Recapitulating the burden of antibiotic resistance

and the health risk of resistance genes

Recapitulating the burden of antibiotic resistance

and the health risk of resistance genes

Perception of the threat

Science: objective appraisal

Far from being magisterial in its

objectivity, science was

conditioned by history, society

and the prejudices of scientists.

Thomas Kühn

Zum einen soll die wissenschaftliche Methode von allen subjektiven Einflüssen abstrahieren

und den Prozess der Erkenntnisgewinnung damit für jeden nachvollziehbar machen

Lukas Elsler (Ludwig-Maximilians-Universität München)

Lorraine Daston,

Peter Galison 2010

A Symposium on Fears

Wendy Lesser (Berkeley, CA)

The Culture of Fear in the XXI Century

In our world, a world of wonders…….

Current fears take the form of the Alexis de Tocqueville paradox:

“plus tout va bien, plus on a peur”, or

“the more better things occur, the more fear we have”

Charlie Hass

Fear of Antibiotic Resistance

Frank Furedi (sociologist) argues that

perceptions of risk,….. controversies over health, the environment and technology have little to do with science or empirical evidence. Rather, they are shaped by cultural assumptions about human vulnerability.

KIDULTHOOD

2015

2016

Examining fears in Antibiotic Resistance

Problems:

• Fear, a cultural construct, tends to fix as proved the worse expectations

• False identity between that we are scared of and that is really dangerous

• Continuous fear without solutions discredit scientific efforts

• Fear might suggest “we are at the mercy of the nature”

• Fear might be sustained and exploited by interested parties

Advantages:

• Fear facilitates analysis and adaptive responses (Ebola, AIDS,…)

• Fear stimulates motivation and creativity: emotion and knowledge

• Fear improves social and organizational cooperation

• Fear rise our awareness not to stop scientific and social progress

Fear in antibiotic resistance is converted in fear to antibiotics

More than 20 years ago…

Identical “fighting strategies against antibiotic-resistance! have been repeatedly

and monotonously proposed over and over again across meetings and years…….

The unmet need of objective threat

ratings in antibiotic resistance

Exist or will certainly happen

We are confident will actually happen

Can happen and is likely to happen

Can happen but is not likely to happen

Will not happen

Threat 1: “Back to the pre-antibiotic era”

A widely repeated over-exaggeration?

• History never comes back again, never back to 1916. The social and medical resources in 2016 cannot be compared with those of 1916.

• Infectious diseases start declining before the discovery of antimicrobial agents: progress of hygiene-ecology and social welfare

• Many severe infectious diseases can be cured in our days without antibiotics, because of the advances of Medicine. (Guerrant RL et al., Cholera, diarrhea, and oral rehydration therapy: triumph and indictment, CID, 2003)

Severe illness, Death

Etiological therapy but therapy of the cascade of pathogenic events

A bacterial

“bullet”?

Threat 1: “Back to the pre-antibiotic era”

A widely repeated over-exaggeration?

• History never comes back again

• Infectious diseases start declining before the discovery of antimicrobial agents: progress of hygiene-ecology and social welfare

• Many severe infectious diseases can be cured in our days without antibiotics, because of the advances of Medicine. (Guerrant RL et al., Cholera, diarrhea, and oral rehydration therapy: triumph and indictment, CID, 2003)

Severe illness, Death

Intensive Care Procedures

Threat 2: Many deaths as a direct result of antibiotic resistance

Need of better studies estimating the magnitude of the burden of antibiotic resistance in relation with mortality

Mantra figures: “At least…”

• 25,000 deaths/year because Ab-R in Europe (EMA-EUROPA, 2012)

• 23,000 deaths/year (CDC Ab-Resistance Threats in the US, 2013)

Very rare (difficult to achieve) case-control studies

• 18 deaths per million/year: 2% of deaths by coronary artery disease (940)

• 9,000 deaths/year in Europe?Kanerva et al. Antimicrobial Resistance and Infection Control 2012, 1:33

Who is dying from antibiotic resistance?

Threat 2: Many deaths as a direct result of antibiotic resistance

The population at risk of dying because antibiotic resistance

• Immuno-depressed patients

• Elderly (>75)

• Admission to the ICU

• APACHE II score at ICU admission

• Large spectrum antibiotics

• Special treatments

• Rhinogastric tube in place

High Risk of Death

Bu

rden

of

Dis

ease

Perfect Health

Population at

risk of dying

because Ab-R

Ab-RAb-S

• Nutritional immuno-deficiency

• Poor medical care, shortage ICUs

• Resistance to cheap available agents

Developing countries:

Threat 3: Antibiotic-R increases the number of severe infections

Antibiotic-selection of antibiotic-

resistant microorganisms, and

elimination of local competitors

results in a increase of the total

number of resistant organisms.

Increase in the probability of

translocation-invasion by resistant

organisms (bacteremia)

The probability of bacteremia

(translocation-invasion) by

frequent but minority commensal

pathogens (as E. coli,

Enterococcus) is proportional to

their total population size.

Inside the host

probability of

translocation,

invasion

Microbiota

Susceptible microbiota

Susceptible

microbiota

Resistant

microbiota

probability of

translocation,

invasion

overgrowth

red

uc

tio

n d

ive

rsit

y

• The incidence of nosocomial bacteremia due to highly-resistant microorganisms increased8.7 times as fast as non-resistant ones (1996-2005)

• Moreover, the increase in resistance does not replace infections with susceptible pathogens, but adds to the total burden of bacteremia

• Hospitalized patients have become progressively more severely ill over the last 10 years. (Ammerlaan HSM, Bonten MJM et al., JAC 63:1064–1070, 2009)

Tedim ASP et al., AEM 2015

Enterococcus faeciumE. coli phylogroup B2

Irene Rodriguez ECCMID 2014

Bacteremia

RYC Hospital (1996-2012)

Threat 3:

Antibiotic-R increases the number of severe infections

resistant

• But it remains unclear if in many severe infections there is a worse outcome when caused by antibiotic resistant microorganisms.

Possible reasons:

• Bias: Bacteremia patients presenting with severe symptoms are probably more likely to have antibiotics administered prior to blood culture draw compared with less ill patients. Only those caused by resistant organisms are able to grow in cultures.

(Stig Lønberg Nielsen, PhD Thesis 2015, Dan Med J 62: B5128)

• Lesser virulence of antibiotic-R bacterial variants:

1- Multi-resistant clones are frequently derived from commensal (less pathogenic) lineages

2- Pathogenic fitness costs of antibiotic resistance (Jon Tyrell, PhD Thesis 2014, Cardiff University)

In neonatal sepsis caused by blaNDM-1-positive Enterobacteriaceae, mortality was lower (13.3%) than cases caused by blaNDM-1-negative (22.2%)

(Datta et al., PLoS One. 9:e112101, 2014)

Threat 3:

Antibiotic-R increases the number of severe infections

• In detailed case-control studies in Greece, overall mortality in ICU patients with carbapenem-resistant K. pneumoniae was not different from the mortality of the control group with carbapenem-susceptible strains (same APACHE II score)

Expectation:

The mortality rates of antibiotic resistant infections should be

higher that in the case of infections by susceptible organisms

Carbapenem-R

K. pneumoniae

IT IS NOT NECESSARILY THE CASE

Antibiotic resistance increases the number of severe

infections (as bacteremia), and hence overall mortality

* Possible role of selective decontamination, SDD, SOD (Plantinga, Bonten, Crit. Care 2015)

• The adverse association between MRSA and all-cause mortality or infection-related mortality, were not

statistically significant after adjustment for important prognostic factors including age,

comorbidities, severity of acute illness, metastatic infections, and long-term care facility resident status

Falagas ME et al., JAC. 60:1124, 2007; Vardakas KZ et al., J. Infect 70:592. 2015; Yaw LK et al., LID 14:967, 2014

Threat 3:

Antibiotic-R increases the number of severe infections

Threat 4:

The invasion by resistant strains of normal microbiota

Treated

patient

Non-treated

Fitness R-bacteria

Treated and favoring condition

for R colonization

(as elderly)

Large R-colonization of non-treated

Age and cases E. coli bacteremia RYC Hospital Non-treated

• Normal microbiota might become

antibiotic resistant microbiota

• More risk for more patients

Threat 5:Antibiotic-R altering the human-microbiota interactions

Human-microbiota common evolutionary history

Bacteroidetes

Clostridium

C-I

Clostridium

C- XIVa

Proteobacteria

(Enterobacteriaceae)

• Most of the significant antibiotic-resistance genes are located in minority

bacterial populations organisms

• When minority bacterial populations reach majority, there is an ecological

disturbance that might be deleterious for the system –unpredictable

clinical consequences under global overuse of antibiotics

• Consequences of acquisition of resistance by members of majorities?

M. Rajilic´-Stojanovic et al.

EM. 2012

Reads/kb (normalized per gene size)

Resistance genes in minority populations revealed in metagenomic capture

platforms, less detectable in conventional metagenomics, addressing majorities

(V. Fernandez-Lanza, Baquero, Coque, ICETAR 2015)

Conventional metagenomics

Resistance genes capture platform

• Increase in total local number of resistant strains means increase the absolute amount of resistance genes, and mobile genetic elements

gene

integron

transposon

plasmid, ICE

Antibiotic resistance

might increase the

density of tools involved

in microbial genetic

interactions,

with

unpredictable

consequences

Threat 6Antibiotic resistance accelerates its own evolution

Transmission of R genes (red) is probably

favored by homology of the incoming R

clone with resident ones (yellow)

Selection of incoming clone +

selection of the resident homologous clones

The risk of propagation of R genes increases with the homology between incoming R clones and

susceptible “kin” resident clones

Threat 7

High-speed “global dissemination” of R-clones

A “chain-reaction-like” spread of resistance in kin clonal populations?

Example of global dissemination: Petty NK et al., Proc Natl Acad Sci U S A. 2014, 111(15):5694-9 (E. coli ST131)

Kin clones already in place acquire resistance: INVASION OR CONVERSION?

Val Fernández Lanza, Coque, de la Cruz, Baquero et al., Bioinformatics 2016

Bipartite network with

Dark Blue nodes: Genomic Unit, GU, here

E. coli strains (27)

Colored nodes: Homologous (accessory)

Protein Clusters, HpCs (6,141)

Edges: Links between GUs and HpCs

(34,459)

Edge weights: Phylogenetic distance

for each HpC and the consensus HpC

AccNET representation of the accessory

genome of 27 Escherichia coli chromosomes

Genome proximity is a consequence of the

similarity between accessory genomes.Pseudo-core genome: HpCs shared by most but

not all genomes: cluster

http://sourceforge.net/projects/accnet

AccNET: Accessory Genes Constellation Network

Detecting clonal families

Threat 8:Antibiotic release and antibiotic resistance altering the environmental life-sustaining microbiosphere

• Possible ecological functional disturbances by the antibiotics in the environment include nitrogen transformation, methanogenesis and sulfate reduction

• For instance, Cyanobacteria, largely susceptible to antimicrobial agents, as such type of organisms accounts for more than 70% of the total phytoplankton mass, and are responsible for more than a third of the total free O2 production, or CO2 fixation.

(Baquero F et al., Curr. Op. Biotechnol. 2008; 19:260–265; Dias E, et al. Frontiers in Microbiology 2015)

• Naturally-antibiotic resistant organisms might substitute under extended antibiotic pollution criticalsusceptible organisms of huge ecological interest. Alternatively, acquisition of antibiotic resistance might alter fitness or critical functional traits.

• Antibiotic disturbance of interbacterial signaling (semiotic space) with microecological consequences

Two final remarks:

“Fighting, defeating antibiotic resistance” A naïve statement.

Leslie Orgel’s Second Rule:

"Evolution is cleverer than you are.“

• We have 1012 E. coli cells in the intestine of a single human host, with about 200,000 mutations per gene and day.

• A gram of soil may contain between 5,000 and 40,000 speciesof microbes

• “Modular engineering of resistance”:

Transposases are the most common and abundant genes in nature.

Unlimited offer of bacterial genetic variation and

engineering in an unlimited number of niches

The Tool and the Goal• Don’t Confuse a Tool with a Goal!

• Our medical goal is NOT to fight antibiotic resistance, but morbidity and MORTALITY of BACTERIAL INFECTIOUS DISEASES.

Resistance

Antibiotic

hammer

The toolkit for controlling infections

The Tool and the Goal

• Don’t Confuse a Tool with a Goal!

• Our medical goal is NOT to fight antibiotic resistance, but morbidity and MORTALITY of BACTERIAL INFECTIOUS DISEASES.

Resistance

Antibiotic

hammer

The toolkit for controlling infections

Awl

Baquero, F., et al (2014). Counteracting antibiotic resistance: breaking barriers among antibacterial strategies. Expert Opinion

on Therapeutic Targets, 18, 851-861.

• Teresa Coque, Val Fernández-Lanza, Ana-Sofía Tedim-Pedrosa, Rafael Cantón,…….. in our Department*

• Marc Bonten (Utrech), ICETAR presentation 2015, Rob Willems and Willem van Schaik (Utrech), coordination EvoTAR FP7

• Tim Walsh and Jon Tyrell (Cardiff) , discussions around Jon PhD Thesis.

• Bruce Levin (Emory)

• … and many others….

Acknowledgements

Integrated Knowledge Map

Universe of genes from

families of basic enzymes

In bacteria!

Acetyl-transferases

Methylases

Nucleotidyl-

transferases

Esterases

Phosphorylases

Peptidases

Thiol-transferases

Hydroxylases

GlycosyltransferasesOxydases….

Antibiotic resistance genes in nature

Universe of genes

encoding basic enzymes

In bacteria!

Enzyme with some

coincidental antibiotic

detoxification activity

Universe of genes encoding

basic enzymes

In bacteria!

Antibiotic exposure

Enzyme with some

coincidental antibiotic

detoxification activity

Universe of

different genes

encoding basic

enzymes

In bacteria!

Selection of organisms

with the natural enzyme

with coincidental

antibiotic detoxification

activity

Concentration high

Effective selection of antibiotic resistance at very small antibiotic

concentrations

(Negri, Levin, Blázquez, Lipsitch, Baquero, AAC 2000); Baquero, Negri.

Selective compartments for resistant organisms in antibiotic

gradients, Bioessays 1997)

Universe of

different genes

from a family of

basic enzymes

In bacteria!

Climbing the hill

Under continuous exposure,

climbing the hill to reach high

antibiotic resistance: from

soft “coincidental functions”

to specialized antibiotic-

resistance functions

Decre

ase i

n β

-m

ino

rity

Antibiotic exposure increases

resistant minority populations

able to produce bacteremia

Threat 3:

Antibiotic-R increases the number of severe infections

0

10

20

30

40

50

60

70

80

90

100

Before During After Before During After

Susceptible Resistant

The importance of proportions of susceptible versus resistant populations

The effects on resistance frequencies of new antibiotics or resistance-inhibitors

Susceptible

and

resistant are

equally

inhibited

If the new drug is

introduced and

used early,

resistance might

collapse