Introduction 29/09/2020 (Prev-Guiliano in Microbiology for Immunology aspect)
2.5 hours of independent reading for every hour lecture. Some lectures will not be live :(.
Practicals: COSHH and Risk Assessment before practical must be read. Antibiotic resistance,
then results-after them, discuss data-no running away. NBT assay, and Primary and Secondary
Lymphoid Tissue Staining. Those are the practicals. Bring your own mask ig. TAP IN!
Workshops: we research topics related to innate immunity; group 2 for adaptive.
Work with 6 students to make 5-7 slides where you use data on your subject
(Immunology SARs/Covid-19). Present to the class for 15-20 min and take questions
on the research. THIS WILL BE ON THE EXAM.
Assessments: 12 Jan-theory (60 min online written). 15 Dec-Practical (same). Not in
the lab, all online. There are questions about results as well! Like how does staining
work. Theory-MCQ of microbiology and immunology. 2 essay questions from those groups.
Could be from either lecture or practical. They usually pick up on themes that are in multiple
lectures. Practical-questions about anything we do (techniques or results). OPEN BOOK EXAM
AND CAN USE NOTES! 1.5-2 hours for the exam.
Where do Infections (Pathogens-viruses/bacteria/fungi/protozoa) come from?
Open wounds/sores. 80% of life was bacterial. Every surface covered in microbes. Pathogenic
microbes globally are the most important cause of human disease and death. 10x more
bacterial cells than human. Infection is a decisive role in history; major cause of death and
misery. Wars have been won because of infections. Public anxieties-meningitis, food poisoning,
mad cow disease, emerging infections. Hospital infection like antibiotic resistant superbugs.
Potential pathogens-commensalism (one species uses body of a larger one; association of
convenience). Mutualism-reciprocal benefits for both. They make vitamin K, we give them
warmth. Parasitism-Symbiotic relationship of benefit to just the parasite. Pathogen-primary and
opportunistic pathogens; all benefits, but cause harm to host. Primary-always cause disease;
not normally associated with the host like Influenza or M. tuberculosis. Opportunistic-cause
disease IF you give them opportunity to do so (food borne, open wounds). Pseudomonas
aeruginosa. This group is larger. Lots of clinical infection from these.
Chain-susceptible host, infectious agent, reservoir host, portal of exit, mode of transmission,
portal of entry. Pathogen sources: exogenous or endogenous. Exo-environment (air, water
fomites), food or from animals
(zoonoses). Endo-post-operative
wound infection with own flora,
normal flora in the wrong place
(opportunistic), Reactivation of
latent infection, and congenital.
Route of entry (pic): inhalation,
ingestion, inoculation/contact.
Infection is like an iceberg.
Infection starts mild/sub clinical.
Then mild disease and moderate.
Eventually severe, and hospital.
Then they go to a doctor or die
(or both).
,Exogenous infection (derived from outside of environment): can be environmental (post
flooding, soil), food-borne infection, zoonoses (animal associated), anthropod-borne infection, or
xenotransplantation (through corneal transplants). Tetanus-clostridium tetani. Stand on rusty
nail, soil into foot, can succumb to the infection.
Nosocomial infection (acquired from hospital):
susceptible individuals (old, immunocompromised,
post-transplant, cancer), sick patients with infections,
post-operative patients, or significant antimicrobial
use. Usually acquired >48 hours after admission. May
occur after discharge. 9% are affected, increases with
length of stay. Large financial burden on NHS. 100k
infections per year in UK. 5k deaths per year.
Contributing factor in 15k further deaths. Presence of
microorganisms in hospital environment, transmission
of pathogens between staff and patients and among
patients, and immunocompromised patients make a
big nosocomial infection.
Food-borne: under-cooked, poor food hygiene, poor
storage (raw next to cooked), or faecal-oral
transmission. Salmonella in peanut/jelly sammiches; 7
deaths. Enteric fever instead of diarrhea-white blood
cells in stool. Pic below <-.
Anthropod-borne: viral (arboviruses)-tick-borne
encephalitis, yellow fever, dengue. During them
blood borne meals they puke. Bacterial-plague,
lyme disease, rickettsiosis. Protozoa-malaria,
leishmaniasis, trypanosomiasis. Prevent-avoid
contact. Cover skin if possible exposure. Insect
repellants. Take prophylaxis. Change/Wash clothes.
Endogenous infections-post-operative wound
infection, meningitis, urinary tract infection.These
are our own flora relocating to a different part of the
body.
Congenital infections. Viral-German measles
(rubella), cytomegalovirus. Bacterial-syphilis,
listeriosis (cross the placenta).
Protozoa-toxoplasmosis. Not so much fungi.
Intrauterine viral infection (usually about trimester it is acquired in)-Hep C/B, HIV, Lassa Fever,
enteroviruses, possibly SARs 2 virus hypothesized. Preconception-minimum risk. 0-12 weeks:
100% risk of fetus being congenitally infected resulting in major congenital abnormalities;
spontaneous abortion occurs in 20% of cases. 13-16 weeks: deafness and retinopathy 15%.
After 16 weeks: normal development, slight risk of deafness and retinopathy. Biggest risk of
virus is during early pregnancy. Placenta is a barrier, but some organisms get across it. More
viruses do this. Toxoplasmosis-parasite lives in cat gut. Excreted in feces, can end up in other
,hosts (livestock) so tissue cysts form in the meat. People in contact with feces with food. Fecal
Oocyst. Lots of microbial organisms that can get into wounds. Staph. Aureus is frequency 20%.
Opportunistic infections have a balance between virulence and host factors (host-susceptibility).
Some viruses can infect more easily.
Urine steps are: kidneys produce urine; ureters transport urine; urinary bladder stores urine;
urethra passes urine to outside. Respiratory infections then UTI are most common infections.
UTI occurs when bacteria (E. coli) from the digestive tract get into the opening of the urinary
tract and multiple. Bacteria first infect the urethra, then move to the bladder and finally the
kidneys. Urine moves from the kidneys, through ureters to the bladder and finally the urethra.
Can migrate up the urethra to establish a UTI. Bigger problem for women; usually due to sexual
activity. Urethra shorter in women, opening nearer the anus. Signs: urinate frequency, painful
burning, discomfort/pressure/bloating in lower abdomen, cramping in pelvic area or back,
cloudy/bloody urine, strong smell, and fever.
Meningitis-opportunistic infection of upper
respiratory tract flora, migrate to CNS. Secondary
to systemic infection. Meningeal
symptoms-headache, fever, stiff neck (arch back
for relief). Typically endogenous organisms.
Biggest cause: Neisseria meningitidis. Several
strains of it; B causes 75% of the meningococcal
cases and highest fatality rate.
Not just intact organisms that is the problem!
Horizontal transfer of antimicrobial resistance
genes (picture to the left). REMEMBER THE SEX
PILI!!! Know some examples of pathogens. Essay
answers should be illustrated with examples.
Antibiotics and Resistance
Antibiotic-a substance produced by living organisms with
activity against bacteria. Mostly made by bacteria. Penicillin
made by fungus (picture to left). Many of our current drugs
are not true antibiotics but are either synthetic or
semi-synthetic antimicrobial agents. Microorganism can be
resistant to penicillin but still infected with penicillin
because of an additional side chain. Bactericidal-drugs
that kill the bacteria. Bacteriostatic-drugs which halt the
growth and replication of bacteria. Graph-after drug is
added, bacteriostatic makes a line across (like K carrying
capacity), but with bactericidal, bacteria over time goes
down (hill shape). MIC-minimum inhibitory concentration:
lowest concentration of a drug which inhibits the growth of
a microorganism. Antibiotics have different MICs, we need
to know how much to give patient; want to use lowest
concentration, as some antibiotics have side effects. We
do doubling dilution series with the drug (25 uL 12.5uL
, etc). Put same concentration of bacteria in all tubes. Low concentration of drug, then bacteria
grows (not transparent). This is all bacteriostatic! Take a sample from all these tubes, put on an
agar plate. See growing bacteria, concentration can stop the growth, but does not kill them. No
growing on plate, then we determined MBC. Subculturing from each tube onto an agar plate
enables determination of the minimum bactericidal concentration MBC.
Measuring selective toxicity-chemotherapeutic index CI = maximum dose tolerated by humans
(high) divided by minimum dose required to treat infection (low). This equals toxic concentration.
High CI is desirable as less likelihood of adverse side effects. Adverse effects can be toxic
(renal/hepatic toxicity, neurotoxicity), suppress normal flora (GI disturbances-diarrhea), or have
allergic reactions (hypersensitivity). Kidney disease-granular surface, decreased function,
smaller size, high uterine protein (should be low).
Picture is the sites of activity, as antibiotics interfere
with metabolic processes in the bacteria. They work on
cell wall synthesis (surrounds cell membrane of
bacteria), some target DNA gyrase or RNA polymerase.
Lots target protein synthesis (made with ribosomes
remember, which can be different in bacteria in size).
Important sites for antibacterial activity: The
peptidoglycan cell wall-unique to bacteria. Protein
synthesis utilises the 70s ribosome. Specific bacterial
enzymes, e.g. RNA polymerase, DNA gyrase. The cell
membrane has some structural differences to eukaryotic
cells.
Cell wall: made with peptidoglycan. Agents which act on
peptidoglycan do so by inhibiting its synthesis. Such
agents will have no activity against stationary phase cells which are not actively laying down
new cell wall material. Because of the uniqueness of peptidoglycan, agents which act at this site
have a high chemotherapeutic index; no effects on humans really (no cell wall nor
peptidoglycan). Bacteria cannot grow without synthesising peptidoglycan (which is blocked with
antibiotics bound). Antibiotic examples: penicillins, cephalosporins, carbapenems, glycopeptides
(vancomycin), bacitracin, cycloserine, fosfomycin.
B-lactams: The original β-lactam drugs have now given rise to a whole series of semi-synthetic
derivatives with improved properties, e.g. broad spectrum (ampicillin); resistance to βlactamase
(methicillin-used when we have resistant to ampicillin and penicillin). Ampicillin is the most
widely prescribed of all the antibacterial drugs due to its low toxicity and broad spectrum (some
patients are allergic to penicillins).
Inhibitors of protein synthesis: Aminoglycosides (e.g. streptomycin, gentamicin, kanamycin),
Tetracyclins, Chloramphenicol (used to be widely used), Fusidic acid, Mupirocin, Macrolides
(e.g. erythromycin), Lincosamides (e.g. clindamycin), Streptogramins. Remember some
examples for essay questions, but not needed to know all.
Aminoglycosides: Binds to 30s subunit of the ribosome (remember there are a big and small
one, 30s is the small one), has a single binding site. At high concentrations: It inhibits formation
of initiation complexes; blocking protein synthesis completely-cell cannot survive. At low
concentrations: It causes misreading of the mRNA codons during elongation, leading to
