BIOL131 Medical Microbiology Lecture Notes PDF
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These notes provide an overview of medical microbiology, including the various types of microbes (viruses, bacteria, fungi, and protozoa), the different methods of classification, and the techniques used in the clinical laboratory. The focus is on the practical application of microbiology in medicine.
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BIOL131 Medical microbiology https://www.lancaster.ac.uk/itpi/attendance-teaching/#/classList Medical microbiology The prevention, diagnosis and treatment of organisms responsible for infectious and communicable disease Microbes: • Viruses • Bacteria • Fungi → (mycology) • Protozoans (parasites)...
BIOL131 Medical microbiology https://www.lancaster.ac.uk/itpi/attendance-teaching/#/classList Medical microbiology The prevention, diagnosis and treatment of organisms responsible for infectious and communicable disease Microbes: • Viruses • Bacteria • Fungi → (mycology) • Protozoans (parasites) → (parasitology) to provide a firm basis for clinical and scientific practice, it is important to include all of these categories Viruses Genetic material and cell components: • Viruses are not cells, not considered ‘living’ • They possess genetic material (DNA or RNA) but lack cell membranes, cytoplasm and the machinery for synthesizing macromolecules • Must reproduce within host cells • Difficult to treat Bacteria Pili/fimbriae Genetic material and cell components: • Bacteria are prokaryotes, all other organisms are eukaryotes nucleoid • Prokaryotes lack a distinct nucleus • Bacterial cell wall confers protection, antigenicity and stimulates certain pathologic responses • DNA in the form of a single, circular chromosome Flagellum Fungi • Eukaryotes, multinucleate or multicellular • thick cell wall • grow as thread-like filaments (hyphae) • Some are part of normal body flora • Pathogenic species digest material externally by releasing enzymes • Infection (mycoses) - superficial mycoses (skin, hair), cutaneous and subcutaneous (nails and deeper skin) or deep mycoses (internal organs) e.g. Genus Aspergillus, Cryptococcus, Trichophyton Protozoa • Single-celled animals • capable of infecting all tissues and organs in the body - human parasites • Infections most prevalent in tropical and subtropical regions, sometimes temperate regions • Transmitted by bites of blood-sucking insects or accidental ingestion of infective stages • Infect as: Intracellular parasites or as Extracellular parasites (in blood, intestine or urinogenital system) • Usually asexual reproduction within host Plasmodium falciparum Classification of cellular organisms Correct identification needed for accurate diagnosis and effective treatment Species classification for eukaryotes based on binomial system – • species (similar, interbreeding organisms) • genus (closely related but non-interbreeding species) Taxa Human Bacteria Fungi Protozoa Genus Homo Escherichia Candida Plasmodium Species sapien coli albicans falciparum Food poisoning Thrush Malaria Associated disease (example) Classification of viruses Classified according to: • type of nucleic acid (DNA or RNA) • mode of replication • symmetry of virus particle - icosahedral, helical or complex • presence or absence of external envelope Identification using antibodies to certain features (epitopes) – serologic reactivity or PCR amplification of viral DNA HIV – human immunodeficiency virus SARS – severe acute respiratory syndrome single stranded RNA Genus: Coronavirus Species: SARS single stranded RNA Genus: Lentivirus Species: HIV1/HIV2 Classification of bacteria Practical characteristics – for example: • size • shape (e.g. cocci, bacilli, spiral) • colour • respiration (e.g. ana/aerobic) • reproduction (e.g. a/sexual) • immunologic • biochemical and molecular analyses Staining properties (e.g. Gram’s stain) • Gram positive = purple e.g. Staphylococcus spp • Gram negative = pink e.g. E.coli cocci bacilli spiral Identification of bacteria below genus level Bacterial strain = genetic variant or subspecies Pili/fimbriae To differentiate pathogenic vs. nonpathogenic • different immunologic properties Cell wall, flagellum and capsule antigens • specific antibodies used for identification • e.g. E.coli, Salmonellae, Streptococci, Shigellae spp. Flagellum Bacterial strain Different strains have distinct biochemical characteristics & different susceptibility to bacteriophage viruses e.g. some strains of Staphylococcus produce catalase (breaks down H2O2, releasing O2) and b-haemolysin (lyses red blood cells). Strain: O157:H7 Strain O83:K24:H31 Not only same species, but both have “Oantigen’ in outer lipopolysaccharide layer Medical microbiology Aims of medical microbiology lab: •Identify microorganisms in specimen → ?disease •Microorganisms grow in artificial media •Viruses in cell cultures & PCR •Identify antimicrobial susceptibility •Detect microbial products e.g. toxins •Analyse patient’s response Precise identification of causative organism depends on quality of specimen Specimen collection • Take appropriate specimen and at correct time in disease, preferably before antimicrobials have been administered • Sterile containers and appropriate transport media • Contamination must be avoided (from normal flora or equipment) • Don’t use histologic fixatives -kill the microbes • Collection of specimen is responsibility of clinician • Label accurately Request form Specimen handling • Hazardous samples – identify & take precautions • Transport to the lab needs to be quick • Some contaminants (flora or environmental) may grow quickly and mask presence of pathogen • False impression of balance between species • Various artificial media are used to maintain viability of microbial samples • Refrigeration of specimens prevents multiplication of most bacteria BUT… • some won’t survive (Neisseriae) • Listeriae grow well at low temperatures Conventional specimen processing Details of specimen are checked against request form Specimen is grown on relevant culture media & incubated • Normal atmosphere • with 5% CO2 • anaerobically at 37oC Microbiology in practice https://www.youtube.com/watch?v=afM7DGjSVn4 Significance of isolates from certain sites Body sites which are normally sterile: • Blood and bone marrow, cerebrospinal fluid, serous fluids, tissues, lower respiratory tract, bladder Body sites which have a normal commensal flora: • Mouth, nose, upper respiratory tract, skin, gastrointestinal tract, female genital tract, urethra Significance depends on identity of isolate, quantity and immune status of patient Note – urine passes through urethra, sputum passes through upper respiratory tract and mouth - contaminated Practicalities of identification Identification of the microorganism or its products or the patient’s immune response? TIME- Conventional microbiological diagnosis depends upon growth and identification. • Minimum 18 h to achieve results; for mycobacteria 6 weeks. Ratelimiting step. Diagnostic techniques that take hours, rather than days: • Microscopy • Antibody response in the patient’s blood • PCR and oligonucleotide probes – identify specific gene sequences – no need to culture. Microbe + host =/ disease • Pathogen = disease causing organism • Infection is a conflict between two organisms, with the outcome (resistance or disease) dependent upon mechanisms of both innate and acquired resistance (immunity) • Commensal microorganisms – one organism survives in another organism without causing it harm • Opportunistic infections – infection that occurs because of weakened immune system • transplant • burns • surgery • AIDS • pre-existing infection Opportunistic infection during ‘flu infection • neutrophil infiltration in section of lung from a 1918 influenza case with acute pneumonia Uninfected lung alveoli Acute pneumonia neutrophils x100 x200 Taubenberger et al. 2019 Sci. Transl. Med. 11 (502): eeau5484 Acute vs. chronic infection • Refers to the longevity of the immune response against the organism • Both can be severe Chronic Acute Clostridium difficile Methicillin-resistant Staphylococcus aureus (MRSA) Influenza HIV E.coli HPV Lower respiratory tract infections • Tend to be severe • Antimicrobial therapy may be life saving • Acute – e.g. bronchitis, pneumonia, influenza • Chronic – e.g. tuberculosis, aspergillosis, lung abscesses, infections in cystic fibrosis Mims Lower respiratory tract infections. p217 (3rd); p227 (4th) Pneumonia Most common cause of infection-related death in USA and Europe Caused by a wide range of microorganisms – children usually viral origin, adults usually bacterial origin Indistinguishable symptoms – lab identification of microbial cause needed for effective treatment Infection occurs through: 1. inhalation of aerosols 2. aspiration of normal flora 3. via the blood Results in interference in air exchange in the lungs Symptoms: Chest pain, cough + sputum, short of breath, difficulty and pain on breathing Pneumonia microbiology • Gram stained sputum showing abundant Gram positive pneumococci • Streptococcus pneumoniae most common bacterial cause of Mims: 3rd p221-225, 4th p231-235 pneumonia Tuberculosis Kills ~ 3 million/year and infects ~ 9 million wherever poverty, malnutrition and poor housing Affects healthy and immunocompromised e.g. AIDS Clinical manifestations: • fatigue, weight loss, weakness, fever → chronic productive cough with blood-stained sputum (due to tissue destruction) Caused by inhalation of Mycobacterium tuberculosis in aerosols and dust. Primary TB → asymptomatic, ~ 10% → disease Primarily a disease of the lungs, may spread to other sites or become systemic (‘miliary’ TB, 1-5 mm size lesions), 1-3% cases. Tuberculosis (cont’d) The body reacts to contain the Mycobacteria within ‘tubercles’ small granulomas consisting of macrophages (‘epithelioid cells’ and ‘giant cells’) Guirado and Schlesinger 2013 Front. Immunol. 4:98 Tuberculosis (cont’d) Tubercles may heal spontaneously, become fibrotic or calcified, and persist (dormant) in otherwise healthy people Particularly in the immunocompromised, the mycobacteria invade the bloodstream → ‘miliary’ TB Mycobacteria may colonize any site in the body