2024 Microbiology Overview PDF

MICROBIOLOGY OVERVIEW Block: Foundations Block Director: James Proffitt, PhD Session Date: Monday, August 12, 2024 Time: 9:00 – 11:00 am Instructor: Saman Nematollahi, MD Department: Medicine Email: [email protected] INSTRUC...

MICROBIOLOGY OVERVIEW Block: Foundations Block Director: James Proffitt, PhD Session Date: Monday, August 12, 2024 Time: 9:00 – 11:00 am Instructor: Saman Nematollahi, MD Department: Medicine Email: [email protected] INSTRUCTIONAL METHODS Primary Method: IM13: Lecture ☐ Flipped Session ☐ Clinical Correlation Resource Types: RE18: Written or Visual Media (or Digital Equivalent) INSTRUCTIONS Please read lecture objectives and notes prior to attending session. READINGS N/A LEARNING OBJECTIVES 1. Describe the organism factors (e.g., virulence) and host factors (e.g., age, nutritional status) that determine susceptibility to an infectious disease 2. Understand the differences between prokaryotes and eukaryotes 3. Describe the structure, function, and characteristics of bacteria, viruses, fungi, and parasites 4. Describe viral replication, viral evolution, and compare strategies among different viruses 5. Describe the factors of bacteria, viruses, and fungi that contribute to their pathogenesis 6. Describe important factors that affect the diagnosis of bacteria, viruses, fungi, and parasites CURRICULAR CONNECTIONS Below are the competencies, educational program objectives (EPOs), course objectives, session learning objectives, disciplines and threads that most accurately describe the connection of this session to the curriculum. Related Related Competency\EPO Disciplines Threads COs LOs CO-01 LO-01 MK--03: The molecular, Microbiology N/A cellular and biochemical Block: Foundations | Saman Nematollahi [1 of 15] MICROBIOLOGY OVERVIEW Related Related Competency\EPO Disciplines Threads COs LOs mechanisms of homeostasis CO-01 LO-02 MK-01: Core of basic Microbiology N/A sciences CO-01 LO-03 MK-09: Critical thinking Microbiology N/A about medical science and about the diagnosis and treatment of disease CO-01 LO-04 MK-01: Core of basic Microbiology N/A sciences CO-01 LO-05 MK-05: The altered Microbiology N/A structure and function (pathology & pathophysiology) of the body/organs in disease CO-01 LO-06 MK-10:L The scientific Microbiology N/A method in establishing the cause of disease and efficacy of treatment, including principles of epidemiology and statistics NOTES Importance of Infectious Diseases We always need to study the reasons that people die so we can improve the healthcare system. Understanding how many people die of which diseases is helpful so we can direct resources to where they are needed most. From the 2020 WHO Global Health estimates, 3 of the top 10 causes of death globally are communicable: lower respiratory infections (#4), neonatal conditions (#5) and diarrheal diseases (#8). People living in a low-income country are more likely to die of a communicable disease than a noncommunicable disease. In low-income countries, 6 of the top 10 causes of death are due to communicable diseases: neonatal conditions (#1), lower respiratory infection (#2), diarrheal diseases (#5), malaria (#6), tuberculosis (#8), and HIV (#9). Even before the COVID-19 pandemic, preventing infectious diseases is critical to improving public health. Framework of Infectious Diseases In order to understand how someone can develop an infectious disease, one needs to realize the interplay between the host, the environment, and the pathogen. These three categories are interconnected, and each one can affect the other. Block: Foundations | Saman Nematollahi [2 of 15] MICROBIOLOGY OVERVIEW Host factors that can affect the susceptibility of acquiring an infectious disease include: - Age: o Neonates- As you will learn, neonates are not born with the same immune system as an adult. Their neutrophils have limited ability to accelerate production. The neutrophils also have decreased adhesion, impaired migration, and decreased phagocytosis. The macrophages have decreased responses to pathogen-derived products (e.g., LPS- lipopolysaccharides). Although some antibodies are transferred from the mother to the fetus, T-cell immunity is not transferred. Finally, neonates show diminished delayed-type hypersensitivity (DTH) skin test reactions to antigens until ~12 months of age. o Elderly- Immunosenescence is a process of immune dysfunction with aging. One can have problems with the innate immune system and have impairments of anatomical barriers or can have issues with adaptive immune system (see tables below). - Nutritional status- The main connection with poor nutrition and the immune system is protein deficiency (either from undernutrition or from a gut abnormality). If you do not have enough protein, then you will have a principal defect in T-cell function. Defects in T- cell function can make a person susceptible to infections such a tuberculosis (TB), disseminated Herpes infections, and pneumocystis. You may also have a defect in neutrophil production, but this is less obvious. - Pregnancy- In the first trimester, pregnancy does not increase the risk of acquiring infectious diseases. As pregnancy advances, T-cell activity, natural killer cell activity, and possibly B-cell activity are reduced. One can have increased susceptibility to infections such as listeria and malaria. Additionally, the severity of infections (influenza, malaria, hepatitis E, herpes simplex virus) increases with advancing pregnancy. - Co-morbidities- Many clinical infections in the United States are situational- meaning, there is a reason why the patient became infected. Some of these reasons include: o Diabetes o Immunosuppressive drugs such as systemic corticosteroids, transplantation regimens, chemotherapy- all of which alter the immune system Block: Foundations | Saman Nematollahi [3 of 15] MICROBIOLOGY OVERVIEW o IV access for surgical incisions, implanted foreign bodies, etc - Genetics- There are many genes that have been discovered that either protect us from infections or make us more susceptible to infections. The classic example of protection is the selective advantage conferred by the sickle hemoglobin heterozygous genotype that is associated with a reduction in the risk of severe malaria. An example of susceptibility is a mutation in the interferon gamma receptor that increases the risk of developing invasive mycobacterial infections. - Behavior- Some examples of behavior that can increase the risk of acquiring infectious diseases include foreign travel (bug bites), IV drug use, unprotected sex with multiple partners, ingesting contaminated foods or water, close contact with people who are sick, improper hand hygiene, and being unvaccinated. Environmental factors that can affect the susceptibility of acquiring an infectious disease include population density, migration, herd immunity, and climate change. Pathogen factors that can affect the susceptibility of acquiring an infectious disease include biochemical factors (virulence factors like LPS), structural factors (lack of a cell wall), and genetic factors (mutations that gain resistance to antibiotics). Put together, the probability of disease (in the appropriate environment) is equal to: Block: Foundations | Saman Nematollahi [4 of 15] MICROBIOLOGY OVERVIEW The 4 Kingdoms Infectious pathogens come in all shapes and sizes. A nice summary table from Dr. Sean Elliott of the 4 kingdoms can be found below: Block: Foundations | Saman Nematollahi [5 of 15] MICROBIOLOGY OVERVIEW Block: Foundations | Saman Nematollahi [6 of 15] MICROBIOLOGY OVERVIEW Bacteria Bacteria are prokaryotes typically measuring 0.3 – 2 μm in size that contain their own DNA and produce RNA. Bacteria are found everywhere on earth. Most bacteria are harmless or helpful, but some are pathogens. Bacteria are prokaryotic because their genetic material (DNA) is not housed within a true nucleus. Most bacteria have cell walls that contain peptidoglycan. Bacteria divide by binary fission (asexual) and can multiply rapidly. Bacteria are often described in terms of their general shape. Common shapes include spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio). Figure 1.13 shows examples of these shapes. The shape of a bacterium is determined by its cell wall. Bacteria have rigid cell walls; components of the cell walls contribute to their Gram staining properties. The Gram stain is useful for bacterial identification, which helps with early initiation of an appropriate antibiotic. Gram-positive bacteria have a large amount of peptidoglycan in their outer envelope (thick cell wall); peptidoglycan absorbs a large amount of crystal violet and thus Gram-positive bacteria appear purple under the microscope. Gram-negative bacteria have only a small amount of peptidoglycan (thin cell wall that is surrounded by an inner and outer membrane), making them appear initially colorless after the decolorization step in Gram staining. However, the counterstain safranin stains Gram-negative bacteria reddish-pink under the microscope. This actually matters for which antibiotics will work… Block: Foundations | Saman Nematollahi [7 of 15] MICROBIOLOGY OVERVIEW Bacteria are further characterized by their use of oxygen for growth (table courtesy of Dr. Sean Elliott): The use of oxygen generates two toxic molecules: hydrogen peroxide (H2O2) and superoxide (O2-). Bacteria need two enzymes to utilize oxygen (superoxide dismutase and catalase) Block: Foundations | Saman Nematollahi [8 of 15] MICROBIOLOGY OVERVIEW Obligate aerobes cannot grow without oxygen because the ATP-generating system is dependent on oxygen as the hydrogen acceptor. An example of this is tuberculosis. Microaerophilic bacteria can tolerate SOME oxygen because they have superoxide dismutase. They require oxygen for energy production, but they are harmed by atmospheric concentrations of oxygen (21% O2). An example of this is Campylobacter jejuni (a GI bug). Facultative anaerobes PREFER to use oxygen to generate energy by respiration if it is present, but they also have the capacity to use the anaerobic fermentation pathway. An example of this Staphylococcus. Obligate anaerobes lack one or both enzymes and cannot generate ATP via the respiratory pathway. Examples of these are Bacteroides and C. diff. Finally, bacteria have several pathogenic factors: - the bacterial capsule may contribute to pathogenesis by helping the bacteria evade phagocytosis. The peptidoglycan provides strength to the cell wall and enables the bacterium to resist osmotic lysis. - Gram-positive bacteria contain lipoteichoic acid, which helps them attach to their host cells - Many Gram-negative bacteria have pili, or protein-strands that help them attach to their host cells. The ability of the pili to attach to host cell receptors determines the type of tissues that a bacterium can colonize. A specialized pilus known as the sex pilus is involved in the transfer of DNA from one bacterium to another - Spores: Clostridium and Bacillus genera produce them (among others). Once the environment is more favorable, enzymes degrade the coat, and germination into a bacterium occurs. The spores are HIGHLY resistant to heat and chemicals. - Biofilms are aggregate of interactive bacteria (single species or multiple species) attached to a solid surface or to each other and encased in a polysaccharide matrix. It provides protection from the host’s immune responses and against antibiotics. Examples: hardware infections (prosthetic joints, central intravenous line infections); dental plaque; etc. Block: Foundations | Saman Nematollahi [9 of 15] MICROBIOLOGY OVERVIEW - Bacteria also produce various enzymes which contribute to their pathogenesis: urease, catalase, and coagulase are some examples. - Bacterial toxins come in two types: 1) Endotoxins, which are structural components of the bacterial cell wall. Lipopolysaccharide (LPS) is an example that causes disease by triggering pro-inflammatory cytokines, followed by an activation cascade which causes shock (low blood pressure). 2) Exotoxins, which are produced and then secreted by bacteria. There are five categories of exotoxins, based on their toxic effects: - Protein synthesis inhibitors - Neurotoxins - Super-antigens (they stimulate T-cell proliferation through non-specific interaction with Class II MHC complex on APCs and specific Vβchains of the TCR resulting in oligoclonal T-cell activation and massive cytokine release) - cAMP inducers - Cytolysins Viruses Viruses are the most common infectious agents in humans and are also the smallest (20-300 nm). They contain only one kind of nucleic acid (DNA or RNA) that is surrounded by a protein shell (capsid). This protein shell MAY be surrounded by a lipid envelope (sensitive to ether). Viruses depend on the host cell (enzymes and other replication factors) for survival; they will hijack host cell machinery to replicate and propagate. The infectious unit is called a VIRION. This is derived from DNA or RNA components of host cells. Viruses are classified by the nucleic acid in the virion (RNA or DNA), the symmetry of the capsid, the presence/absence of envelope, and dimensions of the virion and capsid. The 2 basic types of viral genome structure are RNA and DNA viruses. Within RNA, they can be positive single-stranded, negative single-stranded, segmented single-stranded, or segmented double stranded. Within DNA, they can be single stranded, linear double-stranded, or circular double-stranded. When viruses infect cells, two important and separate events must be done: 1) Production of virus structural proteins and enzymes 2) Replication of the viral genome Block: Foundations | Saman Nematollahi [10 of 15] MICROBIOLOGY OVERVIEW A generic viral replication cycle is shown below: The goal of viruses is to make mRNA. Positive single-stranded RNA is infectious and is equivalent to mRNA. It is directly translated to proteins. Negative single-stranded RNA and double stranded RNA viruses use a viral RNA polymerase (packaged into the virion) that transcribes each segment to mRNA. With DNA viruses, mRNA is achieved by a host-cell enzyme, DNA-dependent RNA polymerase II. Block: Foundations | Saman Nematollahi [11 of 15] MICROBIOLOGY OVERVIEW Pathogenic factors for viruses: - Viruses attach to host cells and insert their nucleic acid for translation, making multiple copies of themselves. - Such infected cells may trigger an immune response during this process and/or after dying. This immune response is the major contributor to viral pathogenesis. - Other factors included in pathogenesis are antigenic drifting and shifting, in which the virus evades an immune response by changing its antigenic appearance. Viruses evolve rapidly, inherently due to the large number of progeny that are produced and that the RNA polymerase lacks proofreading capabilities. When a large number of variant genomes come together and form a population structure, it is called a viral quasispecies. These quasispecies are formed from the high mutation rates during viral replication. In addition to mutations, viruses can evolve by recombination and reassortment. Below is a list and short description of medically relevant viruses. I highly encourage you to read and study this now as opposed to seeing all new content during the I&I block: DNA Viruses Herpes Viruses: o HSV 1: Most commonly causes orolabial disease (“cold sores”) and gingivostomatitis, but can cause genital disease (self-inoculation). Rarely can cause acquired HSV encephalitis, a devastating central nervous system infection that starts by reactivated HSV in the temporal lobes of the brain. o HSV 2: Most commonly causes genital (sexually-transmitted) disease but can be a cause of orolabial disease. When transmitted perinatally, can cause severe neonatal HSV disease which occurs in three potential syndromes: skin/eye/mouth (SEM), disseminated, and encephalitis. When HSV-2 causes neonatal encephalitis, the disease is diffuse (rather than temporal lobe) due to preceding viremia. o Varicella-zoster virus: Causes primary disease (chickenpox) and reactivated disease (zoster, AKA “shingles”). When reactivated, the lesions are seen in a dermatomal distribution – this is important to distinguish them from other vesicular eruptions that typically cross the mid-line and spread past a single dermatome. o Epstein-Barr Virus: Causes infectious mononucleosis and targets B- lymphocytes. The pattern of serologic response to the stages of EBV infection can be used to identify the length of infection: preliminary seroresponse is to the viral capsid antigen, followed by early antigen and then nuclear antigen. o Cytomegalovirus: The other cause of infectious mononucleosis and latent, lymphocytic infection. However, also is an important cause of congenital infection and the most common cause of sensorineural hearing loss in children. o Human herpesvirus 6: Classic cause of Roseola infantum, a common but benign illness of childhood. Classic description is 3 days of high fever, followed by resolution of fever and onset of a rash. The febrile period is highly associated with febrile seizures in children. Block: Foundations | Saman Nematollahi [12 of 15] MICROBIOLOGY OVERVIEW o Human herpesvirus 7: The other cause of Roseola, although somewhat milder on severity. o Human herpesvirus 8: Classic cause of Kaposi sarcoma, highly associated with HIV/AIDS. Causes neoplasm of endothelial cells and thus blood vessel proliferation. Poxviruses: Viruses in this class cause smallpox, cowpox, and molluscum contagiosum. The first two diseases are (hopefully) historic, but molluscum contagiosum is a very common childhood wart-like lesion that is highly contagious via close contact with infected skin lesions. Hepatitis B virus: HBV is transmitted via blood and body fluids, and causes hepatitis which progresses ultimately to cirrhotic liver failure and, possibly, associated hepatic carcinoma. Adenoviruses: Multiple sub-species of adenovirus exist and cause different diseases depending on the tropism of each virus. Diseases range from sinopulmonary infections to gastrointestinal disease. All are quite common in the community. Parvovirus B19: this virus is the classic cause of Erythema Infectiosum (AKA “Fifth Disease”), a common childhood illness that is benign for children. However, pregnant women who contract this illness may experience severe complications for their infants due to the tropism of the virus for various neonatal tissue types (platelets, red blood cells, myocardium). Positive-strand RNA Viruses Rotavirus: Infamous for causing severe, acute enteritis that is both secretory and mal- absorptive in children. Rotavirus gastroenteritis is the focus of several vaccines that, when studied long-term, were associated with increased risk of intussusception and subsequently were discontinued. Caliciviruses (noroviruses): These viruses also cause severe gastroenteritis, most classically “cruise-ship” disease and other outbreak-associated clusters. Picornaviruses: This class of viruses contains Poliovirus, Rhinovirus (cause of the “common cold”), Hepatitis A virus (causes hepatitis that is fecal-orally transmitted), and Enteroviruses. Enteroviruses are further broken down into sub-families of Coxsackievirus, Echovirus, and Enterovirus. All cause multiple types of mostly-mild clinical illness, depending on the cellular tropism of each virus. Flaviviruses: This class of viruses contains Hepatitis C virus (HCV, similar to Hepatitis B virus in transmission and potential progression to cirrhotic liver failure), Yellow Fever virus, Dengue virus, St. Louis Encephalitis virus, West Nile virus, and Zika virus. With the exception of HCV, the other viruses in this class are mosquito-transmitted and cause a variety of clinical syndromes. Zika virus is the most recently-encountered of these viruses and gained international infamy via its association with neonatal microcephaly and other birth defects in Brazil. Togaviruses: This class of viruses contains Rubella (AKA German Measles), Western & Eastern Equine Encephalitis viruses, and Chikungunya virus. With the exception of Rubella, the other viruses are mosquito transmitted (similar to the Flaviviruses) and also cause a variety of disease based on tropism of the virus. Rubella causes a milder form of measles, but is of concern in under-developed countries due to its ability to cause severe, congenitally- acquired disease. Block: Foundations | Saman Nematollahi [13 of 15] MICROBIOLOGY OVERVIEW Coronaviruses: The coronaviruses most commonly cause mild upper- respiratory illness (the “common cold”) similar to rhinovirus. Occasional, rare severe diseases also caused by coronaviruses include SARS (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Syndrome). In late 2019, however, SARS-CoV-2 emerged as a cause of the world’s worst pandemic in over 100 years. This virus caused high mortality among at-risk patient populations and was found to be highly infective, especially in areas of crowding. Negative-strand RNA Viruses Influenza viruses: Influenza A, B, and C are described, but only types A and B cause severe disease. These viruses are subject to the phenomena of antigenic drift and shift (reassortment). They are a source of upper and lower-respiratory disease, and an annual cause of epidemic influenza burden, with severe mortality and morbidity associated. Parainfluenza viruses: These viruses are most commonly associated with Croup, which causes acute laryngotracheobronchitis. While mostly mild, croup can cause severe airway obstruction and secondary respiratory failure. The disease is notable for causing a harsh, seal-like barking cough. Respiratory Syncytial virus: RSV, a common cause of severe bronchiolitis and epidemic disease every winter. RSV-bronchiolitis is most severe in very young infants and those infants with congenital heart disease or prematurity. A monoclonal antibody-based immunotherapy exists to reduce the severity of disease in such infants. Several vaccines have been studied and will likely be distributed for the first time in Winter 2023 Measles virus: This virus and its self-named disease were transiently absent in the U.S., but now have been re-introduced by international visitors and established in large populations of un/under-vaccinated U.S. citizens. The disease itself is notable for the classic “three C’s”: cough, coryza and conjunctivitis, preceded by Koplik spots in the buccal mucosa and followed by a cranial to caudal rash. Complications include severe, central-nervous system disease (1/1000 patients) and risk for SSPE (Subacute, Sclerosing, Pan-Encephalitis, 1/10,000 patients). A vaccine exists and is effective. However, concern exists that waning immunity in older individuals may be insufficient to prevent disease in an outbreak setting. Mumps virus: This virus and its self-named disease have also experienced a resurgence, mostly on college campuses. Similar to measles virus, a vaccine exists but may be subject to waning immunity. Ebola and Marburg viruses: These viruses collectively are named the hemorrhagic viruses, since they cause a severe, hemorrhagic syndrome which is approximately 60% to 80% fatal. Disease caused by these viruses usually occurs in sporadic to epidemic form, and progresses due to the highly contagious nature of the viruses and the extensive exposure to blood and body fluids experienced by healthcare workers and family members. Fungi Fungi are eukaryotic. They have cell walls that contain complex carbohydrates (polysaccharides) and ergosterol (humans have cholesterol). These 2 components serve at targets for both identification and antifungal therapy. Block: Foundations | Saman Nematollahi [14 of 15] MICROBIOLOGY OVERVIEW Pathogenic fungi can be broken down into Yeasts, Dimorphic molds, and Monomorphic molds. Morphology: Fungi exist in hyphal forms (consisting of filamentous units) which, when matted together, can form a Mycelium. Yeasts are single-celled fungi, and sometimes grow to develop Pseudohyphae (such as Candida albicans). Monomorphic molds (such as Aspergillus and Mucorales) only exists in the mold form (hyphal elements - “one morphology”). Dimorphic molds (“two morphologies”) can convert from the mold form (when in the environment at lower temperatures) to the yeast form (when inside the human body at higher temperatures). This is called thermal dimorphism. Examples include Histoplasma, Blastomyces, and Coccidioides. Pertinent to medical students in Tucson, AZ, Coccidioidomycosis “Valley Fever” is endemic to the Southwest US. Most cases are asymptomatic. Primary infection resembles community- acquired pneumonia and is typically self-limited. Disseminated disease rarely occurs. The gold standard for diagnosis of fungal infections is culture, smear, or histology from direct biopsy of the source. The culture requires specific, enriched media; it can be difficult to culture fungal organisms. This is why we rely on serology/antigen tests to augment our diagnostic armamentarium for fungal infections. Unfortunately, serology and antigen detection methods all suffer from some variable differences in sensitivity and specificity. Examples of diagnostic tests include: serum Cryptococcus antigen, urine Histoplasma antigen, Coccidioides serology, serum galactomannan, and serum (1,3)-β-D-glucan. Parasites Parasitology is the study of eukaryotic pathogens that are not fungi. A parasite is an organism that lives on or in a host and gets its food from the host. Parasites are broken down into 3 categories: - Protozoan (unicellular; example- Plasmodium) - Helminths (multicellular; example- flatworms, roundworms) - Ectoparasites arthropods (ticks, lice, fleas) One key point to remember is that protozoan and helminths parasites are fundamentally different. Protozoan parasites replicate in us and can reach high numbers (such as Plasmodium falciparum). They are also unicellular. Helminths do not replicate in us, with two exceptions (Strongyloides stercoralis and Capillaria philippinensis), and disease is a function of infecting worm burden. They have complex life cycles with development stages outside the human host. Block: Foundations | Saman Nematollahi [15 of 15]