Concepts: The Scientific Process - PDF

Concepts WEEK 1 The scientific process Learning objectives: ​ Define, agent, host and environment ​ Describe the general role of the causal model in disease transmission ​ Review descriptive epidemiology as it applies to communicable diseases ​ Review analytic epidemio...

Concepts WEEK 1 The scientific process Learning objectives: ​ Define, agent, host and environment ​ Describe the general role of the causal model in disease transmission ​ Review descriptive epidemiology as it applies to communicable diseases ​ Review analytic epidemiology studies as applied to communicable diseases. ​ Describe differences between case-control and cohort studies. ​ Explain the importance of randomization in randomized controlled trials ​ Understand and calculate odds ratio as a measure of association. Definitions ​ Disease: pathological condition of body parts or tissues characterized by a group of symptoms ​ Infectious disease – a disease caused by an infection agent such as bacteria, virus, fungus, that ca be passed on to others ​ Epidemiology: Study of disease and other health related events in population ○​ Descriptive: examine distribution of disease and observe the features of distribution ○​ Analytic: test a hypothesis about the cause of the disease – by studying how exposures relate to the disease ​ Communicable disease is an illness caused by infectious agents such as bacteria, viruses, parasites, or fungi, which can be transmitted directly or indirectly from one person to another, from animals to humans, or through environmental reservoirs All diseases have host, agent and environment ​ Host: the individual who has the disease ​ Agent: the factor whose presence (or absence) can cause disease – ex: poison, physical trauma ​ Environment: all external conditions and influences on effecting life – ex: water, housing 4 Study Designs Study Temporal NatureCharacterization of Example design Subject at Enrollment Cross-sAt a point in time The exposure, and the They do not follow a group over time, ectional snapshot) disease status are nstead, they collect research of stress Study collected at the same time evels in college students in various years of study (freshman, sophomore, etc.). Case-coPoint in time, or Diseased and Compares the sick and the healthy. Dr do ntrol may collect non-diseased. Look a study to find if Coke intake is associated Study retrospective retrospectively to collect with Colon Cancer data nfo on exposures ​ Already sick ​ Asked if they drink coke or not Cohort Follow subjects Exposed and not Exposed.Compares the exposed and not exposed. over time Follow overtime to Ex: female nurses who smoke, vs those prospectively determine disease status who don’t. Compare for a particular and outcome – Lung cancer. retrospectively) ​ Will BLANK make them sick ​ Whoever is running the experiment already knows who smokes or doesn’t Clinical Follow subjects Similar disease status but Used to study new test or treatments, and Trial over time randomly assigned an evaluates how they effect the patients prospectively) exposure. Followed over outcome ime to determine outcome. Prospectively – individuals are followed over time and data about them is collected as their characteristics or circumstances change Retrospectively – Individuals are sampled and information is collected about their past (by interviews or questions) General role of the Casula Model in Disease Transmision ​ Understanding Relationships: It establishes cause-and-effect relationships between variables, such as how increased contact rates lead to higher transmission probabilities or how vaccination reduces susceptibility ​ Prediction and Forecasting: By quantifying these relationships, causal models can predict future outbreaks, identify high-risk populations, and estimate the potential impact of interventions. ​ Guiding Interventions: The model can identify leverage points for controlling or preventing disease, such as targeting vaccination campaigns or reducing contact rates in specific areas. ​ Supporting Decision-Making: Causal models provide evidence-based insights for public health planning, resource allocation, and policy development.  ​ Incorporating Feedback Loops: These models often account for dynamic feedback, such as how a decrease in susceptible individuals due to immunity reduces the transmission potential over time. 1.​ Example: the Casual Model in Disease Transmision in Covid would focus on variables such as: viral load, mask-wearing behavior, social distancing measures, and the effect of vaccinations, all interacting to determine the rate of disease spread. Descriptive epidemiology as it applies to communicable diseases ​ Descriptive epidemiology examines the distribution of the disease in a population and observes the basic features of the distrubution by examining patterns related to person, place, and time. ○​ Applying to a communicable disease, it focuses on understanding how infections spread and who is most affected, providing possibility for further analysis and intervention planning Analytical Epidemiology as it applies to communicable diseases ​ Analytical epidemiology uses a hypothesis to test about the cause of the disease by studying how exposures relate to the disease, and determining the factors that influence the occurrence, spread, and control of diseases, including communicable diseases. Describe differences between case-control and cohort studies. ​ A case control study looks at the subjects durring a certain point in time, and may also collect retrospective info (interviews) They will compare a group of healthy subjects and a group of diseased subjects. They start recording the groups, once the subjects have already been infected, and try to find out what caused the disease. ​ Whereas a Cohort study follows the subjects over a period of time, where they are able to collect prospective data – as well as retrospective if needed. Rather than comparing the sick and the healthy (case-control), they compare Exposed vs not exposed subjects, and compare for a particular outcome Explain the importance of randomization in randomized controlled trials ​ Randomization is the main strength of a randomized control trial. It aims to ensure that there is a sense of baseline comparability between groups on factors related to the outcome. ​ This design allows researchers to evaluate the safety and efficacy of the new vaccine in a controlled and scientifically rigorous manner. Case-control study of cross-sectional study OR - Understand and calculate odds ratio as a measure of association. ​ Odds ratio is a different expression of probability, the probability of an event/ the probability of the event not happening ​ Can be used to determine if a particular exposure is a risk factor  ○​ OR = odds of disease among exposed/Odds of disease among those not exposed ○​ OR = (a/c)/(b/d) ○​ A= exposed and diseased ○​ B= exposed and not diseased ○​ C= not exposed and diseased ○​ D= not exposed and not diseased OR - Calculations ​ If OR=1 exposure does not affect the odds ​ If OR>1 exposure associated with higher odds of outcome ○​ Positive correlation ​ If OR< 1exposure is associated with lower odds of outcome ○​ Negative correlation Cohort study or clinical trial – Relative Risk ​ RR – proportions of people with the disease among the exposed/proportions of people with the disease among unexposed ​ RR = [a/(a+b)] / [c/(c+b)] ○​ A= exposed and diseased ○​ B= exposed and not diseased ○​ C= not exposed and diseased ○​ D= not exposed and not diseased WEEK 2 Introduction to Microbes and Infection Learning Objectives ​ Name and describe the general features of different types of disease-causing microorganisms. Microscopic: ○​ Bacteria – single celled microoragnisims, some are beneficial to humans, and some cause disease. ​ Roughly 0.001 micor meters ​ Prokaryotes ​ FOOD POISINING ○​ Viruses - Roughly ~0.0001-0.00001 ​ Come in many different shapes ​ They depend on the host cells fro survival/replication ​ MYRAID ○​ Fungi – few micrometers to a few centimters ​ Different shapes (single celled yeasts, multicellular molds) ​ Eukaryotic, or heterotropic ​ Cause a wide range of diseases (yeast infection, jock itch) ○​ Parasites – size varies  ​ Different shapes (unicellular protozoa, multicellular helminths) ​ Eukaryotic, often relies on host for survival ​ Often have complex lifestyles ​ Causes wide range of diseases ​ Malaria [protozoa], tapeworm [helminth] ​ Define microbiology and include some size ranges of microorganisms in this category. ○​ Deffiened by two groups. Microscopic, and macroscopic. ○​ Micro: Bacteria ​ Yeast ​ Ciruses ​ Protozoans ○​ Macro: ​ Worms ​ Mold ​ Describe the historical contributions of Semmelweis, Lister and Koch. ○​ Lister: (British surgeon) ​ Sepsis from a pollen-like dust ​ Use of disinfection greatly improved survival after surgeries and decreased post-operative infection ○​ Semmelweis: in all but a few cases, puerperal fever—also known as childbed fever—was caused by an infection introduced into the birth canal from outside, which could be prevented by chlorinous disinfection of the hands ○​ Koch: Experiment with bacterium, Bacillus anthracis ​ List Koch’s postulates and discuss the limitations. Explain how Koch’s postulates can apply on a molecular scale. ​ With this info he developed Kick's postulates ​ Suspected agent must be present in every case of the disease ​ The agent must be able to be isolated and grown in "pure" culture ​ The cultured agent must cause the disease when its inoculated into a healthy host ​ The same agent must be reisolated from the diseased experimental host ​ Explain the basis for a common naming system used for bacteria. ○​ Typicaly latin or greeke origin ○​ Genus name ex: Escherichia ○​ Species name: coli ​ Makes E coli ​ Understand the unique feature of a bacterial cell wall and how a gram stain is done. ○​ Peptidoglycan is uniqe component of bacterial cell wall. Its made of proteins (Peptido) and sugars (glyco) ○​ Often targeted by antibiotics ○​ A bacteria with thick peptidoglycan wall stains purple meaning gram Positive ○​ A bacteria with outer membrane stains pink meaning gram Negative ​ Explain the difference between horizontal and vertical gene transfer. ○​ Vertical gene transfer – generation to generation ​ Asexual reproduction – less genetic diversity ○​ Horizontal – transfer of genetic material from one organism to another in the SAME generation ​ Ex: transferring plasmids ​ KEY mechanism behind antibiotic resistance ​ Different bacterial shapes: ○​ Coccus – circle ○​ Bacillus – pill shape ○​ Vibrio – arc ○​ Coccobacillus – oval ○​ Spirillum – spiral ○​ Spirochete – more spiral ​ Understand the four types of organisms included in microbes - known as microorganisms and some of their key differentiating characteristics - make a table for this one ○​ Bacteria ○​ Viruses ○​ Fungi ○​ Protozoa ​ Define: infectious disease, pathogen, parasite and virulence. ○​ Infectious disease – damages a host cell, by growing a microbe ○​ Pathogen – a microbe that can cause an infectious disease ​ Ex: bacteria, fungi, viruses, protozoa ○​ Parasites – a protozoa, or worm ○​ Virulence - how successful a microorganism is at infecting the host and causing disease ​ List three factors that affect the outcome of the host-pathogen interaction. ○​ The host immune response, the pathogen virulence factors, and environmental factors  ​ Name and explain the role of virulence factors in disease. ○​ Adhesion molecules – how well the microorganisim can attach to the host cell ○​ Endotoxins – bacterial toxins that contribute to the virulance of gram-negative bacteria ○​ Exotoxins – acts as a supper agent, and causes tissue damage – ex toxic shock ​ Explain the importance of endospore formation and its role in transmitting infectious disease. ○​ Endospore is a tough, non-reproductive structure that allows bacteria to survive in harsh conditions, highly resistant to heat and chemicals ​ Explain what biofilms are and some of their characteristics ○​ Biofilms are a structire made of organisisms,a that ar emade to to a surface, this allows for bacterial to withsnat environmental stress ○​ They can be formed on tissues: wounds, airways, or on foreign bodies: prosthetic joints ​ Causes infection ​ Describe the steps that are needed for a pathogen to cause and infectious disease ○​ They must maintain a reservoir ○​ Transport to, then enter the host ○​ Invade host cells ○​ Evade host defence ○​ Multiply ○​ Damage host ○​ Leave the host and return to reservoir or enter a new host ​ Describe diffrences between gram negative and positive bacteria ○​ Positive: thick peptidoglycan layer, no outer membrane, purple, more susceptible to antibiotics ​ Ex: Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, ○​ Negative: thin peptidoglycan layer, has outer membrane, Pink/red gram stain, more resistant to antibiotics ​ Ex: Escherichia coli, Salmonella typhi WEEK 3 KING, Spring 2025 HSCI 212 Study Guide Week 3: Microbiology Diagnostics, Antibiotics and Antimicrobial Resistance Learning Objectives Know what a gram stain is and how it can differentiate between gram positive and gram-negative organisms ○​ A gram stain test is used to differentiate between gram negative, and gram positive organisms. A iodine die is added to a plate containing the organism ○​ After if the organism turns purple, then then it has died the thick outer layer of proteins, meaning it is a gram positive organism ○​ If it turns pink/red then the organism contains an outer membrane, and thin peptidoglycan layer, meaning it is gram negative Understand different modalities that can be used to identify microorganisms in a microbiology lab (microscopy, biochemistry tests, MALDI-TOF, molecular techniques, serology) ○​ MALDI-TOF – pathogen identification, analyze the protein of a microorganism ​ Exposed to a laser, which causes the proteins to ionize ​ Then the ionz are measured by their mass-to-charge ratio, which generate a mass unique to their organism. ○​ PCR – pathogen detection, amplifies DNA and detects the organisim ​ Highly specific, fast ○​ Culture and biochemical – growing it and observing ​ Routine for bacterial infection, its slow, labor-intense ○​ DNA Sequencing – ginetic identification, accurate but time consuming ○​ Immunological – antigen-antibody reactions, antibody detection and pathogen detection, quick but sometimes less specific Understand 3 different methods to conduct antibiotic susceptibility testing (disk diffusion, etest, minimal inhibitory concentration) ○​ Disk diffusion: uses antibiotic impregnated paper disks placed on an agar plate with the test bacteria, then the disk is watched to see how much the bacteria spreads ○​ Etest: uses antibiotic impregnated strip with a gradient of antibiotic concentration ​ When the strip is placed on an inoculated agar plate, the antibiotic diffuses radially, creating a concentration gradient ○​ MIC – Minimum inhibitory concentration: MIC is the lowest concentration of an antibiotic that inhibits bacterial growth Explain the concept of selective reporting of antibiotics and give reasons why this is used  ○​ Selective reporting is when only certain antibiotic results are reported to healthcare providers or doctors, while others are not, based on their clinical relevance or treatment guidelines Explain parts of a bacterial growth curve ○​ Lag phase – flat line at the beginning ​ No cell division or growth occurs ○​ Exponential phase – growing ​ This is the phase of rapid growth where bacteria are dividing at a constant and maximum rate. ○​ Stationary phase – flat at top ​ The rate of bacterial growth equals the rate of cell death, resulting in a stable population size. ○​ Death phase – declining ​ The rate of cell death exceeds the rate of new cell formation, leading to a decrease in the overall population. Describe methods to control bacterial growth before antibiotics were used ○​ Heat ○​ Pasturization ○​ Refrigeration ○​ Alter acidity ○​ Desiccation – adding salt or sugar – draws water out of the cell, making it hard for the bacteria to stay alive Understand selective toxicity and how antibiotics leverage unique differences of prokaryotic cells ○​ Antibiotics aim to have selective toxicity, this is where they selectively kill, or or inhibit sgrowth of microbial targets causing minimal, or no harm to host. ○​ In Prokaryotic cells: ​ human cells don’t have cell wall, prokaryotes do ​ Bacteria hacve 70s ribosmes, Humans have 80s. ​ Membrane structure is different ​ Bacteria rely on certain metabolic pathways that are not present in human cells, making them prime targets for antibiotic action Understand the difference between bactericidal and bacteriostatic antibiotic ○​ Bactericidal: ​ Kills bacteria directly ​ Disrupts bacteria process ​ Effective on immunocompromised patients ​ Ex: Penicillins, ○​ Bacteriostatic  ​ Inhibits bacterial growth, does not kill ​ Slows down growth by blokcing metabolosim ​ Relies on healthy immune system ​ Tetracyclines Understand antibiotic spectrum (broad vs narrow) and when each would be used ○​ Broad: targets wide variety of bacterial pathogens ​ Use when: empiric therapy (don't know what your treating) ○​ Narrow: targets only one bacterial pathogen ​ Use when: less effect on Microbiome (good bacteria) Know the mechanism of beta-lactam antibiotics and how this is disrupted by betalactamase enzymes. ○​ Beta-lactame antibiotic can have hydrolysis in the beta-lactame ring, because of an enzyme called beta-lactamases, which stops theirability to bind to the lenacillin binding proteins, making the drug not useful. Understand concepts of drug resistance and mechanisms through which it can occur ○​ Modification of target site ○​ Enzyme inactivation of antibiotics ​ Drug resistance occurs as microbes are constatly changing ad evolving to better survive ​ Resistance occurs when random mutations are selected, and passed on to generations – genetic mutations ​ Horizontal gene transfers Know ways that we can reduce antibiotic resistance ○​ Reducing over prescription of unnecessary antibiotics ○​ Reducing antibiotics in farming – consumption ○​ Improve infection prevention and control WEEK 4 KING, Spring 2025 HSCI 212 Study Guide Week 4: Introduction to Virology & HIV Learning Objectives ​ Describe the unique characteristics of viruses ○​ Requires the host cell genomes to reproduce  ○​ Infections, ACELLUCAR – not composed of cells, cant reproduce independently - pathogens ○​ DNA or RNA genome (not both!!!!) ​ Understand the general components of a virion, including the types of genetic material contained ○​ Viron is a fully formed virus partical outside a host cell ○​ The core, contains genetic info: RNA OR DNA ○​ It has a protein shell, and sometimes an envelope (lipid shell) ○​ The genetic info can exit in different forms: ​ Single-stranded DNA (ssDNA) → Example: Parvovirus ​ Double-stranded DNA (dsDNA) → Example: Herpesvirus ​ Single-stranded RNA (ssRNA) ​ Positive-sense (+ssRNA) (acts as mRNA) → Example: Poliovirus ​ Negative-sense (-ssRNA) (must be converted to +ssRNA first) → Example: Influenza virus ​ Double-stranded RNA (dsRNA) → Example: Rotavirus ​ Describe the general steps of a virus lifecycle ○​ Lifecycle ​ attachment – binds to host cell usig receptor molecules ​ Entry - the virus, or its genetic materials enter the host ​ Genome replication and gene expresission – viral genome is copied and its genes expresses to make viral proteins ​ Release – completed viral particles exit the cell and can infect other cells ​ Compare an enveloped to a naked virus. ○​ Enveloped virus: has lipid layer made from the host ells membrane during viral replication or budding ​ Helps better invade the immune system ​ Helps bind to receptors on new host cells ​ Ex: HIV Influenza ○​ Naked Virus: only proteincapsids (no lipid) ​ More resistant to heat, drying , sicne they lack the FRAGILE envelope ​ Ex: norovirus ​ Explain what is meant by viral host range and how this is determine by specific viral receptors on the host cell surface. ○​ Viral host range is based on how many different species of organisms the virus can infect. It is determined by the shape of the protein receptors ​ Understand three different ways that RNA viruses replicate their genome ○​ Positive single starnded = +ssRNA ​ The +ssRNA acts as mRNA and is directly translated by host ribosomes into viral proteins ​ Replication occurs entirely in the cytoplasm, and the genome can be immediately used as mRNA ○​ Negative single stranded = -ssRNA ​ The -ssRNA cannot be directly translated into proteins. ​ Requires an RNA polymerase in the virion to initiate replication since the genome alone cannot be used as mRNA ○​ Double stranded RNA (dsRNA) replication ​ Once inside, the viral capsid remains partially intact to protect the dsRNA from host immune sensors like RIG-I. ​ The viral RNA-dependent RNA polymerase (RdRp) is already present inside the capsid. ​ RdRp transcribes mRNA from the dsRNA genome, using the negative (-) strand as a template. ​ Newly synthesized mRNA serves as a template for dsRNA genome replication. ​ RdRp copies the mRNA back into complementary (-) strands, forming new dsRNA genomes ​ The virus exits the host cell via lysis (breaking the cell) or exocytosis (if enveloped) ​ Describe two ways that viruses can become persistent ○​ Latent viruses – dormant in a cell, not causing symptoms ​ Ex: chicken pocks ○​ Chronic infections – viruses invade the immune system through several mechanisms ​ Ex: hepatitis B, C ​ List four different ways to diagnose a viral infection ○​ Electron microscopy - ○​ Enzyme immunoassay – antibodies used to detect specific antigens ○​ Cytopathic effect – look for abnormalities by light microscopy ○​ Nucleic acid amplification test ​ Understand antigenic shift and drift ○​ Drift: small mutations causing slight chnges in the spike protein ​ Ex: seasonal flu vacines are updated acording to these shifts ○​ Shift: Major changes do to reassortment ​ Ex: when two different viruses from different species infect the same host and exchnage genetic materials ​ Describe the general epidemiology of the HIV/AIDS. ○​ HIV/AIDS remains a global public health issue, with millions of people affected worldwide, particularly in sub-Saharan Africa, where the highest prevalence rates are found. The virus is primarily transmitted through unprotected sexual contact, contaminated blood, shared needles, and from mother to child during birth or breastfeeding, with factors like socioeconomic status, stigma, and lack of healthcare access influencing its spread and management. ​ Describe the virus and the lifecycle of HIV. ○​ HIV is a single stranded RNA retrovirus that passed trhough sex, blood and breast milk ○​ It does not kill on its own, it attacks the hosts immune system ○​ Life cycle: ​ Bind: Binds to receptors on outside of host ell ​ Fusion: the capsid enters and breaks, and viral RNA proteins are released into the host cell ​ Revers transcription: the viral enzyme (reverse transcription) is used to create a complementary strand of DNA, from the viral RNA ​ Integration: new DNA enters the host cell nucleus, then is inserted into the hosts DNA ​ Replication: HIS uses the host cell's machinery to build chains of the viral protein that will build new viruses ​ Assembly: HIV proteins and RNA migrate to cell surface, to create new viruses ​ Budding: the immature HIV leave host cell. Then, Proteases(inside nucleus) breaks Viral protein chain into functioning proteins ​ The virus is now mature, and can infect host cells ​ Understand the associations between viral lifecycle and treatment challenges. ○​ A high mutation rate (replication) ​ 10 million mutations every day ○​ Extended latency period (sits around in the body) ​ 9 weeks to 8 years ○​ Intergration of DNA into host genome ○​ Make HIV VERY hard to treat. ​ Describe antiretroviral drugs and their mode of action. ○​ Integrase inhibitors: prevents viral DNA to integrate the host genome ○​ Protease Inhibitors: prevents the long viral proteins from reaching their viral form – will still exist, but not reproduce  ​ Describe Host, agent, and environment for HIV-1 ○​ Host: immune cell ○​ Agent: Human Immunodeficiency Vrirus ○​ Environment: socioeconomic conditions, healthcare factors, cultural and legan barriers, biological factors ​ Define: serodiscordant, seroconversion, opportunistic infection (OI) ○​ Serodiscordant - refers to a relationship in which one partner is HIV-positive and the other is HIV-negative ○​ Seroconversion - Seroconversion is the process in which the immune system produces detectable antibodies against HIV after infection. ○​ Opportunistic infection (OI) - occur when the immune system is severely weakened, making it unable to fight off infections that a healthy immune system would normally control. In HIV/AIDS, OIs are a major cause of morbidity and mortality, particularly when CD4 T-cell counts drop ​ Explain what happens to an viral levels of an individual living with HIV when they go on ART and then if they go oK ART. ​ Define PrEP, and identify the underlying mechanisms that make PrEP work. ○​ PrEP – is a treatment that deacreases the likelihood f sexual transmission, useful for serodicordant couples, or people who inject drugs. ​ It is a preventive medication taken by HIV-negative individuals at high risk of HIV exposure to significantly reduce the likelihood of infection. ​ It involves taking antiretroviral drugs (ARVs) daily or on-demand before potential exposure to HIV. ​ Be able to describe treatment as prevention, U=U and 90-90-90 ○​ U=U – Undetectable = Untransmitable ​ Describe some challenges to achieving 90-90-90 targets and how this ties in to the end of HIV ○​ 90-90-90's goal was to have ​ 90% diagnosed ​ 90% on treatment ​ 90% suppressed ○​ By 2020... ○​ May low income and rural areas have the most cases, and socioeconomic disparaties stop them from getting help, diagnosis, treatment TasP – treatment as retention WEEK 5 KING, Spring 2025 HSCI 212 Week 5: Host factors: immunocompromised host, fungal infections, intersection of infection & substance use Learning Objectives- ​ Know the unique characteristics of fungi and how these can be targeted therapeutically ○​ Eukaryotic, has nucleus, contains ergosterol, 3-10um ○​ Heterotopic – they get food from their environemnt ​ Know common morphologies of fungal organisms ○​ Yeast: single celled, reproduced by building ○​ Mold: Multicellular fungal bodies made of hyphae, can reproduce asexually ○​ Dimorphic mold: ​ Can be yeast of mold depending on environment ​ Yeast in beast, mold in cold ​ Understand that fungi are an important of normal flora ○​ ​ Know what is meant by opportunisticå infection and factors that predispose to getting an opportunistic infection (OI) ○​ An opportunistic infection is a an infection that would not be harmfull in a healthy, uncompromised immune syteme ○​ only cause disease in situations that compromise the host’s defenses ​ Explain ways to reduce the risk of fungal infection in immunocompromised patients. ○​ We can make changes to their environment, and to the host as well ○​ Environment: air filtration, avoid flowers and plants, No construction around them ○​ Host: Avoid risk behaviors (plant/Mould exposures) ​ Discuss OIs with respect causative agents, anatomical locations of infections and why HIV-1 infected individuals are at higher risk for acquiring OIs. ○​ HIV causes the CD4 count in infected patients to drop, and when host cells have lower CD 4 count, they are more susceptible top opportunistic infections. ​ Describe diagnostics for fungal infections ○​ Laboratory techniques – microscopy  ○​ Molecular methods – MALDI-TOF – identification from protein ○​ Antigen detection – test for polysaccharides ○​ Imaging motilities – CT, MRI ​ Know the mechanism of action of three common antifungal agents ○​ Polyenes - mechanism that binds to ergosterol causing cell leakage and death ​ Ex: Amphotericin ○​ Azoles ​ Mechanisms that inhibits ergosterol synthesis, disrupting cell formation ​ Ex: fluconazole ○​ Echeandias: Mechanism that beta D Glucan synthesis, key component to fungal cell wall ​ Example: Micafungin ​ Understand the ways in which substance use increases risk of infection ○​ Needel sharing, open wounds, increased STI's from influenced decision making ​ Understand social and structural factors related to infection risk for people who use substances ○​ Feeling unsafe or jugged in hospital setting ​ Understand what harm reduction is ○​ Non-judgmental provision of service ○​ Understadning the emotional side of drugs ○​ Recegonize the social inequiteis that impact substance use and treatment ​ Describe harm reduction strategies and how these can decrease prevalence of infectious diseases ○​ At the individual level: safe injection kits Practice questions: WEEK 1 1.​ Explain the difference between a disease and an infectious disease. A disease is a pathological condition of body parts or tissues that is characterized aby symptoms or traits, while an infectious disease is a disease caused by an infectious agent like a bacteria of fungus that can be passed on to others. 1.​ Define Host, Agent and Environment and describe how they may impact each other with respect to infectious disease transmission. The host is a person, animal, or environmental reservoir, that holds the disease. The Agent is the factor whose presence – or sometimes absence - causes the disease (often a bacteria or fungus). The environment is any outside factors that may influence how the host responds to the agent, such as weather, pollution, water housing. 2.​ Select an infectious agent (e.g., Malaria, influenza). Name the host, vector and agent. Suggest a couple of environmental factors that could affect transmission. Malaria Host: a human Agent: Anopheline Mosquitos Environment: Warm environments often lead to a higher possibility of malaria, due to the agent being passed along my mosquitos. 3.​ What are two diseases that could be impacted by climate change? Malaria – Higher average temperatures could lead to more mosquitos Air pollution – increase the likelihood of lung cancer, asthma, heart disease. 4.​ How do socioeconomic conditions affect spread of cholera? Cholera is contracted through dirty, unsafe drinking water. This is often more prevalent in poorer countries, who do not have access to filtered drinking water. 5.​ How might climate change impact mosquito borne diseases? An increase is average temperature – caused by climate change – would lead to an increase in the births of mosquitos, allowing for more mosquitos to transmit the disease. 6.​ Describe a time that an infectious disease has changed the course of history. Use your own knowledge, stories you may have heard, google etc. ​ The Bubonic plague in the 14 hundreds wiped out between 25-50 Million Europeans. It forced government to enforce Isolation of people who were sick in plague hospitals. Hospitals were built throughout Europe and remained as fever hospitals for infectious patients up until the 1900s. ​ This idea of isolation is now used globally to slow/stop the spread of disease. 1.​ What is the main difference between a case-control study and a cohort study (hint: think about participants at enrollment and the timing of exposure)? Case-control looks at subjects who have already contracted the disease, and compares those subjects to a group of healthy subjects, then Drs look retrospectively to collect info on exposures. Cohort Study finds a group of subjects, and exposed half of the group to the disease, to determine disease status overtime – here they are able to follow them prospectively, and retrospectively if needed. 7.​ What are scenarios where a case-control study might be preferred over a cohort study? If you do not have the time or Finacial funds to prospectively follow the group of subjects over a long period of time, and would rather just use retrospective data. 8.​ Explain the difference between correlation and causation. ​ Correlation - a direct association or relationship between two variables, where changes in one variable are related to changes in the other - can be positive or negative ​ Example: There is a correlation between ice cream sales and drowning incidents—both increase during summer months. However, buying ice cream does not cause drowning ​ Causation - changes in one variable directly result in changes in another. There is a cause-and-effect relationship between the two variables. ​ Ex: Example: Smoking causes lung cancer. 9.​ Describe some characteristics that might argue in favor of a causal relationship between an exposure and an outcome (hint: think of Bradford Hill criteria) ​ While none of these criteria alone definitively proves causation, they collectively strengthen the argument for a causal relationship. Temporality is essential, and other criteria add weight to the evidence. Careful evaluation of these criteria helps avoid false conclusions about causality in epidemiological studies. 1.​ Describe processes in science that ensure quality standards of research output before and after publication. ​ Peer review 1.​ You are interested in determining the eHicacy of the new Shingles vaccine to decide if it is worth recommending for the general population. You are provided with the following data in 2x2 table format, obtained from a cross-sectional study of 179 patients. Calculate the odds ratio to determine if those who developed Shingles are at increased odds of having had the vaccine. Based on this information, would you recommend this vaccine (yes/no)? WEEK 2 Study Questions 1.​ What are the differences between the four classes of microorganisms? Give an example of each organism. a.​ Bacteria i.​ Smallest 0.001 micro meter ii.​ Single celled - iii.​ Prokaryotes iv.​ Ex:ood poisining b.​ Fungi i.​ Few micrometers to a few centimeter's ii.​ Single celled – yeast iii.​ Multicellular – mold iv.​ Eukaryotes, or heterotopic v.​ Ex: yeast infections c.​ Virus i.​ Smallest in size ii.​ DEPEND on host cells to grow/replicate/survive iii.​ Myriad d.​ Parasites i.​ Size varies ii.​ Eukaryote iii.​ Unicellular: protozoa multicellular: helminths iv.​ Complex lifestyle a.​ Virusues are the smallest microorganism. They are rougly 0.0001-0.00001 micrometers, while a bac5teria is roughly 0.001 micrometers. You can only see a bacterial cell with a light microscope, viruses require an electron microscope. 1.​ How were the contributions of Lister and Semmelweis similar? How were they different? a.​ Both doctors (lister and Semmelweis) contributed to germ theory. Lister did so by finding a way to prevent infections inbounds after surgery. Semmelweis did so by discovering the importance in washing hands between patients to lower likelihood of infection transmission. 2.​ Describe an experiment that demonstrates Koch’s postulates. Use a flow chart or drawing to enhance your description. a.​ Suspected agent must be present in every case b.​ The agent must be able to be isolated an grown in a pure culture c.​ It must cause disease when put into a healthy host d.​ Must be able to reisolate the agent from the newly diseased host. 3.​ What are some limitations of Koch’s postulates? a.​ The assumption that all carriers will fall ill: some cases can be carriers of the disease, but not get infected b.​ Some pathogens cant be grown in pure culture c.​ Not all diseases can be tested on animals, and some are only carried by humans. 4.​ How can Koch’s postulates be applied to an organism that is unable to be cultured? How about an organism that has pathogenic and non-pathogenic forms? a.​ Molecular Koch's postulate - 5.​ Vibrio cholerae is a ‘comma’ shaped bacterium that causes cholera, an often fatal disease transmitted by fecal-oral route. Does this mean that Vibrio fischeri is also a pathogenic organism? a.​ No. Different strains of different infection can be transmited and carried diffrently. 6.​ What are the steps of a gram stain? What features of bacteria does a gram stain differentiate based upon? a.​ Step one crystal violet stain is added b.​ Iodine is added to bring out the purple color in the gram positive bacteria c.​ Rinse with alcohol, only gram positive cells will remain purple, while gram negative cells will turn pinkish/red d.​ Step Safrin, allows the dye to adhere i.​ Gram stain works because gram positive bacteria have a thicker outer layer of lipids, allowing the die to better stick to the cell. Which gram negative have outer membrane which turns pink in the gram stain processed. 7.​ Name two examples of endospore forming bacteria and the disease they cause. How do endospores contribute to disease spread? ○​ Endospore: tough nonreproductive structure that allows bacteria to survive in harsh environments. ​ Ex: clostridium botulinum – causes botulinum ​ Ex: tetani – causes tetanus 8.​ Bacterium #1 can spread its antibiotic resistance gene exclusively to its own offspring. Bacterium #2 can spread its antibiotic resistance gene directly to other species of bacteria. What are these processes called? Which bacterium will contribute to a broader spread of the antibiotic resistance gene? Why? ​ The spreading of antibiotic resistance through offspring is referred to as antigenic driftr. Where slight chanmges occur over time. ​ The spreading of antibiotic resistance form one species to another is anigrntic shift, where traits from one speceis, jump to another, causingimense change in a new speceis.  ○​ Antigenic drift is more frequent, and is what most comon colds and flus will do year after year, and why we need to keep up to date with shots, and the virulance is constantly changing. 9.​ Compare and contrast bacteria and viruses with respect to structure and reproduction. a.​ Bacteria: i.​ Bacteria can reproduce sexually, or asexually ii.​ Bacteria are single celled b.​ Viruses: i.​ Need a host cell in order to grow, reproduce, and infect ii.​ Acellular, no cellular structure 10.​List and explain 7 steps required for a pathogen to cause infectious disease. a.​ They must maintain a reservoir b.​ Be trasnported to host cell c.​ Adheare hopst cell d.​ Invade host cell e.​ Reproduce/multiply f.​ Damage host cell g.​ Leave host cell and Return to reservoir or new host cell 11.​Describe two different ways that an infectious agent can be transmitted from a reservoir to a suitable host. ​ Direct conatact – bacteria or fungi can often spread through direct contact with open wound ​ Droplet spread – viruses can spead through the droplets produced when coughing or sneezing 12.​Describe three strategies that an infectious disease can use to evade host defenses. a.​ Bind to protein receptors b.​ Attaching through biofilm c.​ 13.​Describe three ways that an infectious disease can damage the host. a.​ damages a host cell, by growing a microbe 14.​List three classes of virulence factors and explain how they affect virulence. a.​ Ability to sick onto the host cell b.​ Ability to survive inside the host cell c.​ Ability to reproduce inside the cost cell 15.​Describe two ways that bacteria can survive in harsh environments. ○​ Envelope  ○​ Endospore: tough nonreproductive structure that allows bacteria to survive in harsh environments. WEEK 3 Study Questions 1. Describe the procedures used in gram staining. What organisms appear purple? Why? (review from week 2) ​ Crystal voilet is added to die all th ebecteria ​ Iodine is added ​ Alc is added to wash away exsese stain ​ Sarfrain is sadded ○​ This is what allows the purple (positive) bacteria to be prevelant. Thi occurs because the gram positive bactreria have a tick outer lipid layer which the sdtair attaches to. 2. You use the Gram staining procedure to stain an L-form bacterium (a bacterium that lacks a cell wall). What color will the bacterium be after the staining procedure is Finished? ​ The bacteria would turn pinkish/red 3. Give reasons why a microorganism might not be seen in a gram stain. ​ If the organism is acellular (virus) a gram stain would not be used 4. Apart from microscopy, explain 4 other ways that microorganisms are detected in clinical samples. Why are multiple diagnostic techniques useful/necessary? ​ Microorganisim culture and identification ○​ MALDI-TOF – pathogen identification, analyze the protein of a microorganism ​ Exposed to a laser, which causes the proteins to ionize ○​ DNA Sequencing – ginetic identification, accurate but time consuming ○​ Immunological – antigen-antibody reactions, antibody detection and pathogen detection, quick but sometimes less specific Different tequniques are required, because different miroorganisims have different cellular makup, and some testts are 5. Explain 3 different ways to test antibiotic susceptibility. ○​ Kirby Bauer testing ○​ 6. What is minimal inhibitory concentration? Use a picture to explain. If an antibiotic has a high minimal inhibitory concentration, what does that mean about its ability to kill that microbe? KING, Spring 2025 HSCI 212 7. You conduct Kirby-Bauer testing on a bacteria that grew in a blood culture and test three antibiotics: A, B, and C. Which antibiotic do you recommend giving and why? ○​ Antibiotic c shows the largest zone of inhibition ( no bacterial growth) therefore I would pick antibiotic C 8. Explain selective reporting of antibiotics and give some ways that this may be helpful to use in clinical settings. ○​ Selective reporting of antibiotics is when doctors choose which information about antibiotic use or effectiveness to report, based on certain criteria, such as the clinical context, treatment outcomes, or research findings ​ This is sometimes beneficial because of: ​ Antibiotic stewardship – most effective ​ Optimizing Treatment Duration – how long optimal 9. Explain the logarithmic stage of bacterial growth and the stationary phase. What is the difference? ○​ Logarithmic growth phase is the beginning of the graph, when the bacterial is producing at a rate faster that the death rate ○​ The stationary growth phase is the top, flat part of the graph when bacteria is dying and being produced at the same rate 10.What stage of bacterial growth are most impacted by antibiotics? Why? ○​ The log phase because as cells are reproducing, they are more susceptible to DNA, Protein, and Cell wall targeted antibiotics 11.Describe ways that humans have adapted the environment of bacteria to prevent microbial growth (Hint: think food industry). ○​ The food industry has started adding antibiotics into the food of livestock – chickens, pigs, cows. This will reduce the likeliness of humans getting bacterial diseases form our animal based foods. However the downside to this is that we are consuming antibiotics on a daily basis, so they end up being less effective when we are actually sick. 12. The optimum temperature for growth of Salmonella is between 35 to 37°C. How does putting a salmonella-contaminated piece of chicken in the fridge affect the growth rate of the bacterial contaminant? Does it kill the bacteria? What happens if you take that piece of chicken out of the fridge and let it rest at room temperature (21°C) for a few hours? ○​ Putting a piece of salmonella containing chicken in the fridge will not kill the bacteria, but just slow down the growth. Once brought bake to room temperature, the bacteria will continue reproducing. The only way to kill the bacteria is by burning it at a temperature of 74 degrees c 13. Give examples of ways that bacterial cells are different from human cells and how these differences are used for targets of antibiotics (at least 4 ways). ○​ Bacterial cells are prokaryotic, meaning they do not contain a nucleus ○​ 70S ribosomes - means they are smaller and easier to target ○​ Peptidoglycan – allows synthesis of the bacterial cell wall ○​ They reproduce by binary (asexual) fusion – so antibiotics can target bacteria before they have the chance to reproduce 14.What is a narrow spectrum antibiotic? What are the advantages of using a narrow spectrum antibiotic? Disadvantages? ○​ Narrow spectrum antibiotics are good for treating and infection, if you know exactly what you are treating for – they are very specific, and only useful for as elect bacteria ○​ The disadvantages are that if you don't know exactly what the bacteria is, it could be useless 15.Draw a diagram showing how beta-lactam antibiotics work. Show how drug modification can occur for beta-lactams and describe how this is overcome with antimicrobial therapy. 16. Explain how antibiotic resistance can occur for bacteria? How is this impacted by overuse of antibiotics? ○​ Antibiotic resistance can occur through antigenic drift or antigenic shift, this can be by a modification of target site, orother ginetic mutations ○​ The mutated bacteria becomes increasingly resistant to the medication 17.Describe four mechanisms by which bacteria can become resistant to antibiotics. ○​ Horizontal gene transfer - ○​ Vertical gene transfer - ○​ Modification of target site ○​ Microbes are constantly changing 18. Explain ways that humans can change behaviors to reduce selection pressure on resistant bacteria. ○​ Reduce over prescription of antibiotics ○​ Reduce antibiotics in farming ○​ Improve over all health in infection prevention and control Readings: Openstax: KING, Spring 2025 HSCI 212 https://cnx.org/contents/[email protected]:ryt9cF1D@6/PrefaceLinks to an external site. Microbiology diagnostics, antibiotic susceptibility testing (Week 3, lecture 1): Microbiology and immunology on-line – Bacteriology, Chapter 2: Culture and identification of infectious agents. https://www.microbiologybook.org/fox/culture.htm Openstax Section 14.6 – Testing the e