microbial interactions in an endotracheal biofilm
TRANSCRIPT
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Microbial interactions in an endotracheal biofilm
Surbhi Malhotra-Kumar, PhDLaboratory of Medical Microbiology
Vaccine & Infectious Disease InstituteUniversity of Antwerp, Belgium
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Contents
• Why study the ETT biofilm?
• The ETT microbiome: molecular analysis and impact on development of ventilator-associated pneumonia (VAP)
• Mono- and -polymicrobial VAP
• Modelling ETT interactions
• Conclusions
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Contents
• Why study the ETT biofilm?
• The ETT microbiome: molecular analysis and impact on development of ventilator-associated pneumonia (VAP)
• Mono- and -polymicrobial VAP
• Modelling ETT interactions
• Conclusions
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Why study the ETT biofilm?
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Biofilm formation on the endotracheal tube
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Bacterial colonization of the ETT
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Sottile et al, 1986; Zur et al, 2004
14 hrs post-intubation 3 days post-intubation
Is it really a biofilm?
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Causative role of ETT biofilm in VAP
Adair et al, Int. Care Med., 1999
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ETT biofilms are associated with microbial persistence and treatment failures
ETT+ETT+
ETT-ETT-
Gil-Perotin et al, Crit. Care, 2012
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Contents
• Why study the ETT biofilm?
• The ETT microbiome: molecular analysis and impact on development of ventilator-associated pneumonia (VAP)
• Mono- and -polymicrobial VAP
• Modelling ETT interactions
• Conclusions
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Molecular analysis of microbial communities in ETT biofilms
– 20 ETTs were analysed by 16S rDNA PCR-cloning-Sanger sequencing and 4 by pyrosequencing
– On average, 16S rDNA sequencing revealed 3 different species per ET biofilm
• Simpson diversity indexes did not differ significantly between both methods (culture and sequencing of the clone libraries)
– Pyrosequencing analysis suggested that the four samples were dominated by members of the normal oral flora such as Prevotella spp., Peptostreptococcus spp. and lactic acid bacteria
Vandecandelaere et al, PLOS One, 2012
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Molecular analysis of microbial communities in ETT biofilms
– Inner luminal surface of 24 ETT from 20 patients analysedby quantitative culture and by denaturing gradient gel electrophoresis (DGGE) profiling of 16S rRNA gene
– DGGE profiling of the endotracheal biofilms revealed complex banding patterns containing between 3 and 22 (mean 6) bands per tube
– Significant inter-patient diversity
– No. of DGGE bands detected was not related to total viable microbial counts or the duration of intubation
Cairns, PLOS One, 2011
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Prevalence of potential pathogens in ET tube biofilms
Hotterbeekx et al, In preparation, 2015
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Analysis of ETTs culture positive for P. aeruginosa or S. epidermidis or both
Sample processing workflow Data analysis workflow
Collection of ET
• Mechanically ventilated patientsin ICU
Culture of ET
• Blood agar, 37.C • Identification by MALDI-TOF• Selection 39 ET positive for P. aeruginosa and/or S. epidermidis
16S sequencing
• DNA extraction: Masterpurecomplete DNA and RNA purification kit (Epicentre)
• Target: V3-V5 region• Platform: Roche 454
Pre-processing
• MG-RAST online software service (default parameters)
• Template alignment and qualtiycontrol
• Chimera removal
Sequenceanalysis
• BLAT1 similarity search againstM5ma database
• Min% identity cutoff 97%• Min alignment cutoff 15
Microbiome discovery
• Common core based on presence/absence of family (50% cutoff)
• Differences in relativeabundance between groupsbased on LefSe2 and LDA2
Hotterbeekx et al, In preparation, 2015
Slide withheld
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Histology of ETT biofilms
• Microtome sectioning
• Paraffin embedding
• Staining– H&E– Gram– DAPI
H&E
H&E
H&E
Courtesy S. Kumar-Singh, Vaxinfectio, Univ. Antwerp
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Histology of ETT biofilmsGramGram
PAS ConA & DAPI
Courtesy S. Kumar-Singh, Vaxinfectio, Univ. Antwerp
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BAL-confirmed VAP and correlation with ETT culture
Pa/Sepi OthersPatient 1 55 35 15 Pa Pa -
Patient 2 55 7 23 Pa PaC. freundiiE. faecium
Patient 3 58 24 12 Pa Pa -
Patient 5 42 21 6 S. aureus SepiS. aureus
C. glabrataothers
Patient 6 68 31 22 Staph spp. Sepi C. albicans
Patient 7 74 30 8S. aureus
K. pneumoniae Sepi E. faecium
Patient 8 58 14 7C. albicans
othersSepi S. capitis
Patient 9 74 25 20 Pa SepiE. faeciumC. glabrata
Patient 10 31 22 19Staph spp.
Acinetobacter Sepi -
Patient 11 47 22 8S. aureus
C. freundii Sepi
S. aureusS. pneumoniae
C. albicansC. freundii
Patient 12 49 23 23 K. pneumoniae SepiK. pneumoniae
C. albicansPatient 13 67 24 4 E. coli Sepi E. coli
Patient 14 39 20 19 PaPa
SepiL paracasei
Patient 15 59 17 16 -Pa
SepiC. albicans
others
P. mirabilisPatient 4 58 35 5Pa
E. coliPa
Patients who developed
VAP
Age (years)
APACHE II
Ventilation days BAL culture
ETT culture
Slide withheld
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Characterizing the ETT biofilm microbiome
Hotterbeekx et al, In preparation, 2015
S. epidermidis ETTs: 290 spp in total and 35 spp/tube on average
P. aeruginosa: 116 spp in total and 20 spp./tube
P. ae + S. epi: 111 spp. In total and 29 spp./tube
Slide withheld
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Core ETT microbiome
Hotterbeekx et al, In preparation, 2015
Slide withheld
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Specific ETT microbiome
Segata et al, Genome Biol., 2011; Hotterbeekx et al, In preparation, 2015
Slide withheld
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Organisms associated with S epidermidis in ETT biofilms
Slide withheld
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Development of VAP and patient survival upon extubation: a cluster analysis
Cluster 1 (n=16) Cluster 2 (n=11) Cluster 3 (n=12)
Patient survival 100% survived 100% died 100% survived
VAP status 81,2% VAP 81,8% nonVAP 100% nonVAP
Biomass visible on ETT 50% no biomass visible 81,8% biomass visible 100% biomass visible
Culture results 56,2% S. epidermidis 63,6% P. aeruginosa 66,7% S. epidermidis
APACHE II 25,50 26,55 18,50
Age 57,69 67,82 60,50
Duration of intubation 13,69 days 12,45 days 11,42 days
Hotterbeekx et al, In preparation, 2015
Can the bacterial consortium on the ETT influence or help predict patient outcome?
Slide withheld
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Impact of the ETT microbiome on patient survival
Segata et al, Genome Biol., 2011; Hotterbeekx et al, In preparation, 2015
Slide withheld
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Contents
• Why study the ETT biofilm?
• The ETT microbiome: molecular analysis and impact on development of ventilator-associated pneumonia (VAP)
• Mono- and -polymicrobial VAP
• Modelling ETT interactions
• Conclusions
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Is ICU pneumonia (VAP) polymicrobial?
• 3 year study in HAP and CAP patients and controls
• 25% BAL samples monomicrobial and 75% polymicrobial from pneumonia patients
Bousbia et al, PLOS One, 2012
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Characteristics of mono- and -polymicrobial VAP
Bousbia et al, PLOS One, 2012
Bacilli
Gamma proteobacteriaBacteriodia Bacilli
BacteriodiaBacilli
Bacteriodia
Gamma proteobacteria Gamma
proteobacteriaClostridia
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Is ICU pneumonia (VAP) polymicrobial?
Bousbia et al, PLOS One, 2012
P. aeruginosa common to both pneumonia patients and controls: core pulmonary microbiota?
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Microbial consortium interactions: ‘Keystone' and dominant pathogens
Hajishengallis et al, Nat. Rev. Microb., 2012
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Contents
• Why study the ETT biofilm?
• The ETT microbiome: molecular analysis and impact on development of ventilator-associated pneumonia (VAP)
• Mono- and polymicrobial VAP
• Modelling ETT interactions
• Conclusions
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In vitro modelling of ETT microbial interactions
Bioflux 200, Fluxion
Static assay
De Backer et al, 2015
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In vitro modelling of ETT microbial interactions
S. epidermidis/C. albicans
S. epidermidis/S. marcescens
S. epidermidis/K. pneumoniae
S. epidermidis/P. aeruginosa
De Backer et al, 2015
S. epidermidis + C. albicans: synergismS. epidermidis + P. aeruginosa: antagonism
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Effect of biofilm supernatant of P. aeruginosa and S. marcescens on S. epidermidis biofilms
Hotterbeekx et al, In preparation, 2015
S. epidermidis + S. marcescens: strain dependent
Slide withheld
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In vivo modelling of ETT microbial interactions
• Pressure-controlled mechanically ventilated on a Servo 900C (Pmax 15–23 cm H2O; Vt 8-12 mL/kg; PEEP = 2–4 cm H2O; RR = 90 breaths/min; TI/E 1:2; FiO2 = 0.21-0.33)
0 1 2 3 40.0
0.4
0.8
1.2
9942.00476.02432.0
2 =
+=
Rxy
Optical density (OD 600nm)
McF
arla
nd (M
cF)
Tracheal intubation
Bacterialinstillation
Courtesy S. Kumar-Singh, Vaxinfectio, Univ. Antwerp
Histopathology and scoringClinical scores Mortality
Slide withheld
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Some conclusions
• Need for more comprehensive ‘Big data’– Role of accessory
organisms in VAP etiology
• ETT fingerprint as a prognostic and, possibly, diagnostic marker
• Rapid molecular diagnostic tools to include fastidious ‘keystone’ and ‘dominant’ pathogens
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Laboratory of Medical Microbiology, University of Antwerp
An Hotterbeekx
Basil Britto Xavier
Christine Lammens
Pieter Moons
Sarah De Backer
University Hospital &University of Antwerp/Vaxinfectio
Prof. P. JorensProf. G. Ieven
Prof. S. Kumar-SinghProf. H. Goossens
COMBACTE-MAGNET