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Emergence and spread
of AMR
Tim McAllisterPrincipal Research Scientist
Agriculture and Agri-Food Canada
Adjunct Professor
Faculty of Veterinary Science, Department of Production Animal Health
Cummings School of Medicine, Department of Physiology and Pharmacology
Email: tim.mcallister@canada.ca
Date: Sept 22, 2020
Learning Objectives
How bacteria became resistance to antibiotics?
How diverse the mechanism of resistance is?
Role of horizontal gene transfer in dissemination of resistance genes in ecosystem
Co-occurrence of resistance genes to antibiotics, biocides and metals on plasmids.
Emergence and spread of AMR Date:
Lecture Content
Antimicrobial resistance
Mechanisms of resistance
Selection of resistance isolate
Resistance before antibiotics
Dissemination of resistance genes
Horizontal gene transfer in different ecosystems
Emergence and spread of AMR Date:
Bacterial warfare- the never ending battle
Emergence and spread of AMR Date:
Lecture Title: Date:
3. Competitive exclusion
1. Competition for nutrients2. Direct antagonism
Approaches to bacterial warfare
Antimicrobial
resistance elements
from 4 human skeleton
Shigella flexneri isolate
resistant to penicillin and
erythromycin Available for
human use
First case of penicillin
resistance
Resistance before antibiotics
Lecture Title: Date:
Discovery of
Penicillin
1927
1941
1947
1915
950–200 CE
Gut-microbiome of pre-
Columbian Andean mummy
from Cuzco, harbor resistance
genes
950-1170 AD
5k yrs.
presence of resistance
genes in Siberian
permafrost
presence of
vancomycin resistance
gene in permafrost
30k yrs.
Reference:Perry J, Waglechner N, Wright G. The Prehistory of Antibiotic Resistance.
Cold Spring Harb Perspect Med. 2016;6(6):a025197. Published 2016 Jun 1.
doi:10.1101/cshperspect.a025197
Forms of antimicrobial resistance
Acquired
➢ Mutation (endogenous and vertically transmission)
➢ Horizontal gene transfer (Conjugation, transformation and transduction)
Intrinsic
➢ Due to structural or functional trait allowing tolerance by all members of a group (species,
genus, etc)
✓ Inaccessibility of the drug into the bacterial cell (Gram-negative cell wall)
✓ Extrusion of the drug by chromosomally encoded active exporters (Pseudomonas)
Emergence and spread of AMR Date:
Decreased uptake
Overexpression of
efflux pump
Enzymatic degradation
DNA
Target alteration
A B
Alterative enzyme
Mechanism of resistance
Pseudomonas aeruginosa can
produce pumps to get rid of
several different important
antibiotic drugs, including
fluoroquinolones, beta-lactams,
chloramphenicol, and
trimethoprim.
Klebsiella pneumoniae
produce enzymes called
carbapenemases, which
break down carbapenem
drugs and most other
beta-lactam drugs
Gram-negative bacteria have an
outer layer (membrane) that protects
them from their environment. These
bacteria can use this membrane to
selectively keep antibiotic drugs
from entering.
Staphylococcus
aureus can bypass
the drug effects of
trimethoprim
mutations in RNA polymerase
and DNA gyrase, resulting in
resistance to the rifamycins and
quinolones
Resistance to macrolide
involves modification of
their target site on the
ribosome.
Emergence and spread of AMR Date:
Tetracycline resistance – a single example
of resistance mechanisms in bacteria
Active efflux: tet(A), tet(B), tet(C), tet(D), tet(E), tet(G), tet(H), tet(I), tet(J), tet(Y),
tet(30), tet(31), tet(K), tet(L), tet(V), tet(Z), tetP(A), tcr3, otr(B), tet(33), tet(35),
tet(38), tet(39)
Ribosomal protection: tet(M), tet(O), tet(Q), tet(S), tet(T), tet(W), tetP(B), otr(A),
tet, tet(32), tet(36)
Enzymatic modification: tet(X), tet(34), tet(37)
Known - Unknown: tet(U), otr (C)
Unknown - Unkowns: ???
Emergence and spread of AMR Date:
Lecture Title: Date:
Overview of microbial drug resistance
Chromosome and
cytoplasm
RNA Polymerase
mutations
Rifamycin
DNA gyrase and
topoisomerase IV
mutations
Quinolones
Novobiocin
Ribosomal mutations
and modification
Aminoglycosides
Acquired metabolic by-
pass
Sulphonamides
Trimethroprim
Mupirocin
Reduction
Nitroimidazoles
Modifying
enzymes
Aminoglycosides
Chloramphenicol
Fosfomycin
Streptogramin A
Tetracyclines
Rifamycins
Inner
membraneCell wall
New or
mutated PBPs
Penicillin
Cephalosporins
Monobactams
Carbapenems
Beta-lactamases
Penicillin
Cephalosporin
Monobactams
Carbapenems
Acquired ligases
Vancomycin
Teicoplanin
Outer membrane
(Gram –ve)
Permeability and porin deficiency
Penicillins
Cephalosporins
Monobactams
Carbapenems
Quinolones
Aminoglycosides
Tetracyclines
Membrane pumps
Tetracyclines
Fusidic acid
Quinolones
Bacitracin
Chloramphenicol
Lincosamides
Betalactams
Aminoglycosides
Macrolides
Antiseptics
Emergence and spread of AMR Date:
One DrugSeveral
Mechanisms
Many
Bacteria
Variable
phenotype
Variable
clinical
importance
Mode of
acquisition
Mechanism Bacterial species
None Reduced
permeability
Pseudomonas spp.
Conjugation Enzymatic
inactivation
Enterobacteriaceae
Staphylococci
Unknown Target replacement Staphylococci
Transformation Target modification Streptococci
Ex: Beta-lactam
resistance
Emergence and spread of AMR Date:
Selection of resistance
The origin of species by means of natural selection,
1859 Charles Darwin
Variation within species occurs randomly and that survival or extinction of
each organism is determined by that organism’s ability to adapt to its
environment
Emergence and spread of AMR Date:
”Snowball rolling downhill effect”
Emergence and spread of AMR Date:
Time
An
tib
ioti
cs s
uscep
tib
ilit
y
Dissemination of resistance genes
Vertical transmission Horizontal transmission
The mobilization of ARGs on
plasmids, transposons, and
integrons has enabled resistance
genes to spread horizontally
across strains and species,
greatly facilitating the
development of resistance in
numerous pathogens.
Emergence and spread of AMR Date:
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• In animal farming
• In community
• In healthcare facilities
• Through travel
https://www.youtube.com/watch?v=4KMWun3Og8I
Drugs makes bugs (3min video)
Horizontal gene transfer in ecosystemsSoil ecosystems harbor an extremely
broad diversity of microbiota reflecting
plant type, soil type, soil management
regime, and other factors
More than 70% of the earth
surface is covered with water,
and the World Ocean is one of
the principal components
forming the climate and
biosphere of the Earth.
biofilm communities are widespread in
many natural ecosystems. Majority of
microbiota found in natural, clinical, and
industrial settings persist in association
with surfaces and not in the planktonic
state
Conditions in the gut can be considered as very favorable for
HGT. Because of continuous inflow of nutrients, the
population densities are extremely high and thus conducive
to the HGT mechanisms requiring intimate cell-to-cell contact
such as conjugation.
Ref: Aminov RI (2011) Horizontal gene
exchange in environmental microbiota.
Front. Microbio. 2:158. doi:
10.3389/fmicb.2011.00158
HGT in soil ecosystem
The microbiota of soil, especially of manure-fertilized soil, harbors a wide variety
of MGEs enabling extensive HGT within and among microbial ecosystems.
Clinically relevant class 1 integrons are also introduced into soil via manure
application.
A novel plasmid type with low G + C content was captured from manure-treated
soil microbiota by conjugation to E. coli recipient.
The species of Acinetobacter are the putative hosts for low G + C plasmids in soil
ecosystem.
Similar to the plasmid-mediated HGT, the diversity, and dynamics of
bacteriophages is also mostly confined to the nutritionally rich hot spots such as
the rhizosphere.
The possibility of natural genetic transformation of B. subtilis and Pseudomonas
stutzeri has been demonstrated in a soil/sediment model system
Emergence and spread of AMR Date:
HGT in aquatic ecosystem
Antibiotic resistance phenotype and the presence of plasmids in marine bacteria tend to
correlate with the degree of pollution, especially by toxic chemical waste.
Resistance phenotype was more frequently encountered in bacteria from seawater samples
collected offshore than for those collected near shore.
Plasmids with an enormous size range are also widespread in the Roseobacter clade (25%
of the total marine bacterial community) and thus play a global role in this ecosystem
Emergence and spread of AMR Date:
HGT in gut ecosystem
The intestinal microbial ecosystem is extremely enriched by MGEs thus making it the
arena of a potentially extensive gene exchange.
The discovery of ICEs among the representatives of Bacteriodetes, the major bacterial
phylum in the mammalian gut.
Indeed, the taxonomically different representatives of gut microbiota may share the pool of
closely related antimicrobial resistance genes.
The occurrence of conjugal plasmid transfer and transduction was also observed in the
flea, house fly gut and ciliate's food vacuole.
Emergence and spread of AMR Date:
HGT in biofilm ecosystem
Biofilms are the matrix-enclosed aggregates of microbiota, attached to each other
and to biological or non-biological surfaces
Biofilm formation is linked to the pathology of many infectious diseases, and
biofilms are notoriously difficult to eradicate because of the increased level of
resistance to antibiotics.
They are the hot spots for HGT because they provide high population densities
and close proximity of cells, cells in biofilms are metabolically active, and the
microbiota is protected against harsh environment, predators, and immune
surveillance by the extracellular matrix in which the cells are encapsulated.
Emergence and spread of AMR Date:
Conjugal plasmid transfer that is implemented through the synthesis of pili and
type IV secretion system contributes to the intimate cell-to-cell contact, thus
facilitating the formation and growth of biofilms.
The presence of prophages in the host’s genome may have a modulatory effect on
biofilm formation.
A partial phage-mediated lysis of a proportion of microbiota in biofilm, due to
spontaneous phage induction, may provide the eDNA supply, thus contributing to
biofilm formation and maintenance by the remaining bacterial populations.
Emergence and spread of AMR Date:
Pollution linked to AMR
Heavy metals in environmental reservoirs may contribute to
selecting antibiotic-resistant strains
Pseudomonas aeruginosa and Escherichia coli - co-occurrence of
resistance to several heavy metals and antibiotic classes.
Cross-resistance – One resistance system confer resistance to
both.
Co-resistance – Resistance gene co-located on same genetic
element
Co-regulation – Transcriptional and translational regulation by
same regulator in response to stress
Emergence and spread of AMR Date:
Reference: Nguyen, C.C., Hugie, C.N., Kile, M.L. et al. Association between
heavy metals and antibiotic-resistant human pathogens in environmental
reservoirs: A review. Front. Environ. Sci. Eng. 13, 46 (2019).
https://doi.org/10.1007/s11783-019-1129-0
Zinc, a common and toxic metal known to
co-select for antibiotic resistance with
industrial and agricultural activities
Bacterial isolates from the sediment were
used to test for patterns of cross resistance
between zinc and cefotaxime, oxacillin and
trimethoprim.
Significant increase in tolerance to these
antibiotics in isolates that exhibit resistance
to zinc.
Emergence and spread of AMR Date:
Reference: Dickinson, Andrew William, et al. "Heavy metal pollution
and co-selection for antibiotic resistance: A microbial palaeontology
approach." Environment international 132 (2019): 105117.
HGT and heavy metals
Emergence and spread of AMR Date:
Heavy metal Cu promotes the plasmid
RP4 mediated conjugative transfer
environmentally by cell damage effect,
facilitating the transmission of ARGs.
Reference: Wang, Qing, et al. "Heavy metal copper accelerates the conjugative transfer of antibiotic
resistance genes in freshwater microcosms." Science of The Total Environment 717 (2020): 137055.
HGT and biocide
The global Biocide consumption is estimated
at $ 6.6 billion
The use of biocides might lead to increased
resistance to antimicrobial agents used for
treatment of humans and animals, through
increasing mutation rates in bacteria or
increasing horizontal gene transfer.
Ethanol, chlorine, chloramine, H2O2 and,
nano-titanium dioxide (TiO2) can promote
conjugal transfer of resistance plasmids.
Triclosan and chlorhexidine induced
horizontal gene transfer at low
concentrations.
Emergence and spread of AMR Date: Jutkina, J., et al. "Antibiotics and common antibacterial biocides stimulate
horizontal transfer of resistance at low concentrations." Science of the total
Environment 616 (2018): 172-178.
Co-occurrence of resistance genes to
antibiotics, biocides and metals on plasmids.
Emergence and spread of AMR Date:
The network shows most
frequently observed co-occurrence
of resistance genes to antibiotics,
biocides and metals on plasmids.
Connection between
metal/antibiotic resistance genes
and markers of MGEs
Reference: Pal, Chandan, et al. "Metal resistance and its association with antibiotic resistance." Advances in microbial physiology.
Vol. 70. Academic Press, 2017. 261-313.
Additional Resources
https://www.nytimes.com/video/health/100000005932983/bacteria-antibiotics-war.html
Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G. The shared
antibiotic resistome of soil bacteria and human pathogens. Science.
2012;337(6098):1107-1111. doi:10.1126/science.1220761
Granato, Elisa T., Thomas A. Meiller-Legrand, and Kevin R. Foster. "The evolution and
ecology of bacterial warfare." Current biology 29.11 (2019): R521-R537.
Bush, K. Past and present prespective on beta-lactamases. Antimicrobial agents and
chemotherapy. https://doi.org/10.1128/AAC.01076-18.
Lecture Title: Date:
Summary
Bacteria have different mechanisms of antibiotic resistance
There may be different ways to confer resistance to one single
antibiotic or vice versa (cross resistance)
Different ecosystems facilitate the dissemination of resistance gene
among different and similar species.
Resistance to heavy metals and biocide are linked to antibiotic
resistance.
Lecture Title: Date:
Questions
Lecture Title: Date:
Break!
10 minutes break
After Break
Discussion session
Lecture Title: Date:
Discussion Question(s)
Lecture Title: Date:
What are some of the factors associated with spread of
antimicrobial resistance from livestock production systems
that should be considered when trying to gage potential
risks to human health?
Thank You!
Email: tim.mcallister@canada.ca
Twitter: timmcallister7
Lecture Title: Date:
Co- Chair VTEC 2021 Web Site: https://vtec2021.org/ https://www.facebook.com/vtec2021 https://twitter.com/vtec2021
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