test 4 micro
I. Skin Diseases
Skin Anatomy and Defenses
Skin Layers:
Epidermis: Outermost layer. Cells actively grow and divide, migrating towards the surface. The top layer is dead and filled with keratin. This is a 30-day process overall. The keratinized epidermis is a tough protective component. Epidermal cells are continuously removed.
Dermis: Lies beneath the epidermis. Composed of connective, fibrous tissue. Contains nerves, muscles, the lymphatic system, and sebaceous glands.
Subcutaneous: Innermost layer. Contains fat cells.
Skin Defenses:
Tough, keratinized epidermis.
Continuous removal of epidermal cells.
Sebaceous secretions: Maintain a low pH, which is inhibitory to some microbes.
Sweat: Salty and maintains a low pH.
Lysozymes: Found in sweat, tears, and saliva.
Normal Skin Flora
Populations vary greatly depending on the location (e.g., dry locations like the back may have less).
Includes Diphtheroids, Micrococci, and yeasts.
Staphylococcus epidermidis: Lives on nutrients from the skin and produces antimicrobial substances.
Propionibacterium acnes: Involved in the development of acne.
Abnormal Flora
Many individuals carry Staphylococcus aureus on their skin and in the nasopharynx area.
Skin infections caused by Streptococcus pyogenes and Staphylococcus aureus
Commonly caused by S. pyogenes and/or S. aureus.
Impetigo:
A superficial infection.
Characterized by peeling of the outer layers of the epidermis.
S. aureus exfoliating toxins, which are coded for by a phage, contribute to the peeling.
Leads to pus-filled lesions.
Cellulitis:
Involves invasion of the dermal and subcutaneous layers.
Extremely painful.
Can be caused by S. aureus, S. pyogenes, and several other bacteria.
Treated with antibiotics.
Can be problematic for individuals with diabetes due to reduced blood flow to extremities; any lesions can lead to infection.
Scalded Skin Syndrome:
Caused by S. aureus.
Exfoliative toxins move systemically through blood vessels.
Affected infants are susceptible to secondary infections.
Treatment is similar to that for a burn victim, focusing on hydration and sterile skin.
Treated with antibiotics.
Toxins degrade desmosomes (filaments connecting skin cells), causing skin cells to fall apart.
The infection is more serious in adults.
Staphylococcus aureus Wound Infections:
The bacterium is commonly found on the skin or in nasal passages.
Produces a variety of virulence factors. Not all S. aureus strains have every virulence factor.
Key virulence factors include:
Protein A: Embedded in the gram-positive membrane, travels through peptidoglycan. Binds to the constant region of antibodies to immobilize them, protecting the bacteria from the immune system.
Clumping factor: Embedded in the membrane, travels through peptidoglycan. Binds to fibrinogen, helping the bacteria stay in place.
Foreign material like a suture greatly enhances the risk of wound infection.
Multiple antibiotic resistance is a serious problem.
MRSA (Methicillin-Resistant Staphylococcus aureus):
A significant form of antibiotic-resistant S. aureus.
In 2017, 125,000 people were infected, resulting in almost 20,000 deaths.
85% of cases were associated with the healthcare system.
The threat of community-acquired MRSA is rising, particularly among healthy people in close proximity.
Around 75% of S. aureus cases were MRSA.
Vancomycin treatment is still effective, but some VRSA (Vancomycin-Resistant Staphylococcus aureus) strains have developed.
Invasive hospital-acquired MRSA infections declined by 54% from 2005-2011, while community-acquired cases declined by only 5% during the same period.
Clusters are found in groups like athletes, military recruits, children, and prisoners.
Shared through personal items (towels, razors, tweezers).
Can live on surfaces contaminated with body fluids.
Treatment involves antibiotics or infection drainage.
Necrotizing Fasciitis:
Known as "Flesh-eating bacteria".
A rapid, invasive infection.
Can be caused by S. aureus, S. pyogenes, and several other bacteria.
Pathogens produce toxins and enzymes, such as hyaluronidase, which digest connective tissue.
Rapid treatment with surgery and antibiotics is essential.
Streptococcal Toxic Shock:
Similar to S. aureus Toxic Shock Syndrome (TSS).
Can occur within a week of symptom onset.
May lead to organ failure, tissue shutdown, coma, or death.
Rapid surgery and antibiotic treatment are necessary.
Varicella-Zoster Virus (a herpesvirus)
Causes Chickenpox and Shingles.
Chickenpox:
Affects only humans.
Primarily a childhood disease.
A vaccine has been available since the mid-1990s.
Much more serious in adults and immunocompromised individuals.
Skin lesions can become infected by bacterial pathogens.
Pre-natal infection is very serious.
Entry is via the respiratory tract or contact.
Moves through the bloodstream to the skin, where a characteristic rash forms.
Immunity for life is usually acquired after recovery.
The virus can become dormant (latent) in thoracic nerves.
Shingles:
Reactivation of the dormant virus in thoracic nerves.
A shingles vaccine is now available.
Reactivation is often triggered by a compromised immune system.
Blister pustules contain live virus and can be transmitted to children, causing chickenpox.
Lyme Disease
First recognized in the mid-1970s.
Can pose a long-term health risk.
Cases clustered in Lyme, Connecticut initially.
Approximately 25,000 new cases occur yearly, making it the most common vector-borne disease in the United States. It is not restricted to the Northeast.
Causative agent is Borrelia burgdorferi.
A large, gram-negative spirochete.
A cousin to the bacteria causing syphilis.
Zoonosis: Humans, dogs, and cats are accidental hosts. It is widespread in the U.S..
Vectors: Several tick species are vectors; the Deer tick (black-legged tick) is the main one. Ticks mature during a 2-year cycle.
Reservoirs: Ticks and mice are the main reservoirs of B. burgdorferi. Deer spread the bacteria.
Cycle: Female ticks lay uninfected eggs; larvae infect mice; mice can be reservoirs and infect larvae.
Early symptoms include a localized infection with a target rash (erythema migrans).
The disease can take up to 6 months for symptoms to fully disappear.
Smallpox Virus
Historically significant as it was the first disease for which vaccination was widely practiced.
Lady Montagu in 1721 observed and introduced variolation (using fluid from smallpox pustules) to England from Turkey. Variolation had a death rate of up to 3%.
Edward Jenner in 1796, a British physician, developed the first true vaccine from smallpox. He noticed milkmaids who got cowpox (Vaccinia virus) did not get smallpox.
The smallpox vaccine is made from live, attenuated Vaccinia virus (cowpox).
It had a relatively high rate of side effects, including a few deaths per million vaccinations and about 1 in 1000 adverse reactions.
Smallpox was the first major disease to be eradicated.
The WHO eradication campaign started in 1967; the last natural case was in Somalia in 1979.
Global eradication was possible because all of the following criteria were met:
There are no subclinical infections; all cases are readily identified.
The virus is eliminated from the body upon recovery; there are no chronic carriers.
Humans are the only host; there are no animal reservoirs.
An effective vaccine was available.
There are still concerns about the bioterrorism threat posed by the virus.
Virus characteristics:
A large, double-stranded DNA virus with ~200 genes.
It is the only DNA virus that does not replicate in the host nucleus.
It carries the enzyme DNA-dependent RNA polymerase.
It codes for DNA polymerase, RNA polymerase, and mRNA maturation functions.
It is a tough virus that can survive well outside the cell.
II. Gastrointestinal Infections
Sanitation is Key for preventing most gastrointestinal infections.
GI Tract Defenses
Supports large and diverse microflora populations that compete with pathogens.
Saliva contains lysozyme and lactoferrin.
The stomach has a low pH.
A mucus layer is present throughout the entire GI tract.
Gut-associated lymphoid tissue provides immune function.
Bacterial Toxins
Exotoxin: A toxin secreted by bacteria, typically protein in nature. Can cause damage to the host by destroying cells or disrupting normal cellular metabolism.
Enterotoxin: A type of exotoxin that specifically targets the intestine, usually causing diarrhea and vomiting.
Endotoxin: A toxic substance bound to the bacterial cell wall and released when the bacterium ruptures or disintegrates. Endotoxins consist of lipopolysaccharide and lipoprotein complexes. An endotoxin that targets the intestines is also called an enterotoxin.
Helicobacter pylori
Causes Gastric ulcers. High levels are often found in individuals with stomach cancer.
A gram-negative bacterium.
Discovered by Robin Warren and Barry Marshall (won the 2005 Nobel Prize). Marshall famously ingested H. pylori to demonstrate its role.
Adapted to survive in the stomach by secreting urease, which converts urea to CO2 and basic ammonia, neutralizing the stomach acid around the bacteria.
Invades and digests the mucus layer, allowing stomach acid to leak and cause ulcers.
Common in healthy people.
Humans are the major, if not only, reservoir.
Transmitted person-to-person via fecal-oral or oral-oral routes.
Stress and diet may trigger disease development.
Could potentially have beneficial roles, such as acid control and influencing appetite.
Vibrio cholerae
Causes Cholera.
A gram-negative, comma-shaped bacterium.
First isolated by Koch.
Invades the small intestine.
Produces an Enterotoxin (Cholera toxin, an exotoxin with A and B factors).
The toxin causes massive loss of ions and fluids by preventing intestinal absorption.
A large infectious dose (10^6-10^8 cells) is needed.
Death can result if fluids are not replaced; most people die from dehydration. Rehydration therapy is important and the most common treatment.
Transmitted almost exclusively through contaminated water supplies, occasionally shellfish.
Not a major problem in countries with good sanitation and public health.
Causes 3-5 million cases and 100,000 deaths yearly worldwide.
The gene for the cholera toxin is acquired and expressed via lysogenic conversion: a lysogenic phage (CTX phage) genome integrated into the bacterial cell genome expresses gene products (cholera toxin) that affect the phenotype of the host bacterium.
Treatment includes salt solution, intravenous fluids, and antibiotics may be used. Hydration therapy is most common.
The Haiti outbreak in October 2010, following the January 2010 earthquake, was caused by the collapse of the country's water, sanitation, and health systems. It resulted in >386,000 cases and 5,885 deaths by July 2011.
John Snow, an English doctor, conducted a classic epidemiological study in 1854, determining that contaminated water (specifically the Broad Street Well) was the source of a cholera outbreak by mapping cases and shutting off the well.
E. coli
Causes Gastroenteritis.
Most E. coli are harmless members of the normal intestinal flora.
Pathogenic strains cause mild to very severe diarrhea and cramps.
Transmission is fecal-oral, usually through contaminated food or drink (can include ruminants as sources).
Antibiotics may make things worse for certain strains by causing the release of toxins.
Rehydration therapy is important.
Types of pathogenic E. coli:
Enterohemorrhagic E. coli O157:H7 (STEC): First described in 1982. O and H refer to antigen numbers. Causes severe, bloody diarrhea. Hemolytic uremic syndrome (kidney failure) can develop. Shiga Toxin genes are carried on a phage via lysogenic conversion. A 1993 outbreak in Washington state was traced to undercooked hamburgers. Recent outbreaks have been linked to contaminated produce.
Enterotoxigenic E. coli: Makes two types of toxin. The cause of "Traveler’s diarrhea". Can be life-threatening in infants.
Enteroinvasive E. coli: Invades mucosal cells of the large intestine.
Enteropathogenic E. coli: Similar to STEC but does not produce toxin. Causes significant infant mortality in developing countries.
Salmonella
S. enterica affects the stomach and GI tract (Salmonellosis).
S. typhi (associated with Typhoid Mary) can enter all the body’s cells.
Prevention is best achieved by proper handling and cooking of food.
Very common, with possibly 2 million cases yearly in the U.S..
Rehydration therapy is important.
Some strains cause typhoid fever: they multiply in macrophages and are carried throughout the bloodstream. Humans are the source for these strains.
Most cases originate from non-human sources.
Produces an Enterotoxin that targets the intestines.
Pet reptiles can pose a risk, as Salmonella is part of the normal microflora of most reptiles. The CDC recommends that households with children under 5 years old do not keep reptiles as pets. Careful hand washing and hygiene are essential. A ban on the sale of small turtles in the U.S. was enacted in 1975.
Campylobacter jejuni
A gram-negative, rod-shaped, motile bacterium.
One of the most common causes of diarrhea in the U.S..
Very low infectious dose, less than 500 bacteria.
Common in domestic animals, especially poultry feces.
Spread is food or waterborne; person-to-person transmission is very rare. It is considered a zoonosis.
Intestinal infection can last over two weeks.
Produces an Enterotoxin derived from exotoxins.
Causes diarrhea, fever, nausea, and vomiting.
Most individuals recover without treatment.
Prevention includes proper cooking, pasteurization, and sanitation.
Clostridium difficile (antibiotic diarrhea)
A gram-positive, endospore-forming, rod-shaped bacterium.
Found in normal intestinal flora.
Disease often follows antibiotic therapy that eliminates competing microbes.
Can cause severe inflammation and sloughing off of layers of cells.
Often leads to chronic infections.
Very painful and can result in death.
Transmission is fecal-oral, especially common in nursing homes and other healthcare settings.
Can also live in soil and water and persist as endospores.
Treatment involves appropriate antibiotics (sometimes) or a fecal transplant.
Antibiotic resistance is a particular problem.
Viral Gastroenteritis
Caused by Rotavirus and Norwalk virus (Norovirus).
Both are spread by the fecal-oral route.
Have a very low infectious dose.
Infect small intestine epithelial cells.
Cause nausea, vomiting, and diarrhea.
Lasts a few days to a week.
Prevention by hand-washing and sanitation.
Rotavirus: Causes the death of millions of children every year in developing countries. Common in livestock, with high morbidity and mortality; genetic exchange occurs.
Norwalk virus: Causes the majority of food poisoning outbreaks on cruise ships. Humans are the only known reservoir.
Porcine Epidemic Diarrhea Virus (PEDV)
A coronavirus.
Fecal-oral transmission.
Causes a high mortality rate in baby pigs (> 90%).
Pigs are the only host.
Now widespread in the U.S..
Food Poisoning (distinct from gastrointestinal infections)
Caused by pre-formed toxins, meaning bacterial growth is not required in the host.
Results in vomiting and severe diarrhea.
Has a short incubation period, typically just a few hours.
Staphylococcus aureus is an important cause. It makes heat-stable toxins that bind receptors in the bowels, stimulating the medullary centers and causing vomiting.
May also be caused by toxins of non-microbial origin, such as arsenic, fertilizer, pesticides, or mercury.
III. Respiratory Diseases
Mucociliary Escalator
Composed of cilia lining the trachea and bronchi.
Propels material, including microbes trapped in mucus, up and out of the respiratory tract.
Swallowing, coughing, and sneezing help move microbes out.
Infections like influenza can cause infected epithelial cells to die, compromising this defense mechanism.
Normal flora of respiratory system
Competes with invading pathogens and helps prevent colonization.
Resident microflora may include some potential pathogens like Streptococcus pyogenes, Staphylococcus aureus, Streptococcus pneumoniae, and Neisseria meningitidis.
COVID-19
Abbreviation for coronavirus disease 2019.
Caused by SARS-CoV-2.
A single-stranded RNA virus (genes coded in RNA). Specifically, it's a positive-stranded RNA virus.
Part of the Coronavirus family, which is large and common in people and many animal species like camels, cattle, cats, and bats. The name comes from the crown-like appearance under electron microscope.
Virus structure includes proteins with key functions in its cycle:
Spike proteins (S): Mediate attachment to host cells via their ACE-2 receptors. They are heavily glycosylated and form distinct surface spikes. They utilize an N-terminal signal sequence for access to the endoplasmic reticulum and are cleaved by host cell proteases.
Nucleocapsid protein (N): Binds to and packages the viral RNA genome.
Envelope protein (E): A transmembrane protein involved in virus assembly and release; needed for pathogenesis.
Membrane protein (M): The most abundant protein, promotes membrane curvature and binds the nucleocapsid.
Hemagglutinin esterase dimer protein (HE): Found in some coronaviruses, enhances cell entry and virus spread.
Attaches to cells via ACE-2 receptors and replicates in the respiratory tract. ACE-2 receptors are found in various locations in the body.
The virus can multiply deep in the lungs and enter the bloodstream.
Its recent emergence is likely from an animal reservoir, spreading via human-to-human transmission.
Symptoms and signs vary from mild to severe, appearing 2-14 days after exposure.
Common symptoms include fever, cough, and shortness of breath.
Seek medical attention for trouble breathing, persistent chest pain/pressure, confusion, inability to get up, or blue lips/face.
Can cause mild follicular conjunctivitis.
Prevention: Disinfection (viral envelope susceptible to >70% alcohol) and masks (reduce spread of viral particles).
Treatment: No specific medicine for prevention or treatment mentioned. Self-care like rest, fluids, warmth, humidifiers/steam for symptoms are suggested.
Tests are primarily PCR-based (RNA detection) or serological (antibody detection).
Vaccination challenges mentioned include the virus not reproducing well in chicken eggs (unlike flu) and the financial risks posed by the pandemic without knowing safety and efficacy.
Long Covid is a risk not linked to the initial symptom severity. A study showed ~5-8% of patients have persistent symptoms past 4 weeks.
Influenza
Annual epidemics are a concern, with 3,000-49,000 deaths/year in the US.
Seasonal flu: Causes 80-90% of flu-related deaths in individuals ≥ 65 years old. Flu season in the US is typically Oct-May. The seasonal vaccine targets the strains predicted to be most common. Traditional vaccines are quadrivalent (protect against 4 viruses), usually heat killed; nasal mist is attenuated. Vaccines are commonly made in chicken eggs, but mammalian cells or recombinant methods (using HA protein) can also be used.
1918 Spanish flu: Killed over 50 million people globally. Predominantly affected previously healthy young adults. Killed through a cytokine storm (overreaction of the immune system). Started in birds. Spread through sneezes/coughs (up to half a million particles). Had high mortality (up to 20% overall, 70% in pregnant women). Showed a W-curve mortality pattern. Research has involved reconstructing this virus.
H1N1 pandemic: First seen in the US in Spring 2009. Very contagious, spreading person-to-person. Spread worldwide; most cases were mild to moderate. High-risk groups for complications included pregnant women, young children, diabetics, asthma, heart disease, etc..
Avian flu ("Bird Flu") strains (H5N1, H7N9): H7N9 was deadly to humans but not birds 10 years ago; now deadly to birds (<24hr death for chickens) and still deadly to humans (>1/3 die). H5N1 has been spreading since 2005 and has a high human mortality rate. Both H5N1 and H7N9 do not spread easily person-to-person currently, but there are fears they could make that jump. Research has manipulated H5N1 to be more transmissible in ferrets, leading to discussions about "gain-of-function" research risks and ethical implications.
Symptoms include cough, weakness, fatigue, muscle aches.
Transmission is via aerosol, inhaled into the lungs.
Secondary lung infections often follow.
Complications are serious in the very young, elderly, pregnant women, and immunocompromised.
Influenza viruses infect birds, hogs, horses, seals, and other mammals.
Vaccines are available and needed annually.
The virus shows significant immunological variation. Concerns exist about the next pandemic.
Antigenic drift: The influenza virus genome is variable, with frequent mutations in surface glycoproteins (HA and NA) recognized by the immune system. This is the reason for the need for a new flu shot every year.
Antigenic shift: Occurs when two different flu viruses infect the same host, allowing viral genome segments to be swapped. This can result in a new virus totally unrecognized by the human immune system. Influenza A virus has 8 RNA segments coding for 11 genes.
Pneumonia
Defined as inflammation of the lungs, where alveoli fill with fluid.
Can infect one or both lungs.
Caused by bacteria or viruses.
Common Bacterial Pathogens: Streptococcus pneumoniae, Legionella pneumophila, Haemophilus influenzae, Mycoplasma pneumoniae, Klebsiella pneumoniae.
Common Viral Pathogens: SARS, COVID-19, Hantavirus, Influenzas, Respiratory syncytial virus.
Causes > 2 million cases and 45,000 deaths annually in the U.S..
Early symptoms are similar to the common cold, including fever, chest pain, difficulty breathing, and discolored sputum.
Tuberculosis (TB)
Caused by Mycobacterium tuberculosis.
Characteristics: Acid fast, lipid-rich cell wall, resistant to disinfectants and drying. It is a rod-shaped bacterium.
Spread is via the respiratory route.
Has a low infectious dose.
Infects lungs, lymph nodes, etc.. Can multiply within macrophages and migrate within them throughout the body.
Symptoms include chronic fever, weight loss, and cough.
Chronic/latent infections can often reactivate.
Prevention: A vaccine is used in some countries.
Treatment: Antibiotics are used, but resistance is a problem. Long-term antibiotic therapy (up to 12 months) is needed.
The Tuberculin test is used for early detection.
A related bacterium, Mycobacterium paratuberculosis, causes Johne’s disease, an intestinal disease of ruminants.
Globally, 1/3 of the world population harbors TB bacteria (~2 billion people).
M. tuberculosis is an important pathogen attacking patients with AIDS. HIV and TB co-infections are very problematic worldwide, especially in developing nations. 1/3 of HIV-infected people are co-infected with M. tuberculosis. TB is a cause of death for many suffering from AIDS.
Whooping Cough
Caused by Bordetella pertussis.
An encapsulated, gram-negative, rod-shaped bacterium.
Attaches to host cells for survival. Produces virulence factors that damage tissue. Contains LPS with unusual structures.
An upper respiratory infection.
Early symptoms are similar to the common cold.
Followed by violent cough attacks where gasping for air makes a "whooping" sound.
Extremely serious in babies under 6 months old.
Highly contagious.
Treatment with antibiotics is available.
Vaccination and boosters are needed for prevention.
Common Cold
Over 75% of cases are caused by Rhinoviruses.
Rhinoviruses are small (20 nm), icosahedral particles with a single-stranded RNA genome.
Over 100 different strains or serotypes are known. Exposure to one strain does not protect against future infections by other strains.
Rhinoviruses are members of the Picornavirus family, which includes poliovirus and foot and mouth disease virus.
Infects mucous membranes lining the nose and throat.
Can survive several hours on skin and up to 4 days on inanimate surfaces.
Aerosol spread is the most common mode of transmission; sneezing is very effective at spreading the virus.
Causes 62 million cases yearly in the U.S., resulting in 45 million missed days of school or work.
Most infections remain symptomless.
Symptoms (coughing, sneezing, runny nose) are primarily caused by the body’s immune response to the infection.
Stress can increase the severity of symptoms.
Symptoms typically last about one week.
IV. Sexually Transmitted Diseases (STDs)
STD Facts
20% of people in the US have had an STD.
50% of sexually active individuals will contract an STD by age 25.
There are 19 million new cases in the U.S. each year.
More than 65 million people are living with an incurable STD.
The U.S. has the highest STD infection rate of any developed country.
Women suffer more from serious complications than men.
Viral STDs are as common as bacterial ones. Viral STDs are often incurable.
Bacterial STDs
Gonorrhea
Caused by Neisseria gonorrhoeae.
A gram-negative diplococcus, non-motile.
Transmitted via sexual contact or to a newborn at birth.
Affects only humans, infecting the penis, vagina, anus, mouth, or eye.
Symptomless infections are common (10% of infected males, 50% of infected females).
Symptoms include painful urination and discharge.
Causes 700,000 new cases in the U.S. every year.
Condoms are effective in preventing transmission.
Antibiotic treatments are effective, but antibiotic resistance is a problem.
Infection rates and serious complications are higher in women, including Pelvic Inflammatory Disease (affecting > 1 million women annually).
Infection of newborns can lead to blindness.
Chlamydia
Caused by Chlamydia trachomatis.
A small gram-negative bacterium.
An obligate intracellular pathogen, meaning it lacks a peptidoglycan-based cell wall.
Humans are the only reservoir.
Symptoms and signs are similar to Gonorrhea.
Newborns can also become infected.
Causes 3-4 million cases each year in the USA.
Condoms can prevent transmission.
Treated effectively with antibiotics, such as Azithromycin.
It is the #1 cause of infertility worldwide. Antimicrobial drug resistance is an important problem.
Viral STDs (as common as bacterial but often incurable)
Genital Herpes (herpes simplex virus HSV-1 and HSV-2)
Very common and often asymptomatic. An estimated 45 million people in the U.S. have had a genital HSV infection.
Causes painful lesions or blisters on the genitalia.
HSV-1 typically causes oral cold sores, while HSV-2 is the most common cause of genital infections; however, both can cause either type of infection.
They are enveloped, icosahedral DNA viruses.
Infection of newborns and infants can be fatal. Cesarean sections are common if the mother has an active infection to reduce the chance of transmission during delivery.
Herpes viruses can become latent. Reactivation results in new lesion outbreaks.
Antiviral drugs may help manage symptoms but do not cure the infection.
Condoms provide some, but not complete, protection as lesions may be outside the protected area.
Human Papillomavirus (HPV)
There are over 40 different strains.
May be the most widespread STD; 75-80% of sexually active individuals acquire HPV at some point. It is the most common STD in the U.S..
Causes genital warts.
Some high-risk strains infect the cervix and can lead to cancer (genitals, mouth, throat). The Pap smear test is used for screening.
The Gardasil vaccine was approved by the FDA in 2006. It protects against 4 strains (6, 11, 16, 18) responsible for 70% of cervical cancers and 90% of genital warts. It is not effective against other HPV strains.
The Advisory Committee on Immunization Practices (ACIP) recommends the vaccine for children ages 11-12. No serious side effects are listed.
It is a non-enveloped DNA virus.
Zika Virus
Spread mostly by the bite of an infected Aedes species mosquito (Ae. aegypti and Ae. albopictus), which bite during the day and night.
Can also be passed from an infected person to a sexual partner.
Can be passed from a pregnant woman to her fetus.
Infection during pregnancy can cause certain birth defects, notably microcephaly. There is a very high correlation between Zika infection during pregnancy and microcephaly in the newborn.
There is currently no vaccine or medicine for Zika.
Local mosquito-borne Zika virus transmission has been reported in the continental United States.
Typically causes a mild flu-like infection.
It is an enveloped, single-stranded RNA virus.
Human Immunodeficiency Virus (HIV) / Acquired Immune Deficiency Syndrome (AIDS)
AIDS is the clinical condition resulting from advanced HIV infection.
AIDS is considered the most significant new infectious disease to emerge during the 20th century.
Over 40 million people are currently infected worldwide; over 20 million have died. New infections occur every 6 seconds, and deaths every 5 minutes.
It is a zoonosis originating from African chimpanzees. Probable spread to humans occurred during butchering chimpanzees for meat in the 1920s in the Democratic Republic of Congo.
AIDS in humans was described in 1981, but probably existed since the 1950s.
The HIV-1 virus was isolated in 1983 by Dr. Luc Montagne (who won a 2008 Nobel Prize).
HIV is transmitted in humans by body fluid exchange. This includes during sexual activity, via contaminated blood transfusions, through contaminated needles used by intravenous drug users, and via perinatal transmission. AIDS can be prevented.
HIV is a retrovirus with an RNA genome. It is an enveloped virus.
The enzyme reverse transcriptase is packaged inside the viral particle. Reverse transcriptase converts the viral RNA into cDNA (a DNA copy). This effectively reverses the usual direction of transcription (DNA to RNA). (This corresponds to option D in a study question).
HIV primarily targets CD4 T-cells (also called TH cells or Helper T-lymphocytes), which recognize antigens presented on MHC II. HIV-1 infection kills these cells.
AIDS develops during the late stages of HIV-1 infection when CD4 T-cell populations become very low, severely compromising the immune system.
Death typically occurs due to opportunistic infections and cancers that invade following the collapse of the immune system. Examples include Encephalitis, Meningitis, Retinitis, Pneumocystis pneumonia, Tuberculosis, various Tumors (lungs, skin, GI), Esophagitis, and Chronic diarrhea.
As noted earlier, HIV/AIDS and TB co-infections are very problematic globally. 1/3 of HIV-infected individuals worldwide are co-infected with M. tuberculosis. TB is a common cause of death for those suffering from AIDS.
Treatment involves drug therapy targeting viral enzymes and functions. Drug mechanisms include inhibition of viral entry, integrase, maturation, reverse transcriptase (nucleoside and non-nucleoside types), and protease.
Development of an effective vaccine is difficult due to the virus's high mutation rate and the lack of a good animal model.
Prevention is the best approach to AIDS management.
Highly Active Anti-Retroviral Therapy (HAART) is the standard treatment. It's a combination or "cocktail" of drugs, typically two reverse transcriptase inhibitors plus one protease inhibitor, potentially also including a fusion or integrase inhibitor. HAART is highly effective and reduces the chance of drug resistance. However, it has high cost and serious side effects. It is not a cure; the virus is not eliminated from the body.
As of 2018, a person in the US diagnosed with HIV has no shorter life expectancy than someone without HIV.
STD Transmission During Pregnancy and Birth
Some STDs can be passed from mother to infant during delivery, often due to skin-to-skin contact as the infant passes through an infected birth canal. Examples include Chlamydia, Gonorrhea, Genital herpes, and Cytomegalovirus (CMV).
A few STDs can infect the fetus before birth during pregnancy by migrating into the placental fluid. Examples include Syphilis, HIV, and CMV.
A cesarean delivery may be recommended to reduce the chance of transmission for certain STDs/STIs during delivery.
V. Soil and Plant Microbes
Importance of Microbes
Microbes play crucial roles in maintaining the health of natural and managed ecosystems.
They are important in biogeochemical cycles, such as the carbon and nitrogen cycles.
In ecosystems, microbes function as producers, consumers, and decomposers.
Soil Environment
Soil is a very complex environment (physical, chemical, biological).
It's important to consider the soil environment at the microhabitat level.
Soil Organisms
Includes micro-organisms (bacteria, fungi, actinomycetes, protozoans, viruses, nematodes, metazoans, algae) and macro-organisms (insects, earthworms, plant roots and seeds, soil animals).
Soil communities can include over 4000 species per gram.
Microorganism distribution varies with soil depth. Estimates are conservative as most soil microbes cannot be grown in culture.
Microbial biomass in soil
For surface soil, estimates include approx. 670 lb/acre of bacteria and approx. 703 lb/acre of fungi.
Competition among soil microbes
Competition is intense in the soil environment; many microbes have antagonistic relationships.
They compete for organic and inorganic nutrients; active microflora keeps nutrient levels low.
Interactions include parasitism, predation, and antibiosis (production of antibiotics).
Almost all medicinal antibiotics used today come from soil-borne actinomycetes, bacteria, and fungi. Little is known about antibiotic production levels or function in the natural soil environment.
Rhizosphere
The thin layer or volume of soil immediately surrounding the plant root.
Nutrients (exudates like organic acids, amino acids, sugars, polysaccharides) leach into the rhizosphere soil from the roots.
Microbial activity is intense due to this nutrient input. The microflora is diverse.
Fungistasis (soils naturally preventing fungal germination) is overcome in the rhizosphere due to nutrient input.
Similar phenomena occur in the spermosphere (soil surrounding a seed).
Significant C transfer from plants to the soil (10-40% of fixed C) occurs in the rhizosphere. This is analogous to gut microflora.
Benefits of the rhizosphere microflora for the plant:
Make minerals (N, P, K, Fe) available to the plant.
Secrete chemicals (plant hormones) that influence root growth.
Create an environment favoring the growth of beneficial microbes.
Protect the plant root from pathogenic microbes.
Symbiotic Relationships of Roots and Microbes
Relationships are beneficial for both partners.
Not all parasites are pathogens; parasitism is a nutritional term, while a pathogen damages the plant. Some parasites can be beneficial.
Nitrogen-Fixing Root Nodules:
Found in legumes.
Involves the soil bacterium Rhizobium.
Rhizobium invades legume roots and forms root nodules. They enter via root hairs and an infection thread, developing into bacteroids within enlarged host cells.
Discovered by Beijerinck in 1887.
This symbiotic relationship benefits both: Rhizobium obtains nutrients, and atmospheric nitrogen is fixed and made available to the plant.
Mycorrhizae ("fungus root"):
Symbiotic relationship involving plant roots and fungi.
The fungi obtain nutrients from the root.
The plant benefits from more efficient uptake of water and nutrients, especially phosphorus.
Benefits include increased mineral/water uptake, nutrient storage/release, increased tolerance to stress (salinity, metals, infertile soil), and disease resistance.
Two main types:
Endomycorrhizae: Fungus penetrates root cortical cells, forming arbuscules (arbuscular mycorrhizal fungi). The fungus is inside the root cells. These are ancient relationships, found in 400 Ma fossils.
Ectomycorrhizae: Fungus is located between the root cells. They take materials leeched from the cell. Hosts include conifers and some broadleaf trees (oaks, beech, willow).
Rhizobium bacteria fix nitrogen while Mycorrhizae fungi do not. This statement is True.
Plant Pathogenic Microorganisms
Include Phytoplasma (EM), Nematodes (LM), Bacteria (EM), Fungi (LM), and Viruses (EM).
Examples of plant disease symptoms include Bacterial wilt (e.g., banana), Rust fungus (e.g., oats), Tobacco mosaic virus, and Soybean cyst nematode.
Virulence factors that help pathogens attack plants
Plant cell wall-degrading enzymes.
Toxins.
Plant growth regulators (hormones).
High molecular weight polysaccharides and glycoproteins.
Molecules that suppress plant defense responses.
Plant Disease Resistance
Plants lack T cells, B cells, antibodies, and phagocytic cells.
They have evolved various mechanisms to defend against pathogen attack.
Defense mechanisms include:
Production of anti-microbial compounds called phytoalexins.
Production of enzymes that degrade pathogen cell walls.
Production of structural barriers to pathogen colonization, such as stomatal closure and lignification. Plant cells produce wall material that becomes lignified to resist pathogen penetration. Lignification resists pathogen enzymes.
Rapid death of infected cells, known as the hypersensitive response.
Plant cells have receptors that recognize Pathogen-associated molecular patterns (PAMPs), similar to innate immunity in animals. Examples of plant receptor analogs include NOD, TOLL, and RIG.
Examples of PAMPs recognized by plants:
Bacteria: Peptidoglycan, LPS, Flagellin.
Fungi: Chitin, Mannans, Ergosterol.
Viruses: Double-stranded RNA.
The Zig-Zag model describes the ongoing evolutionary arms race between plants and pathogens, involving plant recognition of PAMPs versus pathogen suppression and evasion.
Stomata allow for gas exchange (CO2 in, O2 and water vapor out) but also serve as entry points for bacterial pathogens into the leaf.
Stomatal closure is a defense; plant receptors perceive flagellin, causing stomata to close.
However, pathogens can produce effector molecules like coronatine, which cause stomata to reopen.
Plant populations show significant genetic variation for disease resistance. Plant breeders utilize this variation to develop resistant plants.
Genetic engineering tools are now used to create plants with new types of resistance.
VI. Biofuels from Microbes
Environmental Microbiology and Biofuels
Microbes can be utilized to produce biofuels.
Discussed types include Biogas (Methane), Bioethanol, and Biodiesel.
Biogas (Methane)
Produced from materials like manure, sewage, and plant material.
Process involves anaerobic digestion by a consortium of microbes. Methanogenic archaea are responsible for producing the methane gas (CH4).
Often an important energy source in the developing world.
Methane can also be recovered from landfills.
Bioethanol
Ethanol is a fermentation product.
Saccharomyces cerevisiae (yeast) is critical in brewing (anaerobic ethanol production).
Corn-based ethanol is considered a short-term solution, as the energy output typically only breaks even with energy input.
Cellulosic Ethanol production utilizes biomass feedstock like plant residues and energy crops.
The process involves pretreatment (to make cellulose accessible) and fermentation.
Generation 1 Biofuel: Ethanol produced from corn and yeast.
Generation 2 Biofuel: Ethanol or butanol produced from cellulose and yeast or bacteria.
Biodiesel
Generation 3 Biofuel: Produced by photosynthetic algae or cyanobacteria exposed to sunlight and CO2. These organisms produce fats internally, which are then extracted using a chemical solvent and refined into biodiesel. An example is Botryococcus brunii, which can contain over 50% oil.
Generation 4 Biofuel: Uses genetically engineered photosynthetic cells that produce and secrete fats when exposed to sunlight and CO2, allowing for direct refining into biodiesel.
Degradation of Lignocellulose
Efficient degradation of lignocellulose (tough plant fiber) is important for biofuel production. Lignocellulose is difficult to digest and a poor nitrogen source.
Two natural examples of systems with microbes specialized in lignocellulose degradation are the termite gut and the cattle rumen.
Termite Gut: Termites are important for recycling woody biomass but also cause significant damage to timber structures. They thrive on wood as their sole food source. They rely on a diverse symbiotic gut microflora (protozoa, bacteria, archaea) to digest wood and provide nutrients. The gut is an anaerobic environment. Significant methane (CH4) is released during digestion. Few of these microbes have been cultured. Some gut bacteria can fix nitrogen. Each termite species has a distinctive microflora. Protozoa in the hindgut often contain endosymbiotic bacteria (Pseudotrichonympha grassii). Sequencing their genomes allows researchers to study their metabolic pathways. Termite microbiology research could contribute to biofuel breakthroughs.
Cattle Rumen: Shows many similarities to the termite gut in terms of microbial activity. It is an anaerobic environment with very high microbial concentrations (bacteria/archaea, protozoa, fungi, phage). Microbes degrade plant fiber and ferment sugars to produce volatile fatty acids (VFAs), which provide energy for the animal. Significant CH4 is also released. The microbes themselves are digested by the animal, providing protein and vitamins.
VII. General Study Points for Diseases
For each disease covered in detail in the sources, you should be able to identify and describe the following:
Pathogen Type: What kind of microorganism causes the disease (e.g., bacterium, virus, protozoan, fungus)?
Hosts Affected: Which organisms are affected by the disease? Is it a zoonosis (transmissible between animals and humans)?
Reservoir: Where does the pathogen typically live and multiply when not infecting a host?
Transmission: How is the pathogen spread from one host to another?
Symptoms and Signs: What are the characteristic manifestations of the disease in an infected individual?
Prevention and Treatment: How can the disease be prevented (e.g., vaccines, sanitation, behavior changes)? How is it treated (e.g., antibiotics, antiviral drugs, rehydration therapy, surgery)?