Introduction to Microbiology Lecture Notes PDF

Introduction to microbiology Lecture 1 of 3 Dr Ashutosh Deshpande Consultant Microbiologist  Learning outcomes – Understand what microbiology means – Classify microorganisms in very broad terms – Describe the general structure of bacteria and the role of Gram stain in help...

Introduction to microbiology Lecture 1 of 3 Dr Ashutosh Deshpande Consultant Microbiologist  Learning outcomes – Understand what microbiology means – Classify microorganisms in very broad terms – Describe the general structure of bacteria and the role of Gram stain in helping to classify certain bacteria  Microbiology The study of microorganisms and their relationship with humans What is a microorganism? Any organism/replicating entity that is of microscopic size (e.g. bacteria) or small (e.g. certain worms)  Microorganisms – a simple classification Cellular – Bacteria – Fungi – Protozoa/other parasites Acellular – Viruses – Prions  Classification of cellular microorganisms Prokaryotes – Organisms without membrane-bound nucleus – Transcription/translation coupled – Single, circular chromosomal DNA – Additional DNA carried in plasmids – Bacteria  Classification of cellular microorganisms Eukaryotes – DNA carried on chromosomes in a membrane-bound nucleus – Transcription and translation are compartmentalised – Cytoplasm is rich in membrane-bound organelles – Cellular organisms other than bacteria http://water.me.vccs.edu/courses/env108/lesson2_2.htm http://www.ebi.ac.uk/microarray/biology_intro.html  Bacteria Single-celled prokaryotes with characteristic cellular organisation DNA in long circular form +/- plasmids Cell is often surrounded by complex cell wall and often a thick capsule May be motile Reproduce by binary fission Wide range of aerobic and anaerobic metabolic patterns and biochemical variations  Bacteria Classified as: – Gram-positive – Gram-negative – Gram-variable – Gram-stain unreliable Bacteria that are very small, have an atypical life cycle, atypical structure, or don’t have a complex cell wall (e.g. mycoplasma) For such bacteria, serological, molecular (ie PCR), or other methods of detection may be used (specialist microscopy, alternative staining and culture techniques etc) http://www.cehs.siu.edu/fix/medmicro/genmicr.htm http://hugolila.pbworks.com/w/page/4881660/Gram%20Stain http://pmj.bmj.com/content/77/905/148.full  Common GPC: – Staphylococcus aureus – Streptococcus pneumoniae Common GPR: – Listeria monocytogenes – Corynebacterium diphtheriae Common GNC: – Neisseria meningiditis Common GNR: – Escherichia coli – Salmonella species  Learning outcomes – Understand what microbiology means – Classify microorganisms in very broad terms – Describe the general structure of bacteria and the role of Gram stain in helping to classify certain bacteria Introduction to microbiology Lecture 2 of 3 Dr Ashutosh Deshpande Consultant Microbiologist  Learning outcomes – Describe sites of the body that are sterile and those that are colonised with bacteria – Understand the difference between colonisation and infection – State common colonisers and pathogens of different body systems – Understand the concept of host, pathogen and environmental factors that lead to infection  Bacteria and the body: colonisation Colonisation – Commensal organisms, mutualism – Symbiotic and natural living arrangements between two species which may be beneficial to one or both parties and does not cause harm – Normal flora is acquired soon after birth and changes with age Benefits – Competition and natural by-products inhibit establishment of infection – Vitamins (K and B) in the gut produces as metabolic end-products – Immune stimulation http://www2.bc.cc.ca.us/bio16/PAL/Lecture%202.htm  Bacteria and the body Sterile body sites – Blood, tissues and organ systems – CNS – Lower respiratory tract – Sinuses, inner and middle ear – Renal system down to posterior urethra – Female reproductive tract down to the cervix – Eye (exposed conjunctivae colonised)  Bacteria and the body: infection Colonisation +/- multiplication of pathogens or organisms that may cause harm in a vulnerable host, +/- manifestation of disease Organisms may produce manifestations of disease by direct invasion or production of toxins and other virulence factors Some definitions: – Parasite – Opportunistic infection – Nosocomial infection – Carrier state Transient or chronic  Infection: microbial factors Virulence factors – Colonisation factors – Invasive factors – Toxigenicity Other microbial defences – Antigenic mimicry – Antigenic masking – Antigenic shift – Encapsulation – Evasion of host immune response – Induction of inappropriate immune responses Infectious doses  Endotoxin Lipopolysaccharide in outer membrane of Gram-negative bacteria “Endotoxic lipid A” and “O antigen” Elicits strong immune responses and can make patients appear “septic” http://en.wikipedia.org/wiki/File:LPS.svg  Superantigens Exotoxins liberated by certain Gram-positive bacteria – Produced intracellularly and released as mature toxins on infection – Staphylococcus aureus, Streptococcus pyogenes Massive immune stimulation – Non-specific polyclonal T- cell stimulation – Toxic shock syndrome http://en.wikipedia.org/wiki/File:Seb.png  Infection: host and environmental factors Age, gender, ethnicity, personal hygiene, nutrition Other medical conditions, drugs Immunocompromise – Immune deficiency disorders, malignancy, chemotherapy and other drugs – Immunocompromising infections e.g. HIV Presence of foreign objects – Make infection with commensals more likely – Biofilms Vaccination history Crowding, seasonal variations, sanitation, socioeconomic and public health factors  Common infections in different body System systems Example of infection Example of common pathogen Respiratory Pneumonia Streptococcus pneumoniae Haemophilus influenza Sore throat Streptococcus pyogenes Gastrointestinal Cholecystitis Gut flora Food Poisoning Campylobacter, Salmonella, certain strains of E.coli, Shigella Central nervous system Meningitis Neisseria meningiditis Streptococcus pneumoniae Haemophilus influenzae Bone and joint Osteomyelitis Staphylococcus aureus Septic arthritis Skin and soft tissue Cellulitis Staphylococcus aureus Necrotising fasciitis Streptococcus pyogenes Renal Pyelonephritis Gram-negatives e.g. Escherichia coli UTI Genital Pelvic inflamamtory disease Neisseria gonorrhoea Urethritis Chlamydia trachomatis Cardiovascular Endocarditis Streptococci, Staphylococci, various others Ophthalmological Periorbital cellulitis Staphylococci, Streptococci Endophthalmitis Various iatrogenic Conjuncivitis Obstetrics/neonates Chorioamnionitis, neonatal sepsis Group B Streptococci, E.coli, Klebsiella  Natural course of infection Host, microbial and environmental factors will determine the likelihood of getting infected, severity of symptoms, and chances of overcoming the infection Most healthy individuals will mount an immune/ inflammatory response to infection and eventually clear it Both the host immune or inflammatory response, and the offending pathogen itself, may contribute to symptoms and signs http://www.cardiff.ac.uk/biosi/subsites/cold/commoncold.html  Natural course of infection: more definitions Entrance (portal of entry) Colonisation (adherence; adhesion; attachment) Multiplication +/- dissemination (spread) Penetration +/- invasion (not all pathogens are invasive) Signs and symptoms of disease (morbidity, mortality) based on host immune system and pathogenic virulence factors etc Resolution or chronic state may occur Elimination and/or exit of pathogen (carrier state may be established)  Learning outcomes – Describe sites of the body that are sterile and those that are colonised with bacteria – Understand the difference between colonisation and infection – State common colonisers and pathogens of different body systems – Understand the concept of host, pathogen and environmental factors that lead to infection Introduction to microbiology Lecture 3 of 3 Dr Ashutosh Deshpande Consultant Microbiologist  Learning outcomes – Understand the importance of pre-antibiotic sampling and develop an understanding of the specimen journey – Understand the meaning of sepsis and the broad principles of assessment and management of infection – Understand what is meant by the “chain of infection” and the rationale behind standard and transmission-based infection control precautions  Laboratory diagnosis of infection Pre-antibiotic samples are important Samples need to get to the lab on time in the correct containers and media Samples must be labelled correctly, and must have plenty of accurate clinical details on them In emergencies, do not wait for lab results – check previous microbiology results, check the empirical prescribing policy, check for any antibiotic allergies, discuss with a senior, and start treatment Always review empirical antibiotic choices and tailor these to the organisms grown when appropriate  The specimen journey Depending on the clinical details and type of sample, the sample is processed in an appropriate area of the lab  Specimen processing Processing may involve anything from microscopy, culture, sensitivity testing or PCR to serology or referral of the sample to reference laboratory services for techniques such as whole genome sequencing Samples that are heavily contaminated with commensal flora, such as stool samples, require decontamination steps and selective and differential culture media Microscopy, culture and sensitivities 24 hours 24 hours 24 hours 24 hours 1-2 hours  Microbiological emergencies Acutely threatening to organ-system or life Must be assessed and treated empirically immediately – Infection of a normally sterile site – Meningitis/CNS infection/cerebral abscess – Septic arthritis – Deep ocular or periorbital infections – Infection involving breach of the GI tract e.g. peritonitis – Any outbreak scenario or public health risk – Any infection in which a patient is “septic” – Don’t forget agents other than bacteria  Sepsis Physiological response to severe infection involving cytokine cascades, free radical production and vasoactive mediators Many older textbooks describe the old SEPSIS scoring system below. The principles are similar, but this has now been superceded by different scoring systems to measure degree of illness of patient SIRS – 2 or more of: T outwith 36-38 C, HR > 90, RR > 20 or PaCo2 < 4.3 kPa, WCC outwith 4-12, or > 10% immature band forms Sepsis – SIRS in presence of infection Severe sepsis – Sepsis with evidence of organ damage or hypoperfusion e.g. hypoxaemia, oliguria, acidosis, cerebral dysfunction Septic shock – Severe sepsis with hypotension despite fluid resuscitation or vasopressor/inotropic support  Severity Scores SIRS/Sepsis/MEWs/NEWs/SOFA or other similar scores commonly used in most settings Maternal and paediatric settings may have more bespoke guidelines Help objectively assess how critically unwell a patient – early aggressive management can save lives Familiarise yourself with the system used in your local hospital/health board Other organ system-specific scores in common use – Clostridium difficile severity score – CURB 65 score Kumar, A. Early Antimicrobial Therapy in Severe Sepsis and Septic Shock. Curr Infect Dis Rep 12, 336–344 (2010). https://doi.org/10.1007/s11908-010-0128-x  Sepsis “bundles” SEPSIS 6 and other “bundles” are used to help guide early identification and management of septic patients ASAP, ideally within the first hour of assessment  Principles of treatment Management Examples Investigate Imaging, cultures etc – helps guide later managment Conservative Rehydration, nutrition, inotrope/vasopressor support, oxygen, support affected organ systems, drugs Antibiotics “Golden hour” of antibiotics NB contraindicated in E.coli 0157 Surgical Fulminant colitis (C. difficile), peritonitis , collections, abscess etc. Infection control Single room or cohort isolation, enteric precautions, respiratory precautions, hand hygiene Public health Outbreak surveillance, exclusions, microbiological clearance  Infection control precautions Universal precautions – Apply to all patients – Care with body fluids, broken skin and mucous membranes – Handwashing, PPE, environmental cleaning, injury prevention Transmission-based precautions – May involve some sort of isolation and special PPE – Airborne Precautions – Droplet precautions – Contact precautions – Other special precautions e.g. enteric, prions etc. http://instructor.mstc.edu/instructor/csebasti/543102_NursingSKills.html  Learning outcomes – Understand the importance of pre-antibiotic sampling and develop an understanding of the specimen journey – Understand the meaning of sepsis and the broad principles of assessment and management of infection – Understand what is meant by the “chain of infection” and the rationale behind standard and transmission-based infection control precautions