Dr Carola Venturini - Ministry of Health

CIDM-PH_November 2015

Gut microbial ecology:

the side‐effects of antibiotic treatment

Dr Carola Venturini

J. Iredell group, CIDM, WMI

The Microbiome

Microbiome Microbiota

collective and representative

microbial genome;

all interacting microbial genomes

microorganisms;total ecological community of commensal,

symbiotic and pathogenicmicrobes


Adult Gut Microbiota

different microbial communities associated with different nichesupper digestive tract

↑


Proteobacteria (Enterobacteriacae)

Bacteriodetes (rod-shaped Gram negative)

Firmicutes (Gram positive – Staphs; Clostridia)

Fusobacteria

Actinobacteria

Cyanobacteria

Digestive Tract Microbiota

beneficial effects on host physiology

inter-individual variation

complexity and stability ↑ from infancy to adulthood

vulnerable to perturbations

Dysbiosis - altered microbiota & disrupted homeostasis

• associated with disease

• due to genetics, immune status, diet, age, sex,

interventions, drugs (antibiotics)


Antibiotics in the ICU

“A post-antibiotic era…a very real possibility” (WHO, 2014)

Antibiotic use = antibiotic resistance (AR)

ICU: high risk of infection & high antibiotic usage

Timely empiric therapy is critical for survival

E. coli and K. pneumoniae MR ESBL types = major concern

Stewardship = strategies to curtail AR by reducing inappropriate antibiotic use


short- and long-term effects (≠ recovery time-span) including:

Reduction in biomass and diversity

Proteobacteria blooms

Establishment of opportunistic pathogens

(P. aeruginosa; MRSA; S. thyphimurium; C. difficile)

Amplification of AR (resistome; HGT; resistant species)

Antibiotics and Dysbiosis

A

A

www.giantmicrobes.com0


but…

Antonopoulos DA et al. (2009)

Penicillin-like antibiotics → rapid recovery

- long-term (years) changes

- linked to increased prevalence of pathogens and AR markers

different antibiotics have a different impact on the microbiota

3GC/4GC → slower and poorer recovery

Research Focus

Ecological effects of antibiotic intervention on the

microbiome of ICU patients

Enterobacteriacae

Antibiotic resistance


Cefepime vs anti-pseudomonal penicillin combinations (APP-): effects on culturable microflora

ICU cycling protocol alternating FEP with APP-

FEP = ↑ AR infection (Ginn et al., 2012*)

Sub-study: patients (n=206) directly from the community

A. Gram-negative colonisation and resistance rates

B. E. coli population profiles before (B; ≤48 h) and after

(A; ≥72 h) FEP


Cefepime vs APP-

(A) GNB colonisation and resistance rates

TIM resistance rates with ICU stay

FEP exposure = acquired TIM resistance (p=0.027)

FEP = more AR organisms after ≥72h (~2.5x; OR 2.439,

CI 1.096-5.429, p=0.027)CIDM-PH_November 2015

(B) E. coli population profiles: strains

different clones dominate the B and A samples

phylogroups associated with virulent traits (B2; D/E)

are prevalent but increase in the A sample

(B) E. coli population profiles: plasmids

> strains carrying large plasmids in the A samples

> complexity in the A sample with the frequent

introduction of new plasmids

= ↑ HGT/ transmissible ARCIDM-PH_November 2015

(B) E. coli population profiles: resistance genes

mobile genetic elements (Tn; IS) associated with AR genes

also identified


Microbiome wide effects:3GC/4GC and penicillin-like antibiotics

DAY 1 2 3 4 5 to discharge

24h 48h 72h 96h +24h…………ICU admissionB A

Human experiments

Animal experiments

+ Ab n=5(x2)

no Abn=5(x2)

+ Ab3GC

no Ab+ Ab

TZP or amp-clav

no Abn=10

Ab

B A

6 ≥ n ≤ 12

Microbiome wide effects

- metagenomic analysis = 16S rRNA gene sequencing

- relative abundance (phylum; order)

- diversity measure

- microbiology on culturable aerobic flora

- effects on Enterobacteriacae

- opportunistic pathogens

- GBN resistance markers

- BOTTLENECKS

- sampling (individuals; body site)

- specimen collection and storage

- DNA extraction


Summary

Choice of antibiotic is more important than homogeneityfor selection pressure (penicillin-like superior to 4GC)

4GC exposure leads to increased AR

AR increase in E. coli by (1) amplification/establishment ofstrains carrying large mobilisable plasmids and AR genes,and (2) acquisition and transfer of these resistance vectors

Microbiome-wide studies: NB metadata + sampling size +animal experiments

J. Iredell group (Andrew, Sally) CIDM, WMII. Paulsen, S. Tetu, Hasinika Macquarie UniversityBrooke Wilson & Agnieszka Wiklendt Westmead HospitalI. Seppelt Nepean HospitalWestmead & Nepean ICUs

Dr Carola Venturini - Ministry of Health

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