Microbiology Lecture Notes PDF

Takwa khader Abdullah AlRawashdeh Dina Yamen Introduction to Microbiology Modified in red  ENTEROBACTERIACEAE / Classification More than 50 genera and hundreds of species and subspecies, Enterobacteriaceae are ubiquitous (organisms found worldwide in soil, water, and...

Takwa khader Abdullah AlRawashdeh Dina Yamen Introduction to Microbiology Modified in red  ENTEROBACTERIACEAE / Classification More than 50 genera and hundreds of species and subspecies, Enterobacteriaceae are ubiquitous (organisms found worldwide in soil, water, and vegetation and are part of the normal intestinal flora of most animals, including humans ). In humans it can be part of the normal intestinal flora, or always associated with human disease, or opportunistic infections, or normally commensal organisms that become pathogenic when they acquire virulence genes. Enterobacteriaceae are moderate-sized (0.3 to 1.0 × 1.0 to 6.0 μm), non–spore-forming, gram-negative rods , facultative anaerobes that share a common antigen enterobacterial common antigen ENTEROBACTERIACEAE / Pathogenesis and Immunity Endotoxin toxin activity depends on the lipid A component of LPS, released at cell lysis. Capsule, hydrophilic capsular antigens repel the hydrophobic phagocytic cell surface, but anticapsular antibodies diminish the capsule role. ( the way that capsule evade immune response by repelling effect against hydrophobic phagocytic cells, But still the immune system can evade immune response against the encapsulated organisms by producing anti capsular antibodies). Antigenic Phase Variation, somatic O antigens, capsular K antigens, and flagellar H antigens alternately expressed or not expressed (phase variation). these 3 antigens maybe be different gene under enterobacteriaceae family or different species under the same genus or different strains under the same species express variation of these strains  Type III Secretion Systems. (help to evade immune response of host cells) The bacteria counteract iron sequestration by producing their own competitive siderophores or iron-chelating compounds (e.g., enterobactin, aerobactin). Or from Iron released from lysed cells. Resistance to Serum Killing and Antimicrobial Resistance. (ENTEROBACTERIACEAE can be cultured in blood agar as general media, and on selective media such as macConkey agar and EMB) ENTEROBACTERIACEAE/MacConkey's agar It contains bile salts (to inhibit most Gram-positive bacteria), crystal violet dye (which also inhibits certain Gram- positive bacteria) and it induce the growth of gram-negative bacteria, neutral red dye (which turns pink if the microbes are fermenting lactose). Enterobacteriaceae are classified based MacConkey's agar showing on biochemical properties, antigenic both lactose and non-lactose structure, and molecular analysis of fermenting colonies ”Differential media”. Lactose their genomes, protein composition by fermenting colonies are pink mass spectrometry. whereas non-lactose fermenting ones are colourless or appear same as the medium. Modified Diagnosis of enterobacteriaceae as gram negative bacteria depends on -In goal standard method- culturing ( blood, macConkey agar) and series of biochemical reactions for different genera and species give us specific Id to specific species of enterobacteriaceae family One of these biochemical that can be done Abi and vitic AbI : manual way of doing biochemical reactions as a kit and it is very fast way instead of conventional biochemical reactions method. Vitic: semiautomatic method by preparing broth and put it in device contains different biochemical reactions and put it again in machine that responsible for these reactions and incubation period and record reactions and the code that show it is one type of enterobacteriaceae is the causative agent. Another analysis is done based on its antigenic structure (somatic antigen ,capsular ,flagellar ) and differ from species to another even from subspecies to another subspecies. More analysis can be done on molecular level by analyze DNA " genomic " or analyze protein " proteomics" ENTEROBACTERIACEAE/ Antibiotic resistance Resistance of the Enterobacteriaceae to antibiotics, especially of the β lactam type, is increasingly dominated by the mobilization of continuously expressed single genes that encode efficient drug modifying enzymes. Multi drug resistant (MDR) Enterobacteriaceae has been frequently reported from different parts of the world as an emergence of treatment problem. Antibiotics given empirically without proper antibiotic susceptibility testing are one of the major causes for the development of MDR. There is a shift of the "natural" resistance, such as membrane impermeability and drug efflux, to the modern paradigm of mobile gene pools that transmit resistance between bacteria. https://www.bmj.com/content/352/bmj.h6420 Modified How antibiotic resistance can be There? -By the genes that continuously expressed which coding enzymes that can degrade drug molecules very important when we make bacterial identification should accompanied with antibiotics susceptibility testing to prescribe most suitable antibiotic to treat this patient due to this causative agent There are two types of antibiotic resistance: natural resistance and acquired/transmitted - Natural resistant: bacteria itself have an impermeable membrane to these antibiotic or drug efflux which means if the drug enter the cell it collect and extract it outside bacterial cell , Therefore this antibiotic inefficient to treat this type of bacteria. - Acquired resistance: it can be transmitted by genes that responsible for emerging antibiotic resistance genes, and through time it express theses genes and acquire resistance to certain type of antibiotics ENTEROBACTERIACEAE / overview The following pathogens are discussed Escherichia coli Escherichia: The most commonly encountered genus and most imp species from this genus is Escherichia coli Salmonella Shigella Yersinia Klebsiella Proteus  Escherichia coli E. Coli is the model organism of Enterobacteriaceae since it is the most extensively studied. E. coli is the most common and important member of the genus Escherichia. It is both a common commensal inhabitant of the gastrointestinal tract and one of the most important pathogens in humans. It is a frequent cause of diahrrheal disease. It is the most frequent cause of bloodstream infection and urinary tract infections (UTIs) among Gram-negative bacteria. Which collectively called "extra intestinal infections" Escherichia coli it exist as normal flora in GI NOTE: Diarrheal diseases are very common and -in most cases- self- limiting. Diarrhea is defined either as the presence of more than three bowel movements per day, water content exceeding 75%, or a stool quantity of at least 200–250 g per day. Acute diarrhea lasts for no longer than 14 days and is typically caused by viral or bacterial infection or food poisoning Escherichia coli strains Commensal strains innocuously colonize the colon of healthy hosts, causing extraintestinal disease only in the presence of a large inoculum (e.g., with penetrating abdominal trauma) and/or significant host compromise “If immune system is compromised in host”. (must have large number of bacteria that is originally normal flora and undergo transmission to another body region in order to manifest extraintestinal disease) Diarrhoeagenic strains cause diarrhoea syndromes that vary in clinical presentation and pathogenesis-From mild to severe- according to the strain's distinctive virulence traits Extraintestinal pathogenic E. coli (ExPEC) often innocuously colonize the human gut. However, they have a unique ability to enter and survive within normally sterile extraintestinal body sites, and to cause disease when they do so.  important Sorry to say that you Most commonly have to Memorize it 🙂 encountered strain there's no invasion Until now due to this strain,but there is no the presence of invasion and bacteria itself rather no release than the activity of of the blood exotoxins which is the with stool factor that mainly to pathogenesis of organism Enterotoxigenic E. coli (ETEC) one of the most common causes of bacterial diarrheal disease in developing countries, and 30% of traveler’s diarrhea*.Acquired through consumption of fecally contaminated food or water. Person-to-person spread does not occur. 1- to 2-day incubation period and persists for an average of 3 to 5 days. The symptoms: Secretory diarrhea (watery high production of fluid and secretion of electrolytes, non-bloody diarrhea there's no invasion for infected tissues) and abdominal cramps; less commonly nausea and vomiting. Can be fatal in undernourished individuals. Produces 2 classes of toxins: Heat stable toxin leads to increase in cyclic guanosine monophosphate (cGMP) and subsequent hypersecretion of fluids well as inhibition of fluid absorption. Heat labile toxins leads to increase in cyclic adenosine monophosphate (cAMP) levels, resulting in enhanced secretion of chloride and decreased absorption of sodium and chloride *traveler’s diarrhea : When you visit a place where the climate or sanitary practices are different from yours at home, you have an increased risk of developing traveler's diarrhea. Usually, recovery happens within days with no need for treatment. Enterotoxigenic E. coli (ETEC) A second-year medical student experiences watery diarrhea and mild abdominal cramps during his 2-week travel to Egypt. With his little medical knowledge, he makes several assumptions, which of those assumption is false? a) This is probably a case of traveler’s diarrhea that should resolve within a few days. b) Enterotoxigenic E. coli (ETEC) is a probable causative agent. c) He would not have become sick if he washed his hands properly. d) Liquids are important to prevent dehydration and loss of electrolytes. e) If it is traveler’s diarrhea, he probably contracted the pathogen in a meal he ate 2 days ago. The answer is C, because this bacteria is transmitted by the ingestion of contaminated food or water, so washing his hands wouldn’t make a difference in being infected by it or not. Shiga toxin–producing E. coli (STEC) Most infections are attributed to the consumption of undercooked meat products, water, unpasteurized milk or fruit juices uncooked vegetables, and fruits. Ingestion of fewer than 100 bacteria can produce disease, and person-to-person spread occurs. Disease caused by STEC ranges from mild uncomplicated diarrhea to haemorrhagic colitis with severe abdominal pain and bloody diarrhea. Severe disease is more commonly associated with STEC O157:H7. 3 to 4 days of incubation before manifestation a disease, Within 2 days of onset, disease in 30% to 65% of patients progresses to a bloody diarrhea with severe abdominal pain, Complete resolution of symptoms typically occurs after 4 to 10 days in most untreated patients. Shiga toxin–producing E. coli (STEC) Complications of it depend on several factors such as how immune response can stop further manifestation and pathogenesis of this organisms, also on virulence factors of these strains Hemolytic uremic syndrome (HUS), a disorder characterized by acute renal failure, thrombocytopenia, and microangiopathic hemolytic anemia, is a complication in 5% to 10% of infected children younger than 10 years. self recovery may occur without treatment, but it depend on how patient can withstand diarrhea for 10 days ' most medications just taken to replace fluid and electrolyte loss ' Shiga-Toxin E. coli Hemolytic Uremic Syndrome: Review of Management and Long-term Outcome https://link.springer.com/article/10.1007/s40124-020-00208-7 Escherichia coli/ Extraintestinal Infections Urinary Tract Infection: Most gram-negative rods that produce UTIs originate in the colon, contaminate the urethra, ascend into the bladder, and may migrate to the kidney or prostate. (its it is normal flora in GI, however sometimes it transmit to urethra and contaminate it making UTI) Almost every second woman suffers from a bladder infection at some point in her life (E. coli in 80% of UTI cases). Also men are affected by cystitis (bladder infection), though less frequently, probably due to anatomical differences (e.g. shorter urethra in women makes it easier for bacteria to reach the bladder). Neonatal Meningitis : E. coli and group B streptococci cause the majority of CNS infections in infants younger than 1 month. Should be considered strictly to the pregnant women before delivery to ensure it was completely treated from this causative agents preventing its transmission to the baby and prevent cause neonatal meningitis  Septicemia : Typically, septicemia caused by gram-negative rods, such as E. coli, most commonly originates from infections in the urinary or GI tract, with high mortality in immunocompromised patients. Once it spread in the blood stream we cannot get rid or avoid infection from E.coli Escherichia coli/ Extraintestinal Infections Salmonella Salmonella can colonize virtually all animals (especially poultry ‫)الدواجن‬. Serotypes such as Salmonella Typhi and Salmonella Paratyphi are highly adapted to humans and do not cause disease in nonhuman hosts. After ingestion and passage through the stomach, salmonellae attach to the mucosa of the small intestine and invade into the M (microfold) cells located in Peyer patches” are small masses of lymphatic tissue found throughout the ileum region of the small intestine”, as well as into enterocytes(specialized epithelial cells lining the surface of the small intestine). The bacteria remain in endocytic vacuoles, where they replicate. The bacteria can also be transported across the cytoplasm and released into the blood or lymphatic circulation. The inflammatory response confines the infection to the GI tract, mediates the release of prostaglandins, and stimulates cAMP and active fluid secretion. Virulence dependent on pathogenicity island on the bacterial chromosome. Encoding for toxins, attachment proteins and immune evasion mechanisms. Note : In most E.coli strains the pathogenesis is mediated by plasmid mediated virulence factor, in the other hand salmonella virulence dependent in bacterial chromosome rather than plasmid Salmonella Asymptomatic Colonization : -Responsible about Preservation of these strains and source of infection to be transmitted from one person to another -The strains of Salmonella responsible for causing typhoid and paratyphoid fevers are maintained by human colonization. Salmonella Typhi is the causative agent of typhoid fever and salmonella paratyphi the causative of paratyphoid fever  Salmonella / Epidemiology and diseases Route of infection is ingestion The most common sources of human infections are poultry, eggs, dairy products, and foods prepared on contaminated work surfaces, large inoculum (e.g., 106 to 108 bacteria) is required for symptomatic disease. The infectious dose for Salmonella Typhi infections is low, so person-to-person spread is common, occur when food or water contaminated by infected food handlers is ingested. Gastroenteritis is a common form of salmonellosis, nausea, vomiting, and nonbloody diarrhea. can persist for 2 to 7 days before spontaneous resolution. ( self recovery can occur without prior treatment) Septicemia All Salmonella species can cause bacteremia, although infections with Salmonella Typhi, Salmonella Paratyphi more commonly lead to a bacteremic phase. Salmonella / diseases Salmonella Typhi produces a febrile illness called typhoid fever. A milder form of this disease, referred to as paratyphoid fever, is produced by other Salmonella (e.g paratyphi). Symptoms are not distinctive initially but then we can make identification if it typhoid or paratyphoid The bacteria responsible for enteric fever pass through the cells lining the intestines and are engulfed by macrophages. They replicate after being transported to the liver, spleen, and bone marrow. Ten to 14 days after ingestion of the bacteria, patients experience gradually increasing fever, with nonspecific complaints of headache, myalgias, malaise, and anorexia). Peyer's patches are small masses of lymphatic tissue found throughout the ileum region of the small intestine. Salmonella / diseases Typhoid Fever https://www.nejm.org/doi/full/10.1056/nejmra020201 Shigella S. dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei. However, analysis of DNA has determined that these four species are actually biogroups related within the species E. coli. Shigellae cause disease by invading and replicating in cells lining the colon. Virulence factors : - Structural gene proteins mediate the adherence of the organisms to the cells - -as well as their invasion - intracellular replication, and cell-to-cell spread. S. dysenteriae strains produce an exotoxin, Shiga toxin. Similar to Shiga toxin produced by STEC The A subunit in the toxin cleaves the 28S rRNA in the 60S ribosomal subunit, thereby preventing the binding of aminoacyl-transfer RNA and disrupting protein synthesis. The primary manifestation of toxin activity is damage to the intestinal epithelium; however, in a small subset of patients, the Shiga toxin can mediate damage to the glomerular endothelial cells, resulting in renal failure (HUS). As long as there is invasionation there will be bloody diarrhea Shigella passes the epithelial cell (EC) barrier by transcytosis through M cells and encounters resident macrophages. The bacteria evade degradation in macrophages by inducing an apoptosis-like cell death, which is accompanied by proinflammatory signaling. Free bacteria invade the EC from the basolateral side, move into the cytoplasm by actin polymerization, and spread to adjacent cells. Proinflammatory signaling by macrophages and EC further activates the innate immune response and attracts PMN. The influx of PMN disintegrates the EC lining, which initially exacerbates the infection and tissue destruction by facilitating the invasion of more bacteria. Ultimately, PMN phagocytose and kill Shigella, thus contributing to the resolution of the infection. Shigella / Epidemiology and diseases Humans are the only reservoir for Shigella. S. sonnei is responsible for almost 85% of U.S. infections, whereas S. flexneri predominates in developing countries. Epidemics of S. dysenteriae infections occur periodically, most recently in West Africa and Central America. Different environmental conditions=> different virulence factors Shigellosis (Shigella infection) ( is primarily a pediatric disease, with 60% of all infections in children younger than 10 years. Shigellosis is transmitted person to person by the fecal-oral route. Because as few as 100 to 200 bacteria can establish disease- very low inoculum needed to manifest a disease-, shigellosis spreads rapidly in communities where sanitary standards and the level of personal hygiene are low. Shigellosis is characterized by abdominal cramps, diarrhea, fever, and bloody stools ( same as STEC ). The clinical signs and symptoms of the disease appear 1 to 3 days -incubation period- after the bacteria are ingested. Infection is generally self-limited, although antibiotic treatment is recommended to reduce the risk of secondary spread to family members and other contacts.  Klebsiella Klebsiella species are routinely found in the human nose, mouth, and gastrointestinal tract as normal flora. The most commonly isolated members of this genus are K. pneumoniae, which can cause community- or hospital-acquired primary lobar pneumonia. These bacteria also cause wound and soft-tissue infections and UTIs. The ability of K. pneumoniae to colonize the hospital environment, including carpeting, sinks, flowers, and various surfaces, as well as the skin of patients and hospital staff, has been identified as a major factor in the spread of hospital-acquired infections One of its virulence factors that it is encapsulated bacteria Proteus P. mirabilis , the most common member of this genus, primarily produces infections of the urinary tract. P. mirabilis produces large quantities of urease, which splits urea into carbon dioxide and ammonia. This process raises the urine pH, precipitating magnesium and calcium in the form of struvite and apatite crystals, respectively, ( Production of crystal maybe be an indication of Proteus infection) and results in the formation of renal (kidney) stones. The increased alkalinity of the urine is also toxic to the uroepithelium Yersinia The best-known human pathogen within the genus Yersinia is Y. pestis All Yersinia infections are zoonotic (mean that it affect the animals,), with humans the accidental hosts (and can be transmitted to the human). There are two forms of Y. pestis infection: urban plague, for which rats are the natural reservoirs, and sylvatic plague, which causes infections in squirrels, rabbits, field rats, and domestic cats. 3 major pandemics that shaped history :  The third pandemic, the Modern Plague, began in The Justinian Plague began in China in the 1860s and 541 AD and was followed by appeared in Hong Kong by frequent outbreaks over the next 1894. Over the next 20 years, two hundred years that it spread to port cities eventually killed over 25 million The second pandemic, widely known as the “Black around the world by rats on people and affected much of the Death” or the Great Plague, originated in China in steamships. The pandemic Mediterranean basin–virtually all 1334 and spread along the great trade routes to caused approximately 10 of the known world at that time. Constantinople and then to Europe, where it million deaths claimed an estimated 60% of the European population, around 50-200 million lives. Yersinia Bubonic plague caused by Y. pestis is characterized by an incubation period of no more than 7 days after a person has been bitten by an infected flea. Patients have a high fever and a painful bubo (inflammatory swelling of the lymph nodes) in the groin or axilla. Bacteremia develops rapidly if patients are not treated, and as many as 75% die. ( Affected from it : animals transmitor of it : flea) The patients are highly infectious; person-to-person spread occurs by aerosols in case of pneumonic plague. ENTEROBACTERIACEAE/ Antibiotic resistance Carbapenem-resistant Enterobacteriaceae (CRE) or carbapenemase-producing Enterobacteriaceae (CPE) are Gram-negative bacteria that are resistant to the carbapenem class of antibiotics, considered the drugs of last resort for such infections. -If resistance happens to carbapenem this mean that this type of bacteria could be not treated anymore. They are resistant because they produce an enzyme called a carbapenemase that disables the drug molecule. The resistance can vary from moderate to severe. Experts fear CRE as the new "superbug". The bacteria can kill up to half of patients who get bloodstream infections. The main risk factors for CRE acquisition in the United States include exposure to healthcare and exposure to antibiotics. Watch this video https://www.youtube.com/watch?v=plVk4NVIUh8&ab_channel=HarvardMedicalSchool Further reading: Murray - Medical Microbiology 8th Edition Section 4: Bacteriology Chapter 25: ENTEROBACTERIACEAE The End Of This Lecture Good Luck