Microbiology Exam 3 Review

Therapeutic options for coronavirus:

1. *Blocking the binding of S protein to ACE2*. Directly uses the RBD from the S protein of SARS-CoV-2 to bind ACE2 and occupy available sites or could mean directly using ACE2 antibodies or single-chain antibody fragments (scFv) to block the entry of the virus. Another type of blocking uses ACE2 itself to bind to the virus (see diagram for all three types of blocking). 2. *Inhibiting the RNA-dependent RNA polymerase* since it is used only by the virus to make new copies of its own RNA; targeting this process is particularly effective for RNA viruses (that do not have a DNA stage). This uses remdesivir. 3. *Making it toxic for the parasite to digest its host's hemoglobin* by raising the pH of endosomes. The slightly acidic pH of endosomes helps facilitate viral entry so raising this may prevent viral fusion and stops the virus from entering the cell. This uses chloroquine, but there have been cardiac side-effects seen with its use. 4. * Reducing the intensity of cytokine storms* created in response to the virus. A number of different drug approaches are being used for coronaviruses which target each step of the process.

Growth types of fungi

1. *Yeast* - small round single cells 2. *Molds* - long branched filaments called hyphae 3. Dimorphic Some grow exclusively as yeast or molds but there are some that can grow in both shapes. The types that can do both are said to be *dimorphic*. Many medically important fungi are dimorphic.

Mumps

Highly contagious viral illness caused by the mumps virus; it is spread by droplets of saliva or mucus from the mouth, nose, or throat of an infected person. Disease typically starts with a few days of fever, headache, muscle aches, tiredness, and loss of appetite, and is followed by swelling of salivary glands. The most common complication is inflammation of the testicles (orchitis) in males; but rare complications include encephalitis, meningitis, inflammation of the ovaries (oophoritis) and/or breasts (mastitis), deafness The live attenuated vaccine introduced in 1967. Prior to this there were hundreds of thousands of cases per year. In recent years there have been on average a few hundred cases per year, although in 2006 there was an outbreak of over 6000 cases (mostly among Midwestern college students) and in 2009 & 2010 an outbreak involved over 3500 cases (mostly among tradition-observant Jewish communities in New York and New Jersey); recently there have been multiple outbreaks on college campuses (even at Brown!!!) and with the NHL in 2017.

Diphtheria (C. diphtheriae)

INFO--> The C. diphtheriae is gram (+) and is in a rod or club shape for the cells. They are lysogenized by a bacteriophage which encodes the toxin. The cells lodge in the throat, and produce the toxin which leads to pseudomembrane formation. Vaccination against diphtheria has essentially eliminated the disease from the US. *Disease*: There is a formation of a 'pseudomembrane' that interferes with breathing and may lead to suffocation and heart and neurological damage can also be seen. *Pathology*: mediated by a secreted EXOTOXIN; the injection of the toxin in the absence of the bacteria replicates the disease and once internalized, the toxin interferes with protein synthesis (it is an A-B toxin); a single toxin is enough to kill a cell! *Treatment & prevention*: may be treated by passive immunization with antitoxin, or by active immunization which employs formaldehyde-inactivated toxoid, which retains the protective epitopes but can't actually cause disease. EXTRA INFO--> In the late 1800s, Neutralizing Antibodies to Bacterial Toxins (Antitoxins) Were Produced in Animals and Employed to Treat Diphtheria and Tetanus; Balto was one of the lead sled dogs who helped bring diphtheria antitoxin to the children of Nome, Alaska during a diphtheria outbreak in 1925

Preventing respiratory transmission:

In 1925, there were many posters and advertisements about preventing transmission, like one that says "careless spitting, coughing, sneezing spread influenza and tuberculosis." Currently, we have campaigns like "Be a Germ Stopper" and "Cover your Cough" which encourage people to cover coughs/sneezes by using tissues or your arm, and clean hands with soap and water or hand sanitizer. The most efficient ways to prevent airborne transmission are hand soap and flu shots. Note: the supplement Airborne won't protect you from airborne infections (or anything else).

Coronavirus (SARS-CoV-2) protein-mediated membrane fusion

In the first step, receptor binding, pH reduction and S protein proteolysis induces dissociation of S1 from S2 (see picture). In the second step, the fusion peptide (FP) is intercalated into the host cell membrane. In the third stage, the part of the S protein nearest to the virus membrane refolds onto a heptad repeat 1 (HR1) core to form the six-helix bundle (6-HB), which is the final postfusion configuration of the S2 protein. The virus needs the host protease to cleave the S protein (which is called TMPRSS2). This protein could be important for drug targeting as its not needed in normal cellular function.

Dimorphism in fungal pathogens

In the four true pathogenic fungi (Histoplasma, Coccidioides, Blastomyces, and Paracoccidioides), all are dimorphic and temperature regulates the switch between growing as filaments vs. growing as yeast (lower temperature, longer filaments with spores, higher temperature such as body temperature facilitates growth as yeast). Different forms will express different genes and characteristics. Candida albicans is one of the only species that switches to the filamentous form when introduced in body temperature so the filamentous form is the pathogenic form (perhaps because they are commensal and can live in the human for a while without causing disease).

Coliforms (waterborne)

Indicators of fecterm-48al contamination of water since coliforms live in the intestinal tract of humans and other animals. They are rod-shaped, gram (-), non-spore forming bacteria which can ferment lactose with the production of acid and gas when incubated at 35-37ºC. Typical genera include Citrobacter, Enterobacter, Hafnia, Klebsiella, and Escherichia. While not typically pathogenic themselves, the presence of coliforms indicates fecal contamination of water and suggests water is unsafe for human consumption or use. Sometimes they must close beaches because of coliforms! You can tell if it is a fecal coliform because of how it grows on certain types of agar (see picture!).

Giardiasis (waterborne)

Is a parasitic disease caused by a single-celled organism (Giardia protozoa). It is very possible to contract it in the US and other developed nations. It is called "Backpacker's Disease" since people who often camp or hike and drink contaminated water can often contract it. It doesn't cause a fever. Almost everyone historically (~1681) had been exposed to giardia. The cysts are incredibly resistant to kill and can persist for months or even years. It is a ubiquitously distributed protozoan parasite (in 97% of all U.S. waterways) and is a major cause of endemic and epidemic diarrheal disease. The most common protozoal disease in the United States. Has also been called "Beaver Fever". First observed by *van Leeuwenhoek* in 1681 using samples of his own stool. Giardia **cysts** (infectious stage) are resistant to chlorine and dehydration. See picture for life cycle. You essentially ingest the cysts and then and then the motile stage happens once it's in the body (as if it is "hatching") and then the protozoa "sit" on the villi and harden the sides which causes massive diarrhea. About half of infected persons are asymptomatic but may transmit infection. Symptoms typically begin within two weeks of infection. The major symptom is diarrhea (which is mild to severe, may last weeks to months, with exacerbations and remissions). It also causes *Steatorrhea* (fatty diarrhea), abdominal cramps, nutritional deficiencies due to malabsorption, weight loss, fatigue, and in children, delayed growth and failure to thrive. They are incredibly complex single-celled protozoa and essentially have a "suction-up" so that they can sit on the villi. A lot of people can be asymptomatic, and if you have it actively it can happen in cycles. Most of the time there is a good job of preventing giardia in commercial filtration system but can happen if there are large rains or sediment being stirred up. So, municipal water should be properly treated and delivered. If camping or backpacking, ALL drinking water should be treated (with chemicals such as iodine or chlorine, filtration using appropriate equipment, or boiling). Travelers to developing countries should avoid tap water, ice and raw food, as well as avoiding contact with feces and washing hands frequently.

Cholera

It is a severe diarrheal disease caused by Vibrio cholerae, which is a gram(-), comma shaped, flagellated bacteria. Currently found largely in the developing world, although historically outbreaks were common in major cities such as London before water treatment and improvements in waste management. Aside from contaminated drinking water, consumption of raw shellfish from sewage-contaminated beds and raw vegetables washed in contaminated water can transmit V. cholerae and related species. There has been a cholera pandemic going on for the past 60 years. Historically, cholera was a major problem for city-dwellers in any part of the world. Before water treatment, there was a high risk of getting cholera. You can get an infection by eating contaminated shellfish, which has even happened in RI. Since 1817, there have been 7 cholera pandemics. The 7th one began in 1961 and continues today. There are 2 strains of V. cholera: Classic and El Tor. The classic caused the first 6 pandemics, and El Tor is responsible for the 7th pandemic; it is distinguished from Classic by being somewhat less pathogenic and having higher numbers of asymptomatic carriers. There have been 5 million cholera cases since 1961, and at least 250,000 deaths. Cholera tends to require the ingestion of a *lot* of particles to cause infection (10^8-10^9 bacteria compared to some diseases that maybe just need 10 bacteria for infection). They colonize the small intestine and release enterotoxin, which causes severe diarrhea (the patient can lose up to 20L of fluid per day and "cholera cots" are used for patients to dispel their fluids). The mortality rate of untreated cholera is 25-50% and the introduction of oral rehydration therapy has greatly improved survival. The toxin is what causes the severe diarrhea. If you do not treat cholera by rehydrating, the mortality rate is quite high. The *cholera toxin* is produced by Vibrio cholerae and is an A-B toxin. The B-subunit binds to epithelial lining of small intestine and the A-subunit activates adenylate cyclase (cAMP produced from ATP, so water is secreted into the intestine). This causes massive diarrhea (up to 20 liters per day) which necessitates the use of 'cholera cots'. Rapidly fatal if not treated. The massive water movement to the lumen is what causes the cholera symptoms of massive diarrhea A-B Toxins ***TIP***--> The B-unit Binds to the cell (tip to remember a B unit Binds!!) and the A-subunit does the "nasty" stuff inside the cell. The 1854 London Cholera Outbreak: What was different about this outbreak was that the physician *John Snow*, with the assistance of a clergyman, started mapping the cases and fatalities, going door to door and collecting the information from people. They wanted to see what the outbreak looked like on a map and they figured out that the cases were clustered around one of the many water pumps on Broad St. The removal of the handle from the pump kept people from drawing contaminated water. The concept of tracking a disease like this was an incredibly important breakthrough in public health. The Haiti Cholera Outbreak: There wasn't really a cholera problem in Haiti before the earthquake, but it is still a problem up until today. 10 years after the earthquake, there are still parts of Haiti that haven't be repaired so some parts of the countries live in crowded camps and don't have access to clean and filtered water. The cholera may have been introduced by UN peacekeeping forces which may have accidentally kicked off the epidemic. It has sickened more than 800,000 people (over 7% of the population) and killed more than 9,500.

Why should we care about person-to-person microbial disease?

Kind of a no-brainer but at one time or another we will all eventually become infected and infect other people via person-to-person contact. Also, coronavirus is an example, as the total amount of cases is directly correlated with the amount of deaths (even when it comes down to the curve). Also, a lot of people "back then" would die from a number of infectious diseases; there's even a picture of guards quarantining Brown! There would particularly be a lot of young people who would die of infectious diseases, as shown by the number of child graves in the Old Saybrook CT graveyard.

Why do we need fungi??

Life on earth would not exist (as we know it) without fungi! They are critical for proper plant root function, breaking down dead organic material into simple compounds that plants can absorb, and many important plant and human diseases. Overview: Fungi exist from single-celled organisms to multicellular systems including the biggest organism on earth. They are critical for life on the planet and are important causes of plant and animal diseases. They are also beneficial (food, drink, antibiotics, plant growth/resistance). Fungi are critical for life on Earth. They range from single-celled organisms to multicellular systems (including the largest organism on Earth). They can be beneficial (food, drink, antibiotics, plant growth/resistance) and detrimental (cause plant, animal and human diseases). They have complex relationships with other kingdoms.

West Nile Virus (arthropod-transmitted)

Many diseases are named after where they are first identified; this one was first identified in Uganda and spread to Egypt and Israel. Member of the flavivirus groups: symmetrical, enveloped icosahedral capsids with positive, single stranded RNA genomes. It is spread by bite of a *mosquito* and was first identified in Uganda in 1937. Spread to Egypt and Israel by 1950s. In 1999, first cases were reported in US in the Northeast. West Nile is still very much established in some parts of the country, less so on the east coast (possibly by immunity evolving against WNV in either bird or human populations). WNV is primarily a disease of birds. Infected birds either die or become immune, and disease spreads by the mosquitoes to new areas. It is moving west in the US. Symptoms are often mild (fever, headache, aches) but can occasionally progress to West Nile encephalitis. Some bird species are susceptible and are killed by the virus and some are immune now; it used to be such a concern that if you saw a dead bird you had to report it to be tested for West Nile Virus. Symptoms are actually pretty mild but the mortality for encephalitis is quite high. 20% of infected people develop West Nile fever, which consists of headache, nausea, myalgia, rash, lymphadenopathy, and malaise and has a 2-3% mortality rate. Less than 1% develop West Nile encephalitis or meningitis and it mainly occurs in adults over 50.

Glomerulonephritis (S. pyogenes)

Mediated by immune complexes that deposit in the kidneys

LECTURE 17

Microbial disease (Animal, arthropod, and soilborne)

Molds

Molds are filamentous fungi; cells may contain more than one nucleus, but sometimes 100s. A single filament is known as a *hypha* (a nucleated tube containing cytoplasm). Some grow below the surface. The largest organism on earth may be armillaria which spreads over 1000s of acres and several feet deep; the total mass larger than a blue whale! Biologists have long debated what constitutes an individual organism. The record-breaking A. solidipes clonal colony passes the test based on a definition of being made up of genetically identical cells that can communicate, and that have a common purpose or can at least coordinate themselves. Common molds that we find are Rhizopus and Aspergillus. The Basidiomycota are normally the mushrooms.

Key genes in SARS-CoV-2

Some of the genes, like the ones coding for RNA-dependent RNA polymerase, are important since it allows RNA--> replication (represented by the blue box in diagram). Many genes code for the complex replication machinery proteins in the virus. The replicase complex is made up of many nonstructural proteins (nsps) in the gene including Nsp12, which is RNA dependent RNA polymerase. Both SARS-CoV-1 and SARS-CoV-2 genomes are very similar to the genomes of the viruses in bats as well as some in civets/pangolins....so SARS-CoV-2 could be the recombinant product of bat/pangolin viruses. RECAP of above: There is evidence that the virus originally came from bats due to the genomes. There are, however, closely related genomes in pangolins, so that is suspected to have passed on the virus as well. It is thought that a pangolin and bat circulating virus may have recombined and created the human virus due to the sequencing of the human virus genome. We can see that the virus is evolving a bit (which could be good if it is becoming less pathogenic but also bad if it is becoming more pathogenic).

Arthropod-transmitted diseases

Spread from host-to-host by the bite of an insect. Examples are listed above in the previous flashcard. Arthropod-transmitted diseases are normally part of the *diptera* group a lot of the time (insects like flies and mosquitoes) and are spread by the bite *or* feces of an insect.

Examples of foodborne diseases:

Staph. aureus, Clostridium, Salmonella E. coli, Campylobacter, Listeriosis, Prions

Staphylococcal food poisoning

Staphylococcus aureus is a common cause of food poisoning. It is a normal inhabitant of skin and respiratory tract, and produces several heat stable toxins. Causes nausea, vomiting, diarrhea within 1-6 hrs of ingestion. This is a common cause of food poisoning; it has several heat-stable toxins which means that you can heat the food and kill the bacteria but the toxin will still stay there. Foods commonly contaminated include custard and cream filled baked goods, poultry, meat, gravies, mayonnaise- based salads (which are commonly kept in kitchens and outdoor parties at room temperature; such conditions promote rapid growth of S. aureus and toxin production). Toxin is heat stable - reheating foods may kill the bacteria but does not inactivate toxin. Bacteria like mayonnaise/hollandaise sauces because they have a bunch of stuff that bacteria like as well as the texture and temperature they they are normally served at.

Examples of person-to-person diseases:

Streptococcus spp.; Corynebacterium diphtheriae; Bordetella pertussis; Mycobacterium spp.; Neisseria meningitidis; Measles virus; Mumps virus; Common cold viruses; Influenza viruses; Staphylococcus spp.

Candida albicans toxin

The 1st peptide toxin identified in a human fungal pathogen. Candida produces a toxin which is not common at all to fungal pathogens (is the only one). *Candidalysin* is a fungal secreted peptide toxin (Ece1). It is produced during hyphal growth and generates pores in host epithelial cells; critical for mucosal infection and responsible for the activation of epithelial and Th17 immunity.

"Swine Influenza" (2009 H1N1)

The 2009 H1N1 "Swine" Flu Virus Contains Gene Segments From Four Different Viruses; Virus described as a new subtype of A/ H1N1 not previously detected in swine or humans. The virus contains gene segments from 4 different influenza types: North American swine, North American avian, North American human, and Eurasian swine. Overall, it caused 61 million infections, 274,000 hospitalizations, and 12,470 deaths. The majority of infections, hospitalizations, and deaths in the 2009 pandemic occurred in persons under 65 years old.

Life cycle of coronavirus

They have a particularly large genome (30,000 base pairs which is quite large for a virus). They have positive strand single stranded RNA in the virus. 1. The spike (S) protein is critical for binding on the human cells; the protein on the coronavirus binds to the receptor ACE2, which is a receptor present on many different human cells (epithelial cells, blood cells, nasal cavities, the gut, etc.) so there are many subsets of cells that can be infected by this virus. 2. After receptor binding, the conformation change in the S protein facilitates viral envelope fusion with the cell membrane through the endosomal pathway. Then, SARS-CoV-2 releases its RNA into the host cell which can be directly used for translation. 3. One polypeptide is clipped into more proteins which seems to form a replication complex that can make RNA from RNA. This may be a good target for drugs since our cells don't have RNA to RNA polymerases. 4. One half of the genome goes into making the replication complex, and the other goes into making the new virus proteins. There are also accessory proteins, but we don't completely know the functions of those. 5. The virus completely assembles, as the RNA replication and packaging step combines with the assembly of proteins step. The new virus is enveloped and then is released into the cell.

Cytokine storm (coronavirus)

This is when immune responses turn toxic. This virus seems to be so deadly due to the cytokine storm which is a very large immune response which gets to a level where it is hypo-reactive response driven by IL-6 that can damage tissues and organs, which can lead to a lot of side effects from the disease (lung injury, cell death, renal failure, and blood clotting) which result from the body trying to fight off the virus. People are looking at reducing these cytokine storms to manufacture some potential medicines.

Direct Contact Transmission

Transmission of an infectious agent from one person to another through touching. Examples: skin-to-skin contact, kissing, sexual intercourse. It typically involves contact with blood or bodily fluids from the infected person, and this is often facilitated by wounds, skin lesions, etc. Many respiratory diseases with airborne transmission are also spread by direct contact!

Clostridial food poisoning

Two members of the genus Clostridium can cause food poisoning: Clostridium perfringens, and Clostridium botulinum. Both are gram (+) spore formers. Canning and cooking may not destroy the spores (since they are obligate anaerobes; if you don't correctly can your own food, the spores can enter, and then grow and germinate under the conditions). Under *anaerobic* conditions the spores will germinate. *Clostridium perfringens* is one of the most common bacterial causes of food poisoning in the US and is commonly found in soil and intestinal tract of animals (also found in sewage). Results from ingestion of a large number of cells (10^8 cells), and is found in cooked and uncooked meat, poultry, and fish. The enterotoxin alters permeability of intestinal epithelium, leading to diarrhea and cramps which begin 7-15 hrs after eating, resolves within 24 hrs. Rarely fatal in this form. *Clostridium botulinum* causes severe, often fatal food poisoning (you can definitely die from botulinum). Is caused by consumption of food containing the botulinum toxin. Normally inhabits soil or water, but spores may contaminate raw foods before harvest or slaughter. If the spores are not killed during canning they may grow in food and produce toxin. Damage to packaging (e.g. dented cans) may introduce spores. The spores are basically everywhere in the environment but we don't get the disease all the time because there has to be the right conditions for it. The botulinum toxin causes flaccid paralysis (and paralysis of the diaphragm). Destroyed by high heat - heating to 80°C for 10 min will inactivate toxin. Most cases of botulism occurs from eating home-canned foods that are not cooked after opening, and all forms of botulism are rare in the US (about 150 cases per year, of which 25% are fatal). Antitoxin is given to people with botulism to neutralize toxin, and mechanical ventilation is also necessary. Infant botulism is usually self-limiting and most infants recover with assisted ventilation. There have been numerous outbreaks of botulinum in the past caused by different food sources (prison-wine, baked potatoes, sautéed onions, fermented fish, and chili sauce).

Fungi uses and roles in environment

USES--> for food or in the manufacture of foods (like bread, some cheeses, alcoholic beverages) and produce important drugs: (antibiotics like penicillin and cephalosporin; cyclosporin is an anti-rejection drug). But some are parasitic in animals and also cause significant diseases of plants. *Yeast*--> Yeasts can be considered man's oldest industrial microorganism. It's likely that man used yeast before the development of a written language. Hieroglyphics suggest that that ancient Egyptians were using yeast and the process of fermentation to produce alcoholic beverages and to leaven bread over 5,000 years ago. The biochemical process of fermentation that is responsible for these actions was not understood and undoubtedly looked upon by early man as a mysterious and even magical phenomenon. ENVIRONMENT--> Extremely beneficial, as they decompose dead organisms and recycle nutrients. 90% of plants form *mycorrhizae*: fungal associations with roots that helps absorb water and minerals. Reminder!!! They are eukaryotes!! They are actually pretty close to animals (more than plants).

Viruses (waterborne and foodborne)

Viruses can be transmitted by water and food. These viruses are an issue because people who are infected shed a very large amount of the virus particles so it is really hard to completely eliminate or eradicate it, but water purification and chlorination kill these viruses. *Poliovirus*: eliminated from the western hemisphere and on track to global eradication. Paralytic polio only actually happened in 1 out of 100 cases and mostly polio would just cause diarrhea. *Norovirus* and *hepatitis A* virus may also be spread in water contaminated with feces. Diarrheal outbreaks of viruses can happen very readily on cruise ships (there have been outbreaks of norovirus even recently in 2019 on cruise ships).

Social distancing

Voluntarily limiting one's interactions with others in order to prevent potential exposure to pathogenic microorganisms; the importance of social distancing is crucial for the coronavirus pandemic, as it can drastically reduce the amount of cases.

Plague (arthropod-transmitted)

Was one of the most widespread diseases in human history. The arthropod in this scenario is the *flea* as it ingests the Yersinia pestis when feeding from an infected animal like a rat (which are the primary reservoir). It killed between 25-33% of the population of Europe in the Middle Ages, and is caused by *Yersinia pestis* a gram (-) bacteria. It is a disease of rodents with rats a primary reservoir. It is spread by fleas - ingest Y. pestis when feeding on an infected animal then transfer to new animal when feed again. Was discovered by Alexandre Yersin. Just before the outbreak, there are normally large numbers of dead rats around the area. It is possible that gerbils could've caused the black death as well. Once infected, the bacteria travels to lymph nodes - causes swollen areas called buboes which causes *bubonic plague*. The capsule prevents phagocytosis - escape the immune system. Bacteria eventually enter the bloodstream causing *septicemia*. Yersinia pestis causes multiple hemorrhages under the skin (black splotches) which is why it is called Black Death. The plague causes death in 3-5 days. The septicemic plague is a combination of the bubonic plague and pneumonic plague. It is deadly as it causes death in 3-5 days. The bacteria's capsule may help it in infecting the host. The bursting blood vessels cause the black splotches underneath the skin. Pneumonic plague is more deadly than the bubonic plague, but septicemia is the deadliest. *Pneumonic plague* occurs when cells are inhaled directly into lungs. People rarely survive more than 2 days. It is highly contagious and can spread rapidly. With septicemic plague, the bacteria rapidly spread through the bloodstream and death occurs very quickly - even before it can be diagnosed. Its not so much of a problem now in the US but there are flare-ups around the globe where people aren't so careful with hygiene or used to dealing with these kinds of infections. Antibiotics must enter the patients at an early stage. It can be treated in rapidly diagnosed and is treated with antibiotics. Mortality is 1-5% if treatment begins early enough. It is a rare disease today (1006 cases since 1990 in US and around 1500 cases per year worldwide). Recent evidence confirms that Y. pestis caused the black death, but more than one strain was involved. It appears that there are two lineages of Yersinia pestis (shown by the purple and red line). So, there were probably more than one strain involved. Historically, the black death had a huge impact on the human race. The plague was even used as an early strategy of bioterrorism! They did not abide to good quarantine standards!! In 1345, while attacking the city of Kaffa, the Mongol army essentially threw bodies of dead soldiers into the city as a form of bioterrorism (it is possible that throwing rats into the city could have been more potent in spreading disease). When it came to Kaffa people left because they didn't want to get infected but that spread the plague even more.

LECTURE 18

Water & Foodborne Diseases

Human fungal pathogens

When fungi are human pathogens, they tend to be very fatal (especially with a combination of predisposing factors). Fungal infections affect ~1.7 billion people/year and there are approximately 13 million life-threatening infections every year. *Predisposing factors:* use of antibiotics, steroids, and immunosuppressive conditions. The mortality rates > 50% for some species, and there are approx. 1.6 million deaths a year. Only FOUR FUNGI are true human pathogens, and most disease-causing fungi are *opportunistic* and take advantage of a weakened immune system. They have different phyla, size, shape, and mode of infection. *Histoplasma, Coccidioides, Blastomyces,* and *Paracoccidioides* are the four fungi that are true human pathogens (rather than 'accidentally' growing and spreading).

Tuberculosis (TB)

Also known as "consumption" or the "white plague". It is caused by the *Mycobacterium tuberculosis*. It is easily spread, and acquired by inhalation. TB is the leading cause of death from an infectious agent (1.5 million deaths per year worldwide; over 2 billion are currently infected). And although largely eliminated as a public health threat from U.S. in mid 20th Century, TB re-emerged in 1990s as a result of HIV/AIDS. The family of mycobacterium are *acid fast bacilli* and remember their cell walls!!! They clump together, and TB stains pink. *Disease*: 90% of those infected mount effective cellular immune response in the lung that contains bacteria in a granulomatous tubercle. 10% develop chronic TB, leading to extensive pulmonary lesions and disseminated bacteria *Diagnosis* is typically done by a PPD skin test (a positive test will produce a sort of rash) and pulmonary X-ray. *Treatment*: Various antibiotics for at least 6 months; lapsed treatment has allowed multidrug resistant TB (MDR-TB), XDR-TB and TDR-TB to emerge, so it's SUPER IMPORTANT! to take the antibiotics for the proper amount of time. *Prevention* is traditionally done by public health measures and quarantine; the BCG vaccine effective in some areas, but complicates skin testing (may give a positive PPD test result) so it's not used in U.S. FACT: x-rays of skeletal remains show that prehistoric humans (4000 BC) had TB, and tubercular decay has even been found in the spines of Egyptian mummies. *Multidrug-resistant tuberculosis* (MDR TB) is a form of tuberculosis that is resistant to two or more of the primary drugs (isoniazid and rifampin) used for the treatment of tuberculosis. The bacillus that causes tuberculosis was first identified in 1882 by *Robert Koch* and he received a Nobel Prize for his work in 1905. The *BCG vaccine* was developed by*Calmette* and *Guérin* in 1906 and it was named after them. The US has never used mass immunisation of BCG, relying instead on the detection and treatment of latent tuberculosis. The UK introduced universal BCG immunisation in 1953 and until 2005, the UK policy was to immunise all school children at the age of 13, and all neonates born into high risk groups.

Rheumatic fever (S. pyogenes)

An autoimmune disease induced by bacterial molecules that are similar to host molecules and leads to heart and valve joint damage.

Examples of non person-to-person diseases:

Arthropod-transmitted diseases (Rickettsial disease, Lyme disease, Malaria, West Nile Virus, Zika, Plague), animal-transmitted diseases (Rabies and Hantavirus), and soilborne diseases (Pathogenic fungi and Tetanus).

Prions (food infection)

'Prion' = proteinaceous infectious particle; proteins that adopt altered structures and cause disruption of neural tissue. Causes Variant Creutzfeldt-Jakob Disease (vCJD) - slow acting degenerative neurological disease. Spread by eating meat from cattle infected with bovine spongiform encephalitis (BSE) - mad cow disease. Prions are not destroyed by heat - can affect related human protein configuration. Stanley Pruisner received the Nobel Prize in 1997 for his discovery of prions. The misfolding of one protein can cause other proteins to misfold, which when it gets into the brain, is very harmful and causes several degenerative neurological diseases. It's not even alive as there's no nucleic acids or anything else, so the scientific community was a bit resistant to the idea at first, but then it was accepted. They can cause serious neurological symptoms; an outbreak of prions causing diseases was discovered in the Kuru epidemic in the 1960s resulting primarily from cannibalism (Kuru is a neurodegenerative disorder that surfaced among the Fore people of New Guinea). The vast majority of victims among the South Fore were women. In fact, eight times more women than men contracted the disease. There are multiple ways that the prions can actually spread the disease and there are speculations as to why prions encourage the misfolding of other proteins. Seeding of prions is said to cause disease as amyloid fibers get deposited in the brain which may overload the proteasome and cause cell death. *Spongiform encephalopathy* is essentially gaps and holes in the brain; Neurons develop vacuoles. As the disease progresses, vacuolization becomes more pronounced and the cortical cells develop a spongy appearance, hence the term spongiform encephalopathy.

S. cerevisiae

(Baker's yeast or Brewer's yeast) can divide asexually via budding or can enter the sexual cycle and form spores. It is said to be a cellular toolkit for biology since it is a generator of ethanol by synthetic biology. It is great at fermentation but can't break down many substrates; so, we have engineered it by adding enzymes from other species. Commercial production of cellulosic biofuel via fermentation pathways has been hampered by inefficient fermentation of xylose and the toxicity of acetic acid, which constitute substantial portions of cellulosic biomass. The engineering of model yeast, especially this kind, has been used to make useful compounds which can be used in antimalarial drugs, diesel, gasoline, and isoprene. This is done by manipulating what cells do by the metabolic pathway. And it's also been used for the impossible burger! The "meaty" taste comes from the hemoglobin, so they put that hemoglobin gene into yeast.

Zika Virus (arthropod-transmitted)

(a flavivirus) was first discovered in 1947 and is named after the Zika Forest in Uganda. The most common symptoms of Zika are fever, rash, joint pain, or conjunctivitis (red eyes). Other common symptoms include muscle pain and headache. This was a more recent virus spreading primarily in 2015. It's suspected that the virus made its way to Brazil from French Polynesia during the 2014 World Sprint Championship canoe race held in Rio de Janeiro. Pregnant women were most at risk of severe complications with contracting Zika as it could cause microencephalitis. *Microencephaly* is when head size is significantly smaller than normal and brain development is impaired. The CDC reported that genetic material of the Zika virus was found in brain tissue from two infants with microcephaly who had died. Vast swaths of populations have probably become immune to the virus; this "herd immunity" has reduced the number of susceptible people until the virus could no longer easily move between humans and mosquitoes. We don't know why exactly the virus fell off quickly. It is possible that the virus continues to mutate and can flare up again.

Mushrooms (fruiting bodies)

*Basidiomycetes* are filamentous fungi that form fruiting bodies. The sexual spores (basidiospores) are formed on the underside on the cap of the mushroom. These spores are dispersed by the wind, and then form into mature mushrooms later on. These fruiting bodies form in wet, cool weather.

Coronavirus overview

*Covid-19* is the name of the disease and *SARS-CoV-2* is the name of the virus causing the disease of the current pandemic. There have been approximately 500 coronaviruses circulating in bats. The coronaviruses is a large family of viruses, with a seventh and new strain identified in Wuhan, China. Common signs of infection are fever, cough, shortness of breath, breathing difficulties, gastrointestinal symptoms, and diarrhea. Other symptoms may be the loss of smell and taste in some patients (caused by the infection of neurons), as well as fatigue, muscle or joint pain, a sore throat, headache, chills, and nasal congestion. Severe cases may lead to pneumonia, severe acute respiratory syndrome, kidney failure, and death. Currently, there are no vaccines or antiviral drugs available for these viruses and so the symptoms are treated. The coronavirus normally starts in bats and then goes to another animal (civet cats for SARS-CoV, and camels for middle east respiratory syndrome, speculated to be pangolins for current SARS-CoV-2 outbreak). Transmission circulates in animals, and can be transmitted to humans as it is spread through the air, close personal contact, or touching contaminated objects. Previous outbreaks: In Nov. 2002 in China with the SARS-CoV outbreak (8,000 cases, 9.6% mortality, spread to 26 countries; Severe Acute Respiratory Syndrome) and in Sept. 2012 in Saudi Arabia (2,500 cases, 34.4% mortality, spread to 27 countries; Middle East Respiratory Syndrome). The current pandemic, compared to SARS and MERS, is much more contagious but less deadly. *Current pandemic:* For the new strain of the 2019-2020 novel coronavirus, hundreds of cases were detected in china with thousands of deaths. Then, the disease spread to Japan, Thailand, South Korea, Taiwan, the US, etc. A seafood/animal market in Wuhan, China has been identified as the center of the outbreak. The evidence for this virus shows that it is present in natural populations which then gave it to us; it may have been released by a lab but it certainly isn't suspected to be manufactured by a lab (due to the genome). Currently, there are 4,175,284 confirmed cases in the world and 285,971 total deaths. This means that currently *the mortality rate for the coronavirus pandemic is 6.5%*. The US now makes up roughly a third of all coronavirus cases worldwide.

Plant fungal pathogens

*Dutch elm disease* is caused by a fungus and there have been 'vaccines' for elms that can be injected consisting of spores of a strain of the fungus that has lost much of its pathogenic capabilities, protecting it from DED for one growing season. *Corn smut* causes millions of dollars of crop damage every year. It normally feeds off the corn plant and decreases the yield, so the crops are destroyed. The pathogenic fungus causes smut of maize and forms gals on all above-ground parts of the corn species. In Mexico, it is eaten! *Rice blast* destroys enough rice to feed more than 60 million people each year. These pathogens were looked into as being used as bio-weapons in the past.

Convalescent plasma (coronavirus)

Following the infection with SARS-COV-2, our body mounts an immune response, generating specific antibodies that (hopefully) neutralize the virus. Passive antibody therapy involves administration of neutralizing antibodies isolated from a person who has survived the infection into a susceptible person. Convalescent plasma offers what's called "passive immunity." The body doesn't create its own antibodies, but instead "borrows" them from another person or animal who has successfully fought off the disease (blocking the life cycle of the virus). Unlike a vaccine, the protection doesn't last a lifetime. Then, the antibodies are injected as either prophylaxis for someone who has been exposed to coronavirus, or therapy (using a larger amount) for someone who currently has coronavirus.

Pathogenic E. coli (food infection)

200 known pathogenic E. coli strains - can cause life threatening diarrheal disease and urinary tract infections. Divided into several groups - depending on toxin produced and disease they cause. Enterohemorrhagic E. coil (EHEC) causes hemorrhagic diarrhea and kidney failure (causes 60,000 infections and 50 deaths each year). We all kind of have E. coli in our gut but it isn't as pathogenic. If you get it there are treatments (supportively, kidney dialysis, antibiotics, etc.) Treatment is supportive therapy and in severe cases antibiotic therapy. Prevention of E. coli O157:H7 is by cooking meat thoroughly. Irradiation of ground beef was approved specifically to prevent infection by this strain. This is a disease that is completely preventable; as long as meat is cooked thoroughly, it can still infect people and irradiation has been approved specifically to prevent infection by this strain. All types of food poisoning/infections can occur (even if its organic, artisanally sourced, etc.). Pedestal formation (see picture) is associated with *attaching and effacing (AE) lesions* in epithelial cells. When pathogenic E. coli bind they form pedestal legions; photos show the pathogenic E. coli sitting on top of the pedestal (not all of them do this, but the pathogenic ones do). Some E. coli are pathogenic and others are not because of pathogenicity islands (which are regions of the genome encoding virulence factors that are inherited by horizontal transfer; they can be part of the chromosome or on plasmids).

Streptococcus pyogenes

A bacteria that can cause infection if defenses are weakened or infected with a highly virulent strain. In these cases, it causes 'strep throat' which is a group A strep infection (*beta*-completely-hemolytic which creates clear zones around bacterial colonies grown on blood agar and happens when there is a complete disruption of erythrocytes and the release of hemoglobin) characterized by a severe sore throat, enlarged tonsils and glands, as well as a mild fever. It can also cause otitis media (inner ear) mastis (mammary glands) and impetigo (skin infection). Untreated strep infections may progress to serious systemic disease!!! Septic shock can be very fatal despite aggressive treatment with multiple antibiotics. However, it may be isolated from the upper respiratory tract of healthy adults.

Staphylococcus

A gram (+) cocci which is resistant to drying and readily dispersed in dust and on surfaces. Common pathogens of humans, especially of skin wounds. Staphylococcus occasionally causes life-threatening infections, and most infections are from contact with an asymptomatic carrier. They can cause a variety of diseases: acne, boils, impetigo, pneumonia, osteomyelitis, carditis, meningitis, and arthritis. Suppurative infections of staphylococcus produce pus. Coagulase released by the staphylococcus bacteria causes fibrin to accumulate around bacterial cells, which makes it difficult for the immune system to get to them. Many strains of Staphylococcus are resistant to antibiotics. *Methicillin-Resistant Staphylococcus aureus* (MRSA) is a significant problem due to increasing resistance to antibiotics, leading to "superbugs" (as it is resistant to all penicillins). Hospital acquired strains are usually drug resistant and are often acquired from hospital staff who are carriers. Techniques used to control MRSA include surface sanitation, hand washing, isolation, restricting antibiotic use, and "decolonization".

Influenza

A highly contagious viral illness; it causes thousands to tens of thousands of deaths each year in the U.S. The virus was first isolated in 1933 and cultured in embryonated chicken eggs in 1936. The first recognized pandemic was in 1580. There have been at least four pandemics in the 19th century, three in the 20th, one (so far) in the 21st, with an estimated 21 million deaths worldwide in the pandemic of 1918-1919. *STRUCTURE*--> The virus is an enveloped virus with two major surface antigens, *Hemagglutinin* (H) and *Neuraminidase* (N). There are three major types: *Influenza A, Influenza B, and Influenza C*. Type A viruses are further classified based on what combination of H and N they have (for example: H1N1 or H3N2). There have been 18 H subtypes and 9 N subtypes discovered so far. The viral genome consists of single-stranded, negative-sense RNA, which is segmented, with roughly one protein encoded by each segment. This gives Influenza A viruses their special ability to undergo "antigenic shift" ANTIGENIC CHANGES--> Hemagglutinin (H) and Neuraminidase (N) proteins are expressed by circulating virus strains which change with time under the influence of selective pressure exerted by host immunity. Changes occur as a result of: point mutations in the virus gene (*antigenic drift*) or exchange of a gene segment with another subtype of influenza virus (*antigenic shift*). The epidemiological impact of antigenic changes depends on extent of change (more change usually means larger impact). The 1918-1918 influenza pandemic killed at least 21 million people, and influenza mortality compared to other infectious diseases is significantly higher. On October 5th 1918, Brown put a strict quarantine in place due to influenza!! Scientists have attempted to isolate the 1918 virus from samples of bodies that died of the pandemic that year.

Antigenic Shift (influenza)

A major change in H and/or N may generate new subtype. Occurs at irregular intervals (10-40 yr) and is caused by exchange of gene segments. This may result in pandemics. Examples of antigenic shift: H2N2 virus circulated from 1957-1967; H3N2 virus appeared in 1968 and completely replaced H2N2 virus; Novel H1N1 appeared in 2009 and largely displaced the previously circulating H1N1 strain ('Swine Flu').

Enterotoxins

A specific class of exotoxins that act on the small intestine. They cause massive secretion of fluid into the intestinal lumen, which leads to diarrhea and vomiting. Associated with food poisioning. Produced by a variety of bacteria: Staphylococcus aureus, Clostridium perfringens, Bacillus cereus, Vibrio cholerae, E. coli, and Salmonella enteritidis.

Rubella

A viral illness caused by the rubella virus, also known as "German measles". It is spread by airborne droplets derived from the upper respiratory tract of an active case. Symptoms are fever and rash for 2-3 days; generally mild and self-limited in children and adults. The major complication is *congenital rubella syndrome*. If this complication arises, there is a high chance of damage to the fetus if a woman is infected within a month of conception or during first two trimesters of pregnancy. The affected infants may exhibit deafness, cataracts (shown in the picture above), heart defects, mental disability, and liver and spleen damage The live attenuated vaccine was introduced in 1969; prior to this, there were epidemics that could involve millions of cases every 6-9 years in the U.S. In 2009 there were 3 reported cases in the U.S, but no endemic cases have been reported since.

Spores (molds)

Aerial hypha form *conidia* (asexual spores). Fungi are so good at spreading onto food because of the asexual spores that spread readily with mitotic divisions.

Transmission methods of infectious microbes:

Airborne, bites, body fluids, fecal-oral, food, sexual contact, surfaces.

P. destructans ("White-Nose Syndrome" - WNS)

Bat fungal disease. A filamentous ascomycetous fungus that afflicts bats. It is an emerging disease of hibernating bats, as it awakens bats from winter hibernation before there are enough insects to keep them from starving. The lesions caused by WNS, including invasion of the underlying connective tissue by fungal hyphae (see arrows on diagram), are most visible in the wings of a bat infected with the fungus. It causes extensive tissue damage, particularly to the fragile membranous wings. WNS has killed more than 5.7 million bats with mortality rates of up to 100% at some sites. It was introduced to the US from Europe and since has spread to many states. This fungal disease is temperature dependent; preferring colder temperatures as when the bats are hibernating in the winter, their body temperature matches that of the cave which allows the fungus to grow. Fungus grows on nose, ears and membranous wings; spread via direct contact between bats that are sharing hibernation caves. It spreads from cave to cave as it can live on surfaces, and spreads very rapidly through the colony. Infection causes increased arousals from hibernation, and thus a premature depletion of stored body fat leading to starvation. Infection is almost 100% lethal. Bennett lab has identified secreted protease that can degrade a component of the connective tissue, and hydrolytic enzymes are the major proteins secreted by P. destructans. There's not too much WNS research going on, however. A lab in Michigan took a different approach to the disease and analyzed the bats that survive infection; a genetic analysis of bats surviving infection may give clues for resistance against WNS. Deeper hibernation has shown to allow bats to survive infection since there seems to be a gene in some bats that lets them hibernate more deeply and store up more fat than the other bats.

Candida biofilm formation

Biofilms are critical for infections and often form on medical implants. They let the pathogen grow better and are very tough to break. It happens when yeast cells attach to the surface, grow up several layers of cells, switch to the hyphae form, make an extracellular matrix around the complex, and then disperse yeast into new sites. This biofilm formation often contains other bacterial species and are resistant to penetration by antifungal drugs. This is because of low drug accessibility; physical barriers to the drug (the extracellular matrix); non-dividing (stationary) cells are more resistant to antifungal drugs; and since cells in biofilms can activate responses that decrease drug efficiency (like upregulating efflux drug transporters).

LECTURE 19

COVID & Fungi

Fungal pathogens overview

Can cause a destruction of plant crops, animal extinctions, and function as major human pathogens.

Mycobacterium leprae

Causative agent of *leprosy*, also called Hansen's disease; it cannot be grown in culture, but can be grown in experimentally infected armadillos. It is transmitted by direct contact *and* respiratory routes. The incubation time ranges from weeks to decades and this mycobacterium grows within macrophages. It is hard to grow in the lab because the organism is an obligate intra-cellular parasite that lacks many necessary genes for independent survival. The complex and unique cell wall that makes members of the Mycobacterium genus difficult to destroy is apparently also the reason for the extremely slow replication rate. Virulence factors include a waxy exterior coating, formed by the production of mycolic acids unique to Mycobacterium. Intracellular and extracellular masses, called *globi*, are often found in victims of lepromatous leprosy. The bacilli never form chains. So, armadillos!! Armadillos are used because the armadillo has a relatively low body temperature of 32-35ºC, which the bacillus prefers; they are also used because armadillos produce litters of identical quadruplets that can live a relatively long life span of 10-15 years; they also have a tendency not to bite and tolerance to laboratory procedures, and they are a large population in the US—about 30 million. Most cases are found in Madagascar, Mozambique, Tanzania, and Nepal and it is currently diagnosed in 1.2 million people worldwide (but may be unreported in up to 12 million people). The less serious form is *tuberculoid* leprosy which is characterized by vigorous cell-mediated immunity and contained lesions. The most serious form is multibacillary or *lepromatous* leprosy which is characterized by folded, bulblike lesions on the body that contain ~109 bacteria per gram of tissue. This form has a poor prognosis and results in the destruction of motor nerves and loss of motor function and sensation. Contrary to popular conception... leprosy does NOT cause body parts to simply fall off, rather, a long investigation by Paul Brand yielded that insensitivity in the limbs and extremities was the reason why unfelt wounds or lesions, however minute, could lead to undetected deterioration of the tissues is because the lack of pain not triggering an immediate response as it would in a fully functioning body. Since 1995, WHO has supplied MDT (a combination of rifampicin, clofazimine and dapsone for MB leprosy patients and rifampicin and dapsone for PB leprosy patients) free of cost to leprosy patients in all endemic countries.

Malaria (arthropod-transmitted)

Caused by 4 species of the protozoa Plasmodium: P. vivax, P. ovale, P. malariae, and P. falciparum. Malaria is spread by female mosquitoes from the genus Anopheles and is predominantly found in the tropics and subtropics. Annually, there are roughly 214 million malaria cases and an estimated 438,000 malaria deaths. The cells causing malaria can lay dormant in the liver for a while and then become active and infect the red blood cell. Essentially this cycle uses the human as a host for both an asexual and sexual reproduction. There are threats to pregnancies as infected blood cells can fuse to the placenta and adhere more (they can also adhere more to the endothelium which can cause blood clots). See picture for life cycle, which has three stages: 1. *Exoerythrocytic stage*: outside the red blood cells involving the liver before the red blood cells are targeted. The mosquito injects sporozoites, which travel to the liver. This produces schizonts in the liver cells, and after 6-15 days, merozoites rupture and enter the blood. Hypnozoites - dormant and reactivate later causing disease again. 2. *Erythrocytic stage*: inside the blood cell. Merozoites enter blood cell - become trophozoites, which phagocytize hemoglobin. Form schizonts - produce merozoites. Merozoites released and infect new RBCs. Some merozoites become male and female gametocytes. A cycle of infection can increase the amount of parasites. 3. *Sporogonic stage*: begins when a mosquito ingests an RBC with gametocytes. Gametocytes become gametes in the mosquito's gut, then fertilize and become an oocyst. 10-20 days later oocyst releases sporozoites and the mosquito can infect a new host. This is a SEXUAL life cycle; both male and female gametocytes become gametes and fertilize; the sporozoites go into the mosquitoes saliva and now the mosquito can infect a new host. As far as we know right now, the mosquitoes aren't harmed by the malarial bacteria cycle. The disease is characterized by cycles of high fever followed by chills. Usually relapses with treatment - small number remain dormant in liver. The relapses with treatment involve the hypnozoites in the liver as they are spores and can remain dormant. Many strains have developed resistance to current drugs. Prevention --> Most effective control is to break the life cycle by eliminating the mosquito by rain swamps and other breeding areas.Malaria used to be a huge problem in the US but they were eliminated through spraying DDT everywhere; now, the pathogenic mosquitos are essentially gone. In 1933 in southern US, they drained 544,000 acres of mosquito breeding area and sprayed millions of gallons of oil on swamps. In 1946, they established malaria eradication program in south and sprayed DDT. Malaria and human evolution--> In parts of Africa people produce hemoglobin S - a single amino acid change from hemoglobin A, which binds O2 less efficiently, causes RBC to become curved, homozygotes (sickle cell anemia), heterozygotes (sickle cell trait), growth of P. falciparum causes sickle cell shape, and sickle cell shape allows K+ to flow out of cell - inhibits P. falciparum growth. We have seen a hemoglobin mutation in parts of Africa that causes a sort of sickle-cell trait where the RBC are curved and malaria can't infect as readily. The *sickle trait* provides a survival advantage in regions where malaria is endemic. People (and particularly children) infected with P. falciparum are more likely to survive the acute illness if they have sickle cell trait. If infected with P.f. - trait cells start to sickle and parasite growth blocked. If you have the trait, you would be heterozygous and have some RBC with the trait; having both copies of the trait is harmful as you will not have enough oxygen carried in your cells. Research right now is trying to find when this mutation arose and the proliferation of it. Sickle cells are stiff and sticky. They tend to block blood flow in the blood vessels of the limbs and organs. Blocked blood flow can cause pain, serious infections, and organ damage. The stretching of the cell is caused by abnormal hemoglobin which form strands in the red blood cells. The decreases in malaria cases have been due to the implementation of malarial nets and other interventions, etc. Unfortunately malaria still takes the lives of many. The WHO is very important in terms of malarial prevention; the Bill and Melinda gates foundation is also very instrumental in the decrease of malaria.

Lyme Disease (arthropod-transmitted)

Caused by Borrelia burgdorferi (spirochete which is contained within the tick, which is the vector for lyme disease). The spirochete is spread primarily by the bite of the deer tick. Deer and the white footed mouse are main mammalian reservoirs for B. burgdorferi in Northeast, but it is also found all over the US. The wood rat is the reservoir in western US. Spread by bite of tick. A disease *vector* is any agent that carries and transmits an infectious pathogen into another living organism. The Centers for Disease Control and Prevention reports an estimated 30,000 cases of Lyme disease each year to state health departments. It is called Lyme disease since its named after the town Lyme in Connecticut (so it's named a bit after the place it is discovered). Similar illnesses found in Europe and Asia and are caused by similar species of Borrelia. Each area has own rodent reservoirs and tick vectors. The bacterium involved with Lyme disease was first discovered by William Burgdorfer. Primary infection - headache, backache, chills, fatigue. Around 75% of cases develop "erythema migrans" at site of tick bite, which is a spreading bulls eye rash that clears in center. Lyme disease is treatable with tetracycline or penicillin at this stage. Its lucky if you catch it early as there is then the bulls eye rash. If you see the rash, it's a warning sign that you have Lyme disease. If you get it early enough, you can treat it with antibiotics. Untreated lyme disease may progress to the chronic stage. The real problem of lyme disease is if you don't catch it early and treat it with antibiotics. If you don't, the chronic stage can cause arthritis and long-term antibiotics usage. Arthritis develops in 40-60% of chronic cases, neurological involvement in 15-20% of chronic cases (palsy, weakness of limbs, facial tics), and cardiac damage occurs in 8% of chronic cases. The chronic stage requires antibiotics that can cross the blood-brain barrier. Diagnosis is difficult - antibodies don't appear for 4-6 weeks following infection; antibodies persist for years - may not indicate active infection. The disease is prevented by wearing protective clothing and insect repellent. A vaccine used to be available for people at risk - now not recommended (vaccine had an unusual method of action: it stimulated antibodies that attacked the Lyme bacteria in the tick's gut as it fed on the human host, before the bacteria were able to enter the body. This was about 78% effective in protecting against Lyme infection after all three doses of the vaccine had been given.) There is still a vaccine available for dogs in particular, but you needed multiple doses of the original vaccines but it was taken off the market partly due to the anti-vaccination movement as well as the side effects that were reported by the vaccine.

Cryptosporidiosis (waterborne)

Caused by Cryptosporidium parvum, a gastrointestinal protozoan parasite that causes watery diarrhea. Infection is usually self-limiting but can be life-threatening in immunocompromised persons. Can be found in most bodies of water in the United States, and it is a major global agent of disease. The parasites live on the intestinal surface and they didn't really realize how big of an issue cryptosporidiosis was until about the 1970s. Cryptosporidium is known to be among the most common intestinal diseases worldwide. The CDC estimates that crypto causes 300,000 infections annually in the United States. It wasn't recognized until recently since symptoms are similar to other gastrointestinal pathogens, and most cases are self-limiting and few are tested. Crypto oocysts cannot be killed by standard chlorination, and it is difficult to filter them out of water (crypto oocysts have been estimated to be present in >65% of surface water in the U.S.) Besides humans, crypto infects sheep, cattle, birds, rodents, and non-human primates. What complicates the epidemiology of diarrhea is that there are so many organisms that can cause the infections; also, a lot of people who get the diarrhea get better and don't end up interacting with the health systems anyways. Crypto has been found in almost 2/3 of water supplies in the US. It affects a lot of animals (both domestic and wild) which increases the organisms who can carry it. Milwaukee Outbreak--> There was a run out of anti-diarrheal medicine in Milwaukee with a lot of people missing school and work because of diarrhea; they eventually found cryptosporidium samples in patient stool samples and then in the water treatment plants. There was essentially so much cryptosporidium in the plant that it overloaded the filtration capacities. This happened in the spring of 1993, and was a wake-up call that even in developed countries, you can have a massive outbreak of waterborne disease. Life cycle (see picture): Basically, if you are infected you shed oocysts that can get into the water supply through a variety of means; if someone ingests them, then it will cause pathogenesis by affecting the epithelial part of the small intestine. The trophozoites is the feeding stage of Cryptosporidium in the small intestine.

Amebiasis (waterborne)

Caused by Entamoeba hystolytica transmitted by contaminated water. It is an amoebic, single-celled organism that has a feeding form (trophozoite) and creates cysts which are extremely resistant to water treatment and environmental factors. Anaerobic amoeba (so it lacks mitochondria), which produces cysts (one they are ingested, they release trophozoite into the intestine). Many infections are asymptomatic, but it can lead to amoebic dysentery. Can invade liver (best case), lungs (causes big holes), and brain (amoeba in the brain is game over like basically every time). 50 million people develop amoebic dysentery worldwide each year (100,000 die from it). The US has several hundred cases per year, mostly in the Southwest near the Mexican border. INTESTINAL PATHOLOGY: Severity of pathology depends on the extent of damage to the colonic mucosa. Chronic diarrhea is the least severe, ulcerative colitis is more severe (which consists of abdominal pain, cramping, and bloody stools) and amebic dysentery which is the most severe. This causes frequent watery stools containing blood and mucus, as well as severe abdominal pain and dehydration. The perforation of the colon may lead to peritonitis. The amoeba essentially invade and digest their way into the colonic mucosa. They can perforate the colon, get into the liver, and cause abscesses (containing liters of fluid that can be drained out of patients) in the liver and other places like the abdominal wall. EXTRAINTESTINAL PATHOLOGY: Most frequently involves the liver, leading to large abscesses (leads to hepatic tissue destruction; may extend through the diaphragm, causing pulmonary symptoms; may erode through the abdominal wall). E. histolytica may also spread to the brain (via the blood), causing cerebral abscesses. This is rare (about 0.1% of cases), but almost always fatal. Usually, they're happy just living in the intestine but sometimes (for reasons that aren't entirely clear) they can start to damage the intestinal tract and invade the mucosa. There are two forms of it: trophozoites, and cysts. *Trophozoites* average 20mm in diameter, and are highly motile (use pseudopodia) and have a prominent karyosome in the center of the nucleus. It feeds on the host cells and bacteria and has anaerobic metabolisms. *Cysts* are 10-15 mm in diameter and have 4 nuclei; each cyst releases 8 trophozoites when ingested, which can reproduce asexually and produce many more trophozoites. The outer wall of the cyst contains chitin and can survive outside the host for weeks to months.

Legionellosis/Legionnaires' Disease (waterborne)

Caused by Legionella pneumophila. It is named for the first recognized outbreak, which occurred during an American Legion convention in 1976 (where more than 200 people infected, 29 died, so a >14% fatality rate). It is a gram (-) rod, with complex nutritional requirements, such as requirement for high iron levels. It isn't related to any other organism associated with respiratory infections. It can live in areas where other bacteria may not do that well in; it's pretty novel in that it has jumped into humans very recently, and there have been concerns that it could jump into a larger outbreak of respiratory disease. Present in small numbers in lakes, streams, and soil, but also in "commercial" sources like hot tubs and hot water tanks and spas, where they grow to high numbers in warm, stagnant water. They are also found in large numbers in cooling towers and evaporative condensers of large air conditioning systems. They are resistant to heating and chlorination. Infection occurs by inhaling airborne droplets, as they get into your respiratory tract and invade the alveoli and grow there. It's an intracellular parasite - invades and grows in alveolar macrophages and monocytes. Can be asymptomatic or cause mild cough. In the elderly infections are more serious - intestinal disorders and pneumonia.

Rickettsial diseases (arthropod-transmitted)

Caused by Rickettsia which are small bacteria, intracellular parasites in the vertebrate. They are associated with blood-sucking arthropods at some point in their life cycle, like fleas, lice, or ticks. They are closely related to mitochondria and there are three groups (typhus group, spotted fever group, and the ehrlichiosis group). Named after Howard Taylor Rickett. The *typhus group* of rickettsial diseases (caused by Rickettsia prowazekii). It causes typhus which is transmitted from human to human by the body louse. Infection occurs when puncture from the louse bite becomes contaminated with louse feces. There were epidemics during wartime (killed more military than combat and 3 million people in WWI). Charles Nicolle received the 1928 Nobel Prize for his identification of *lice* as the transmitter of the epidemic typhus. Typhus causes fever, headache, weakness, followed by rash that spreads everywhere except face, palms, and soles as well as damage to CNS, kidneys, lungs, heart. It has a mortality rate of 6-30% and is treated with tetracycline and chloramphenicol. We have antibiotics today that can treat typhus well, but without that the mortality rate is quite high. DDT was commonly used to control lice; traps were also used to limit disease. The book Silent Spring talks about the widespread effects of harmful chemicals and is said to have started the green movement (talking about the harmful effects of DDT and how it decreased the bird population).

Measles

Highly contagious viral illness (probably the most contagious disease known). The illness has a respiratory transmission of virus (coughing, sneezing, direct fluid contact), with viral replication in nasopharynx and regional lymph nodes. Measles was first described in the 7th century, and in the 10th century Persian physician Rhazes described it as "more dreaded than smallpox". It had a near universal infection of childhood in the pre-vaccination era (90% infected by age 15) and despite availability of a vaccine, measles is common and often fatal in developing nations. Measles cases have become so rare that doctors are even failing to recognize the disease; however, it can quickly spread through populations as one person has the potential to infect 18 other people. There have been some recent outbreaks in airports and hospitals, as well Disney! The measles outbreaks have brought up the issue of anti-vaxxers and how some people are against vaccinating their children as they believe it may cause autism or other complications, which really doesn't have much or any scientific evidence to support it. The effect of vaccines on the prevalence in the United States of the major childhood viral diseases now controlled by the MMR (measles, mumps, rubella) vaccine. (a) Measles. (b) Mumps. (c) Rubella.

Typhoid Fever (waterborne and foodborne)

Caused by Salmonella typhi; humans are the only hosts. Infection occurs by ingestion of contaminated food or water contaminated with feces from asymptomatic carrier. The infectious dose is between 1000-10,000 cells, and the bacteria pass through intestinal wall and into the bloodstream. These diseases could be waterborne or foodborne since someone infected can contaminate both food and water and the actual bacteria can be found in water. This disease historically killed both rich and poor alike. The son of Abraham Lincoln is thought to have died of Typhoid fever which he acquired from a well with contaminated water in the White House, so it certainly wasn't a disease just large with people who had limited means. Now, typhoid is an issue in developing nations and remains a major pathogen in these regions. With typhoid fever, bacteria in the blood are phagocytized, but not killed, by macrophages. Then, they are carried to liver, spleen, bone marrow, and gallbladder. The bacteria in gallbladder may released back into the intestine, causing another round of gastroenteritis and bacteremia. It causes gradually increasing fever, headache, muscle pains, loss of appetite and "rose spot" rash. Typhoid Mary--> One of the best known cases is with "Typhoid Mary" as she cooked for many people and was an asymptomatic carrier. So, she was constantly secreting typhoid bacteria and, at the time, proper hygiene didn't really include washing hands (surgeons even had to be convinced to wash their hands!). There were 3 deaths linked to her (as well as 51 cases) and they tracked down Mary because several families who were involved with her were exhibiting typhoid symptoms. They essentially incarcerated her in involuntary quarantine which she stayed in for 25 years; she actually died in quarantine.

Impetigo (S. pyogenes)

Caused by Staph. aureus & Strep. Pyogenes and is most common in preschool-aged children and also is seen in players of close contact sports as it is spread by direct contact with lesions or with nasal carriers. It's seldom serious, and minor infections may even clear on their won in two to three weeks. Since impetigo can lead to complications, doctors may choose to treat it with an antibiotic ointment or oral antibiotics. Most people only suffer mild infections, but it's important to understand the full pathogenic potential of the bacteria to understand how to identify, treat, and avoid these infections.

Rabies (animal-transmitted)

Caused by the rabies virus, a member of the *Rhabdovirus* family. It has negative-sense single-stranded RNA. The shape of the rabies virus is very much bullet-shaped. Rabies continues to be a problem across the globe; there are a whole host of animals that can be the primary reservoir. Its typically transmitted by bite. Animals infected with rabies tend to have more saliva and foam at the mouth due to spasms in the mouth. Around 55,000 people die each year worldwide, and 1 million people treated for rabies each year. Wild animals are major reservoir: raccoons, skunks, coyotes, foxes, and bats. Rabies isn't a huge problem in the US, but it continues to be a big problem in the world. Rabies happens in virtually every state in the country but it depends on which animal is causing the rabies to proliferate: for example, a bat on a plane exposed some people to rabies, and the rabies epidemic in racoons has caused an increase in rabies cases in the mid-atlantic and north-east. The virus infects cells of central nervous system in most warm-blooded animals, and is present in saliva of infected animal. It enters body by bite wound, multiplies at site of bite, then travels to CNS. Then, the virus proliferates in brain, causing fever, excitation, pupil dilation, excessive salivation, and anxiety. Death occurs by respiratory paralysis. The virus quickly gets into the central nervous system; depending on where you are bitten it depends the progression of the disease (if you are bitten in the peripheral nervous system, then it can take longer—maybe even months—to progress). It is very dangerous and 100% fatal when left untreated. As treatment, exposed humans get rabies immunoglobulin. There is also an immunization with an inactivated rabies virus. For animals, all domestic animals are vaccinated and a rabies coat protein is expressed in the vaccinia virus. If you are exposed, you really should get treated which happens with rabies immunoglobulin. There are also some people (who work with bats, for example) who get immunized with an inactivated rabies virus. Wild animals are vaccinated sometimes by putting the vaccine available with food or bait sites which are normally a mixture of fish oils which is used to attract the raccoons but it also contains the vaccine.

Examples of waterborne diseases:

Cholera, Giardiasis, Cryptosporidiosis, Legionellosis, Typhoid, Viruses, Amebiasis

TB granuloma formation

Chronic activation of T-cells; Accumulation of macrophages; Formation of a "granuloma"; Tissue necrosis and cavitation. Basically forms holes in the tissue which are filled with a bunch of cheesy-like substances (ew). *Tubercles* are seen under the microscope as rings of macro-phages & other inflammatory cells surrounding infected cells. This creates *caseous necrosis* (solid cheese-like material) forms in the center as a result of cell death.

Common Cold

Colds (and influenza viruses) make up almost 90% of the acute infectious diseases in the US. Each person averages three colds a year. *Rhinoviruses* (upper panel) account for majority of colds and *coronaviruses* (lower panel) account for 15% of colds (this includes SARS). Other viruses account for 10% of colds. Cold viruses are spread mainly by aerosol transmission but direct contact with people and contaminated objects also spreads cold viruses.

Scarlet fever (S. pyogenes)

Common in the pre-antibiotic era and is caused by strains of S. pyogenes containing a lysogenic phage that codes for pyrogenic toxins, which cause a pink-red rash to develop; toxins damage small blood vessels and initiate fever. The scarlet fever is caused by the exotoxin that is released by the bacteria and is characterized by a red rash on the chest that may spread to the rest of the body.

Airborne pathogens

Disease-causing microorganisms (viruses, bacteria, or fungi) that are suspended in the air; aerosols from sneezing, coughing, and talking are important means of person-to-person transmission. A single sneeze contains 10,000-100,000 bacteria, and also may have millions of viruses during an acute infection. Indoor air actually contains more microorganisms than outdoor air, as it contains mostly organisms found in the human respiratory tract. Outdoor air contains mostly soil organisms. Airborne pathogens infect people by RESPIRATORY TRANSMISSION or by DIRECT CONTACT! **travel**--> windblown dust may carry microbial populations long distances, across continents and even oceans; most microorganisms don't survive for long in the air, but some gram (+) bacteria can survive for long periods as they're more resistant to dessication (drying out) and are generally more robust than gram (-) bacteria.

Water Purification

Effective water treatment practices were not developed until 20th century. At first, water was filtered to reduce turbidity (cloudiness). However, in 1905, coliform counting procedures were developed. In 1910 *chlorine* was introduced as a disinfectant. This is the most significant procedure developed for preventing waterborne disease. Typhoid fever in philadelphia shows the importance of water purification (and how chlorination is much more effective than chlorination). Due to urbanization in general, as well as immigration, cities were gaining a lot of population at the time and there were numerous outbreaks of typhoid. This is just one waterborne illness of many others, but after filtering water there was a big drop in cases; when chlorination was introduced there was another drop. Philadelphia was pretty representative of other cities in this time period (1885-1945).

Salmonellosis (foodborne INFECTION)

Food infection caused by species of Salmonella. Once infected, you will present GI symptoms (fever, diarrhea, chills, stomach aches, etc.). The bacteria are normal inhabitants of animal intestinal tracts but all Salmonella species are pathogenic to humans (there are over 1400 serotypes of known pathogenic Salmonella. 45,000 documented cases per year in US (estimated 1.3 million cases per year in US). Sources of infection are the intestinal tracts of humans and animals. Chickens and cattle harbor Salmonella (so eggs, meat, dairy products can be contaminated). Outbreaks and infections are often traced to custards, cream cakes, meringues, pies, eggnog, meat pies, cured uncooked meats, poultry, milk and milk products). Requires the ingestion of 10^5 - 10^8 organisms. Symptoms typically begin 8-48 hours following ingestion and include headache, chills, vomiting, and diarrhea. Typically resolves in 2-3 days, but can be fatal in the elderly and immunocompromised. Salmonella is shed in feces for several weeks, and some people shed Salmonella for months or years as asymptomatic carriers. If enters the blood it causes typhoid fever. Bioterrorism attack using salmonella--> People involved in a religious cult based in Oregon decided they wanted to "control" the government because they were a bit mad at them; they essentially grew salmonella and then contaminated salad bars so that everyone got salmonella so that they couldn't go vote in the elections. This was in 1984. wack!!

Foodborne Diseases

Foodborne diseases can be separated into 2 categories: *Food Poisoning*: eating food containing preformed microbial toxins. The organism doesn't grow in the host, and doesn't need to be alive. Symptoms may begin within 30 min. *Food Infection*: active infections resulting from eating pathogen-contaminated food. 76 million people in the United States are sickened each year with foodborne illness, causing 325,000 hospitalizations and 5,000 deaths. They have $14-152 billion in economic impact. Normally, one out of four people are getting a foodborne illness every year and it is very unreported, even in the developed world. Globally, many healthy lives are lost (children account for one out of three deaths of foodborne diseases).

Systemic mycoses (histoplasmosis, coccidiomycosis, aspergillosis, and cryptococcosis)

Fungal infections affecting blood and internal organs which are often initiated by spore inhalation. *Histoplasmosis* is caused by inhaling Histoplasma capsulatum spores and is common in N. and Central America (areas of wet, humid soil where the spores are aerosolized and dispersed). Once the spores are inside the human, they switch to yeast form and cause infection. *Coccidiomycosis* (or valley fever) is common in the SW US, Mexico, Central and S. america since it lives in dry soil. It is caused by Coccidioides and causes bronchitis, pneumonia, muscle, and joint pain (aka 'desert rheumatism') and can progress to disseminated infection. *Aspergillosis* is a common mold found indoors and outdoors; it causes a lung infection that can progress to disseminated infection in people with weakened immune systems and lung problems. We breathe in around 100 spores a day and COVID-19 and aspergillus coinfections likely, but there is little data available so far. More associated with human environments; in a healthy individual, the spores that we breathe in every day normally don't cause infection. *Cryptococcosis* is caused by the cryptococcus species and causes one of the largest human death burdens; causes a pneumonia infection and potentially meningitis in the brain. The most frequent form is Cryptococcus neoformans and is found ins oil, decaying wood, and bird droppings; disease in immunocompromised hosts (ex: HIV/AIDS patients) is very dangerous. Life cycle of *Histoplasmosis*; they can travel from the lung to the lymph nodes eventually to the blood, causing systemic infection. More specifically, the environment gets contaminated with mold with aerial hyphae, the spores are inhaled and enter into an environment ~37ºC, the yeast form in the lung and are transported to lymph nodes, the yeast move to the blood and other organs, causing systemic infection. *Coccidiomycosis * has a similar symptom presentation to histoplasmosis but a different way of infection, and climate change seems to have caused more of these spores to be aerosolized and spread around due to a variety of factors (rain drying up, fires, dust storms, etc.) Multiple *aspergillus* species are pathogenic; they are highly aerobic and are found in almost all O2 rich environments. They form conidiospores and can form different pigments (they are very diverse). Environmental exposure to antifungal drugs is associated with increased resistance in these species For *Cryptococcosis* phagocytes are kind of called a 'Trojan house' in that they carry the pathogenic yeast. The pathogen is a facultative intracellular pathogen; can utilize phagocytes to travel through the body; non-lytic escape from cells; ability thought to have evolved from environmental selective pressure by amoebae. The yeast cell can escape the phagocyte without killing it which is specific to Cryptococcosis and is called vomocytosis. In the host, cells undergo an unusual change in size, from small haploid yeast to large polyploid titan cells, which are too big to be engulfed by phagocytes! For decades, titan cells couldn't be induced in the lab but now minimal media, hypoxia, low pH and exposure to bacterial cell wall induces titan formation; they have a thick capsule + dense cell wall. It is an *encapsulated fungus* and the capsule is comprised of glucose and glucosamine polysaccharides; it is remodeled during infection and melanin is deposited in the cell wall which confers cell integrity and protects from phagocytosis and hides the cell from the host immune system (required for dissemination). The cell wall and capsule are very important during infection! Cryptococcus species are *radiotrophic fungi*: perform radiosynthesis = use the pigment melanin to convert gamma radiation into chemical energy for growth; produced by melanocytes and the amount of melanin in fungal cells is regulated by the environment; the increase in biomass was faster in an environment with 500X higher radiation. OUTBREAK--> Highly virulent Cryptococcus gattii outbreak in the NW US; ongoing outbreak the Pacific Northwest since 1999; found in tropical and subtropical regions assoc. with various tree species, notably eucalyptus tree. Infections in apparently immunocompetent individuals. It infects the lung and brain and disease is slow ~ 6-7 months to onset. Healthy individuals can get the disease but infections are particularly pathogenic in immunocompetent individuals; the disease progression is slow and chronic.

LECTURE 20

Fungi [Part II]

Fungi metabolism

Fungi are often *heterotrophs* and feed on preformed organic material. Unlike animals which ingest then digest, fungi digest then ingest. Fungi produce hydrolytic enzymes that are secreted and break-up organic material, and then the digested food then absorbed. Most fungi are *saprobes* which means they get nutrients from dead organisms. *Saprobes* use non-living material and they are important scavengers. *Parasites* use organic material from living hosts, harming them in some way. *Mutualists/symbionts* are fungi that live in association with the host without harming it (and often helping it).

Human mycobiome

Fungi cover mucosal and epithelial surfaces of the human body; some can grow in virtually every mammalian niche, and some fungi train the immune system against other fungi. Some of these fungi can become pathogens but also can be beneficial. The Candida species can live in a lot of different locations (see picture). The human mycobiome is few in number than bacteria and viruses, but larger in size (it's bigger in number than helminths). There are *mutualistic interactions* with the host and with other microbiota. The interactions are shaped by host physiology, immunity, and competition for nutrients. Our viral microbiota is the largest (but they are very small in size), then the bacterial microbiota, then the fungal microbiota (which is smaller in number but much larger in size than either the bacteria or viral microbiota).

Fungi explositvity

Fungi have evolved unique modes of dispersal...and are the most explosive organisms on earth. For a sporangiophore less than 1 cm tall, this involves acceleration from 0 to 20 km/h in only 2 µs, subjecting it to over 20 000 G, equivalent to a human being launched at 100 times the speed of sound; it grows in dung and then fires the spores (up to 2 m away) to areas where animals graze. *Pilobolus* is the dung cannon fungus that is also called the hat thrower fungus. They go up to 20,000-180,000G since they accelerate so quickly due to osmotic pressure caused by water build up below the spore. It is a zygomycete. It's called a *sporangiophore* but fruiting body may work as a description, too.

Waterborne diseases

Globally, water is the most important potential source of infectious disease. Water quality breakdown can cause massive spread of infectious disease, which can be life-threatening, especially for the very young, elderly and immunocompromised. Although certain microorganisms are pathological, others may be used to remove pollutants and organic material from water as part of the treatment process. Around 801,000 children died from diarrheal illnesses, most of which are caused by unsafe water, poor sanitation, and inadequate hygiene. There are '*aerated lagoons*' which use microbes to break down organic material in wastewater (in the picture of one of these lagoons in RI, you can see a gaseous presence). Drinking contaminated water (as it is improperly treated) can get you sick, but even when you are swimming around in recreational water like ponds, streams, lakes, pools, and fountains, you can get sick (because you swallow a little bit of water). Animals and humans can contaminate water supplies. Waterborne diseases are a massive problem in developing countries. No matter how clean the water looks, you don't know how it looked upstream. Microorganisms transmitted in water are *intestinal organisms* that leave the body in the feces. The source of the pathogens may be animals (domestic or wild) or other humans. In developing countries, cholera, typhoid fever, and amebiasis are important public health problems.

Penicillin

Growth of bacteria on the agar in a culture dish has been inhibited by the fungus Penicillium notatum (see picture). The first antibiotic, penicillin, was discovered in 1929 by *Sir Alexander Fleming*, who observed inhibition of staphylococci by a Penicillium mold. Ancient treatments for infections included using moldy bread! The ancient Egyptians, the Chinese, and Indians of central America all used molds to treat infected wounds. However, they did not understand the connection of the antibacterial properties of mold and the treatment of diseases.

Hantavirus (animal-transmitted)

Hantavirus is caused by mice and other rodents. The 1993 hantavirus outbreak in US killed 32 of 53 infected people. Hantavirus is a member of Bunyaviridae family, and the virus consists of enveloped negative-sense single stranded RNA viruses. This virus is associated with rodent pellets or rodent feces which can be aerosolized and spread via airborne transmission. Symptoms include fever and pulmonary capillary leakage. Death occurs in 50% of cases due to shock and cardiac complications due to pulmonary edema. There is no treatment or vaccine, so you can reduce exposure by eliminating rodents.

Candida species

Most frequent - Candida albicans (ascomycete). Normal microbial flora on skin and mucous membranes, and a normal component of the GI microbiome. *Commensals* live in association with other organisms but don't derive their nutrition from them. They can cause *mucosal infections* (oral thrush, vaginal infections) and *bloodstream infections* (typically in immunocompromised individuals) have 50% mortality rates. Candida can infect every organ and tissue. The species can switch between yeast and hyphae (filamentous) life-forms quite easily. They also form rod-shapes when mating and can form biofilms (made of hyphae) which are critical in an infection. It is commensal, but since it is the most opportunistic fungus, it will grow anywhere and such cause infection to the host "by accident" (as in, it is not doing it on purpose to take advantage of host processes). So, candida requires a delicate balance between colonization (low fungal load - microbiome competition, intact epithelial barrier, shielding from the immune cells) and invasion (high fungal load - disruption of the microbiome, disruption of the epithelial layer, immune responses and inflammasome activation). The host can be damaged by too many pathogens (weak immune response) or an exaggerated immune response (strong immune response). Candida auris is an emerging fungal pathogen recently, which is worrying. It is frequently misidentified and normally happens with localized outbreaks. It is highly lethal (60%) in susceptible groups and is very hard to clean from hospitals. Most strains of it are resistant to at least one antifungal drugs and many strains are multi-drug resistant (MDR). This species has expanded families of drug transporters and lipases as well as mutations in drug resistance genes.

Superficial fungal infections (cutaneous mycoses)

Most fungal infections are superficial and the most serious '*mycoses*' are not contagious (ex: skin, nails, hair). They result from environmental sources. *Cutaneous mycoses* (like ringworm and athlete's foot) are caused by dermatophytes and ARE contagious. They live in the dead layers of the skin and secrete keratinase to degrade keratin. In cutaneous mycoses, there are multiple dermatophytes present (Tinea pedis, Trichophyton) and multicellular hyphae with asexual spores. They are contagious and spread through contact. They result in scaling, flaking, and itching of the feet and are very treatable and very common (not fatal).

Microsporidia (insect fungal pathogen)

Nosema apis was recently considered fungi (before they were categorized as protozoa); associated with *colony collapse disorder* so this is a major threat for agriculture; picture above shows the spores of the species (they spread through the feces of the honeybees and when infecting, causes dysentery, etc. and reduces the population of bees) ~20% of bee species are in decline in N America because Nosema apis is most common disease of honeybees. This is crucial since bee pollination produces 30% of our food. Nosema spores are spread to other colony members via feces; and *fecal staining* is a major symptom of the disease and a colony will show this when it is on the way to collapse. The spores infect epithelial cells of the midgut causing intestinal injury, this leads to dysentery and a reduction in food gathered, so ultimately the colony collapses.

Avian Influenza

Occurs mainly in birds and can be deadly to them; avian influenza does not usually infect people. When it does, it doesn't usually spread person-to-person. The H5N1 avian strain was first reported to cause human infections in 1997 and most of the cases resulted from people having direct or close contact with H5N1-infected poultry. The mortality rate in humans has been about 60%, and public health officials are concerned that H5N1 will mutate and be able to spread directly from human-to-human (eeeek!!). This might lead to another pandemic with much more serious consequences than 2009. The 1918 Spanish Influenza may have originated from an avian strain that mutated to spread easily among humans. H7N9 Avian Flu has also been found: as of March 2014 there have been over 350 reported cases of H7N9 in China, with over 100 deaths. This is the first time that H7N9 has been reported in humans, and sustained human-to-human transmission has not yet been documented, but remains a possibility. The virus was detected in pigeons at a market in Shanghai. It also happened in a 2015 Midwestern Avian Flu outbreak in Minnesota which eventually led to the death or euthanization of 43 million chickens and turkeys in 15 states.

Cordyceps

Parasitic fungus that alters host behavior; it enters the insect, takes them over, and eventually erupts out of them and infects others. More specifically, it sends them upward and then develops a fruiting body from the head, then the spores burst from its tip. Gahhh!!

LECTURES 15 & 16

Person-to-Person Microbial Disease

Antigenic Drift (influenza)

Point mutation; minor change, same subtype. Caused by point mutations which may lead to amino acid substitutions. This may result in more serious seasonal epidemics than observed in a typical 'flu season'. Can also lead to pandemics if the changes allow person-to-person spread of novel animal-infecting strains (1918 flu pandemic may have started this way). About two-thirds of the H3N2 viruses circulating during the 2014-2015 flu season were a drifted variant of the H3N2 strain in the vaccine, leading to reduced efficacy (19% effective). The 2015-2016 vaccine is well matched to the circulating strains and has been estimated to be 60% effective.

Respiratory Transmission (airborne pathogens)

Since many droplets can be produced by a single sneeze, with the droplets carrying one to two bacteria per sneeze (the air can reach speeds of 70 m/s and the droplets travel at 100 m/s; so, sneeze into your elbow!!), as well as other means of respiratory transmission (coughing, talking, etc.), infectious diseases spread by respiratory transmission are among *THE MOST CONTAGIOUS!!!* See the picture (the blue dots represent airborne transmission).

Antibody (serology) diagnostics - coronavirus testing

Some coronavirus tests use recombinant N protein and S protein conjugated with colloidal gold and anti-human IgM and IgG antibody coated on different test lines respectively (see diagram). The gold-labelled N protein and S protein will bind with CoV IgM or IgG antibody and form marked antigen-antibody complexes. These complexes move by capillary action. Marked antigen-antibody complexes will be captured on different test lines by anti-human IgM (which are used since they're short-lived and may indicate that the virus is still present; they usually disappear a couple weeks after infection) and IgG antibody (appear after IgM antibodies and are more durable; no one knows yet how long they last and provide resistance to reinfection). HOWEVER, positive results may be due to past or present infection with non-SARS-CoV-2 coronavirus strains, and we don't know yet how much protection antibodies give against CoV-2.

Bordetella pertussis

The bacillus is gram(-) and produces a specific adherence factor (filamentous hemagglutinin antigen), adheres to cells of respiratory tract. It produces an exotoxin which induces cAMP production, also has endotoxin. The disease is also called *whooping cough* as the symptoms (cough) worsens over two weeks, when it reaches the "paroxysmal" stage. A paroxysm is a burst of rapid, short coughs. This is when the cough is very severe and has the characteristic "whoop" sound associated with an attempt to breathe through an obstructed airway after a paroxysm. This is what gives pertussis the colloquial name, "whooping cough". Then, the paroxysmal stage slowly subsides and over 2-6 weeks. Paroxysms can be extremely exhaustive, especially for children. Pertussis toxin is an oligopeptide AB-type exotoxin that is the major cause of pertussis (abnormal cough). It has a similar mechanism to the cholera toxin - a modification of G protein. It causes T cell lymphocytosis and has adjuvant properties. The pertussis vaccine is part of the DTaP (diphtheria, tetanus, acellular pertussis) immunization. Before a vaccine was available, pertussis killed 5,000 to 10,000 people in the United States each year. Now, the pertussis vaccine has reduced the annual number of deaths to less than 30. There is a bit of a rise in cases of pertussis (after the significant drop once DTP was introduced). Maybe there is a resistance to the vaccine that is emerging? Teenagers and adults usually recover from whooping cough without complications. At worst, excessive coughing may cause a bruised or broken rib or a hernia. It mostly affects kids.

Neisseria meingitidis (meningitis)

The bacteria is a gram(-) encapsulated diplococcus. Approximately 30% of people carry N. meningitidis in their nasopharynx. It is transmitted to host through air, attaches to cells in nasopharynx, and causes upper respiratory tract infection. It can lead to *meningococcemia* which consists of septicemia, intravascular coagulation, and shock and this is fatal in 17% of cases; survivors may require amputations. It can also lead to *bacterial meningitis* which consists of an inflammation of the meninges (lining around the brain and spinal cord), sudden onset of headache, vomiting, and stiff neck, and can even progress to coma and death in a few hours. Epidemics of these forms of meningitis often occur in young adults living in close quarters, such as military bases and college campuses. Currently there are 13 different strains of this bacteria known and there is an overall 2% mortality rate. Different viral infections can lead to viral meningitis. But in most cases in the US, particularly during the summer and fall months, the meningitis is caused by enteroviruses (which include enteroviruses, coxsackieviruses, and echoviruses). Most people who are infected with enteroviruses either have no symptoms or only get a cold, rash, or mouth sores with low-grade fever. And, only a small number of people with enterovirus infections develop meningitis. Normally, the bacteria live harmlessly in the throat. However, they can start to produce 100-1000x of endotoxin. The bubbles of toxin act to confuse the host immune system so the white blood cells engulf the bacteria. Then, the toxin causes the blood vessels to get sticky and the white blood cells get trapped and leave a stream of damage as the clots increase as platelets attach to the wall. This is what ends up giving meningitis the distinctive rash and kills tissue.

Necrotizing fasciitis (S. pyogenes)

The extensive destruction of subcutaneous tissue through 'flesh eating bacteria' (a misnomer as the bacteria don't actually eat the tissue and cause the destruction of tissue by releasing toxins) and is mediated by superantigens that cause a massive activation of the immune system, causing inflammation that leads to tissue destruction. The S. pyogenes produces an exotoxin known as a superantigen which causes an over-production of cytokine which over-stimulates macrophages and cause the actual tissue damage singe the oxygen free radicals normally intended to destroy bacteria can damage nearly everything they're in contact with in the body. It's very rare but very serious (around 30% mortality rate).

Chytrids (amphibian fungal disease)

The fungus attacks the parts of a frog's skin that have keratin in them. Since frogs use their skin in respiration, this makes it difficult for the frog to breathe. The fungus also damages the nervous system, affecting the frog's behaviour. A sick frog may: have discoloured skin and be sloughing, or peeling, on the outside layers of its skin. This can vary from an obvious peeling of skin (particularly on the feet), to a roughness of the frog's skin that you can barely see. The frog may sit out in the open, not protecting itself by hiding, be sluggish, and have no appetite, and have its legs spread slightly away from itself (rather than keeping them tucked close to its body). In more extreme cases, the frog's body will be rigid, and its back legs will trail behind it. The disease is caused by Batrachochytrium dendrobatidis (Bd) is called chytridiomycosis. It produces a toxin that kills amphibian or mammalian B and T cells. It has caused the decline or extinction of 200 species and can have 85-100% fatality. The life cycle is relatively unique due to the **flagellar** state, and the fact that the spores release through the discharge tubes in the discharge papillae in the sporangium. Scientists estimate up to 170 species of frog have become extinct in the past decade from the fungus and other causes, and an additional 1,900 species are threatened. These are unique as they can form a flagella (no other fungi have this strength). They may have increased due to climate change, which has expanded the distribution for this pathogen. The trading of amphibians as pets has seemed to spread this disease even more. It is also causing decreases in other species (threatens more species than any known to science). It ALSO occurs in ***SALAMANDERS*** and is caused by Batrachochytrium salamandrivorans (Bsal). It's an invasive fungus threatening European and N. American salamanders (fire salamander). It causes skin lesions, apathy, loss of appetite, and eventually death. The damage to the epithelial layer can cause problems eventually leading to sepsis.

The amount of time the virus can live on different surfaces

The surgical mask one is particularly concerning.

Upper and lower respiratory tracts

The two parts of the tracts offer very different environments and thus favor different microbes. The nasal cavity, oral cavity, pharynx, and larynx make up the *upper respiratory tract.* S. aureus is found here (which causes skin lesions) as well as S. pyogenes (which causes strep throat and impetigo). The trachea, primary bronchus, secondary bronchus, respiratory bronchiole, terminal bronchus, alveolar ducts, and alveolar sacs, and alveoli make up the *lower respiratory tract*. Coxiella burnetii live here (which cause Q fever), as well as Chlamydophila psittaci (which are lethal bacteria that cause respiratory issues in humans and outbreaks in zootic populations). See the picture for different microbes that live in the different areas!!

Animal-transmitted diseases

These spread directly from animals to humans (rather than having an arthropod as a bridge between us and animals). Humans can become a host for these diseases. It is very difficult to completely eradicate these diseases through vaccination due to the nature of them originating in animals. Animal diseases transmissible to humans are called *zoonoses*. The natural host is a vertebrate other than humans (wild animals are reservoirs for these diseases). Transmission occurs by contact, aerosols, or bites.

Mycorrhizae

literally means 'fungus-root'; Roots of most terrestrial plants are mycorrhizal. Mycorrhizal fungi get their carbon from root secretions and inorganic minerals from the soil. Mycorrhizal plants get more nutrients from the soil due to greater surface area from fungal filamentous cells. This mutualistic association provides the fungus with relatively constant and direct access to mono- or dimeric carbohydrates, such as glucose and sucrose produced by the plant in photosynthesis. The carbohydrates are translocated from their source location (usually leaves) to the root tissues and then to the fungal partners. In return, the plant gains the use of the mycelium's very large surface area to absorb water and mineral nutrients from the soil, thus improving the mineral absorption capabilities of the plant roots. MUTUALISTIC--> fungus provides inorganic materials for the plant (nitrogen and phosphorus) and the plant provides organic materials (carbon based) for the fungus which come from photosynthesis. There are ectomycorrhizal (outside, do not penetrate root cell) and endomycorrhiza (inside, the hyphae penetrate the root cell; this type is more common) that exist. An example of ectomycorrhizal fungi are truffles! They are usually found in close association with the roots of trees and are the most expensive food in the world. It improves plant growth since mycorrhizal mycelia are much smaller in diameter than the smallest root, and can explore a greater volume of soil, providing a larger surface area for absorption. Also, the cell membrane chemistry of fungi is different from that of plants. Mycorrhizae are especially beneficial for the plant partner in nutrient-poor soils. Mycorrhizal fungi release powerful chemicals into the soil that dissolve hard to capture nutrients such as phosphorus, iron and other "tightly bound" soil nutrients.