X-rays and ultraviolet rays to mutate and acquire nutritional deficiencies type. 
Their research on auxotrophy can not only further understand the role and nature of genes, but also lay the foundation for molecular genetics.

In 1944, O. T. Avery confirmed for the first time that the substance that causes the transformation of pneumococcal capsular genetic traits is deoxyribonucleic acid (DNA).

 In 1953, J. D. Watson and F. H. C. Crick proposed the double helix structure model of DNA molecules and the semi-retained replication theory of nucleic acids. 

H. Frankel-Conrad et al., through the tobacco mosaic virus recombination test, proved that ribonucleic acid (RNA) is a carrier of genetic information and played an important role in laying the foundation of molecular biology.

Since then, it has successively discovered important theories in microbiology such as the mechanism of action of transporting ribonucleic acid (tRNA), the theory of gene triple coding, the fine structure of viruses and the process of infection and proliferation, and the mechanism of biological nitrogen fixation which shows the broad application prospects of microbiology.

In 1957, A. Kornberg and others successfully performed in vitro DNA assembly and manipulation. 
Research on gene recombination of prokaryotic microorganisms has continued to make progress. 

Insulin has been fermented and produced using gene-transferred E. coli, and interferon has also been produced using bacteria.

The research of modern microbiology will continue to deepen at the molecular level, and to the depth and breadth of production.

What are the Branches of Microbiology?

After more than a century of development, microbiology has differentiated a large number of branch disciplines. According to incomplete statistics (1990), it has reached 181.

According to its nature, it can be simply summarized into the following 6 categories:

1. According to the study of the basic life activities of microorganisms, the general subject is called General Microbiology, and the sub-disciplines such as microbiology taxonomy, microbial physiology, microbial genetics, microbial ecology and molecular microbiology, etc.

2. According to the researched microbial objects such as bacteriology, mycology (mycology), virology, prokaryotic biology, autotrophic bacteria biology and anaerobic bacteria biology, etc.

3. According to the ecological environment where microorganisms are located, such as soil microbiology, microecology, marine microbiology, environmental microbiology, water microbiology and cosmic microbiology.

4. According to the field of microbiology, the general subject is called Applied Microbiology (Applied Microbiology), sub-disciplines such as industrial microbiology, agricultural microbiology, medical microbiology, medicinal microbiology, diagnostic microbiology, antibiotics, food microbiology, etc.

5. According to the interdisciplinary and interdisciplinary integration, chemical microbiology, analytical microbiology, microbial bioengineering, microbial chemical taxonomy, microbial numerical taxonomy, microbial geochemistry and microbial informatics, etc.

6. According to experimental methods and techniques, such as experimental microbiology, microbiological research methods, etc.

Kind

The meaning of microorganisms: non-taxonomic nouns, from the French word "Microbe". Is a small body, single cell or individual structure is very small.

Generic term for cells, even lower organisms without cell structure.

Type: Microorganisms are very diverse, including: cell-free viruses, viroids, viroids, etc.,

Bacteria, actinomycetes, rickettsiae, chlamydia, etc. belonging to prokaryotes.

Yeasts and molds belonging to eukaryotes, unicellular algae, protozoa, etc.

Two world system

Animalia: There is no cell wall, it can be moved, and there is no photosynthesis.

Plantae: It has a cell wall, does not move, and can carry out photosynthesis.

Three Realms

Protista: (E.H. Haeckel, proposed in 1866)

Five World System

1. Monera in prokaryotes: bacteria, actinomycetes, etc.
2. Protista in the protozoa: algae, protozoa, slime molds, etc.
3. Fungi: yeast, mold
4. Animalia
5. Plantae

The five-world system is based on the level of cell structure differentiation and the types of tissues related to the three main nutritional modes of photosynthesis, absorption, and feeding. 

Six realms plus the virus realm.

Three Realms (Domain) System

Woese compared the 16SrRNA sequences of more than 60 strains of bacteria with the oligonucleotide sequence catalog analysis method, and was surprised to find that the methanogenic bacteria were completely E.coli

E.coli

There are no sequences that are characteristic of bacteria, so a third form of life is proposed-archaebacteria. Subsequently, he conducted a 16SrRNA (18SrRNA) sequence analysis and comparison of a large number of strains, including certain eukaryotes. 
He found that extreme halophilic bacteria and extreme acidophilic bacteria are the same as methanogens.

Bacteria are also different from the sequence characteristics of their nuclear organisms, and they share many common sequence characteristics. So it was proposed to divide the organism into three kingdoms (later renamed the three domains):

1. Archaea
2. Eubacteria
3. Eukaryotes

 In 1990, in order to avoid treating archaebacteria as a type of bacteria, he renamed the three realms (domains): Bacteria (bacteria), Archaea (archaea), and Eukarya (eukaryotes), and constructed Phylogenetic tree of the three realms (domains).

Features

1. Small size and large specific surface area

The size of microorganisms is measured in μm, but the specific surface area (surface area / volume) is large, there must be a huge nutrient absorption, metabolic waste excretion and environmental information receiving surface.

This feature is also the key to distinguishing microorganisms from all large organisms.

Examples:

• Lactobacillus: 120,000
• Eggs: 1.5
• Human (200 pounds): 0.3

2. Absorb more and transform faster

This feature provides a sufficient material basis for high-speed growth and reproduction and the production of large amounts of metabolites.

For example: 3 grams of hamsters consume food equivalent to body weight.

1 gram of hummingbird consumes twice the weight of food per day.

Escherichia coli consumes 2000 times the weight of sugar per hour. Lactose-fermenting bacteria can kill within 1 hour It can decompose lactose equivalent to 1,000 to 10,000 times its own weight to produce lactic acid.

1 kg of yeast cells can ferment thousands of kilograms of sugar in one day to produce alcohol

3. Prosperous growth and fast reproduction

Very high growth and reproduction speed, such as E.coli split once every 20-30 minutes, if it keeps splitting, 48 hours 2.2 × 10 ^ 43 bacterial count increase, nutrient consumption, metabolic accumulation, limit growth rate. This feature can transform a large number of substrates into useful products in a short time and shorten the scientific research cycle.

There are also downsides, such as disease and mold mildew. For example: Escherichiacoli (E. coli) can divide cells every 12.5-20 minutes under the most suitable growth conditions.

In liquid medium, the concentration of bacterial cells is generally 108-109 cells / ml.

Brevibacterium glutamicum : Shake flask seeds → 50 tons fermentor: The number of cells can be increased by 3.2 billion times in 52 hours.

Using this characteristic of microorganisms, short-cycle, high-efficiency production in the fermentation industry can be achieved. For example, when producing fresh yeast, it can be harvested almost every 12 hours and hundreds of times a year.

4. Strong adaptability and easy mutation

Extremely flexible and adaptable, with amazing adaptability to extreme environments, genetic material is easily mutated. What is more important is that there are many types of microbial physiology and metabolism, and many kinds of metabolites.

For example: microbes have been found in sedimentary rocks of 10,000 meters deep sea, 85 kilometers altitude, 128 meters below ground and 427 meters below ground.

The number of microorganisms, according to 1972:

Types of |  Lower Limit |  Predisposed Species | Higher Limit

Virus and Rickettsia | 1217 |  1217                        | 1217

Mycoplasma             |  42    |  42                            |  42

Bacteria and actinomycetes |> 1000 | 1500            | 1500

Cyanobacteria           |1227  |1500                          | 1500 

Algae                        |15051 |  23100                     | 23100 

Fungus                      |37175 |  47300                     | 68939

Protozoa                    |24068 | 24068                      | 30000

Total                          |79780|  98727                     | 127298

5. Wide distribution and variety

Wide distribution area and wide distribution environment. There are many types of physiological metabolism, many kinds of metabolites and many kinds. 

More important is the physiological metabolism of microorganisms.

Penicillin

There are many types and many kinds of metabolites. Microorganisms can be found in any environment where other organisms survive, and microbes exist in extreme environments where other organisms cannot survive.

For example: Penicilliumchrysogenum (penicillium chrysogenum) yields 20 units of penicillin per milliliter of fermentation broth in 1943.

Over the past 40 years, through the unremitting efforts of microbial genetic breeding workers from all over the world, the variation in the production of this fungus has gradually accumulated.

Coupled with the improvement of fermentation conditions, the fermentation level of advanced countries in the world has exceeded 50,000 units per milliliter, or even close to 100,000 units.

Variations in the quantitative traits of microorganisms and the extent to which breeding increases yields are absolutely impossible to achieve in animal and plant breeding.

Because of this, almost all microbial fermentation plants attach great importance to strain selection.

6. Easy to mutate and produce mutation

The small individual microorganisms and large specific surface area make the microorganisms susceptible to environmental conditions. 

The changes in ultraviolet rays, biological mutagens, and certain nutrient factors in the environment cause the individual microorganisms to consciously and be forced to produce genetic structure changes, resulting in Variants.

According to statistical natural conditions, the probability of individual microbial variation is 1 in 1 million.

Because microorganisms are prone to producing mutants, people use the characteristics of microorganisms to carry out microbial mutagenesis, and then select strains of microorganisms with certain characteristics, such as increased yield and auxotrophy.

 

What are the Effects of Microbiology?

1. Role in the material cycle in nature

2. Air and water purification, sewage treatment

3. Industrial and agricultural production: bacteria, metabolites, metabolic activities

4. Contribution to life sciences

 

Research Direction

Microbiology subject direction: China is one of the countries with the richest microbial resources in the world.

Microbial resource research reflects the level of microbiology basic research. 

It is the basis of national situation investigation, resource protection, development and sustainable use.

It is the basis of biodiversity research and endangered species protection, including microbial molecular biology and biotechnology. It is the foundation of various branches of microbiology.

Research in this field will accelerate the investigation, collection, and systematic classification of micro-physical resources, expand the collection of microbial strains and specimens, and establish a microbial species resource library, making it the largest collection center of microbial strains in Asia and the largest in Asia.

Mycobacterium herbarium. Introducing new methods, new technologies and new ideas in systematic taxonomy research, carrying out biodiversity, system evolution, microbial ecology research, and providing materials for large-scale screening of functional substances.

Among them, extreme microorganisms and microorganisms that are harmful or beneficial to crops. The research has gradually become the current hot research field.

The major research directions of microbiology include: fungi and lichenology, microbial resources, taxonomy, systematics, diversity, population genetics and evolution, cooperative metabolic molecular mechanisms, environmental microbiology, industrial microbiology, systems biotechnology, microbial physiology, microbes Physiology, microbial metabolism, microbial ecology, microbial biochemical engineering, molecular virology, molecular immunology.

Concrete Application

Modern clinical microbiology is an interdisciplinary subject combining clinical medicine, basic medicine and preventive medicine, and it is also one of the important and mature majors in laboratory medicine.

This emerging discipline requires microbiologists and laboratory technicians to work together. 

There are four specific tasks:

1.  Make rapid and accurate test reports on microbiological specimens to meet clinical needs in a timely manner
2.  Conduct antimicrobial resistance Various trials on medicinal properties, accepting consultation on the rational application of antibacterial drugs.
3.  Closely integrating with the clinic, discussing, researching and dealing with issues related to infectious diseases with clinicians.
4.  Participating in the management and rational use of antibacterial drugs in clinical applications Hospital infection monitoring, control and management. This requires that clinical microbiology workers not only complete the laboratory work, but also complete the relevant clinical work, and become the staff and consultant for infection control and clinical application of antibacterial drugs.

Etiological Diagnosis

1. Ensure the reliability of clinical specimens: proper specimen collection is the most important step in the diagnosis of infectious diseases.

Clinicians are required to correctly collect clinical specimens that can represent the site of infection.

Protective swabs, qualified containers, and transport media are widely used to avoid the death of microorganisms in the specimens due to toxic substances.

2. Fully understand the normal flora of the body: Understanding the normal flora of the human body is a necessary prerequisite for bacterial testing.

It is necessary to understand the concept, distribution and types of normal flora, conditional pathogens and endogenous infections, dysbiosis and double.

In the concept of infection, neither the bacteria isolated from all specimens should be regarded as pathogenic bacteria, nor the endogenous infections caused by normal hermit bacteria.

3. Combination of three definitions and one: Qualitative, quantitative and localization analysis should be done during separation and identification, and combined with the condition.

It is required to determine the inspection procedure according to the specific situation of the clinical and specimen, select the medium and the appropriate identification test.

To determine whether the isolated bacteria are pathogenic bacteria, conditional pathogenic bacteria, or non-pathogenic bacteria (qualitative), at the same time there should be a rough estimate of the number of bacteria, if necessary, semi-quantitative and quantitative cultivation.

Bacteria isolated in parts of the human body must be judged with reference to the qualitative and quantitative analysis of microorganisms.

If bacteria are isolated in sterile parts (such as blood and cerebrospinal fluid), no matter what kind of microorganisms and the number of them, they are important meaning (location analysis).

When conducting the three determinations analysis, we must combine the condition and observe whether it is consistent with the condition.

4. Provide fast and accurate etiological diagnosis: when clinicians provide clinical diagnosis information and appropriate clinical specimens of patients, and obtain epidemiological data as much as possible, microbiological examination and antimicrobial sensitivity tests are required.

Comprehensive analysis of test results, provide clinical and accurate etiological diagnosis, in order to make appropriate treatment for patients.

Although the isolation and identification of microorganisms is still the gold standard for pathogenic detection, this traditional "bacterial growth" -based traditional bacteriological identification method is slow and cannot meet the clinical needs, requiring direct inspection of specimens as the basis, such as morphology, staining, antigen detection and nucleic acid detection (nucleic acid hybridization,

PCR and 16S rRNA analysis), detection of pathogenic genes (pathogenic islands, virulence islands) and drug resistance genes, as much as possible in rapid diagnosis.

5. Timely reporting: To effectively convert laboratory data into clinically useful information, the pathogen microbiological diagnosis report should implement a three-stage reporting system, that is, when a smear or culture positive result appears, when a sensitive test result comes out, and after the final result comes out Report in time.

6. Strengthen quality control and increase inspection items:

The clinical microbiology laboratory must strengthen quality control to ensure the inspection quality of various specimens, provide a reliable basis for the clinic, and meet various clinical inspection needs.

The current clinical microbiology laboratory should add inspection items according to the actual situation of the unit. 

Some items that are concerned by clinical requirements are:

 1) bacteriological screening and semi-quantitative cultivation methods of respiratory specimens

 2) detection of atypical pathogens of respiratory tract, including chlamydia and mycoplasma Legionella

 3) Culture and drug sensitivity of non-tuberculous mycobacteria

 4) Detection of special pathogens in patients with immunosuppression or organ transplantation, such as cytomegalovirus, Pneumocystis carinii, etc.

5) Pathogens of antibiotic-related diarrhea ( Mainly Clostridium difficile) detection

6) rapid detection of invasive fungi and drug sensitivity tests.

Participate in clinical consultation

(1) Obtain clinical information and make timely and accurate microbiological reports

Clinical infectious diseases often involve multiple pathogens, and no single test can detect all potential pathogens. Therefore, clinical information is an important reference basis for selecting test methods. 

Clinicians should write out the speculative diagnosis of the patient when opening the test order, so that the laboratory personnel can choose a reasonable test procedure and test method based on this, and can guide the clinic to correctly collect the appropriate specimen. When the laboratory begins to have experimental results clinicians must be notified in time to allow them to re-evaluate the diagnosis and treatment plan.

(2) Interpretation and consultation of difficult microbial reports

Many infectious diseases, especially the spectrum of pathogens and drug sensitivity spectrum of hospital infections, have undergone great changes. 

In the past, rare microorganisms have frequently appeared on the inspection report, and there have been many changes in the methods of drug sensitivity tests, tested varieties, and interpretation of results.

Clinicians often have difficulty understanding and using clinical microbiological testing data. 

Faced with this situation, the clinical microbiology department should actively communicate with the clinic to help:

• Solve the difficulties of clinicians in interpreting the microbiological examination and drug sensitivity report.
• Identify the identification and judgment of normal flora, contaminated bacteria and infected bacteria.
• The significance of rare or rare bacteria. 
• Possible causes when cultured negatively. 
• The criteria and limitations of drug sensitivity test results.
• The resistance characteristics of special drug-resistant bacteria, etc. If necessary, add comments to the report.

(3) Setting up a microbiologist as a bridge between clinical and microbiology

Many foreign hospitals have a consultation and consultation system of clinical microbiologists or laboratory physicians. 

If there is a problem with the smear at the beginning of the test, the laboratory physician will actively contact the clinic to discuss the significance of the smear.

Every day, the doctors and technicians in the microbiology department look at the culture and drug sensitivity results together, especially the sputum culture results should be checked with the direct smear, and if problems are found, contact the ward in time.

It is recommended that a doctor in the clinical microbiology department participate in the morning meeting of the Department of Infection, Respiratory Medicine or ICU of the hospital every day, and come back to report the situation of the infected patient to the physician in the department.

Or regularly send a doctor to bring the relevant test results, participate in infection seminars in some clinical departments, and specifically solve the treatment of infectious diseases.

For example, if you participate in seminars such as ICU, transplantation, oncology, neurosurgery and pediatrics, for patients with positive blood culture, positive cerebrospinal fluid test, or severe burn infection, microbiologists should take the initiative to visit the ward and participate in the discussion of treatment options.

For patients with bacteremia or sepsis, help to find the primary focus. After visiting the patient, the clinical microbiologist should record the opinions on the medical record. 

If necessary, discuss with the clinical doctor in charge and the director.

Each clinical department can contact the clinical microbiology department if they have infection problems, inquire about the significance of the test report or request a consultation.

The Department of Microbiology holds a weekly discussion of infection cases to discuss the situation of infected patients, communicate the problems found, and communicate the opinions of the clinical microbiology department with the clinical departments.

Microbiologists should also participate in daily inspection work and accept clinical consultations on microbiological issues.

Participate in antibacterial drugs

Reasonable application of antibacterial drugs to reduce or avoid the emergence of resistant strains is a major problem in the field of anti-infection. 

The clinical microbiology laboratory plays an important role in the rational use of antibiotics.

First, we must pay attention to the etiological diagnosis of infection. 

Clinicians should collect multiple microbiological specimens for bacterial culture and drug susceptibility testing before using antibacterial drugs, and the microbiology department provides fast and accurate bacterial testing and drug susceptibility results for the clinic.

In addition, close contact between microbiologists and clinicians and participation in the treatment of patients are also important ways to control the amount of antibiotics. 

Microbiologists should participate in the hospital's pharmacy committee, participate in the development of antibiotic use guidelines, education and training, supervision and inspection.
 In this regard, the practice of the Hong Kong Mary Hospital is that the infection monitoring nurse is responsible for visiting the infection cases. 

When the antimicrobial drugs are misused or unreasonably used, the director of the microbiology department will give feedback to the dean, director of the department and the parties concerned, and good results have been achieved.

Participate in the monitoring, control and management of hospital infection

Most countries' “Hospital Infection Management Standards” clearly states that the laboratory should perform the following duties in the management of hospital infections:

To be responsible for the monitoring of routine microbiology of hospital infections

To carry out the cultivation, isolation and identification, drug susceptibility tests and drug resistance of special pathogens.

Sexual monitoring, regular summary, analysis, feedback to the relevant departments, and announcement to the whole hospital.

When the hospital infection is prevalent or outbreak, undertake the relevant testing work.

The role of clinical microbiology laboratories in the monitoring, control, and management of hospital infections includes:

(1) strengthening pathogenic monitoring as the basis for determining hospital infections

(2) strengthening drug resistance monitoring to guide the rational use of antibiotics

(3 ) Strengthen microbiological surveys of the environment and equipment to meet the requirements of hygienic indicators

(4) Ensure the quality of disinfection and sterilization in the hospital

(5) Through epidemiological surveys and bacteriological typing tests, trace the source of infection and carry out control.

(i) Strengthen monitoring

The Clinical Microbiology Department is an inevitable member of the Hospital Infection Control Committee. Microbiology testing plays an important role in the monitoring of hospital infections.

If a hospital infection problem is found in the clinical microbiological examination, it is necessary to contact the hospital infection control department, ward doctor and head nurse in time, and pay attention to the development trend.

Some special drug-resistant bacteria in hospital infections, such as GRE, MRSA and ESBL-producing Enterobacteriaceae bacteria, are often transmitted through cross-infection.

Aspergillus and Legionella are often present in air conditioning, water supply systems, and atomization devices and cause infection. 

The sources carrying these pathogenic bacteria are routinely monitored and reminded of clinical attention, which can usually effectively prevent spread and save a lot of anti-infection costs.

(ii) Education and training of hospital infection

The clinical microbiology department should participate in the education and training of nosocomial infections for relevant personnel.

For example, to explain the requirements and precautions for the collection. Storage and transportation of clinical microbiological specimens. 
What preparations should be made to patients before specimen collection. 
What timing and location should be selected for specimen collection. 
How many times a day to collect, how much to collect, and sampling locations. 
A series of problems such as how to disinfect should be explained. Training on the normal flora, colonization bacteria, contaminated bacteria and infectious bacteria common in the human body.

The detection and significance of various bacterial resistance enzymes and their significance in the selection of antibiotics Regular communication with the clinic, etc. 

Various methods such as lectures, seminars, newsletters, posters, and even participation in rounds can be used. 
It can also be integrated into continuing education and training programs for hospital infection management.

(iii) Participate in the management of disinfection and isolation

The correct and scientific implementation of disinfection and isolation technology is very important for the prevention and control of nosocomial infections.

Correct guidance and supervision of disinfection and isolation is also one of the tasks of the clinical microbiology department. 

When an outbreak of nosocomial infection or special drug-resistant bacterial infection occurs, clinical microbiology professionals should participate in the formulation of disinfection and isolation measures, and provide professional opinions on microbiology for relevant personnel management and waste disposal.

(4) Regular release of bacterial resistance monitoring results

The choice of antimicrobial agents for many infectious diseases is empirical. But empirical medication also requires the support of evidence-based medicine and epidemiological data.
 It is recommended to keep all the pathogen isolation and drug susceptibility data with WHONET software, regularly publish the bacterial resistance monitoring results, at any time to statistically analyze the distribution and resistance status of common pathogens in key departments such as ICU, select antibiotics for clinical experience, and improve severe infections.

 The success rate of treatment is very helpful.

(5) Controlling hospital infection through molecular typing technology

Commonly used molecular typing techniques include PFGE, RAPD, etc. A molecular typing laboratory is set up in the microbiology laboratory to carry out routine typing of drug-resistant bacteria that are more harmful and more prevalent, which is of great significance for the timely detection and control of the prevalence of pathogenic bacteria.

The practice of some foreign hospitals is to conduct molecular typing of uncommon drug-resistant bacteria such as VRE as soon as they are discovered. 

Based on the genotyping, determine the possibility and scope of epidemics and take corresponding measures to control the infection. For example, a hospital classified 19 strains of VRE isolated from 16 patients within 2 months. 

The results showed that 14 strains were of one type and the others were of one type, which highly indicated the prevalence of VRE. 

After investigation and analysis, it was found that 14 Eleven of the patients have direct contact. 

Based on these analyses, targeted control measures were taken to stop the infection. 

Other hospitals address the prevalence of infections such as Klebsiella pneumoniae, Staphylococcus epidermidis, Staphylococcus hemolyticus and Serratia marcescens, all controlled by molecular typing. 

According to statistics, the cost of establishing a molecular typing laboratory (equipment and personnel) in the microbiology room is $ 180,050, and the annual molecular typing-related expenditure is $ 400,000. 

Assuming that all hospitals (United States) routinely perform molecular typing, the experiment-related costs amount to $ 2 billion. , But the cost of saving hospital infections will be more than 5 times (10 billion).

Name

Taxonomic unit of microbes: boundary, phylum, phylum, order, family, genus, species.

Species are the most basic taxonomic units, and each taxonomic unit can be followed by sub-phyla, subclass, suborder, subfamily.

Taking beer yeast as an example, its status in taxonomy is:

• Kindom: Fungi
• Door (Phyllum): Fungal door
• Class: Ascomycetes
• Order: Endospora
• Family: Endosporaceae
• Genus: Saccharomyces
• Species: Beer Yeast

Species (species): is a basic taxonomic unit. It is a general term for a large group of strains with highly similar phenotypic characteristics and extremely close genetic relationships, which are significantly different from other species in the same genus.

i. Strain means any purebred population and all its progeny (a group of purebred progeny bacteria that originated from a common ancestor and maintained the characteristics of the ancestor) and are produced by a single cell that is isolated and reproduced.

Therefore, pure cultures of different sources of a microorganism can be called a strain of the strain.

The strain emphasizes a pure genetic lineage. 

For example: two strains of Escherichia coli: EscherichiacoliB and EscherichiacoliK12.

Representation of strains: If the species is the basic unit of taxonomy, the strain is actually the basic unit of application, because different strains of the same strain will have very different types of enzymes or metabolite production. difference!

ii. Subspecies (variety): reclassification within species.

When there are a few obvious and stable variation characteristics or genetic traits of different strains within a certain species, but they are not enough to distinguish them into new species, these strains can be subdivided into two or more small taxa-sub Species.

Variant is a synonym for subspecies, because the word "variant" is likely to cause confusion in the meaning of the word.

Since 1976, the word variant is not used. Generally, the mutant strains obtained in the laboratory are called subspecies.

For example: E.colik12 (wild type) does not require special aa, and after laboratory mutation, a defective type of aa can be obtained from k12, which is called E.colik12 subspecies.

iii. Form: often refers to the subdivision below subspecies. When the traits of different strains within the same species or the same subspecies are not enough to be divided into new subspecies, they can be subdivided into different types. 

For example: Divided into different serotypes according to the difference of antigen characteristics

Naming of microorganisms: There are two types of microorganisms: common names and scientific names. Such as: Red bread mold-Neurospora crassa. Pseudomonas aeruginosa-Pseudomonas aeruginosa.

Scientific name-is the scientific name of microorganisms, it is named according to the rules formulated by the International Committee on Classification of Microorganisms. The scientific name consists of Latin words, or Latinized foreign words. 

There are two ways of naming scientific names: double name method and three name method. 

i. Dual name method: scientific name = generary name + species name + (first time celebrity name) + current celebrity name + year name name:

Latin noun or adjective used as a noun, singular, capitalized, indicating the main characteristics of microorganisms, Constructed by microorganisms, shaped or named by scientists.

Species: Latin adjectives with lowercase initials, which are secondary characteristics of microorganisms, such as microbial pigments, shapes, sources or names of scientists.

 Example: Escherichiacoli (Migula) Castellaniet Chalmers 1919

Staphylococcus aureus Staphylococcusaureus Rosenbach1884 

When referring to a certain genus of microorganisms, but not specifically to one of the genus (or unspecified species name), you can add sp. Or ssp. (Representing the singular and Plural form).

• For example: Saccharomycessp. Represents a species in the genus Saccharomyces. Strain name: add numbers, place names or symbols after the species name, for example: BacillussubtilisAS1.389AS = AcademiaSinica
• BacillussubtilisBF7658BF = Beifang
• Clostridiumacetobutylicum ATCC824 Clostridium acetobutylicum
• ATCC =  American Type Culture Collection

When a scientific name has appeared in the front of the article, the genus name can be abbreviated to 1 to 3 letters in the back.

For example: Escherichiacoli can be abbreviated as E.coli

Staphylococcusaureus can be abbreviated as S.aureus

ii. Three names method: This is usable to name sub-species, then add a subsp. After the genus and species name, and then attach the subspecies name (italic).

For example: Bacillusthuringiensissubsp. Galleria Bacillus thuringiensis.

Author's Bio

Dr. Shawna Reason

Name: Shawna Reason

Education: MBBS, MD

Occupation: Medical Doctor / Virologist 

Specialization: Medical Science, Micro Biology / Virology, Natural Treatment

Experience: 15 Years as a Medical Practitioner

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