A pilot integrative knowledgebase for the characterization and tracking of multi resistant Acinetobacter baumannii in Colombian hospitals

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1 A pilot integrative knowledgebase for the characterization and tracking of multi resistant Acinetobacter baumannii in Colombian hospitals Our funding partners: EPFL Leading House Swiss Bilateral Programmes

2 The partners Prof. Emiliano Barreto-Hernández Institutode Biotecnología - Universidad Nacional de Colombia, Bogotá, Colombia Dr. Laurent Falquet University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland Msc. Jaime Moreno InstitutoNacional De Salud, Bogotá, Colombia

3 Acinetobacter baumannii Photo Credit: CDC / Janice Carr A.baumannii is a Gram-negative bacterium that can become an opportunistic pathogen in patients with compromised immune systems. In Colombia, it is increasingly found as a hospital -derived infection (nosocomial) carrying multiple drug-resistance genes since Carbapenems resistance: Meropenem 65,7% in 2013 and 69,2% in 2014 Cyclinsresistance: Tigecycline 0% in 2013 and 4,2% in 2014 Susceptibility to colistin remains high, however, development of resistance has already been detected in some colombian hospitals

4 General objectives of the project Design and develop a pilot integrative knowledgebase combining clinical, epidemiological and genomic data for tracking the multidrug resistant Acinetobacter baumannii 1. Sequence a collection of A.baumannii isolates, assemble and annotate the draft genomes. A. baumannii ( bp) 2. Extract a genomic profile based on the known resistance and virulence genes (using HMMs). 3. Strengthen monitoring and surveillance of healthcare associated infections (HAIs).

5 120 isolates of A. baumannii Collection of the Microbiology Laboratory Surveillance program for antibiotic resistances from the Colombian Hospitals of all 22 departments From 2012 to May 2015

6 Analysis of antibiotic resistance profile (VITEK;PHOENIX; KIRBY BAUER) 120 Colombian isolations Extraction of DNA - Resistance genes - Resistance genomic elements Library Whole genome sequencing (80 sequenced genomes) A. baumannii ( bp)

7 Bioinformatics Pipeline Quality Control FastQC (1) Cleaning Sickle (2) Assembly SPAdes (3) Rapid prokaryotic Annotation PROKKA & HMMs (4,5,6,7,8) 1. Andrews S Joshi & Fass, Bankevich et al, 2012 Journal of Computational Biology 19(5) (2012), Seemann T Bioinformatics.15;30(14): McArthur et al, 2013, Antimicrob. Agents Chemother. 57, Gibson et al, 2014, The ISME Journal, doi:ismej Chen et al, 2016, NAR 44(Database issue):d Llorens et al, 2011, NAR 39 (suppl 1): D70-4 Upload data into knowledgebase

8 Status of the 80 sequenced genomes 66 A.baumannii 3 A.pittii 1 A.haemoliticus 10 atypical assemblies Sequence typing based on genomic data reveals ST-79 and ST-25 as the major strains with some minor known ST and some new STs. 40 additional strains to be sequenced by the end of the year

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11 Comparative genomics of the 66 A.baumannii strains ST-79 Non ST-79 ST-25

12 Outreach of the project Publication Saavedra SY, Prada-Cardozo D, Rincón V, Pérez-Cardona H, Hidalgo AM, Gonzalez MN, Reguero MT, Valenzuela de Silva EM, Mantilla JR, Falquet L, Barreto-Hernández E, Duarte C. Whole genome sequence of a Acinetobacter baumanni ST920 Colombian strain co-producer of OXA-72 and OXA-255-like. Genome Announcements (in press) Workshop with 18 participants and publication Falquet L, Calderon-Copete S, Moreno J, Barreto-Hernández E. Report on the Swiss-Colombian workshop, assembly, annotation and comparison of bacterial genomes. EMBnet.journal 2016 (in press)

13 Funding already obtained following the project From the seed money we applied for funding to the National University of Colombia with the project: CARACTERIZACIÓN GENÓMICA DE CEPAS COLOMBIANAS DE Providencia rettgeri PRODUCTORAS DE METALOBETALACTAMASAS AISLADAS DURANTE EL PERÍODO (Genomic characterization of Colombian Providencia rettgeri strains producers of metal-betalactamases, collected between ) The project was approved for USD for a year.

14 Next steps? Extension of the knowledgebase to other bacterial species (Pseudomonas aeruginosa and Klebsiella pneumoniae) of the ESKAPE group. Application to the R4D open thematic call this winter (CHF500K for 3 years) For a joint project between Paraguay, Colombia and Switzerland.

15 Thank you for your attention