One-Health approach for the assessment of antimicrobial resistance dynamics across compartments through phenotypic, genetic and metagenomic methods

Stefano Pongolini - IZSLER

• AMR spreads through resistant bacteria and resistance genes

• AMR can be seen as a complex ecological issue

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Italian MoH-funded project – objectives:

• To study the contribution of humans, animals and environment

to AMR in human pathogens

• To assess the correlation between drug consumption and

AMR in human and vet compartments (strong, week, cross-

compartment, stable, unstable)

• To understand transmission dynamics across compartments

(how intense? Bidirectional? clonal vs horizontal)

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How can this be done? One-health collaborative project

• leveraging the high coverage of the study population of 4.5

millions people for AMR pathogens, zoonotic agents and

indicator bacteria along with the same isolates from the

parallel animal/food population

• collecting harmonized data on antimicrobial consumption in

animals and humans in the study population

• through metagenomics of samples representative of the

compartments and through investigation of individual isolates

from population screening (human) and farm screening

• Investigating the phenotypic and genetic features of AMR

across compartments (types and diversity)

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In the lab...

• metaresistomics of samples

from sewage of hospitals,

community, farms

• Characterization of resistant

isolates from humans and

animals

CLASSYFARM platform for epidemiosurveillance

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Antibiotico Concentrazione*

Ampicillina 8 mg/l

Cloramfenicolo 16 mg/l

Colistina 2 mg/l

Ciprofloxacina 0,064 mg/l

Meropenem 0,125 mg/l

Florfenicol 16 mg/l

Cofetaxime 2 mg/l

5.305 isolates tested

1) 3.865 clinical

2) 1.440 veterinary

total: 37.135

Salmonella phenotypic screening

AMR screening 2012-2015 of 5.305 isolates (4,473 for colistin)

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AMP FFN CIP CTX CHL COL MEM

%Isola

R

Human

Vet

AMP = AMPICILLIN CTX=CEFOTAXIME MEM=MEROPENEM

FFN = FLORFENICOL CHL = CLORAMFENICOL

CIP = CIPROFLOXACIN COL=COLISTIN

mcr-1: source by sub-group

mcr-1 by subgroup and serotype

mcr-1 in Salmonella spp. by source mcr-1 in Salmonella 4,[5],12:i:-

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Open questions:

• Is mcr-1 more prevalent in animal than human isolates

because of

o dynamic disequilibrium due to recent introduction in

animals?

o instability in the human compartment due to low selective

pressure?

Phylogenetic tree of

S. 4,[5],12:i- genotype

mcr-1: swine to human transmission?

Thank you for attention

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