BIOL131 Medical Microbiology Lecture Notes PDF

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