Bacteriology-1 PDF

07.02.2024 Bacteriology-1 Dogukan Ozbey, Lecturer Medical Faculty, Department of Medical Microbiology [email protected] ❑Prokaryotes ▪ Unicellular organism. ▪ Does not contain a nuclear membrane-enclosed nucleus and lack of any other membranebound organelles. ▪ Based upon molecular analysis,...

07.02.2024 Bacteriology-1 Dogukan Ozbey, Lecturer Medical Faculty, Department of Medical Microbiology [email protected] ❑Prokaryotes ▪ Unicellular organism. ▪ Does not contain a nuclear membrane-enclosed nucleus and lack of any other membranebound organelles. ▪ Based upon molecular analysis, prokaryotes are divided into two domains Bacteria and Archaea ▪ Flagellum provides structural backgrounds of chemotaxis. ▪ Plasmid is a small, extrachromosomal DNA molecule ▪ Cell Membrane Surrounds the cell's cytoplasm and regulates the flow of substances in and out of the cell. ▪ Cell Wall is outer covering of most cells that protects the bacterial cell and gives it shape ▪ Cytoplasm is a gel-like substance composed mainly of water that also contains enzymes, salts, cell components, and various organic molecules ▪ Ribosome is responsible for protein production ▪ Nucleoid is an area of the cytoplasm that contains the prokaryote's single DNA molecule. ❑Binary Fission ▪ Organisms in the domains of Archaea and Bacteria reproduce with binary fission. ▪ This form of asexual reproduction and cell division is also used by some organelles within eukaryotic organisms ▪ Binary fission results in the reproduction of a living prokaryotic cell (or organelle) by dividing the cell into two parts, each with the potential to grow to the size of the original. ❑Bacterial Growth Curve Lag Phase: Bacteria try to adapt to the environment. There is cellular activity but not growth. Log Phase: Cells are dividing by binary fission and doubling their numbers. Metabolic activity is high. Stationary Phase: Available nutriens depleted, waste products accumulated. Dividing and Dying cells are equal. Bacteria try to survive. Death Phase: Nutrients become less availabe. Number of dyings cells increase. ❑Koch’s Postulates Koch's postulates are four criteria designed to establish a causative relationship between a microbe and a disease. 1. The microorganism must be found in abundance in all organisms suffering from the disease, but should not be found in healthy organisms. 2. The microorganism must be isolated from a diseased organism and grown in pure culture. 3. The cultured microorganism should cause disease when introduced into a healthy organism. 4. The microorganism must be reisolated from the inoculated, diseased experimental host and identified as being identical to the original specific causative agent. ❑Diagnosis ❑ Acute Phase Reactants Acute phase reactants (APR) are inflammation markers that exhibit significant changes in serum concentration during inflammation. During the response to the inflammation plasma concentration of acute phase reactants may decrease (Negative acute phase reactants) or increase (Positive acute phase reactants) Positive Acute Phase Reactants: CRP, PCT, Serum Amyloid A, Complement Factors, Lectin, Fibrinogen, Ferritin, Haptoglobin... Negative Acute Phase Reactants: Albumin, Transferrin, Retinol-Binding Protein, Antithrombin, Complement 3 (C3) ❑Diagnostic Methods ▪ Culture Based Methods ▪ Non-Cultural Methods ✓ Microscope ✓ Biochemical Tests ✓ Immunological Methods ✓ Molecular Methods ❑Culture Methods ❖ Anaerobic Culture Kanamycin-Vancomycin (KV) Agar Phenylethyl Alcohol (PEA) Agar Thioglycolate Broth ❖ Aerobic Culture Blood Agar Chocolate Agar MacConkey or Eosin Methylene Blue Agar ❑ Microscopic Techniques Staining Peripheral Blood Smear ❑ Biochemical Tests Catalase Oxidase Urease Esculine Hydrolysis IMViC Triple Sugar-Iron Motility… Analytical Profile Index (API) Test ❑ Maldi-TOF MS Ionization technique that uses a laser (UV) energy It can be analyze biomolecules (DNA, proteins…) and various organic molecules Provides species-level diagnosis (25 minutes for 96 samples) ❑ Immunological/Serological Diagnostics Can be done by detecting bacterial antigens (Direct diagnosis) Legionella pneumophilia antigens can be detected from Urine sample Helicobacter pylori antigens can be detected from Stool sample Chlamydia trachomatis antigens can be detected from endocervical and urethral swab Haemophilus influenzae antigens can be detected from Body fluids Or can be done by detecting antibodies against bacterial antigens (Indirect diagnosis) ❑ Molecular Diagnostic Methods Molecular diagnostics is a collection of techniques used to analyze biological markers in the genome and proteome. In medicine the technique is used to diagnose and monitor disease, detect risk, and decide which therapies will work best for individual patients For microbiology; molecular diagnostics are used to identify microorganism or to determine specific strains of a microorganism Steps DNA/RNA extraction Nucleic Acid Amplification Electrophoresis Sequencing Types of Polymerase Chain Reaction (PCR) that used for nucleic acid amplification ❑Dental Infections Dental infections originate in the tooth or its supporting structures and can spread to the surrounding tissue. Dental infections were, historically, a common cause of death. Due to improved dental hygiene, modern dentistry, and antibiotics, dental infections are rarely life-threatening today. Periodontal infections first involve the gingival tissues causing gingivitis and, over time, periodontitis. ❑Dental Abscess A dental abscess is a build-up of pus in the teeth or gums caused by an infection. There are three types of dental abscess. Gingival abscess Periodontal abscess Periapical abscess It needs urgent treatment Without treatment, it can be life-threatening Common symptoms; ✓ Intense toothache or pain in gums ✓ Redness inside the mouth, or outside the mouth on the face or jaw ✓ Sensitivity to hot or cold food and drink in the affected area ✓ Bad taste in mouth ✓ Difficulty opening the mouth and chewing food ✓ Swollen face or jaw ✓ High temperature ❑Biofilm Formation Dental plaque is an example of a biofilm, which occurs naturally on the teeth structures The plaque biofilm is a tenacious microbial community embedded in an extracellular polysaccharide matrix ✓ Living and dead bacteria and their extracellular products ✓ Host compounds, mainly derived from the saliva. Biofilm infections are characterized by persisting and progressive pathology due primarily to the inflammatory response surrounding the biofilm Microorganisms universally attach to surfaces and produce extracellular polysaccharides, resulting in the formation of a biofilm. ❑Cavities It can be caused by cariogenic bacteria, that dissolves the hard tissues of the teeth (enamel, dentin and cementum). Streptococcus mutans, Streptococcus sobrinus and Lactobacillus Root cavities are caused by Lactobacillus acidophilus, Actinomyces spp., Nocardia spp., and Streptococcus mutans Comorbid diseases (SjS or DM) or medications (Antihistamines or antidepressants) are risk factors. Neutral pH: 7.0 Dentin: 6.5 Enamel: 5.5 ❑Biomineralization Enamel demineralization is the primary mechanism involved in the etiopathogenesis of caries When the oral microenvironment reaches low pH values the demineralization process is triggered When the microenvironment reaches pH values higher than 7.0 and there is an availability of calcium and phosphate ions, remineralization can occur Demineralization Remineralization ❑White Spot Lesions The white spot lesion is the first visual finding of enamel caries. The mineral content in the affected area is reduced, which in turn affects the translucent feature of the enamel, and the color of these areas appears more opaque white ❑Disclosing Solution Dental plaque disclosing solutions are dyes that color dental biofilm and dental plaque to make observation easier ❑Periodontal Diseases Gingivitis: Inflammation or infection of the gingiva ❑Periodontitis Periodontitis, also called gum disease, is a serious gum infection that damages the soft tissue and, without treatment, can destroy the bone that supports the teeth Periodontal disease can establish itself when the gums detach from the teeth as a result of an inflammatory response to plaque. Periodontitis can cause teeth to loosen or lead to tooth loss Periodontal infections are usually mixed, most often involving anaerobes such as Treponema denticola and Porphyromonas gingivalis Actinobacillus actinomycetemcomitans causes localized juvenile periodontitis ❑Acute Necrotizing Ulcerative Gingivitis (Vincent Gingivitis) It is an acute and painful infection of the tooth margins and gums that is caused by the symbiotic microorganisms, Prevotella intermedia, Bacillus fusiformis and Borrelia vincentii The main features are painful, swollen, bleeding gums; small, painful ulcers covering the gums and tooth margins; and characteristic fetid breath. ✓ Severe gum pain that characterizes ANUG distinguishes it from chronic periodontitis The ulcers may spread to the throat and tonsils The infection is readily treated by bed rest, the administration of penicillin or other antibiotics, and the use of antiseptic mouth rinses Treatment is removal of dead gum tissue and antibiotics (usually metronidazole) ❑Pericoronitis Pericoronitis is an inflammatory and infectious complication accompanying the clinical emergence of the third molars in the oral cavity It is caused by an accumulation of bacteria and debris beneath the operculum, or by mechanical trauma The microbial flora that develop at the site of eruption are contained within a periodontal pocket-like crevice Pericoronal infection is normally caused by a mixture of bacterial species present in the mouth, such as Streptococci and particularly various anaerobic species Prevotella, Veillonella, Bacteroides, Capnocytophaga can accompany ❑Dental Implant Infections A dental implant is one of the treatments to replace missing teeth. They can be used in the treatment of complete and partial edentulism. They can be prone to infection Dental implant infection is a condition that can be likened to gum disease. It causes inflammation and infection of the gums and bone tissue surrounding dental implants ✓ Local debridement ✓ Implant surface decontamination ✓ Anti-infective therapy (Antibiotics [Ornidazole, Metronidazole or Amoxicillin] or Antiseptics [Chlorhexidine]) ✓ If there is advanced bone loss, Removal of the implant itself. ❑Oro/Facial Gangrene Cancrum oris (Noma) is a devastating, non-contagious, bacterial infectious disease which destroys the soft and hard tissues of the oral and para-oral structures. The risk factors are poverty, malnutrition, poor oral hygiene, residential proximity to livestock in unsanitary environments, and infectious diseases, particularly Measles and those due to the Herpesviridae Acute Necrotizing Gingivitis and herpetic ulcers are considered the antecedent lesions Rapid progression of these precursor lesions to Noma requires infection with Fusobacterium necrophorum and Prevotella intermedia Enzymes and toxins (Dermonecrotic Toxin) are responsible for tissue destruction Early treatment with antibiotics and nutritional support may slow the spread of the disease. ❑Bad Breath (Halitosis) It can develop due to various reasons. Its persistence creates a major psychological disturbance in humans. Although the most common cause is poor oral hygiene, it can also be seen in people who pay attention to hygiene. Halitosis cases may not be caused by a single type, so two or more types of halitosis can be diagnosed at once. Being edentulous, periodontitis, crowns, fillings and brackets do not cause bad breath. Dense teeth, full dentures, gingivitis, excessively recessed tongue papillae, fistula, pericoronary infection, alcohol habit, containing alcohol mouthwashes, bacterial plaques can cause bad breath. ❑Bad Breath (Halitosis) Type 0 (Physiological bad breath): Bad breath that occurs in the morning and disappears by itself during the day Type 1 (Tongue smell): It is caused by volatile aromatic gases produced on the back of the tongue. Response to odor treatment can be obtained. Can be prevented with zinc or tongue cleaning Type 2 (Bad breath caused by throat-sinus): It is caused by any bacteria in the pharynx, tonsils, paranasal sinuses, nasal mucosa and surrounding tissues. May not be identified with Waters X-ray, should be supported by MRI or CT Type 3 (Bad breath caused by the digestive tract): There is a source of aromatic gas anywhere in the digestive tract and this gas reaches the mouth. If there is Helicobacter pylori gastritis in the stomach, there is a nitrite odor in the mouth. Type 4 (Breath odor): It may develop due to an infection in the lower respiratory tract. Even if there is no infection, volatile gases dissolved in the blood can create this odor. Diagnosed with blood gas biochemistry. Type 5 (Psychological bad breath): The patient's obsession with bad breath ❑Bloodstream infections Bloodstream infections are infectious diseases defined by the presence of viable microorganisms in the bloodstream Bacteremia: Bacteria are present in the bloodstream. Sepsis: Reproduction of a microorganism in the blood ❑Systemic Diseases Caused by Oral Infection Bacteremia was observed in 100% of the patients after dental extraction, in 70% after dental scaling, in 55% after third-molar surgery, in 20% after endodontic treatment, and in 55% after bilateral tonsillectomy Three mechanisms or pathways linking oral infections to secondary systemic effects have been proposed Metastatic infection Metastatic injury Metastatic inflammation ❑Systemic Diseases Caused by Oral Infection ▪ Metastatic infection from oral cavity via transient bacteremia Metastatic infection is defined as a deep, distal, or secondary infection, anatomically unrelated to the primary site infection ✓ Subacute infective endocarditis, acute bacterial myocarditis, brain abscess, cavernous sinus thrombosis, sinusitis, lung abscess/infection, Ludwig's angina, orbital cellulitis, skin ulcer, osteomyelitis, prosthetic joint infection ❑Systemic Diseases Caused by Oral Infection ▪ Metastatic injury from circulation of oral microbial toxins Some bacteria have the ability to produce diffusible proteins, or exotoxins, which include cytolytic enzymes and dimeric toxins ✓ Cerebral infarction, acute myocardial infarction, abnormal pregnancy outcome, persistent pyrexia, idiopathic trigeminal neuralgia, toxic shock syndrome, systemic granulocytic cell defects, chronic meningitis ❑Systemic Diseases Caused by Oral Infection ▪ Metastatic inflammation caused by immunological injury from oral organisms Soluble antigen may enter the bloodstream, react with circulating specific antibody, and form a macromolecular complex. These immunocomplexes may give rise to a variety of acute and chronic inflammatory reactions at the sites of deposition ✓ Behçet's syndrome, chronic urticaria, uveitis, inflammatory bowel disease, Crohn's disease ❑Gram Positive cocci Staphylococci Micrococci Enterococci Streptococci ❑Staphylococci Staphylococci are spherical cells about 1 μm in diameter arranged in irregular clusters Single cocci, pairs, tetrads, clusters and chains Gram positive, facultative anaerob, non-spore forming, non-motile Grow rapidly at 37°C, pigmentation (Gray-Golden Yellow) at room temperature (18-25°C) They are frequently isolated from the oral cavity. S. aureus, S. epidermidis, S. saphropyticus, S. lugdunensis Can be found in the saliva of healthy subjects older than 70 years. ❑Staphylococcus aureus They can be seen in clusters (multiple dividing zones) ✓ Clumping factor The habitat is the human skin, especially the anterior nares and the perineum. They are disseminated through air and dust and are always present in the hospital environment. Most strains are resistant to ß-lactam antibiotics Semi-synthetic penicillins (nafcillin, oxacillin, methicillin) cephalosporins, vancomycin, daptomycin, telavansin or linezolid ❑Staphylococcus aureus Toxins Super antigen Cytotoxins; Lyses cell Leukocidin (PVL); It causes lysis by opening pores in leukocyte membranes. Epidermolytic toxin; Exfoliation and splitting of epidermis Toxic Shock Syndrome Toxin; Shock, Rash or Desquamation Enterotoxin; Vomiting and Diarrhea Enzymes Exoenzymes Coagulase; Clots plasma (Fibrinogen→Fibrin) Catalase; Catalyzes the decomposition of hydrogen peroxide to water and oxygen Penicillinase; Breaks down ß-lactam drugs Protein A; Antiphagocytic Hyaluronidase; Connective tissue breakdown Lipase; Breaks lipids of cell membranes DNase; facilitates the spread of the pathogens in the tissue. ❑Staphylococcus aureus Cell surface components Capsule: It is found in more than 90% of S. aureus strains. Provides antiphagocytic properties. Peptidoglycan: Shows endotoxin-like activity. It provides IL-1 release and complement activation. It induces the production of antibodies that will opsonize. Teichoic acid: Provides complement activation. It plays a role in adhesion to mucosal cells. Adhesins: It is responsible for adhesion to skin and mucosal surfaces. It is associated with the adhesion of matrix molecules on the bacterial surface to host proteins. The main ones are clumping factor, fibronectin binding protein, collagen binding protein and protein A. Biofilm: Has a polysaccharide structure. It plays a role in the pathogenesis of foreign body infections. ❑Staphylococcus aureus Infections Skin and soft tissue infections ✓ Carbuncles, pustules, abscesses, conjunctivitis, mastitis and wound infections Bone and joint infections ✓ Osteomyelitis, Prosthetic joint infections… Toxin-related diseases ✓ Scalded skin syndrome, toxic shock syndrome, Food poisoning Bacteremia/sepsis Endocarditis Pericarditis Meningitis Lung infections ❑Staphylococcus aureus Folliculitis Furuncle Carbuncle Impetigo ❑Staphylococcus aureus Localized growth of toxin-producing strains of S. aureus, followed by release of the toxin into blood A diffuse, macular erythematous rash can be seen Multiple organ failure and shock Toxic Shock Syndrome ❑Staphylococcus aureus Staphylococcal scalded skin syndrome ❑Coagulase Negative Staphylococci Staphylococcus epidermidis: Skin Staphylococcus saprophyticus: GIS and Genital Tract Staphylococcus lugdunensis: Skin They can rapidly colonize on foreign bodies Biofilm ❑Staphylococcus epidermidis This species is found on the skin surface and is spread by contact. Grows as white colonies on blood agar. Being a normal commensal of the skin, this bacterium causes infection only when an opportunity arises. Can be treated with Vancomycin ❑Staphylococcus saphrophyticus This organism causes urinary tract infections It has the ability to colonize the periurethral skin and the mucosa. It can be differentiated from Staphylococcus epidermidis by the mannitol fermentation reaction ❑Staphylococcus lugdunensis S. lugdunensis may produce a bound coagulase, but unlike S. aureus, it does not produce a free coagulase ✓ Slide Coagulase (+), Tube Coagulase (-) Decarboxylates ornithine Pyrrolidonyl arylamidase-PYR (+) It can cause cardiovascular infections, empyema, osteomyelitis and prosthetic/native joints infections, skin and soft-tissue infections, central nervous system infections, peritonitis, endocephalitis, and urinary tract infections Treated with Penicillins ❑Micrococci Micrococci are catalase-positive organisms similar to Staphylococci. They are coagulase-negative and usually grow as white colonies on blood agar, although some species are brightly pigmented: pink, orange or yellow Micrococcus is generally thought to be a saprotrophic or commensal organism, though it can be an opportunistic pathogen, particularly in hosts with compromised immune systems It can be difficult to identify Micrococcus as the cause of an infection, since the organism is a normally present in skin microbiota ❑Streptococci Pyogenic Streptococci Streptococcus pyogenes Streptococcus agalactiae Streptococcus dysgalactiae Viridans Streptococci Streptococcus bovis Streptococcus anginosus Streptococcus mutans Streptococcus mitis Streptococcus sanguinis Streptococcus salivarus Streptococcus pneumoniae ❑Streptococci Residents of normal microbiota Non-Motile, Non-spore forming Facultative anaerobe They form a chain because they divide in one direction. Nutrient requirements are complex Predominant in dental plaques ❑Streptococci Lancefield Groups Lancefield grouping is a serological method for classifying streptococci into one of 20 groups (A to H and K to V) based on the presence of polysaccharide and teichoic acid antigens in the bacterial cell wall Some of these groups include human pathogens. Group A includes Streptococcus pyogenes (β hemolysis) Group B includes Streptococcus agalactiae (β hemolysis) Group D includes Enterecoccus species (α or γ hemolysis) ❑Streptococcus pyogenes The normal habitat of this species is the human upper respiratory tract and skin. Some strains produce mucoid colonies as a result of having a hyaluronic acid capsule (Resistance). ß-hemolytic colonies (Streptolysin O and S) Penicillin / Macrolide ❑Streptococcus pyogenes ❑ Toxins S. pyogenes produce biologically active substances Streptokinase: A proteolytic enzyme that lyses fibrin Hyaluronidase: Spreading factor. DNase: Destroys cellular DNA Haemolysins (Streptolysins and Leukocidins) Pyrogenic Exotoxins: Assocaited with severe diseases ❑Streptococcus pyogenes It is the most common cause of bacterial pharyngitis and tonsillitis, especially in children aged 5-15 years. S. pyogenes is an important cause of skin and soft tissue infections and pharyngitis and can cause many other suppurative infections tonsillitis and pharyngitis, necrotizing fasciitis (streptococcal gangrene), scarlet fever, mastoiditis and sinusitis, otitis media, wound infections, impetigo and erysipelas After an episode of infection, some people develop complications Rheumatic Fever (bacterial antigen-heart tissue) Glomerulonephritis (immune complexes) Erythema Nodosum Scarlet Fever Pharyngitis Impetigo Necrotizing fasciitis ❑Streptococcus agalactiae S. agalactiae is the only species that has the group B antigen. They form short chains in clinical specimens and longer chains after cultivation S. agalactiae has polysaccharide capsule (Antiphagocytic) It is the causative agent of neonatal meningitis and sepsis. Found in the human vagina and also can colonize in the lower GIT Babies acquire infection from the colonized mother during delivery. CAMP (+) Macrolide and Flourokinolon (R), Penicillin reduced susceptibility Ampicillin, Cephalosporin, Meropenem, Teicoplanin, Vancomycin ❑Streptococcus agalactiae ❑ Clinical Disease Early-Onset Neonatal Disease Bacteremia, Pneumoniae, Meningitis Clinical symptoms of group B streptococcal disease acquired in utero or at birth develop during the first week of life. Late-Onset Neonatal Disease Bacteremia with Meningitis Late-onset disease is acquired from an exogenous source and develops between 1 week and 3 months of age Infections in Pregnant Women Postpartum endometritis, wound infection, and urinary tract infections occur in women during and immediately after pregnancy Infections in Non-Pregnant Women and Men The most common presentations are bacteremia, pneumonia, bone and joint infections, and skin and soft-tissue infections. Underlying conditions ❑Viridans Streptococci Oral streptococci, which live principally in the oropharynx, are a mixed group of organisms with variable characteristics They typically show α-haemolysis on blood agar. They are easily killed with common disinfectants. Oral streptococci can be divided into four main species groups as follows: ✓ anginosus group ✓ mitis group ✓ mutans group ✓ salivarius group ❑mutans group S. mutans is naturally present in the human oral microbiota, along with at least 25 other species of oral streptococi Can contribute to oral diseases with S. sobrinus Differentiating is not necessary S. mutans is most prevalent on the pits and fissures, constituting 39% of the total streptococci in the oral cavity. Fewer S. mutans bacteria are found on the buccal surface Candida albicans supports biofilms formed by S. mutans. ❑Streptococcus mutans It is the primary organism involved in dental caries. Easily adheres to hard tissues Can eliminate many other bacteria by secreting Mutacin It can synthesize all the amino acids it needs by fermenting carbohydrates. It can lower the pH of the environment in which it grows up to 4 They synthesize large polysaccharides such as dextrans or levans from sucrose and contribute importantly to the genesis of dental caries. ❑Streptococcus sobrinus Enhances the formation of caries within teeth Biofilm from the mixture of sugar and plaque create a suitable environment for S. sobrinus to grow. S. sobrinus is also affiliated with early childhood caries, which are responsible for the majority of dental abscesses and toothaches in children ❑Streptococcus salivarus They can use urea by breaking it down into ammonia Can grow at 10-45°C It can be found on the tongue, saliva and Deciduous teeth. May cause infective endocarditis when bacteremia ❑Streptococcus mitis Streptococcus mitis, previously known as Streptococcus mitior, is a mesophilic α-hemolytic species of Streptococcus that inhabits the human mouth It is most commonly found in the throat, nasopharynx, and mouth It can cause infective endocarditis, brain abscesses, sepsis, pneumonia, and peritonitis In children with leukemia or lymphoma, it can cause meningitis ❑Streptococcus sanguinis (sanguis) May delay cavities caused by Streptococcus mutans or other bacteria They can coexist in biofilms. There is a competitive relationship between each other. S. sanguinis may gain entrance to the bloodstream when opportunity presents (dental cleanings and surgeries) and colonize the heart valves, particularly the mitral and aortic valves, where it is the most common cause of subacute bacterial endocarditis May require short-term antibiotic use before and after surgery. ❑Streptococcus pneumoniae Gram-positive cocci in pairs (diplococci) or short chains, cells are often capsulate, fastidious, α-haemolytic on blood agar. Draughtsman colonies after 2 days of incubation Since they are lack of catalase enzyme, they need exogenous source of catalase to grow (H2O2) S. pneumoniae causes several common diseases, such as pneumonia and meningitis in adults and otitis media and sinusitis in children. Can colonize oropharynx and nasopharynx Vaccine is available Penicillin is the first choice, Vancomycin+Ceftriaxone is used for emphric therapy ❑Streptococcus pneumoniae ❑Virulence factors Peptidoglican layer (binds to NAMA and NAGA) and teichoic acid (binds to plasma membrane lipids) of cell wall Capsule: Antiphagocytic. Only capsulated strains are infectious Adhesins: Attaches to epitelial surfaces IgA Protease: Destroys secretory IgA (sIgA) Pneumolysin: Lysis of epithelial and phagocytic cells ❑Streptococcus pneumoniae ❑Clinical Outcomes Pneumonia Pneumococcal pneumonia develops when the bacteria multiply in the alveolar spaces. Most patients have a productive cough with blood-tinged sputum, and they commonly have chest pain Meningitis S. pneumoniae can spread into the central nervous system after bacteremia, infections of the ear or sinuses, or head trauma that causes a communication between the subarachnoid space and the nasopharynx. Otitis Media The disease is usually preceded by a viral infection of the upper respiratory tract, after which polymorphonuclear neutrophils infiltrate and obstruct the sinuses and ear canal Bacteremia Bacteria are generally not present in the blood of patients with sinusitis or otitis media. Endocarditis can occur in patients with both normal or previously damaged heart valves. Destruction of valve tissue is common. ❑Enterococci (Enterococcus faecalis and Enterococcus faecium) The enterococci are gram-positive cocci, typically arranged in pairs and short chains. The cocci grow both aerobically and anaerobically in a broad temperature range (10° C to 45° C), in a wide pH range (4.6 to 9.9), and in the presence of high concentrations of sodium chloride (NaCl) and bile salts. Glucose is fermented with L-lactic acid as the predominant end product Usually non-hemolytic Antibiotic-resistant strains has become a serious problem in hospitalized patients. VanA, VanB / VanC Daptomycin, Linezolid, Streptogramins, Tigecycline Differential diagnosis can be made with "arabinose fermentation« E. faecalis (-), E. faecium (+) ❑Oral Cavity Infections of Enterococci Enterococcus faecalis is part of microbiota in the oral cavity, but also it has a relation with different oral diseases Enterococcus faecalis causes several infections in the oral cavity as an opportunistic pathogen, such as marginal periodontitis, root canal infections, primary endodontic infections, persistent/secondary infections, dental caries, peri-implantitis, periradicular abscesses and oral mucosal lesions It is commonly found in root canal failures and root-filled tooth treatment failure. They participate in mixed infections with other bacteria in the necrotic root canal 14.02.2024 Bacteriology-2 Dogukan Ozbey, Lecturer Medical Faculty, Department of Medical Microbiology [email protected] Gram Negative Cocci ⮚ Neisseria ⮚ Moraxella catarrhalis Neisseria meningitidis G M S Neisseria gonorrhoeae G M S Moraxella catarrhalis G M S ❑ Neisseriaceae family Non-motile, Gram-negative cocci ranging from 0.6 to 1.0 μm in diameter. It can be seen inside the leukocytes Two species of Neisseria are human pathogens: ✔ Neisseria gonorrhoeae (the gonococcus) ✔ Neisseria meningitidis (the meningococcus). ❑ Neisseriaceae family Pathogenic Neisseria species are nutritionally fastidious, especially on initial isolation from clinical specimens Though aerobic, most strains of N. gonorrhoeae are capnophilic Members of this genus grow optimally at 36°–39°C ❑ Neisseriaceae family ❑ Neisseria gonorrhoeae The human urogenital tract is the usual habitat Humans are the only reservoir May transmitted sexually or pass from infected mother to baby It can evade the immune system by preventing the formation of the phagolysosome complex. Can cause different clinical outcomes Gonorrhea: Characterized by purulent discharge for involved site (e.g., urethra, cervix, epididymis, prostate, rectum) after a 2- to 5day incubation period Disseminated infections: Spread of infection from genitourinary tract through blood to skin or joints; characterized by pustular rash with erythematous base and suppurative arthritis in involved joints Ophthalmia neonatorum: Purulent ocular infection acquired by neonate at birth Oral gonorrhea ❑ Neisseria meningitidis Glucose (+) Maltose (+) The main reservoir is the nasopharynx in healthy individuals Droplet spread is the most common transmission mode. Encapsulated In susceptible individuals, meningococci spread from the nasopharynx into the blood stream (septicaemia), and then to the meninges. It is seen in and around the leukocytes on gram staining. ✔ Meningitis: purulent inflammation of meninges associated with headache, meningeal signs, and fever. ✔ Meningococcemia: disseminated infection characterized by thrombosis of small blood vessels and multiorgan involvement. ✔ Pneumonia: milder form of meningococcal disease characterized by bronchopneumonia in patients with underlying pulmonary disease. ❑ Other Neisseria species N. flavescens N. subflava N. mucosa N. sicca N. cinerea N. lactamica N. denitrificans N. elongata ❑ Moraxella catarrhalis Glucose (-) Maltose (-) Oxidase (+), Catalase (+), DNase (+) Causes Acute otitis media (AOM) in children and leads to exacerbations of chronic obstructive pulmonary disease (COPD) in adults In cases with bacteremia, there are usually a comorbid disease. Resistant to decolorization with ethanol. Acetone-alcohol is used for decolorization. Most of the isolates produce Beta Lactamase (95%). Beta Lactamase enzyme facilitates the growth of Haemophilus influenzae and Streptococcus pneumoniae Beta-Lactamase-resistant cephalosporins (Cefixime or Cefuroxime), Amoxicillin-Clavulanic Acid, Macrolides, Tetracyclines or Quinolones are used in the treatment. Gram Negative Rods Glucose (+) Enteric gram negative rods (Enterobacteriaceae) Lactose (+) Glucose (-) Non-fermentative gram negative rods Lactose (-) Oxidase (+) Oxidase (-) Escherichia Serratia Pseudomonas Acinetobacter Klebsiella Shigella Burkholderia Stenotrophomonas Enterobacter Yersinia Citrobacter Salmonella Proteus Plesiomonas* Gram Negative Rods Enteric gram negative rods (Enterobacteriaceae) ✓ Glucose (+), Oxidase (-) Non-fermentative gram negative rods ✓ Glucose (-) Gram Negative Rods Enteric gram negative rods (Enterobacteriaceae) Lactose (+) ✓ Escherichia ✓ Klebsiella ✓ Enterobacter ✓ Citrobacter Lactose (-) ✓ Serratia ✓ Shigella ✓ Yersinia ✓ Salmonella ✓ Proteus ✓ Plesiomonas* ❑Enteric Gram Negative Rods (Enterobacteriaceae) The Enterobacteriaceae are a large, heterogeneous group of gramnegative rods whose natural habitat is the intestinal tract of humans and animals. All Enterobacteriaceae are potentially pathogenic. Patients who are immunosuppressed, undergoing mechanical or medical manipulation, and have underlying disease are most susceptible to infection Common features are that they multiply under both aerobic and anaerobic conditions and metabolize glucose and other sugars to form acid both oxidatively and in the absence of oxygen (fermentative) ❑Enteric Gram Negative Rods (Enterobacteriaceae) There are approximately 109 Enterobacteriaceae member per gram of feces. However, the predominant species in the gut is Bacteroides. Up to 15% of the population may harbour enterobacteria in the oral cavity, mostly as transient commensals. Sometimes it leads to reduced salivary flow (xerostomia). All species are endotoxigenic because of the LPS outer cell wall. They also possess pili (adhesion) and flagella (locomotion) ❑Enteric Gram Negative Rods (Enterobacteriaceae) Grow well on ordinary media (e.g., blood agar, MacConkey’s agar), producing characteristic circular, convex and glistening/mucoid colonies. Some species form swarming patterns on cultures. Most species are non-pigmented; a few produce red, pink, yellow or blue pigments. Enterobacteriaceae ferment a large number of carbohydrates. This property, together with other biochemical tests, is used to identify and differentiate species. ❑Enteric Gram Negative Rods (Enterobacteriaceae) They form circular, convex, smooth colonies with distinct edges. Enterobacter colonies are similar but somewhat more mucoid. Klebsiella colonies are large and very mucoid and tend to coalesce with prolonged incubation. Green metallic sheen on Eosin-Methylene Blue agar specific for E.coli ❑Enteric Gram Negative Rods (Enterobacteriaceae) Growth on indicator media is used for the initial categorization of Enterobacteriaceae into two groups: lactose fermenters and lactose non-fermenters. ❑Enteric Gram Negative Rods (Enterobacteriaceae) Species can be determined according to the carbohydrates they utilize and the H2S or acid they produce in Triple Sugar Iron (TSI) Agar (1:10:10=Glucose:Lactose:Sucrose) The normal color of the medium is pink-red. If your pink color turns yellow, it indicates that the bacteria is utilize a carbohydrate. The formation of air pocket in the medium indicates that the bacteria also produces gas while utilizing that carbohydrate. The formation of black precipitate in the medium indicates that the bacteria form H2S. ❑Enteric Gram Negative Rods (Enterobacteriaceae) Enterobacteriaceae have a complex antigenic structure. They are classified by O (lipopolysaccharide) antigens, K (capsular) antigens and H (flagellar) antigens. O antigens are the most external part of the cell wall K antigens are external to O antigens on some but not all Enterobacteriaceae. Some are polysaccharides, including the K antigens of E coli; others are proteins. H antigens are located on flagella. The determinants in H antigens are a function of the amino acid sequence in flagellar protein (flagellin) ❑Escherichia coli Motile, sometimes capsulate, facultative anaerobe, bile-tolerant. Commensal of the human intestinal tract Motile with the peritrichous flagella Infections are either endogenous or exogenous. Escherichia strains possess specialized virulence factors that can be placed into two general categories: adhesins and exotoxins. E. coli is a major agent of sepsis and can cause UTIs (simple urethritis to pyelonephritis) After surgery of the lower intestinal tract, it may cause neonatal meningitis, septicaemia and wound infection ❑Diarrheal diseases caused by E. coli These range from simple diarrhoea to severe disease leading to excessive fluid loss and dehydration, which may be fatal in malnourished infants and elderly debilitated adults. Many strains of enteropathogenic Escherichia coli have powerful toxins and other mechanisms by which they cause diarrhoea: Enterotoxins: Two types, one is heat-labile (LT) and the other is heat-stable (ST). Enteroinvasiveness: Some strains invades intestinal epithelial cells and cause inflammation. Adhesive factors: adhesion to mucosae Vero cytotoxicity is caused by strains that have the ability to induce cytopathic effects on Vero cells (grown in tissue culture). Verotoxin (VT) producers can cause diarrhoea with haemorrhagic symptoms ❑Diarrheal diseases caused by E. coli Diarrhea-causing Escherichia coli can be divided into five types: Enteropathogenic Escherichia coli (EPEC) ✓ Small intestine / Infant diarrhea Enteroinvasive Escherichia coli (EIEC) ✓ Large intestine / Fever, Cramping Enterotoxigenic Escherichia coli (ETEC) ✓ Small intestine / Traveler’s diarrhea Enterohaemorrhagic Escherichia coli (EHEC) ✓ Large intestine/ Initial watery diarrhea followed by grossly bloody diarrhea (hemorrhagic colitis) Enteroaggregative Escherichia coli (EAEC) ✓ Small intestine / Infant diarrhea ❑Sorbitol MacConkey It is used to distinguish O157:H7, which is considered the most pathogenic E.coli type because it produces Shiga-Like toxin, from other E.coli. All other E.coli strains can ferment sorbitol, while O157:H7 cannot E.coli that can ferment sorbitol (A) form pink colonies E.coli O157:H7 (B) forms colorless colonies on the medium. ❑Klebsiella Most strains have fimbriae and form a thick polysaccharide capsule that has an antiphagocytic effect and this capsule also responsible for the mucoid appearance of isolated colonies. Klebsiella have no flagella and are therefore non-motile When first grown, they form mucoid colonies on the medium. Klebsiella is resistant to all β-lactam antibiotics including the carbapenem The most commonly isolated members of the genus are K. pneumoniae and K. oxytoca, which can cause community-acquired or hospital-acquired pneumonia. ❑Klebsiella pneumoniae Klebsiella pneumoniae is present for the 5% in the respiratory tract and feces of normal individuals K. pneumoniae can cause pneumoniae in immunocompetent individuals. The most common nosocomial manifestations of Klebsiella infection are UTIs, pneumonia, severe soft tissue infections, and sepsis. In addition, Klebsiella can cause exacerbations of chronic bronchitis. The virulence of the organism is mainly due to its large antiphagocytic capsule ❑Other Klebsiella species Klebsiella oxytoca ✓ This species can cause a spectrum of diseases similar to that of K. pneumoniae (particularly nosocomial urinary tract infections) but is isolated much less frequently. Klebsiella aerogenes ✓ This species is also isolated as the causative agent of nosocomial infections at various localizations in immunocompromised patients. Klebsiella granulomatis ✓ It is the causative agent of chronic genital ulcers (donovanosis), which occurs particularly in the tropics and cannot be cultivated on artificial culture media. Klebsiella rhinoscleromatis ✓ It causes granulomatous disease of the nose Klebsiella ozaenae ✓ It is the cause of chronic atrophic rhinitis. ❑Enterobacter Enterobacter species are indigenous to the intestinal tract but can be found on plants and as free-living saprophytes They differ from the Klebsiella essentially by their flagellation, which gives them mobility. In addition, they form less capsule substance They may cause nosocomial urinary tract infection and very rarely a primary infection. E. cloacae and E. aerogenes are the most frequently isolated as transients in the oral cavity. ❑Serratia Representatives of the genus Serratia share many similarities with the genera Klebsiella and Enterobacter and are combined with them in the KES group. Serratia species are also similar to Klebsiella in terms of their demands on the culture medium and the range of diseases. They differ from all other Enterobacteria in their ability to produce three hydrolytic enzymes: DNase, gelatinase and lipase. ❑Serratia marcescens Serratia marcescens is a common opportunistic pathogen in hospitalized patients and they causes pneumonia, bacteremia, and endocarditis Only about 10% of isolates form the red pigment (prodigiosin) S. marcescens may also be found in the subgingival biofilm of teeth, especially in bedriddens. Due to this, and because S. marcescens produces prodigiosin, it may cause tooth discoloration. S. marcescens is often multiply resistant to aminoglycosides and penicillins Infections can be treated with third-generation cephalosporins ❑Shigella Shigellae are slender gram-negative, non-motile rods; coccobacillary forms occur in young cultures. They are facultative anaerobes but grow best aerobically. The natural habitat of Shigella is limited to the intestinal tracts of humans and other primates, where they produce bacillary dysentery. The genus is divided into four species (Shigella dysenteriae, Shigella sonnei, Shigella flexneri and Shigella boydii) Shigellae are non glucose fermenters, with the exception of Shigella sonnei (Lactose). Can degrade the phagolysosome complex ❑Shigella Fecal contamination of food and drinking water is of concern in developing countries. Shigella do not multiply in food. Convalescents and asymptomatic carriers are the only reservoirs of the pathogen. Shigella infections are almost always limited to the gastrointestinal tract (Shigellosis); bloodstream invasion is quite rare. Shigellae are highly communicable; the infective dose is 103 organisms ❑Shigella After passing through the stomach, the Shigella reach the small and large intestine. First, they multiply in the small intestine, where they reach high germ counts (107 microorganisms/ml). In the colon, they penetrate the intestinal wall and are taken up by the macrophages there. Using proteins secreted by a type 3 secretion system, they resist killing in the phagosome, replicate, and eventually lead to phagocytic cell death (apoptosis). ❑Shigella Shigellosis is characterized by abdominal cramps, diarrhea, fever, and bloody stools. The clinical signs and symptoms of the disease appear 1 to 3 days after the bacteria are ingested. Complications are; Dehydration, Seizures, Rectal prolapse, Hemolytic uremic syndrome, Toxic megacolon, Reactive arthritis, Bloodstream infections Treatment: Rehydration and Antibiotics (Ciprofloxacin, ampicillin, doxycycline or trimethoprim–sulfamethoxazole) ❑Salmonella Gram-negative, motile, non-spore-forming rods. All except Salmonella Typhi are non-capsulate Salmonellae grow readily on simple media, but they almost never ferment lactose or sucrose. Salmonellae are often pathogenic for humans or animals when acquired by the oral route. They are transmitted from animals and animal products to humans, where they cause enteritis, systemic infection, and enteric fever They are resistant to certain chemicals (eg, brilliant green, sodium tetrathionate, sodium deoxycholate) that inhibit other enteric bacteria Can live inside the phagolysosome complex ❑Salmonella There are two species, Salmonella enterica and Salmonella bongori. Salmonella enterica is divided into various serogroups according to O and H antigens. Organisms may lose H antigens and become nonmotile. Loss of O antigen is associated with a change from smooth to rough colony form. Vi antigen may be lost partially or completely. Antigens may be acquired or lost via transduction ❑Salmonella The major types of salmonellosis are enteric fever, enterocolitis and bacteremia with focal lesions. Infectious dose is 106 CFU/mL Infections therefore usually occur after the bacteria multiply in contaminated food. Salmonella Typhi produces a febrile illness called enteric (typhoid) fever. A milder form of this disease, referred to as paratyphoid fever, is produced by Salmonella Paratyphi Gastroenteritis: The most common form of salmonellosis, and can be due to any of the Salmonella enteritidis serotypes Bacteremia: Frequently caused by Salmonella dublin or Salmonella choleraesuis. After oral infection, there is early invasion of the bloodstream ❑Yersinia The genus Yersinia includes Yersinia pestis (the cause of plague) Y. enterocolitica and Y. pseudotuberculosis (enteric pathogens that are relatively uncommon) and several others considered nonpathogenic for human ❑Yersinia All Yersinia infections are zoonotic Humans are the accidental hosts. Humans usually get plague after being bitten by a rodent flea that is carrying the plague bacterium or by handling an animal infected with plague Urban Cycle is maintained in rat populations and is spread among rats or between rats and humans by infected fleas. In contrast, Sylvatic Cycle is difficult or impossible to eliminate because the mammalian reservoirs and flea vectors are widespread ❑Yersinia The two clinical manifestations of Y. pestis infection are bubonic plague and pneumonic plague. Bubonic plague 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 in the groin or axilla. Bacteremia develops rapidly if patients are not treated, and as many as 75% die. Initial symptoms of the pneumonic plague are fever and malaise, and pulmonary signs develop within 1 day. The patients are highly infectious; person-to-person spread occurs by aerosols. The mortality rate in untreated patients is 90%. ❑Proteus Proteus is a genus of Gram-negative Proteobacteria. They show swarming motility on an agar plate Proteus bacilli are widely distributed in nature as saprophytes, being found in decomposing animal matter, sewage, manure soil, the mammalian intestine, and human and animal feces. Proteus species produce infections in humans only when the bacteria leave the intestinal tract. They are opportunistic pathogens, commonly responsible for urinary and septic infections, often nosocomial. Most commons are P. vulgaris and P. mirabilis ❑Proteus Proteus vulgaris is a rod-shaped, nitrate-reducing, indole-positive and catalase-positive, hydrogen sulfide-producing, Gram-negative bacterium that inhabits the intestinal tracts of humans and animals By making the urine alkaline through urease enzymes, it has a toxic effect directly on the kidney tubules and causes stone formation. About 10–15% of kidney stones are struvite stones, caused by alkalinization of the urine by the action of the urease enzyme of Proteus species P. vulgaris known to cause wound infections ❑Citrobacter Citrobacter is a genus of Gram-negative coliform bacteria in the family Enterobacteriaceae. The species C. amalonaticus, C. koseri, and C. freundii can use citrate as a sole carbon source Citrobacter species can cause urinary tract infections and sepsis principally among debilitated hospitalized patients. Citrobacter freundii can cause enteritis by producing plasmid-encoded heat-stable enterotoxin or phage-induced Shiga toxin. In addition, Citrobacter koseri has been associated with meningitis and brain abscesses in infants less than 2 months of age. Bacteria Nitrofurantoin Polymyxin B, Colistin Tigecycline Tetracycline Cefuroxime Cefoxitin Cefazolin, Cephalothin, Cephalexin, Cefadroxil Ticarcillin Ampicillin-Sulbactam Amoxicillin Clavulanic acid Ampicillin ❑Unexpected phenotypes Gram Negative Rods Non-fermentative gram negative rods Oxidase (+) ✓ Pseudomonas ✓ Burkholderia Oxidase (-) ✓ Stenotrophomonas ✓ Acinetobacter ❑Pseudomonas Pseudomonas and related nonfermentative rods are opportunistic pathogens of plants, animals, and humans. P. aeruginosa is frequently present in small numbers in the normal intestinal flora and on the skin of humans, and is the major pathogen of the group ❑Pseudomonas aeruginosa P. aeruginosa is motile, rod-shaped, gram-negative bacteria It occurs as single bacteria, in pairs, and occasionally in short chains P. aeruginosa is an obligate aerobe that grows readily on many types of culture media, sometimes producing a sweet or grape-like odor. Can contaminate disinfectants Can grow at 42°C It forms smooth round colonies with a fluorescent greenish color. Often isolated from Cystic Fibrosis (CF) patients Causes treatment-resistant infection in CF patients by producing alginate Piperacillin + Tazobactam is used in the treatment ❑Pseudomonas aeruginosa P. aeruginosa often produces the nonfluorescent bluish pigment pyocyanin, which diffuses into the agar. Many strains of P. aeruginosa also produce the fluorescent pigment pyoverdin, which gives a greenish color to the agar. Some strains produce the dark red pigment pyorubin or the black pigment pyomelanin Pigmented strains may cause tooth discoloration ❑Pseudomonas aeruginosa Pulmonary infections: range from mild irritation of the bronchi (tracheobronchitis) to necrosis of the lung parenchyma (necrotizing bronchopneumonia) Primary skin infections: opportunistic infections of existing wounds to localized infections of hair follicles Urinary tract infections: opportunistic infections in patients with indwelling urinary catheters and after exposure to broad-spectrum antibiotics Ear infections: can range from mild irritation of external ear (“swimmer’s ear”) to invasive destruction of cranial bones adjacent to the infected ear Eye infections: opportunistic infections of mildly damaged corneas Bacteremia: dissemination of bacteria from primary infection to other organs and tissues; can be characterized by necrotic skin lesions ❑Burkholderia Aerobic, straight or slightly curved, non-spore forming rods. Catalase (+), Lactose (-) Species that infect humans are Burkholderia cepacia, B. mallei, B. pseudomallei It can be isolated from CF patients. Responsible for the rapid deterioration of lung function in these individuals Its incidence is high in Chronic Granulomatous Disease (Phagocyte Ox defect) All species, except B. mallei, are motile It was formerly classified in the genus Pseudomonas. ❑Burkholderia May require selective media to differentiate from Pseudomonas (for B. cepacia; PC, OFPBL, BCSA, for B. pseudomallei; Ashdown medium) Cannot grow at 42°C Clinical strains can survive in macrophages, environmental strains cannot It is intrinsicly resistant to most antibiotics used in gram-negative bacterial infections. Meropenem, TMP-SXT, Chloramphenicol or Minocycline are used in the treatment of B. cepacia. ❑Stenotrophomonas Gram-negative rods in straight or slightly curved morphology that do not form spores, can be found singly or in pairs Can be found in environmental sources It can grow between 5-40°C. Catalase, Lysine decarboxylase DNase (+), Lactose (-) Polar flagella are present Can grow on most routinely used media Forms Lavender-Green colonies ❑Stenotrophomonas In experimental models, it has been observed that sepsis may not develop even if the bacteria are injected IV. In case of coinfection, it may act synergistically with other bacteria. Due to its low pathogenicity, it is common in people undergoing mechanical ventilation in the ICU. Intrinsicly resistant to most antibiotics and disinfectants, including carbapenems Sensitive to TMP-SXT Not using foreign body implants for a long time is one of the most important prevention methods. ❑Stenotrophomonas ❑Acinetobacter It is smaller than other gram-negative rods. Indole (-), Catalase (+), non-motile Some strains may stain as gram-positive as they may be resistant to decolorization. During the logarithmic phase may be seen as rod, and during the stationary phase may be seen as cocci It can be confused with the genus Neisseria because it appears as diplococcus in its cocci form. Multiple drug resistance is common in Acinetobacter baumanii New generation antibiotics are usually tried in the treatment. Can be treated with colistin ❑Acinetobacter Acinetobacter baumanii can be seen in oral biofilms Subgingival colonization increases risk of refractory periodontitis A. baumannii has a significantly higher prevalence in patients with chronic or aggressive periodontitis A. baumannii infection originated from oral lesions may be associated with bacteremia and fatal outcome in oncologic pediatric patients Cellulitis in the orofacial region Bacteria Polymyxin B, Colistin Tigecycline Tetracycline Fosfomycin Trimethoprim Aminoglycoside Cefotaxim Ceftriaxone Ceftazidime Cefepime Aztreonam Ertapenem Imıpenem Meropenem Ciprofloxacin Chloramphenicol Piperacillin-Tazobactam Cefazolin, Cephalothin, Cephalexin, Cefadroxil Piperacillin Ticarcillin-Clavulanate Ticarcillin Ampicillin-Sulbactam Amoxicillin-Clavulanic acid Ampicillin ❑Unexpected phenotypes ❑External Tooth Discoloration It can be caused by poor oral hygiene, the use of iron preparations, or by chromogenic bacteria that settle on the teeth. It can occur in both primary teeth and permanent teeth. It is more common in the upper jaw anterior teeth, which are less affected by the washing effect of saliva. The most common discoloration is black. It can also be in red, orange, green or blue colors. May cause social and psychological problems ❑Black Discoloration It can also be seen in children with good oral hygiene and low caries incidence. The black colored material is formed as a result of the interaction of hydrogen sulfide produced by bacteria and iron in saliva or gingival fluid. Usually caused by Actinomyces, Prevotella, Porphyromonas ❑Green Discoloration Green discolorations are thick, tightly adhered band-shaped formations, usually on the lip surface of the maxillary primary incisors. Among the chemical components of this coloration are aluminum, barium, nickel, copper, boron, strontium and potassium. Primary cause is Pseudomonas aeruginosa ❑Orange-Yellow Discoloration Occurs on the lip surface of the incisors close to the gingivaOften seen in children with poor oral hygiene Primary causes are Serratia marcescens, Flavobacterium lutescens ve Micrococcus roseus. It may also caused by Sarcina rosea, Bacillus roseus, Bacillus prodigieus ❑Blue Discoloration Seen rarely Usually caused by P. aeruginosa Top: Lactose and Sucrose Bottom: Glucose 21.02.2024 Bacteriology-3 Dogukan Ozbey, Lecturer Medical Faculty, Department of Medical Microbiology [email protected] Gram Negative Comma or Spiral Shaped Bacteria Vibrio Campylobacter Helicobacter Spirillum ❑Vibrio Vibrio species are small (0.5 to 1.5 to 3 μm), curved, gram-negative rods Their natural habitat is water. The main symptom of cholera is watery diarrhoea that can be fatal as a result of severe dehydration Most vibrios have polar flagella and pili All strains possess lipopolysaccharides consisting of lipid A (endotoxin), core polysaccharide, and an O polysaccharide side chain. V. cholerae O1 and O139 produce cholera toxin and are associated with epidemics of cholera ❑Vibrio ❑ Clinical Outcomes Vibrio cholerae Cholera: it begins with an abrupt onset of watery diarrhea and vomiting and can progress to severe dehydration, metabolic acidosis and hypokalemia, and hypovolemic shock. Gastroenteritis: milder forms of diarrheal disease can occur in toxin-negative strains of V. cholerae O1 and in non-O1 serotypes. Vibrio parahaemolyticus Gastroenteritis: it is generally self-limited, with an explosive onset of watery diarrhea and nausea, vomiting, abdominal cramps, headache, and low-grade fever. Wound infection: it is associated with exposure to contaminated water. Vibrio vulnificus Wound infection: severe, potentially fatal infections characterized by erythema, pain, bullae formation, tissue necrosis, and septicemia. ❑Vibrio cholerae Virulence factors Cholera Toxin→Hypersecretion of electrolytes and water Toxin coregulated pilus→Surface binding site receptor for bacteriophage CTXΦ; mediates bacterial adherence to intestinal mucosal cells Chemotaxis protein→Adhesin factor Accessory cholera enterotoxin→Increases intestinal fluid secretion Zonula occludens toxin→Increases intestinal permeability Neuraminidase→Modifies cell surface to increase GM1 binding ❑TCBS (Thiosulfate-Citrate-Bile Salts-Sucrose) Agar TCBS Agar is used for the selective isolation of Vibrio cholerae and other enteropathogenic vibrios. Thiosulfate and sodium citrate, as well as the alkalinity of the medium, considerably inhibit the growth of Enterobacteria Bromthymol Blue is used as a pH indicator On this medium, Vibrio cholerae forms yellow colonies, and other Vibrios form green colonies. ❑Campylobacter The genus Campylobacter consists of small (0.2 to 0.5 μm wide and 0.5 to 5.0 μm long), motile, comma- or seagull-shaped, gram-negative rods They require microaerophilic conditions ( sacral ganglia A latent infection is established in the nervous tissue 35 36 Herpes Simplex Viruses Clinical Syndromes HSV can cause significant morbidity and mortality on infection of the eye or brain and on disseminated infection of an immunosuppressed person or a neonate. In the classic manifestation, the lesion is a clear vesicle on an erythematous base (“dewdrop on a rose petal”) and then progresses to pustular lesions, ulcers, and crusted lesions Winding Winding HSV 1 and HSV 2 are painful, benign lesions and recurrent hst. creates 37 Herpes Simplex Viruses Oral Herpes Primary infection is usually asymptomatic; If symptomatic, it is seen as gingivostomatitis in children and pharyngotonsillitis in adults. Secondary infection is herpes labialis. Herpetic keratitis _ Always limited to one eye, dendritic ulcer, cause recurrent disease, leading to permanent scarring and blindness Herpetic whitlow is an infection on the finger often occurs in nurses or physicians who attend patients with HSV infections, in thumb-sucking children Eczema herpeticum İs acquired by children with active eczema Genital Herpes Usually with HSV-2 (10% cases HSV-1) ; painful genital vesicle, ulcer Transient viremia occurs ( fever, myalgia ,glandular inflammation ) Herpes encephalitis usually caused by HSV- 1 and seen one of the temporal lobes most common cause of the sporadic viral encephalitis 38 Herpes neonatorum often fatal, usually HSV-2 ; contagious vaginal canal at birth (A) Primary herpes gingivostomatitis. Site of viral latency: trigeminal ganglia (B) Herpes simplex virus establishes latent infection and can recur from the trigeminal ganglia. Transport along peripheral sensory nerves Site of active lesion: virus replication in the epithelium 39 Herpes gladiatorum Contracted by wrestlers Spreads by direct contact from skin lesions Usually appears in the head and neck region Also seen in other contact sports such as rugby (Herpes rugbeiorum, or scrum pox) ) 40 41 Herpes Simplex Viruses Diagnosis: Tzanck smear is made with scraping from the vesicle base of lesion : stained with Giemsa or Wright stain Cytopathic effects include; Syncytia, ballooning cytoplasm and Cowdry type A intranuclear inclusions Ballooned cells Multinucleated giant cell 42 The three types of inclusion bodies: Cowdry A ( long arrow), fulltype ( intermediate length arrow) and smudge-type (short arrow) are identified in the affected tubules ( hematoxylin -eosin stain, magnification x40). 43 HSV Laboratory Diagnosis Approach Test/Comment Direct microscopic examination of cells from base of lesion (Tzanck smear) Multinucleated giant cells and Cowdry type A inclusion bodies in cells Cell culture Identifiable cytopathologic effect in most cell cultures Assay of tissue biopsy, smear, cerebrospinal fluid, or vesicular fluid for HSV antigen or genome Enzyme immunoassay, immunofluorescent stain, in situ DNA probe analysis, or PCR HSV type distinction (HSV-1 versus HSV-2) Type-specific antibody, DNA probe analysis, and PCR Serology Serology is not useful except for epidemiology 44 HSV Treatment Nucleoside Analogs Acyclovir valacyclovir penciclovir famciclovir Antiviral drugs are ineffective against latent virus 45 Varicella Zoster Virus (VZV) Only nfects humans. VZV causes chickenpox (varicella) and, on recurrence, causes herpes zoster (shingles) Varicella: VZV is extremely communicable; the disease is spread principally by the respiratory route but may also be spread through contact with skin vesicles.. Infects the upper respiratory mucosa ; spread to the skin through the blood and become vesicular creates a rash. Childhood examtem ; skin lesions are macule , papule , vesicle, pustule Unlike smallpox, varicella rash shows polymorphism, so lesions at all stages can be seen simultaneously and ** Rash is more prevalant on the trunk than extremities The virus becomes latent in the dorsal root, cranial nerve,and other ganglia after the priary infection.. 46 Droplets Respiratoy tract Lymphatics Liver, spleen, reticuloendothelial system, T cells Fever, malaise, headache Vesicle progression Macules Papules Vesicles Pustules Crusts Skin Mucous membrane Latency in neuron Mechanism of spread of varicella-zoster virus (VZV) within the body. VZV initially infects the respiratory tract and is spread to the reticuloendothelial system and T cells and then by cell-associated viremia to the skin. 47 Varicella Zoster Virus (VZV) Shingles ( herpes zoster ): The virus can be reactivated in older adults when immunity decrease or in patients with impaired cellular immunity Herpes zoster is a recurrence of a latent varicella infection acquired earlier. Severe pain in the area innervated by the nerve and chickenpox-like lesions are seen. The rash is limited to a dermatome. Ramsay Hunt's syndrome (herpes zoster oticus) Reactivation of latent VZV in the N facialis geniculate ganglion; acute peripheral facial paralysis, vesicular in the auricle and external auditory canal rash, severe ear pain 48 49 Varicella Zoster Virus (VZV) Diagnosis : – Tzanck smear shows multinucleated giant cells and intranuclear Cowdry A inclusions. – PCR , serology Treatment: Adult, immunosuppressed , Children do not need treatment. Local and systemic acyclovir , valacyclovir a live attenuated vaccine for the prevention of chickenpox. Immunosuppressed VZIg ( immunoglobulin ) may be given. 50 Epstein Barr Virus (HHV-4) It is usually transmitted by saliva; kissing disease enveloped virus that infects only humans. Tissue tropism : EBV, C3d complement for cell entry uses its receptor (CR2; CD21 ); ( therefore infect only certain cell types) can) These receptors – In B lymphocytes – Some oropharynx and nasopharynx located on the surface of epithelial cells İnfection begins in epithelial cells of the oropharynx and nasopharynx,, B lymphocyte it reproduces the feature of continuous reproduction ( immortal cell ). Have four important antigens: early antigen, membrane antigen, viral capsid antigen (VCA), nuclear antigen (EBNA) 51 Pathogenesis of Epstein-Barr virus (EBV). EBV is acquired by close contact between persons through saliva and infects B cells. Resolution of the EBV infection and many of the symptoms of infectious mononucleosis result from activation of T cells in response to theinfection. Resolution/Latency Liver EBV in saliva B cells and epithelial cells of oropharynx B-cell activation Lymph nodes Spleen T-cell activation Swelling Malaise Shedding in saliva Pharyngitis Heterophile antibody Atypical lymphocytes (Downey cells) 52 Progression of EBV Infection : Infection can result in lytic , latent , and immortal infection patterns that can be distinguished by the expression of different viral proteins and antigens. T cells limit the proliferation of EBV- infected cells and perpetuate latent infection. 53 Epstein-Barr Virus Diagnosis 1. Symptoms a. Mild headache, fatigue, fever b. Triad : lymphadenopathy , splenomegaly , exudative pharyngitis c. Other : hepatitis, rash due to ampicillin 2. complete blood cell count a. hyperplasia b. atypical lymphocytes ( Downey cells, T cells ) 3. Heterophilic antibody (temporary ): ( monospot -Paul Bunnel Test; Differentiation from 4. EBV-antigen-specific antibody VCA IgM is most commonly used in the diagnosis of acute infection. Immunity diagnosis with VCA IgG 5. Genome detection by PCR 54 Ebstein Barr Virus (HHV-4) Heterophile Antibody–Positive Infectious Mononucleosis Endemic Burkitt lymphoma , Hodgkin's disease , Nasopharyngeal carcinoma, Epstein-Barr Virus–Induced Lymphoproliferative Diseases Hairy Oral Leukoplakia HIV (+)patients Treatment : There is no 55 INFECTIOUS MONONUCLEOSIS : In peripheral blood smear, the cytoplasm is large, blue and lymphocyte ( downey cell ) adhered around the erythrocytes 56 Cytomegalovirus (CMV / HHV-5) CMV has the largest genome of the HHVs CMV replicates only in human cells. Fibroblasts, epithelial cells, granulocytes, macrophages, and other cells are permissive for CMV replication. The histologic hallmark is: the cytomegalic cell, which is an enlarged cell that contains a dense, central, “owl’s eye,”basophilic intranuclear inclusion body** Transmission occurs via blood, organ transplants, and all secretions (urine, saliva, semen, cervical secretions, breast milk, and tears). Heterophile-negative mononucleosis syndrome. Congenital Infection (CMV is the most prevalent viral cause of congenital disease. Transmission via Transfusion and Transplantation Infection in the Immunocompromised Host pneumonia, retinitis (HIV) 57 CMV establishes latency in hematopoietic stem cells and monocytes Virus reactivates on – immune suppression ( corticosteroids , HIV inf ) – allogeneic stimulation ( host response to transfused or transplanted cells). CMV is released sporadically throughout life Cell-mediated immunity is required for resolution and maintenance of latency There are escape mechanisms from the immune system: Since viral antigens are not expressed on the cell surface, they are not killed by Cytotoxic T cells. DIAGNOSIS : owl eye inclusion, virus culture, PCR CMV DNA, viral antigen ( pp65 ) and antibody search; CMV IgM positivity or quadruple increase in IgG every two weeks (acute inf ); IgG avidity test in pregnant women. TREATMENT: ganciclovir , foscarnet CMV Inf. owl-eye view with da HE staining 58 Glycoprotein B: fusion Glycoprotein H: adhesion Human Herpes Virus Type-6 (HHV-6 ) Similar to CMV, HHV-6 is lymphotropic Transmitted in saliva Sixth disease in children ( Exanthema subitum - Roseola infantum ) is the caused by HHV-6 or HHV-7 fever decreases, maculopapular rash appears Human Herpes Virus Type-7 (HHV-7) It is a virus that infect T lymphocytes, such as HHV-6 Exanthema subitum - Roseola infantum It is considered as another factor of. 59 Human Herpes Virus Type-8 ( HHV-8) Kaposi 's Sarcoma Associated Herpesvirus Kaposi sarcoma ( opportunistic disease in AIDS ; vascular endothelial cell malignancy ; dark purple lesions mostly on the skin ) Primary effusion lymphoma (a rare B-cell lymphoma) Multicentric Castleman disease Main target is B lymphocytes and endothelium (like EBV) 60 Adenovirus Non-enveloped, icosahedral , linear dsDNA in the capsid structures called penton (cell toxicity ) , hexone and fiber (tropism). These are the major antigens of the virus. Fibers emerge from the penton ( capsid ): the only virus with a fiber ridge** Capsid virus is resistant to inactivation by gastrointestinal tract , drying, and detergents. It is infective between pH 2-9. Causes lytic ( mucoepithelial cells etc. ), latent ( macrophage , T lymph, adenoid cell. etc ), transforming ( hamster, not human) infections Transmission: direct contact, fecal -oral, respiratory droplets, fomites Epidemics in crowded areas. Respiratory infections , pharyngoconjunctivitis (pink eye), hemorrhagic cystitis, gastroenteritis Diagnosis: It is made by showing virus antigen , antibodies or viral DNA. Treatment: There is no specific treatment, symptomatic treatment is done. Prevention: Handwashing and chlorination of swimming pools Administer Live attenuated oral vaccine: can be administered to soldiers.. 61 PAPOVAVIRIDAE Papillomavirus and Polyomaviruses _ Pa pillomavirus Polyomavirus _ Simian vacuolating virus Small, non-enveloped, icosahedral, ds DNA viruses 62 Human Papilloma Virus (HPV) Non-enveloped , small viruses, icosahedral capsid. The only known host is humans. They cause latent infection. Transmission; direct contact ,sexual contact from mother to baby during birth or, shared use of objects; STDs. HPV causes cervical cancer ! High-risk HPV types (e.g., HPV-16, HPV-18) can initiate the development of cervical carcnoma and oropharyngeal, esophageal, penile, and anal cancers. HPV types 16 and 18 are responsible for 70% of cervical cancers ! It causes localized infections of the skin and mucous membranes: Skin warts , anogenital warts ( condyloma acuminatum ) , cervical dysplasia , laryngeal papilloma , oral wart, conjunctival infections 63 Human Papilloma Virus (HPV) DIAGNOSIS: PAP smear , Molecular methods Treatment: Burning warts with cryotherapy , 5FU, cidofovir with local ted. Liquid nitrogen is used for skin warts. Protection: Recombinant vaccine is administered.** 64 Polyomaviruses non-enveloped , icosahedral symmetrical capsid , latent inf BKV: JCV: It is in this group. close contact, breathing is transmitted by the oral and perinatal routes. Diagnosis: PCR, ELISA and IFA are used. Treatment: No specific treatment, recovery of immunosuppression is sufficient. 65 Parvoviruses The Parvoviridae are the smallest of the deoxyribonucleic acid (DNA) viruses. 18-26 nm , non-enveloped , icosahedral capsid, singlestranded ssDNA parvoviruses They are the smallest single- stranded DNA viruses with a genome. Only Parvovirus B19 causes disease in humans. replication takes place in the nucleus. Bone marrow erythroid series precursors are target cells (lytic enf ): rash and arthralgia Parvovirus B19 and Human Boca virus It is transmitted via droplet route and oral secretions , parenteral (factor transfusion) and placenta. 66 parvoviruses Erythema infectiosum (fifth disease) Parvovirus slapped-cheek appearence in children Aplastic crisis in persons with chronic anemia Non-immune hydrops fetalis : crosses the placenta , risk of fetal loss fetal infections, meningitis, myocarditis , hepatitis Diagnosis : Clinical findings are sufficient. Anti B19 IgM in serological diagnosis ; PCR is used. Treatment: No specific treatment , 5. Disease / Slapped cheek appearance: Parvovirus B19 67 PRIMARY HEPATOTROP VIRUSES Viral hepatitis agents: mainly HAV, HBV, HCV, HDV, HEV and new viruses HFV, HGV, TTV ( transfusion transmitted virus) and It is Sen-V. These viruses cause infection, inflammation and damage to the liver ; icteric symptoms and an increase in liver enzymes. They differ considerably in their structure, replication, transmission routes and in the time course and sequelae of the disease they cause. (A and E fecal -oral route , B, C, D parenteral route, HAV and HEV does not cause chronic liver disease, HBV and HCV be able to) 68 HEPATITIS VIRUSES 69 Hepatitis A Virus (HAV) Picornaviruses ( enterovirus 72) Non-enveloped, icosahedral capsid positive sense ssRNA Virus can be transmitted via the fecal-oral* route: ** – Ingestion of contaminated food and water – shellfish from contaminated water – dirty hands (food handlers, day-care workers, children). Transmission with blood, blood products or mother to baby very rare. HAV is resistant to detergents, acid (pH of 1), and temperatures as high as 60°C, and it can survive salt water; (inactivated by chlorine) Enters the blood circulation through the oropharynx and small intestine mucosa; replicates in hepatocytes then released into the bile and excrete stool Does not cause chronic liver disease and rarely causes fatal disease. (Not associated with hepatic cancer) 70 Hepatitis A Virus (HAV) İmmun mediated damage Symptoms occur abruptly 15-50 days after exposure; İnitial symptoms include fever, fatigue, nausea, vomiting The icteric phase indicated by jaundice, dark urine (bilirubinuria), pale stool Recovery 71 Hepatitis A Virus (HAV) The virus spreads readily in a community Groups at high risk for HAV infections: – People in overcrowded, unsanitary areas (day-care centers.etc) – Travelers to high-risk regions Laboratory Diagnosis: Serology : most reliable Anti-HAV IgM positivty in acute infection* (ELISA) Anti HAV IgG : Past infection lifelong immunity* Molecular: PCR 72 Hepatitis A Virus (HAV) Protection Oral- fecal precautions for water contamination , personal hygiene rules* Passive immunization: after exposure within 2 weeks standardimmune globulin (HSIG) Active immunization: Two doses of vaccine (six months apart) are administered. Not for children under 1 year old. Who should be vaccinated against Hepatitis A? Children All children aged 12–23 months Unvaccinated children and adolescents aged 2–18 years People at increased risk for HAV infection International travelers Men who have sex with men People who use injection or noninjection drugs (all those who use illegal drugs) People with occupational risk for exposure People who anticipate close personal contact with an international adoptee People experiencing homelessness 73 Unique Features of Hepadnaviruses Virus has enveloped virion containing partially doublestranded, circular DNA genome. Replication is through an overlapping circular RNA intermediate. Virus encodes and carries a reverse transcriptase. Virus encodes several proteins (HBsAg [L, M, S]; HBe/HBc antigens) that share genetic sequences but with different in-frame startcodons. HBV has a strict tissue tropism to the liver. HBV-infected cells produce and release large amounts of HBsAg particles lacking DNA. The HBV genome can integrate into the host chromosome. 74 Hepatitis B Virus (HBV) Hepadnavirus , DNA virus, enveloped 42 nm, partially double-stranded circular DNA , icosahedral genome The virions are unusually stable for an enveloped virus; they resist treatment with ether, low pH, freezing, and moderate heating. (important for transmission and disinfection). Hepatitis-B virion It is called Dane particle. The viral genome consists of S, C, P and X gene regions. – S gene region: encodes HBs Ag (surface proteins) – C gene region: encodes HBcAG (core antigen) and HBeAg ( precore antigen ) – P gene region: encodes viral DNA polymerase – X gene region: HBxAg protein (oncogene ) codes. Transmission: Sexual, parenteral and perinatal routes*** Contaminated blood&blood components tx (reduced donor screening programmes),*needle sharing,tattoo, close personel contact (semen, saliva, vaginal secretion exchange) medical personnel (accidental) sexual contact, perinatal (from mother to baby), body secretions horizontal (family) 75 transmission Hepatitis B Virus (HBV) Pathogenesis :Replication of hepatitis B virus (HBV). 1. After entry into the hepatocyte and uncoating of the nucleocapsid core, the partially double-stranded deoxyribonucleic acid (DNA) genome is delivered to the nucleus and completed. 2. Transcription of the genome produces four messenger RNAs (mRNAs), including an mRNA larger than the genome 3. The mRNA then moves to the cytoplasm and is translated into protein. 4. Core proteins assemble mRNA, and negative-sense DNA is synthesized by a reverse transcriptase activity in the core. 5. The ribonucleic acid (RNA) is then degraded while a positive-sense (+) DNA is synthesized. 6. The filled core associates with HBsAg-containing endoplasmic reticulum membranes, is enveloped before completion of the positive-sense DNA, and is then released by exocytosis with HBsAg-containing particles. 7. Cell-mediated immunity and inflammation are responsible for causing the symptoms and effecting resolution of the HBV infection by eliminating the infected hepatocyte. 8. Necrosis (ground glass) develops in liver parenchyma cells. The virus itself does not harm the liver, the cause of liver damage is hepatocytes destruction by cytotoxic T cells. Eight genotypes from A to H and D is the most common (95%) genotype in Turkey 76 Hepatitis B Virus (HBV) Acute hepatitis develops after about 30-100 days of incubation. It can be asymptomatic , icteric or anicteric course. 90% cases heal; 10% become chronic enfection Weakness, nausea, vomiting, yellowing of the sclera and body, tea-colored urine, diarrhea, increased transaminase levels are seen. Immune complex rxn: (urticaria, arthritis, glomerulonephrits, PAN ) in acute hepatitis. Supportive therapy. In chronic hepatitis, interferon alpha + antiviral ( lamivudine, adefovir etc.) 77 HBsAg : The surface antigen found in the envelope. The first to appear Ag. Anti HBs: stays for life ; immune indicator HBeAg : shows replication and infectivity. It appears in the blood shortly after HBsAg. HBV DNA: The most reliable indicator of replication. * HBcAg (core antigen): It is not found in blood, it is found only in hepatocytes. It cannot be detected serologically in serum. Anti- HBc IgM Acute HBV inf. indicator; diagnosis during the window period** Anti- HBc IgG : is not protective, it only shows that it has encountered the agent. 78 DIAGNOSIS Serological tests are very important. PCR HBV-DNA. https://www.cdc.gov/hepatitis/hbv/interpretationOfHepBSerologicResults.htm 79 Protection 1. Pre-contact prevention with HBV a) non-specific protection Universal blood body fluid precaution Screening blood and blood products for HBsAg Sterilization and disinfection b) Specific Protection Active immunization : Vaccine. HBV immunoglobulin ( HBIG) 2. Protection after exposure to HBV a) Babies born to HBV (+) mothers  HBIG+ vaccine (first 12 hours). Vaccination protocol is completed (0-1-6. months) b) Needle injury (parenteral contact) – healthcare personnel notification. Anti HBs negative: HBIG + vaccine in the first 48 hours ** then vaccination protocol is completed (0-1-6 months ) In the vaccinated individual, the protective antibody titer is checked; reminder dose? 80 Hepatitis C Virus (HCV) HCV is the only member of the Hepacivirus genus of the Flaviviridae family. Enveloped, positive-sense RNA genome There are seven different genotypes (types 1-7). Most common HCV- genotype in Turkey is 1b The genome of HCV encodes 10 proteins, including two glycoproteins (E1, E2) Structural proteins are Nucleocapsid (cor, C), and envelope (E1 and E2) glycoproteins The fastest changing gene is E2 non-structural (NS) proteins The viral RNA-dependent RNA polymerase is error prone and generates mutations in the glycoprotein and other genes. This generates antigenic variability and antiviral drug resistance and vaccine development diffuculty 81 HCV Transmission: HCV is transmitted primarily and efficiently in infected blood and less efficiently sexually. ** In blood, semen, and vaginal secretions (HBV: saliva and mother’s milk) Risk groups: High risk: Intravenous drug abusers and tattoo recipients are at the highest risk of acquiring HCV infection. Screening procedures have led to a reduction in the levels of transmission by blood transfusion and organ donation Babies born of HCV-positive mothers are also at increased risk for infection and hemodialysis healthcare personnel (needlstick injury) Clinical Syndromes HCV causes three types of disease (1) acute hepatitis with resolution of the infection and recovery in 15% of cases, (2) chronic persistent infection with possible progression to disease much later in life for 70% of infected persons, and (3) severe rapid progression to cirrhosis in 15% of patients The most important complications of chronic hepatitis C are cirrhosis and hepatocellular carcinoma (HSK ) ** 82 HCV Diagnosis The diagnosis and detection of HCV infection are based on ELISA recognition of anti-HCV antibody or detection of the RNA genome. ELISA: Anti-HCV (not indicate recovery) PCR: HCV-RNA Treatment PEG IF+Ribavirin Prevention Prevent transmission NO vaccine : due to genetic and antigenic variability 83 Hepatitis D Virus (HDV) HDV RNA genome is very small Single-stranded, defective RNA virus The genome is surrounded by the delta antigen core, which, in turn, is surrounded by an HBsAg-containing envelope. The delta agent can replicate and cause disease only in people with active HBV infections. Because the two agents are transmitted by the same routes, a person can be coinfected with HBV and the delta agent. A person with chronic HBV can also be superinfected with the delta agent. The delta agent exacerbates the HBV disease. 84 Hepatitis D Virus (HDV) Parenteral (in blood), sexually transmitted, and perinatally. Acute ( coinfection , superinfection , fulminant hepatitis), chronic or latent infection may develop. If infection develops at the same time (HBV+HDV) , it is called coinfection , If it is added to the existing HBV infection, it is called superinfection More rapid, severe progression occurs in HBV carriers superinfected with HDV than in people co-infected with HBV and the delta agent 85 Hepatitis D Virus (HDV) DIAGNOSIS ELISA  anti - Delta IgG and IgM , HDAg RT-PCR Demonstration of HDV-RNA Anti-HBc IgM (if positive, coinfection) test is performed to distinguish between coinfection and superinfection. TREATMENT: Support + close monitoring PROTECTION: HDV decreases with HBV vaccination. 86 Hepatitis E Virus (HEV) HEV (the E stands for enteric or epidemic) is predominantly spread by the fecal-oral route, especially in contaminated water. with a positive-strand RNA genome and naked capsid structure. it is most problematic in developing countries. The symptoms and course of HEV disease are similar to those of HAV disease; it causes only acute disease. HEV infection is especially serious in pregnant women (mortality rate of ≈20%). 87 RNA VIRUSES Properties of RNA Viruses RNA is labile and transient. Most RNA viruses replicate in the cytoplasm. Cells cannot replicate RNA. RNA viruses must encode an RNA-dependent RNA polymerase. The genome structure determines the mechanism of transcription and replication. RNA viruses are prone to mutation. The genome structure and polarity determine how viral mRNA is generated and proteins are processed. RNA viruses, except for (+) RNA genome, must carry polymerases. All (−) RNA viruses are enveloped. 2 Insert Table 25.1 RNA viruses 3 Families of RNA Viruses and Some Important Members Familya Members PARAMYXOVIRIDAE Parainfluenza virus, Sendai virus, measles virus, mumps virus, respiratory syncytial virus, metapneumovirus ORTHOMYXOVIRIDAE Influenza virus types A, B, C and thogotoviruses CORONAVIRIDAE Coronavirus, SARS virus, MERS virus Arenaviridae Lassa fever virus, Tacaribe virus complex (Junin and Machupo viruses), lymphocytic choriomeningitis virus Rhabdoviridae Rabies virus, vesicular stomatitis virus Filoviridae Ebola virus, Marburg virus Bunyaviridae California encephalitis virus, La Crosse virus, sandfly fever virus, hemorrhagic fever virus, hantavirus Retroviridae Human T-cell leukemia virus types I and II, HIV, animal oncoviruses Reoviridae Reoviridae Rotavirus, Colorado tick fever virus 4 Families of RNA Viruses and Some Important Members Familya Members Togaviridae Rubella virus; western, eastern, and Venezuelan equine encephalitis virus; Ross River virus; Sindbis virus; Semliki Forest virus; chikungunya virus Flaviviridae Yellow fever virus, dengue virus, St. Louis encephalitis virus, West Nile virus, hepatitis C virus Caliciviridae Norwalk virus, calicivirus Picornaviridae Rhinoviruses, poliovirus, echoviruses, parechovirus, coxsackievirus, hepatitis A virus Hepeviridae Hepatitis E virus Astroviridae Astrovirus Delta Delta agent 5 ORTHOMYXOVIRIDAE The orthomyxoviruses are enveloped and have a segmented negative-sense ribonucleic acid (RNA) genome The genome of the influenza A and B viruses consists of eight helical nucleocapsid segments, each of which contains a negative-sense RNA Influenza C has only seven genomic segments. The envelope contains two glycoproteins, hemagglutinin (HA) and neuraminidase (NA), and the membrane (M2) protein and is internally lined by the matrix (M1) protein. 6 Unique Features of the Influenza A and B Viruses The enveloped virion has a genome of eight unique negative-sense RNA nucleocapsid segments. Hemagglutinin glycoprotein is the viral attachment protein (sialic acid receptor)and fusion protein; it elicits neutralizing, protective antibody responses. Influenza transcribes and replicates its genome in the target cell nucleus but assembles and buds from the plasma membrane. The polymerase uses capped cellular mRNA as primers for mRNA synthesis. Amantadine and rimantadine (antiviral drugs ) target the M2 (membrane) protein for influenza A only to inhibit the uncoating step. The antiviral drugs zanamivir, oseltamivir, and peramivir inhibit the neuraminidase protein of influenza A and B. The NA cleaves the sialic acid on glycolipids and glycoproteins, including the cell receptor. The segmented genome promotes genetic diversity caused by mutation and reassortment of segments on infection with two different strains. Influenza A infects humans, other mammals, and birds (zoonosis). 7 Orthomyxoviruses: Influenza There are four types of influenza viruses: A, B, C, and D. Influenza A viruses are the only influenza viruses known to cause flu pandemics (i.e., global epidemics of flu disease). (CDC) Virus attaches to, and multiplies in, the cells of the respiratory tract; finished viruses are assembled and budded off. Unlike other RNA viruses, replication takes place in the nucleus. Functions of hemagglutinin:** Hemagglutinin, viral attachment protein, fusion protein, target of neutralizing antibody: Allows the virus to bind to sialic acid (N-acetyl neuraminic acid) receptors and enter* Functions of neuraminidase: Neuraminidase (cleaves sialic acid and promotes virus release): It allows the virus to be expelled from the infected cell. 8 Influenza (flu) A virus. Influenza A viruses are classified by subtypes based on the properties of their hemagglutinin (H or HA) and neuraminidase (N or NA) surface proteins. There are 18 different HA subtypes and 11 different NA subtypes. Subtypes are named by combining the H and N numbers – e.g., A(H1N1), A(H3N2).** 9 Insert figure 25.1 Influenza cycle 10 The morphology of influenza A virus particles is characterized by distinctive spikes, which are readily observable in electron micrographs of negatively stained virus particles.These spikes, comprised of HA and NA. HA protein is the major antigenic component of the virus. 11 Orthomyxoviruses: Influenza The segmented genome of these viruses facilitates the development of new strains through mutation and reassortment of the gene segments among different human and animal (influenza A) strains of virus. This genetic instability is responsible for the annual epidemics (mutation: drift) and, for influenza A, periodic pandemics (reassortment: shift) of influenza infection worldwide. Antigenic drift Minor antigenic changes resulting from mutation of the HA and NA genes are called antigenic drift. This process occurs every 2 to 3 years, causing local outbreaks of influenza A and B infection. epidemic 12 Antigenic shift – Antijenik shift Major antigenic changes (antigenic shift) result from reassortment of genomes among different strains, including animal strains. This process occurs only with the influenza A virus. Such changes are often associated with the occurrence of pandemics. In contrast to influenza A, influenza B is predominantly a human virus and does not undergo antigenic shift. one of the genes or RNA strands is substituted with a gene or strand from another influenza virus from a different animal host. Antigenic shift involves major antigenic changes in which a new HA or NA subtype is introduced into the human population. Shifts occur only with influenza A virus. The newly introduced proteins are immunologically distinct from the previously circulating strains and result in high infection rates in the immunologically naive population, leading to pandemics. An antigenic shift is caused by reassortment, typically between human and avian viruses. During the last century, four antigenic shifts occured: – – – – – – in 1918; with the appearance of H1N1 viruses that caused the Spanish influenza; in 1957; whith the appearance of H2N2 viruses that caused the Asian influenza; in 1968; with the appearance of H3N2 viruses that caused the Hong Kong influenza; in 1977; when the H1N1 subtype reappeared (Russian influenza) The pandemic of 2005-Avian flu-Asian H5N1 2009 H1N1, swine flu *** 1957 and 1968 pandemics both resulted from reassortant between human and avian 13 viruses. Duck influenza virus Human influenza virus Insert figure 25.3 Antigenic shift Antigenic drift: HA/NA mutations Antigenic shift: genetic reassortment 14 15 Influenza (Avian and other zoonotic) There are four types of influenza viruses: types A, B, C, D Type A causes most infections Influenza type A viruses are classified into subtypes according to the combinations of different virus surface proteins hemagglutinin (HA) and neuraminidase (NA). Depending on the origin host, influenza A viruses can be classified as avian influenza, swine influenza, or other types of animal influenza viruses. Examples include avian influenza "bird flu" virus subtypes A(H5N1) and A(H9N2) or swine influenza "swine flu" virus subtypes A(H1N1) and A(H3N2). Signs and symptoms in humans Avian, swine and other zoonotic influenza infections in humans may cause disease ranging from mild upper respiratory infection (fever and cough) to rapid progression to severe pneumonia, acute respiratory distress syndrome, shock and even death. Gastrointestinal symptoms such as nausea, vomiting and diarrhea has been reported more frequently in A(H5N1) infection. Conjunctivitis has also been reported in influenza A(H7). Disease features such as the incubation period, severity of symptoms and clinical outcome varies by the virus causing infection but mainly manifests 16 with respiratory symptoms. Influenza A Acute, highly contagious respiratory illness Seasonal, pandemics; among top 10 causes of death in the World- most commonly among elderly and small children Respiratory transmission Binds to ciliated cells of respiratory mucosa Causes rapid shedding of cells, stripping the respiratory epithelium; severe inflammation Fever, headache, myalgia, pharyngeal pain, shortness of breath, coughing Weakened host defenses predispose patients to secondary bacterial infections, especially pneumonia. 17 Diagnosis, Treatment, Prevention The diagnosis of influenza is usually based on the characteristic symptoms, the season, presence of the virus in the community Laboratory tests are required to diagnose human infection with zoonotic influenza. (WHO, through its Global Influenza Surveillance and Response System (GISRS) RT-PCR; hemaglütinasyon inhibisyon Rapid influenza diagnostic tests (RIDTs) have lower sensitivity compared to PCR; RDTs in general cannot provide subtype information. Rapid immunofluorescence tests to detect antigens in a pharyngeal specimen; serological testing to screen for antibody titer Treatment:Control of symptoms is important in treatment, oseltamivir (Tamiflu) is recommended in advanced cases (although amantadine and rimantadine are used, resistance to them is increasing) Annual trivalent vaccine recommended 18 19 Annual vaccination is recommended for; Everyone 6 months and older should get a flu vaccine every season with rare exceptions. Vaccination is particularly important for people who are at higher risk of serious complications from influenza. (CDC) Vaccination is routinely recommended for all individuals and especially persons older than 50 years, health care workers, pregnant women who will be in their second or third trimester during flu season, people living in a nursing home, people with chronic pulmonary heart disease, and others at high risk. 20 Unique Features of the Paramyxoviridae Large virion consists of a negative-sense RNA genome in a helical nucleocapsid surrounded by an envelope.(The difference from orthomyxoviruses is that the genome is not segmented.) The three genera can be distinguished by the activities of the viral attachment protein: – HN of parainfluenza virus and mumps virus binds to sialic acid and red blood cells (hemagglutinin and neuraminidase activity), neuraminidase facilitates release from cell; – H of measles virus binds protein receptors and is also a hemagglutinin; – G of RSV binds to cells but is not a hemagglutinin. Virus replicates in the cytoplasm. Virions penetrate the cell by fusion with the plasma membrane and exit by budding from the plasma membrane without killing the cell. Viruses induce cell-to-cell fusion, causing multinucleated giant cells (syncytia). Cell-mediated immunity causes many of the symptoms but is essential for control of the infection. Paramyxoviridae are transmitted in respiratory droplets and initiate infection in the respiratory tract. Measles and mumps establish viremia and spread to other body sites. 21 Insert figure 25.5 Effects of paramyxoviruses 22 PARAMYXOSOVİRİDAE A new group of highly pathogenic paramyxoviruses, including two zoonosis-causing viruses, Nipah virus and Hendra virus, was identified in 1998 23 PARAMYXOSOVİRİDAE Differences in envelope peplomers of paramyxoviruses Virus Hemagglutinin Neuraminidase Fusion glycoprotein Measles + - + Mumps + + + parainfluenzavirus + + + RSV - - + human metapneumo virus - - + Main target tissues : respiratory system in envelope F (fusion) and HA ; Under the envelope is the M protein – HA: attachment to target cell – F: It causes the formation of giant cells by making a cytopathic effect. 24 Mumps Virus is the cause of acute, benign viral parotitis (painful swelling of the salivary glands). Parotid is painful and tender. The hemagglutinin-neuraminidase (HN) protein and fusion protein (F) are surface glycoproteins. The HN protein mediates adsorption of the virus to the host cell, and the F protein mediates the fusion of lipid membranes, allowing the nucleocapsid to enter the cell. Transmission Inhalation of large-droplet aerosols Virus infects epithelial cells of respiratory tract and by viremia; Infection of parotid gland, testes, and central nervous system. only infects humans; lifelong immunity 25 Mumps Virus Oral examination reveals redness and swelling of the ostium of the Stensen (parotid) duct. The most common complications are meningitis and orchitis. It can cause deafness or infertility Diagnosis – is the most common ELISA IgM – Clinic+RT-PCR – Multinuclear in cell culture giant cells can be seen. Symptomatic medication and rest Live attenuated vaccine measles-mumps-rubella vaccine:MMR The first dose is administered 12-15 months and the second dose is 4-6 years of age. 26 Respiratory Syncytial Virus The two major glycoproteins on the surface of the RSV virion are the attachment glycoprotein (G) and the fusion (F) glycoprotein – G targets the ciliated cells of the airways, – F causes the virion membrane to fuse with a target cell membrane Infects upper respiratory tract and produces giant multinucleate cells (RSV induces syncytia) The most common cause of fatal acute respiratory tract infection in infants and young children. (bronchiolitis and pneumoniae) It infects virtually everyone by 2 years of age, and reinfections occur throughout life Enveloped, RNA Transmission Inhalation of large-droplet aerosols. Moderate cold in winter Epithelia of nose and eye portal of entry; replicates in nasopharynx Fever, rhinitis, wheezing, otitis, croup The most common complication is otitis media No viremia and systemic infection. Treatment: ribavirin inhalation 27 Measles virus (Rubeola) Morbillivirus; contains Hemagglutinin H and F (fusion) protein on the envelope. Thanks to the F protein , it creates giant cells. The nucleocapsid associates with the matrix (M) protein lining the inside of the virion envelope. plays a role in budding. Virus infects epithelial cells of respiratory tract; spreads systemically in lymphocytes by viremia. Virus replicates in cells of conjunctivae, respiratory tract, urinary tract, lymphatic system, blood vessels, and CNS. transmitted through the respiratory route and is highly contagious 28 Measles virus (Rubeola) The maculopapular rash on the skin (starts behind the ear) is caused by T lymphocytes that attack infected cells. Cell-mediated immunity is essential to control infection. It does not cause anomaly in pregnant women, does not cause congenital infection, but it can cause abortion and stillbirth. Sequelae in the CNS may result from immunopathogenesis (postinfectious measles encephalitis) or development of defective mutants (Subacute Sclerosing Panencephalitis) Initial prodromal symptoms are fever, malaise, anorexia, followed by cough, coryza, and conjunctivitis. After 2 days of prodromal illness, the typical mucous membrane lesions known as Koplik spots appear. They are seen most commonly on the buccal mucosa across from the molars, Humans are the only reservoir. 29 Measles virus (Rubeola) Koplik spots (white in the middle, erythematous around) are white-colored lesions that appear in the form of salt sprinkled on the buccal mucosa in the mouth. If there is fever after the third day of the rash, complications are considered. The most common complication causing death is pneumonia. Rashes fade by pressing 30 Diagnosis: Measles virus (Rubeola) It is established by clinical findings. Definitive diagnosis of measles IgM Treatment: Symptomatic medications and rest. Vitamin A reduces mortality ; NO specific antiviral treatment Protection: Attenuated viral vaccine MMR Live vaccine (NOT GIVEN to pregnant, immunocompromised , AIDS patients!) MMR It is given under the skin with mumps and rubella vaccines at 12 months. 4-6 year rapel Lifelong immunity Ekzantem Subacute sclerosing panencephalitis (SSPE)* Most serious complication, is a progressive neurological degeneration of the cerebral cortex, white matter and brain stem. 31 Parainfluenza Viruses Enveloped, RNA Transmission: inhalation Four serologic types within the parainfluenza genus are human pathogens. Types 1, 2, and 3 are second only to RSV as important causes of severe lower respiratory tract infection in infants and young children – mild coldlike upper respiratory tract infection (coryza, pharyngitis, mild bronchitis, wheezing, and fever) to bronchiolitis and pneumonia. They are especially associated with laryngotracheobronchitis (croup)* (most common cause croup in children under 5 years old) Type 4 causes only mild upper respiratory tract infection in children and adults. – The most common complication is otitis media Parainfluenza virus does not cause viremia and systemic infection. 32 Human Metapneumovirus ( hMPV ) _ Enveloped, RNA fusion protein. 5 days of incubation, moderate upper respiratory tract infection 33 Rubella (German Measles) Togavirus family, Rubivirus genus (+) RNA, icosahedral , enveloped It is transmitted through the respiratory tract. Infant with skin lesions the upper respiratory tract and multiplying h