exclude: true --- class: top left hide-count background-image: url(img/giorgio-trovato-IclGoWB6wEY-unsplash.jpg) background-size: cover .move-top20[ .title-text[Empty Islands] .title-subtext[<span style='font-size:0.9em'>The Bacterial Ecology of Infection & Antibiotic Failure</span>] ] .callout-url-leftcorner[ .title-nametext[ Brendan J. Kelly, MD, MS Infectious Diseases & Epidemiology University of Pennsylvania 14 February 2022 <!-- 12 October 2022 --> ] ] .footnote-right[<span style='color: white'>photo: Giorgio Trovato @unsplash</span>] --- ## Disclosures .pad-left[ - No conflicts of interest. - Research supported by: - NIAID K23 AI121485 - CDC BAA 200-2016-91964 - CDC BAA 200-2016-91937 - CDC BAA 200-2018-02919 - CDC BAA 200-2021-10986 ] --- ## Objectives .pad-left[ - How do antibiotics fail? - failure of pathogen identification → wrong antibiotic - high-grade phenotypic resistance or inadequate source control - <u>post-antibiotic repopulation</u> - Bacterial ecology of infection: VAP, _C. difficile_ - Microbiome change during & after antibiotics - Engineering post-antibiotic repopulation ] --- class: top left hide-count background-image: url(img/yudi-haryasa-HEpUyHwJuzQ-unsplash.jpeg) background-size: cover ## <span style='color: #093b85;'>Introduction: Island Ecology</span> .footnote-right[<span style='color: white'>photo: Yudi Haryasa @unsplash</span>] --- class: hide-count .pull-left[ <img src="img/tibg_title_authors.png" width="55%" style="display: block; margin: auto;" /> <img src="img/tibg_figure7_equilibrium_model.png" width="75%" style="display: block; margin: auto;" /> ] .pull-right[ <img src="img/wilson_simberloff_ecology_1969_fig3map.png" width="80%" style="display: block; margin: auto;" /> <img src="img/wilson_simberloff_ecology_1969_tab1.png" width="80%" style="display: block; margin: auto;" /> ] .footnote-left[Macarthur & Wilson 1967; Simberloff & Wilson _Ecology_ 1969] --- class: hide-count .pull-left[ <img src="img/wilson_simberloff_ecology_1969_fig2.png" width="90%" style="display: block; margin: auto;" /> ] .pull-right[ <img src="img/wilson_simberloff_ecology_1969_fig8.png" width="90%" style="display: block; margin: auto;" /> ] .footnote-left[Wilson & Simberloff _Ecology_ 1969] --- class: hide-count .pull-left[ <img src="img/wilson_simberloff_ecology_1969_fig8_crop.png" width="90%" style="display: block; margin: auto;" /> ] .pull-right[ <img src="img/simberloff_wilson_ecology_1969_fig1_fig2.png" width="60%" style="display: block; margin: auto;" /> ] .footnote-left[Wilson & Simberloff _Ecology_ 1969; Simberloff & Wilson _Ecology_ 1969] --- class: hide-count .pull-left[ <img src="img/wilson_simberloff_ecology_1969_fig8_crop.png" width="90%" style="display: block; margin: auto;" /> ] .pull-right[ <img src="img/icu_patient_and_doc_crop.png" width="85%" style="display: block; margin: auto;" /> ] .footnote-left[Wilson & Simberloff _Ecology_ 1969; photo: _New York Times_] --- ## Repopulation & Recurrent Infection .pad-left[ - Why does <u>post-antibiotic repopulation</u> matter? - Failed repopulation risks recurrent infection: - healthy subjects time to post-antibiotic repopulation ~ 3 months - recurrent _C. difficile_ infection (R-CDI): ~ 20% post-treatment recurrence - bloodstream, respiratory and urinary tract infections? ] .footnote-left[Blaser _Science_ 2016; Raymond et al _ISME J_ 2016; Kelly & Tebas _Chest_ 2018; Al-Hasan et al _J Infect_ 2010; Jensen et al _CMI_ 2011; Munoz et al _CMI_ 2016] --- exclude: true ## Repopulation & Recurrent Infection .pad-left[ - Study of post-infection recurrence: - 10,855 heme-onc patients admitted to HUP from 2010-2011 - 7819 (72%) with blood, respiratory, or urine culture obtained - 1042 (9.6%) +blood cx, 215 (2.0%) +resp cx, 845 (7.8%) +urine cx - same genus recurrence: 286 (28.6%) blood, 58 (29.0%) resp, 272 (34.0%) urine - other genus recurrence: 208 (20.8%) blood, 35 (17.5%) resp, 88 (11.0%) urine - examine time to post-infection recurrence ... ] .footnote-left[Ziegler MZ et al. Submitted.] --- ## Repopulation & Recurrent Infection .pad-left[ - Study of post-infection recurrence: - 10,855 heme-onc patients admitted to HUP from 2010-2021 - 7819 (72%) with blood, respiratory, or urine culture obtained:
Infection
Total Subjects
Recurrent - Same Genus
Recurrent - Different Genus
Bloodstream
1042 (9.6%)
286 (28.6%)
208 (20.8%)
Respiratory
215 (2.0%)
58 (29.0%)
35 (17.5%)
Urine
845 (7.8%)
272 (34.0%)
88 (11.0%)
- Examine time to post-infection recurrence ... ] .footnote-left[Ziegler MZ et al. Submitted.] --- background-image: url(figs/p_hurdle_gap_same_vs_other_genus_tp.png) background-size: contain .footnote-left[Ziegler MZ et al. Submitted.] --- background-image: url(figs/p_hurdle_gap_same_genus_f_cxtype_r_genus_after14_tp.png) background-size: contain .footnote-left[Ziegler MZ et al. Submitted.] --- ## Repopulation & Novel Therapies .pad-left[ - Why does <u>post-antibiotic repopulation</u> matter? - Repopulation → novel therapies: - Fecal microbiota transplant (FMT) for _C. difficile_ - FMT to overcome resistance / potentiate therapies for cancer: → immune checkpoint inhibitors (e.g., anti-PD-1) → chimeric antigen receptor (CAR-T) therapies - FMT with synthetic bacteria for metabolic disease ] .footnote-left[Davar et al _Science_ 2021; Schubert et al _Frontiers Immun_ 2021; Cubillos-Ruiz et al _Nat Rev Drug Disc_ 2021] --- ## Work to Understand Repopulation .pad-left[ - Bacterial ecology of infection: - ventilator-associated pneumonia (VAP) - _C. difficile_ infection - Microbiome change during & after antibiotics - Engineering post-antibiotic repopulation: - antibiotic conditioning & transplant - post-induction consolidation therapy with bacteriophage ] --- class: top left hide-count background-image: url(img/cdc-aQOe0Ri267U-unsplash.jpg) background-size: cover .move-bottom20[ ## <span style='color: #fce60e'>The Bacterial Ecology of Infection</span> ] .footnote-right[<span style='color: white'>photo: CDC @unsplash</span>] --- ## The Bacterial Ecology of Infection .pad-left[ - What is the shape of the bacterial community during bacterial infection? - ventilator-associatec pneumonia (VAP) - _C. difficile_ infection - What bacterial community features aid diagnosis of infection? ] --- ## Pilot Study: Bacterial Ecology of VAP .pad-left[ - **Aim**: respiratory bacterial community change during critical illness & ventilation - **Population**: 15 adult subjects admitted to medical ICU - **Sampling**: upper & lower respiratory q48-72h for 16S rRNA gene sequencing - **Comparison**: healthy controls sampled via bronchoscopy - **Outcome**: change in community composition, ventilator-associated pneumonia (VAP) ] .footnote-left[Kelly et al _Microbiome_ 2016] --- background-image: url(figs/kelly_microbiome_2016_heatmap.png) background-size: 65% .footnote-left[Kelly et al _Microbiome_ 2016] --- background-image: url(figs/kelly_microbiome_2016_boxplot.png) background-size: 65% .footnote-left[Kelly et al _Microbiome_ 2016] --- ## Validation Study: Bacterial Ecology of VAP .pad-left[ - **Aim**: respiratory microbiome disruption indices (MDIs) to predict VAP - **Population**: 84 long-term acute care (LTACH) patients on mechanical ventilation - **Sampling**: upper & lower respiratory q24-48h (1066 specimens for 16S & qPCR) - **Comparison**: within-subject change over time - **Outcome**: VAP (with sensitivity analysis) ] .footnote-left[Harrigan et al _CID_ 2021] --- background-image: url(figs/harrigan_cid_2021_oddsratio.png) background-size: 65% .footnote-left[Harrigan et al _CID_ 2021] --- background-image: url(figs/harrigan_cid_2021_outcomes.png) background-size: contain .footnote-left[Harrigan et al _CID_ 2021] --- ## Island Biogeography & Lung Microbial Ecology .pull-left[ <img src="img/AnnalsATS.201501-029OC_f2.jpg" width="50%" style="display: block; margin: auto;" /> <img src="img/lung_microbiome_adapted_island_model.png" width="90%" style="display: block; margin: auto;" /> ] .pull-right[ - lower respiratory tract an "island" off shore of the upper respiratory tract & gut - lung microbiome more influenced by microbial immigration and elimination - local growth conditions impact bacterial reproduction rates in disease ] .footnote-left[Dickson RP et al _Annals ATS_ 2015] --- ## Bacterial Ecology of _C. difficile_ Infection .pad-left[ - **Aim**: microbiome features that discriminate _C. difficile_ colonization / infection - **Population**: 384 consecutive positive _C. difficile_ tests (in- & outpatient)
C. difficile
Category
Subject
Count
Proportion
GDH+ Toxin EIA- NAAT-
94
24.5%
GDH+ Toxin EIA- NAAT+
213
55.5%
GDH+ Toxin EIA+
77
20.1%
- **Sampling**: stool 16S rRNA gene sequencing & 16S rRNA gene qPCR - **Comparison**: toxin EIA+ (infection) versus NAAT+ only (colonization) - **Outcome**: EIA+, with fecal lactoferrin as sensitivity analysis ] .footnote-left[Tkatch et al _ASM World Microbiome Forum_ 2021] --- background-image: url(figs/p_cdi_cat_fecal_lacto_boxplot_tp.png) background-size: 65% .footnote-left[Tkatch et al _ASM World Microbiome Forum_ 2021] --- background-image: url(figs/p_toxineia_clostridioides_boxplot_tp.png) background-size: 65% .footnote-left[Tkatch et al _ASM World Microbiome Forum_ 2021] --- ## The Bacterial Ecology of Infection .pad-left[ - Bacterial infection associated with dominance of single strain: - ventilator-associatec pneumonia (VAP) - _C. difficile_ infection - Low diversity predicts the risk for respiratory infection - **Low diversity / dominance → <u>repopulation</u>** ] .footnote-left[Dickson _Eur Resp J_ 2018; Sulaiman et al _Eur Resp J_ 2018] --- class: top left hide-count background-image: url(img/cdc-y--8fqaK1kY-unsplash.jpeg) background-size: cover .pull-farright[ ## <span style='color: #c7b8e3'>Antibiotics & Empty Islands</span> ] .footnote-right[<span style='color: black'>photo: CDC @unsplash</span>] --- ## Antibiotics & Empty Islands .pad-left[ - How do different antibiotics impact gut & respiratory bacterial communities? - well defined spectrum of activity in vitro - complex interactions in vivo - Implications of antibiotic selection & duration for repopulation? ] --- ## Impact of Antibiotics During Induction Chemotherapy .pad-left[ - **Aim**: impact of antibiotics on gut microbiome during chemo/SCT admission - **Population**: 60 adults with acute myeloid leukemia (42%) or multiple myeloma (37%) - **Sampling**: stool specimens for 16S rRNA gene sequencing - **Comparison**: across antibiotic classes - **Outcome**: bacterial community diversity & membership ] .footnote-left[Ziegler et al _OFID_ 2019] --- background-image: url(figs/ziegler_ofid_2019_flow.png) background-size: contain .footnote-left[Ziegler et al _OFID_ 2019] --- background-image: url(figs/ziegler_ofid_2019_table.png) background-size: contain .footnote-left[Ziegler et al _OFID_ 2019] --- background-image: url(figs/ziegler_ofid_2019_pcoa.png) background-size: contain .footnote-left[Ziegler et al _OFID_ 2019] --- ## Antibiotics & Risk for Pseudomonas Recurrence .pad-left[ - **Aim**: define <u>post-antibiotic</u> factors a/w risk for recurrent _Pseudomonas_ VAP - **Population**: 84 long-term acute care (LTACH) patients on mechanical ventilation - **Sampling**: lower respiratory metagenomic sequencing & culture for WGS - **Comparison**: subjects with and without recurrent _Pseudomonas_ infection - **Outcome**: recurrent _Pseudomonas_ VAP ] --- background-image: url(figs/r01_psa_persistence.png) background-size: 65% .footnote-left[Harrigan et al. Manuscript in preparation.] --- background-image: url(figs/r01_psa_SNV.png) background-size: 65% .footnote-left[Harrigan et al. Manuscript in preparation.] --- background-image: url(figs/r01_psa_strep.png) background-size: 65% .footnote-left[Harrigan et al. Manuscript in preparation.] --- ## Environmental Microbiome & Repopulation .pad-left[ - **Aim**: define environmental multidrug-resistant organism (MDROs) contamination - **Population**: 51 hospital rooms with MDRO-associated patient admitted - **Sampling**: composite near, intermediate, far swabs for culture & 16S - **Comparison**: bacterial contamination & MDRO detection by distance - **Outcome**: culturable MDRO from the healthcare environment ] .footnote-left[Kelly et al _ICHE_ 2021] --- background-image: url(figs/kelly_iche_2021_cx.png) background-size: contain .footnote-left[Kelly et al _ICHE_ 2021] --- background-image: url(figs/kelly_iche_2021_gram.png) background-size: contain .footnote-left[Kelly et al _ICHE_ 2021] --- background-image: url(figs/kelly_iche_2021_asv.png) background-size: contain .footnote-left[Kelly et al _ICHE_ 2021] --- ## Antibiotics & Empty Islands .pad-left[ - Large effects of antibiotic selection on post-antibiotic gut community: - differences betwen BSBL, levofloxacin, oral vancomycin - Differential repopulation impacts _Pseudomonas_ re-infection risk - **Passive repopulation ← MDRO-rich environmental microbiome** ] --- class: top left hide-count background-image: url(img/PMT3_pop.jpeg) background-size: cover .move-bottom35-center[ ## <span style='color: #ffe9d6'>Engineering Post-Antibiotic Repopulation</span> ] .footnote-right[<span style='color: black'>photo: Laura Cowden</span>] --- ## Microbial Community Engineering .pad-left[ - How can we control bacterial community succession in the post-antibiotic period? - What is the effect of fecal microbiota transplant (FMT)? - What is the effect of bacteriophage therapy? ] .footnote-left[Seekatz et al _mBio_ 2014; Dedrick et al _Nature Med_ 2019] --- ## Fecal Microbiota Transplant (FMT) .pad-left[ - **Aim**: define the utility of FMT for severe/complicated _C. difficile_ infection - **Population**: 24 subjects with severe/complicated CDI - **Intervention**: Penn Microbiome Therapy (PMT) -001, -002, -003 - **Control**: standard of care antibiotic treatment - **Outcome**: time to resolution of severe CDI symptoms ] .footnote-left[Dutcher et al. Manuscript in preparation.] --- background-image: url(figs/p_fmt_richness_tp.png) background-size: 65% .footnote-left[Dutcher et al. Manuscript in preparation.] --- ## Endogenous Inducible Prophage (EIP) .pad-left[ - **Aim**: define the impact of prophage induction on _Pseudomonas_ VAP risk - **Population**: 45 LTACH subjects with _Pseudomonas_ from lower respiratory culture - **Sampling**: lower respiratory metagenomic sequencing, culture for phage induction - **Comparison**: _Pseudomonas_ with or without inducible prophage - **Outcome**: time to eradication of _Pseudomonas_ from lower respiratory tract ] .footnote-left[Loughrey et al. Manuscript in preparation.] --- background-image: url(figs/r01_phage_growth.png) background-size: 65% .footnote-left[Loughrey et al. Manuscript in preparation.] --- background-image: url(figs/r01_phage_table.png) background-size: 65% .footnote-left[Loughrey et al. Manuscript in preparation.] --- ## Microbial Community Engineering .pad-left[ - Post-antibiotic bacterial community succession can be altered by: - introduction of bacterial communities via FMT - induction of integrated bacteriophage (or introduction of ) - Two models for engineering post-antibiotic bacterial communities: - antibiotic conditioning & transplant - post-induction consolidation therapy with bacteriophage ] --- class: top left hide-count background-image: url(img/christina-victoria-craft-WHSnkIwWpec-unsplash.jpeg) background-size: cover ## <span style='color: #226252'>Conclusion: Into the 'LBP' Era</span> .footnote-right[<span style='color: white'>photo: Christina Victoria Craft @unsplash</span>] --- ## Live Biotherapeutic Products (LBPs) .pull-left[ <img src="img/ser_109_nejm.png" width="45%" style="display: block; margin: auto;" /> ] .pull-right[ - first approval expected 2022: - Seres, Rebiotix, Vedanta, Finch - applications: - _C. difficile_ - IBD - PD-1 potentiation - MDRO colonization - food allergy ] .footnote-left[Feuerstadt et al _NEJM_ 2022] --- ## Conclusions .pad-left[ - Bacterial infections like VAP, _C. difficile_ are characterized by low-diversity / dominance, emphasizing the importance of post-treatment repopulation. - Antibiotics exacerbate low-diversity state in a class-dependent manner. - Late reinfection may represent a failure of <u>post-antibiotic repopulation</u>. Passive repopulation from the healthcare environment risks MDRO colonization. - FMT/LBPs and bacteriophage therapy (exogenous or induced) are methods by which we can exert control over post-antibiotic repopulation and prevent recurrent infection. ] --- ## Acknowledgements .pull-left[ - __ARES Group @ Penn__ Laurel Glaser, Kyle Rodino, Sean Loughrey, Laura Cowden, Magda Wernovsky, Jennifer Han, Erik Clarke, Michael David, Matt Ziegler, Lauren Dutcher, Ebbing Lautenbach, Jim Harrigan, Hatem Abdallah - __Bushman Laboratory @ Penn__ Arwa Abbas, Aoife Roche, Andrew Marques, Aubrey Bailey, Jacob Leiby, Rick Bushman - __PennCHOP Microbiome Program__ Lisa Mattei, Casey Hofstaedter, Huanjia Zhang, Kyle Bittinger ] .pull-right[ - __Collman Laboratory @ Penn__ Ize Imai, Aurea Simon Soro, John McGinniss, Ron Collman - __Division of ID @ Penn__ Ian Frank, Pablo Tebas, Robert Gross, Emily Blumberg - __Rutgers University & Penn DBEI__ Jason Roy, Arman Oganisian - __CDC Prevention Epicenters__ Clifford McDonald, Alison Laufer Halpin - __Funding__ <u>CDC</u>: BAAs 200-2016-91964, 200-2018-02919, 200-2021-10986, 200-2021-10986 & <u>NIAID</u>: K23 AI121485 ] .center[ ### brendank@pennmedicine.upenn.edu ] --- class: middle center hide-count background-image: url(img/giorgio-trovato-IclGoWB6wEY-unsplash.jpg) background-size: cover .title-subtext[Questions?] .callout-url-bottom[ .fade-in[<span style="font-size:0.5em; color:white">slides ↓ </span>] <span style="link-color:white">[bjklab.org](http://www.bjklab.org)</span> ]