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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
CIDM-PH_November 2015
Adult Gut Microbiota
different microbial communities associated with different nichesupper digestive tract
↑
CIDM-PH_November 2015
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)
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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
CIDM-PH_November 2015
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