Year in Clinical Microbiology
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Madrid, April 21-24 SY024 - Year in Clinical Microbiology Prof. Carlo Federico Perno ESCMID eLibrary © by author Contributors • Claudia Alteri, PhD University of Rome Tor Vergata • Stefania Carta, PhD Niguarda Hospital, Milan • Valeria Cento, MD PhD University of Milan • Luna Colagrossi, PhD UniversityESCMIDof Milan eLibrary © by author Game-changers in the setting of diagnosis- treatment integration • Microbiome: a new tool for disease prediction and intervention??? • Cytomegalovirus: from pre-emptive therapy to effective prophylaxis??? • ViralESCMIDhepatitis and HIV eLibrary: new approaches for the cure??? © by author INCREASED INTEREST AND PUBLICATIONS ON MICROBIOME Search term on PubMed "Microbiome" 1950- 2017 pubmed - MICROBIOME Published papers in PubMed Most frequent category, pubmed - GUT MICROBIOME after «microbiome» 10000 9000 8000 7000 6000 5000 4000 3000 2000 1° «Microbiome» paper 1000 ESCMID0 eLibrary 1956 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 © by author KEY QUESTIONS RELATED TO THE HUMAN MICROBIOME • What is the identity of the microbes (bacteria, archea, fungi, eukaryotic viruses and phages, protozoa) that populate their host? • Which is their role? • How is the host responding to them? • What are the forces that maintain equilibrium among the populations? • Can we define a core health microbiome? • Is the microbiome the cause or the effect of the disease? • Can we use the microbiome as diagnostic tool for diseases? ESCMID eLibrary © by author Blaser, Cell 2018 The Role of the Microbiome in cancer: • A “causative” agent?????? Science 2018 Science 2018 ESCMID eLibrary Cancer Discovery 2018 © by author Science 2018 ESCMID eLibrary © by author ESCMID eLibrary © by author Tumor prone mice co-colonized with E.coli (expressing clbB) end heterotoxigenic B. fragilis (ETBF) showed increased IL-17 in the colon, DNA damage in colonic epithelium, faster tumor onset, and greater mortality compared to mice with either bacterial strain alone A: Total colon tumor detected in sham (placebo), ETBF monocolonized, pks+E.coli monocolonized and co-conolized mice. C: Histopathology of an invasive adenocarcinoma in a cocolonized AOM mouse at 15 weeks..D: KM survival plot in ETBF monocolonized, ESCMID eLibrarypks+E.coli monocolonized and co -conolized mice © by author • These results arise the possibility that persistent co-colonization in the colon mucosa from a young age contributes to the pathogenesis of familial adenomatous polyposis (FAP). • Cause-effect phenomenon? ESCMID eLibrary © by author Gopalakrishanan et al., Science 2018 The landscape of the oral and gut microbiome was assessed in all samples available in patients (n=122) with metastatic melanoma via 16S sequencing ESCMID eLibrary © by author • Diversity of the gut microbiome was significantly higher in individuals responding to anti-PD1 therapy (R) compared to non responders (NR). • Higher abundance of Bacteroidales was found in non-responders respect to responders, while enrichment of Ruminococcaceae bacteria was found in responding patients ESCMID eLibrary C: Diversity scores of the gut microbiome in R and NR. D: LDA scores for differentially-abundant taxa in fecal microbiomes of R and NR. © by authorGopalakrishanan et al., Science 2018 Favorable gut microbiome is associated with enhanced systemic and anti-tumor immunity ESCMID eLibrary © by authorGopalakrishanan et al., Science 2018 ESCMID eLibrary © by author ESCMID eLibrary © by authorRouty et al., Science 2018 Kaplan-Meier estimates for progression-free survival (PFS) or overall ESCMIDsurvival (OS) of cancer eLibrarypatients. (D) patients with advanced non–small cell lung cancer (NSCLC, n = 140) © by author ESCMID eLibrary © by authorRouty et al., Science 2018 ESCMIDCystic Fibrosis eLibraryand Microbiome © by author • Subjects affected by cystic fibrosis (CF) experience a progressive loss of pulmonary functions accompanied by an increased burden of chronic infections. • The respiratory microbial composition is particularly relevant for patients with CF. In fact, bacterial lung infections reduce life expectancy in patients with CF (the median predicted survival age is equal to 41.6, as reported in the Cystic Fibrosis Foundation Patient Registry), and represent the primary cause of morbidity and mortality in CF patients. • In the last decade, the emergence of high-throughput sequencing approaches, coupled with the development of new bioinformatics pipelines designed to cope with metagenomics data, has revolutionized the study of complex bacterial communities such as the airway microbiota of CF patients, thereby improving our understanding of this largely unknown “microbial black-box”. We aimedESCMIDto investigate whether patients witheLibrarydifferent disease severities may indeed have a different representation of “keystone genes” in their lung microbiota. © by authorBacci G. et al., Int J Med Sci 2017 Microbes in CF airways encode a diverse set of antibiotic resistance mechanisms; among them, the multidrug resistance efflux pumps are the most represented ESCMID eLibrary © by authorBacci G. et al., Int J Med Sci 2017 • Understanding the threats and stopping the damage are the first orders of business. • Interventions could be drugs, prebiotics, or combinations of these compounds, and even some vaccines. • We will have to restore our lost microbiota to optimize human health and to reverse the disease epidemics. ESCMID eLibraryM. Blaser, Cell 2018 © by author GAME-CHANGERS IN CMV MANAGEMENT: Prophylaxis or Pre-emptive therapy??? ESCMID eLibrary © by author PROPHYLAXIS PRE-EMPTIVE THERAPY . Primary prophylaxis with ganciclovir is . Gancclovir is recommended as first line pre- not generally recommended as toxicity emptive therapy for CMV in HSCT patients outweighs efficacy in HSCT patients (Grade 1A). (Grade 1B). Oral valganciclovir is a valid alternative when . Primary prophylaxis with acyclovir or gastrointestinal absorption is normal or only valaciclovir can be deployed but only in minimally impaired (Grade 1A). conjunction with appropriate monitoring . Foscarnet is recommended as an alternative of CMV in blood (Grade 1B). first-line agent if neutropenia is present or for . Valacyclovir or valgancyclovir are valid ganciclovir treatment failure (Grade 1A). treatment options for secondary . Pre-emptive therapy with cidofovir can be prophylaxis with appropriate monitoring considered as third-line in patients of CMV in blood (Grade 1C). unresponsive to, or intolerant of, both a . Intravenous immunoglobulin is not ganciclovir preparation and foscarnet (Grade recommended for prophylaxis of CMV 2B). infection (Grade 1A). In patients in whom CMV DNA loads in blood increase by 1 log10 over 2 weeks of pre- ESCMID eLibraryemptive therapy with a first line drug, an alternative agent and drug resistance profiling should be considered (Grade 2C). © by author Emery et al., bjh 2013 ESCMID eLibrary © by author Trial Design Prophylaxis Follow-up Randomization Week 14 (≈100 days) Week 24 Week 48 (within 28 days post-transplant (6 months) post-transplant post-transplant) (end of study therapy) post-transplant (final follow-up visit) Letermovir arm n=373 Dose: 240 mg qd w/ cyclosporine or 480 mg qd w/o cyclosporine Placebo arm n=192 ESCMID eLibrary QD=once daily. Marty FM et al. N Engl J Med. 2017. doi:10.1056/NEJMoa1706640. 2 © by author 5 End-points Primary end point Secondary end point Prespecified exploratory end pointsESCMID eLibrary © by author Marty et al., N Engl J Med 2017 Incidence of Clinically Significant CMV Infection ESCMID eLibrary 27 © by authorMarty FM et al. N Engl J Med. 2017. doi:10.1056/NEJMoa1706640. The lower mortality among letermovir recipients than among placebo recipients was more pronounced among high-risk patients than among low-risk patients ESCMID eLibrary 28 © by authorMarty FM et al. N Engl J Med. 2017. doi:10.1056/NEJMoa1706640. In conclusion In a diverse population of patients who had undergone hematopoietic- cell transplantation, letermovir prophylaxis was effective in preventing clinically significant CMV infection when used through day 100 after transplantation. Letermovir was associated with only mild toxic effects, which allows for the administration before hematologic engraftment, was not associated with a higher rate of myelotoxic or nephrotoxic events, and was associated with lower all-cause mortality than placebo. ESCMID eLibrary © by author Marty et al., N Engl J Med 2017 ESCMID eLibrary 30 Correspondence. F.M. Marty, J. Maertens, C. Badshah. © N Engl J Med 378;10by nejm.org March author 8, 2018 The combination of UL56 and terminase complex UL51 mutations can increase significantly the overall level of letermovir resistance ESCMID eLibrary © by author Viral hepatitis B and HIV: new approaches for the cure??? ESCMID eLibrary © by author cccDNA plays a pivotal role allowing HBV to establish a persistent infection ESCMID eLibraryTong et al., J Hepatol 2016 © by author New therapeutic approaches to achieve HBV functional cure ESCMID eLibrary © by Levreroauthor et al., Current Opin Virol 2018 • This highlights the need to identify novel virological markers to better measure cccDNA metabolic activity and cccDNA silencing HBV Core related Antigen -To monitor treatment response -To predict HCC risk HBV-RNA: - To monitor treatment response qHBeAg: - To monitor treatment response in e+patients ESCMID eLibrary © by author The correlations of serum qHBcrAg (A), qHBsAg (B) and HBV DNA (C) with intrahepatic cccDNA among different phases of CHB ESCMID eLibrary © by