Week 2 - Antimicrobial Resistance Flashcards
What are the three major purposes of antimicrobial prescriptions?
What are the consequences of some of these purposes?
- Therapeutics - if an individual is sick, treat the patient to cure.
- Metaphylactics - if one patient is noticed in a herd, treat the whole herd to control its spread.
- Prophylactics - seasonal prescription of drug to prevent the most susceptible population within a herd.
The consequences of 2 & 3 –> Antimicrobial overuse in intensive farms (pigs & poultry), dry cow therapy, and shipping of animal
Antimicrobialswasusedfor?
Growth promotion. Increases weight gain by up to 15-20%. Banned in the EU in 2006, USA in 2016.
Understanding the routes of AMR bacteria ______, why and how AMR spreads in _____, _______, ____ bodies, ____, and _____ helps for controlling its spread.
mobility, animals, environment, water, food, humans
Unregulated use of antimicrobials in animal or humans leads to _______ ______.
AMR bacteria
Use of _____ (or _____) contained with AMR bacteria as fertilizer –> ?
feces, water
________ containing the AMR bacteria from feces –> ?
Food
AMR bacteria spread to the public via _____ and ____.
food, water
AMR Morbidity
___ ________ people in the US.
2 million
AMR Mortality
__-____ ______ people worldwide.
1-27 million
Usually affects the most immune-susceptible people (children, elderly)
Projected AMR Mortality annually by 2050?
10 million
Projected total global economic cost of AMR by 2050= ?
$100 trillion
Describe the plankton life stage as depicted below
- Attachment (e.g. flagella)
- Immobile/Sessile growth
- Biofilm maturation = hibernation
- Dispersal
Bacteria are classified into 5 major groups by their ____ _____ architecture.
cell wall
Describe the cell wall architecture of a classic Gram positive bacterium.
Several layers (tiers) of peptidoglycan with lipo/teichoic acid.
Describe the cell wall architecture of a Mycobacterium.
Mycobacterium peptidoglycan is covered by mycolic acid (wax or lipids).
Describe the cell wall architecture of a Classic Gram - bacterium.
Outer membrane (OM) made up of proteins and lipopoylsaccharide (lipid A and sugar or endotoxin).
Describe the cell wall architecture of Chlamydia.
Cell wall with either tiny OR no peptidoglycan. OM with proteins and lipopolysaccharide (lipid A and sugar or endotoxin).
Describe the cell wall architecture of Mycoplasma.
No cell wall, steroids in cell membrane.
Can’t destroy cell wall with penicillin?
Biofilms are a dense community of ______.
bacteria
Info for this slide
Bacteria have differnt enzymes that synthesize the cell wall, such as peptidase, ribosomes, polymerases, etc.
Folic acid = only exists in bacteria
pilli = methin conjugation
porins = pore
What are the mechanisms of action of antimicrobials?
- Cell wall synthesis
- Metabolism – folic acid synthesis
- 30S – protein synthesis
- 50S – protein synthesis
- RNA polymerase – mRNA
- DNA gyrase/topoisomerase
There are compounds tht inhibit or destroy the enzymes of bacteria; cell wall synthesizing enzyme penicilin binding protein is inactivated by beta ,actans such as pencilins, cephalo, etc.
Ribosomes of bacteria also attack bacteria using tetracyclines, mycol, etc.
RNA polymeas of bacteria is ianctivated by flrifancyins
DNA poly are ianctivated by fluoro and nitro
Folic acid is inhibited by sulfonamides
Bacteria are versatile to survive in nature and immediately acquire AMR to ____ _______.
new antimicrobials
What are the four AMR mechanisms?
- Reduced permeability
- Efflux pumping (vomiting).
- Drug inactivation by enzymes
- Target site change, modification, or protection.
______ formation is also a mechanism of AMR in addition to the four major AMR mechanisms.
Biofilm,
Biofilms limit uptake, aka _______ ________ which leads to:
- Induced ________ ______ (matrix) production as a barrier.
- Thick _________ communities as a barrier
- Low ______ & _______ supply to the center
- _______ _____-like cell in the ______ for persistence
decrease permeability, extracellular polymer, impenetrable, nutrient, oxygen, Dormant, spore, center
Of the 4 AMR mechanisms, the most efficient AMR mechanism varies with __________ ______.
antimicrobial type
Notes on this slide
Bacteria can use all possible strategies simultaneously to survive. Not all strategies are equally efficient. Some are more efficient than others. E.g. Tetracycline = about 70-80% of the tetracyclines are inactivated or made useless by resistant bacteria by efflux pumping.
20-30% remaining are either killed by enzymatic degradation, changing target site, or restriction/reducing permeability.
Majority of antimicrobials, like chloramphenicols, bacteria changes target site or hides it.
Beta lactams and amon = major mechanism if by enzymatic degradation.
AMR mechanism to beta-lactams may vary slightly between ____ vs. ____.
G+, G-
Gram positive (uptake _____) leads to a change in the _______ ____ of beta-lactams (mutation of ______/____).
SCC, binding site, peptidase, PBP
resist beta lactam by changing binding site
Gram negative (uptake of _____ &/or _____ ________) leads to beta-lactamase ______ production.
ESBL, carba plasmids, enzyme
Resist beta lacta by enzymatic degradation
What are some examples of beta-lactam inactivating enzymes that are transmitted by plasmids (ESBL and carbamenenmases)?
In gram negatives, there are two major enzymes that are very dominants in inactivating drugs (extended spectrum beta lactadasees) = inactivate microbials listed below).
Up to 40% of gram negative, aprticualrly enterobacteria, have resistance against these.
Carbapenams was created because of AMR. Such as ertapenem, imi, etc. Bacteria developed a new strategy to overcome this; they made an enzyme called carbapenamse; engulf plasmid and use it and secerete ezymes KPC, etc. When bacteria get carbapenemase, they are super dangerous because they are multi drug resistant to all betalactans including penicilins, etc. The option is to shift to tetracyclines, etc.
The origin of AMR in the ecosystem is from ______ and _______ transfer of AMR _____.
vertical, horizontal, genes
Acquired gene resistance via Horizontal gene transfer –> (3)
Free DNA in nature (transformation), Plasmid (conjugation), Bacteriophage (transduction).
Vertical gene transfer –> (1)?
intrinsic
E.g.Mycoplasma (no cell wall) –> resistant to antimicrobials acting on cell wall (beta lactams = penicillin, cephalosporin, carbapenem, monobactum).
What organizations established the guidelines for AMR detection by phenotypic methods?
- Clinical & Laboratory Standards Institute
(CLSI), USA - European Committee on Antimicrobial
Susceptibility Testing (EUCAST) or - International Standardization Organization (ISO)
notes from this slide
Do we need to know the bacteria?
The following six bacteria species, termed as ESKAPE are famous in AMR globally
- Enterococcus
- S. aureus
- K. pneumoniae
- A. baumannii
- P. aeruginosa
- Enterobacter
Which bacteria can be isolated in mannitol salt agar?
- Staphylococcus,
- Enterococcus,
- Listeria
- Micrococcaceae
Which bacteria can be isolated in Edward media?
- Streptococcus
- Enterococcus
Which bacteria can be isolated in Kenner-fecal agar media?
Enterococcus (selective media)
Which bacteria can be isolated in MacConkey Agar?
- Enterobacteriaceae
- Enterococcus
What are the types of Media that can be used for aerobic vs. anaerobic bacteria for screening isolates for AMR?
- Broth (liquid media)
- Agar (solid media)
depending on what you are trying to isolate
What are the types of Media that can be used for aerobic bacteria for screening isolates for AMR?
- Cation-adjusted mueller-hinton broth
- Cation-adjusted mueller-hinton agar
Fastidious bacteria requires 3-5% of lysed horse blood.
What are the types of Media that can be used for anaerobic bacteria for screening isolates for AMR?
- Brucella broth + 5 micrograms/ml hemin, micrograms/ml vitamin K and 5% lysed horse blood
- Brucella agar + 5 micrograms/ml hemin, micrograms/ml vitamin K and 5% lysed horse blood
Describe the disc diffusion AMR detection method
solid media format
qualitative method
1. E.g. ampicillin - immerse it in 10 microgram of antimicrobial, then put on bacterai already on agar, For cephatoxin - use 30 microgrm of microbial then incubate
Describe the E test AMR detection method
solid media format
Quantitative method
A strip impregnated with a drug on solid media
Describe the agar dilution AMR detection method
solid media format
quantitative method
agar dilution on solid media
Add concentrations of ampicillin to agar media
Start at 4 and go up
Describe the macrodilution AMR detection method
liquid media format
Microdilution
What is the standardized protocol for AMR testing for nonfastidious fast growing aerobic bacteria in 16-20 hours?
What is the standardized protocol for fastidious aerobic bacteria?
(Campylobacter, Erysipelothrix, Haemophilus, Helicobacter, Listeria,Neisseria, Pasteurella, and Streptococcus)
Same number of bacteria to innoculate the different media type, but incubation is different - time is longer and temp is longer and suffocate with CO2.
What is the standardized protocol for anaerobic bacteria ?
(Actinomyces, Bacteroides, Clostridium, Fusobacterium)
Use brucella agar or broth media
The guidelines instruct to include ________ ________ ______ reference bacteria strains for quality control.
genetically stable, known
Quality control during survey on beta-lactamases-
producing bacteria
E.coliATCC 35218
KlebsiellapneumoniaeATCC 700603
KlebsiellapneumoniaeATCC BAA-1705 or BAA-2814
AcinectobacterbaumanniiNCTC 13304
Quality control for testing bacteria of bioterrorism
E.coliATCC 25922
Staphylococcus aureusATCC 29213
Quality control for non-fastidious bacteria for agar/broth (MIC)
E.coliATCC 25922
PseudomonaaeruginosaATCC 27853
EnterobacterfaecalisATCC 259212
Staphylococcus aureusATCC 29213
Invalidate the test if there is no _____ & ____ growth of the quality control strains or their cut-off value inhibition zone by ____ or ____ is not ____ the range defined by CLSI, EUCAST or ISO
viable, pure, disk, MIC, within
MIC cut off values of most antimicrobials ranges between?
0.5 to 64 micrograms/ml
You should test against a several antimicrobials that you use in your state or farm/clinic because?
You cannot do the AMR testing for all of the antimicrobials on the market.
Consult CLSI manual for interpretation of the disk diffusion inhibition zone diameter (mm) and MIC (µl/ml) of your isolate.
Ampicillin, found isolate has a diamter of 17 mm means ampicillin killed isolate, if less than 13 = isolate is resistant.
Describe the steps of the disk diffusion test protcol.
Describe the disk diffusion method for detection of ESBL-producing bacteria.
Describe the disk diffusion method for detection of carbapenemase-producing bacteria.
Surveillance is defined as a ______ survey to measure in the ______, _____, ____, _____, etc.
periodic, population, food, feed, water
Describe how surveillance can be used to control AMR on farm, national, and global level(s)
- Survey on drug use pattern and prioritize the different drugs for use.
- Develop and use faster diagnostic testing of AMR
- Survey regularly antimicrobial resistance patterns in pathogens.
Describe how education can be used to reduce the spread of AMR.
Educate expertise for reducing drug use in animals and regulate, monitor, and evaluate if the drug use is as per the set priority.
Therapeutic use of antibiotics is defined as using antibiotics only to treat _____ individuals with a ______ dose, ______, and ______.
sick, required, duration, frequency
Metaphylactic use is defined as using antibiotics to treat an ____ herd/flock if you observe ____ sick ________.
entire, one, individual
Prophylactic use is defined as blanket ______ use if there is ___ sick animal.
seasonal, no
What are some alternatives to antibiotic usage for animals?
- Improve animal husbandry and nutrition
- Use vaccines and invest in new vaccine development
- New antimicrobial discoveries
- Phage therapy.
Bacteria use at least 4 mechanisms for AMR - name these four mechanisms.
porin, binding site, enzyme, and pumping
Bacteria can acquire AMR genes from at least 4 sources - name these sources.
plasmid, phage, free DNA, & parents
Testing of isolates for AMR can be done by 5 culture based assays - name these assays.
Disc diffusion, E-test, agar dilution, macrodilution, and microdilution
• PCR, whole genome sequencing, serology can also be used to detect AMR
AMR may be controlled by 6 broad interventions -
name these interventions.
judicious drug use, surveillance, diagnosis, discoveries, collaborations, & policy/practice change
