Project Title: “Mobile genetic elements mapping – first bioinformatic insight into the resistome of ESKAPE clinical and environmental isolates from Romania”
Project Number: PN-III-P1-1.1-PD-2021-0540
Funding Agency: UEFISCDI
Project Leader: Marius Surleac
Mentor: Carmen Mariana Chifiriuc
Acronym: EMPIRE
Project Duration: 2022 – 2024
Project Description:
Among European countries, Romania is experiencing one of the highest rates of antibiotic resistance (AR) as revealed by most recent data reported by international surveillance programs such as ECDC, justifying the urgent need for monitoring the AR dynamics in the clinical and environment isolates. This project aims to contribute to the study of mobile genetic elements (MGEs) which are important contributors to the worldwide dynamics of resistance spreading. This project attempts to characterize in detail the ESKAPE resistome by bioinformatic analyses of various MGEs (e.g., plasmids, insertion sequences, transposons, genomic islands) representing huge pools of resistance genes and sets of such genes. These aspects will be correlated with bioinformatic studies focused on the phylogenetic relationships between such factors, between the isolates from the same species and among species, which in turn will cover some vital aspects of clinical interest, namely, functional traits with impact on the metabolic pathways, biological processes. Another important objective of this proposal is to validate the bioinformatic analysis by the use of experimental methods such as the MinION (Oxford Nanopore) technology for 3rd generation sequencing; this will improve the results by increasing the coverage and the degree of confidence: by using such a method we’ll be able to capture the full length of genes with correct orientation as well as of big MGEs such as genomic islands and plasmids.
Objectives:
2022
A1. Obtaining the bacterial mobile genetic elements’ reference sequences.
A2. New bioinformatic approaches based on NGS sequencing data – Adnotation of the assembled Romanian genomes and the pangenome analysis – Part I
Results – 2022:
Scientific papers:
Gheorghe-Barbu, I., Barbu, I.C., Popa, L.I. et al. “Temporo-spatial variations in resistance determinants and clonality of Acinetobacter baumannii and Pseudomonas aeruginosa strains from Romanian hospitals and wastewaters”, Antimicrob Resist Infect Control, 11, 115 (2022). PubMed [36104761]. (Equal contribution – Main Author).
IF: 6.454; AI: 1.382
Oral and Poster presentations:
“An Overview On The Dynamics Of Mobile Genetic Elements In Clinical And Environmental WGS ESKAPEE Pathogens In Romania” (Marius Surleac, Ilda Czobor Barbu, Simona Paraschiv, Irina Gheorghe, Robert Hihan, Carmen Chifiriuc, Dan Oțelea) – 6th Conference on the Environmental Dimension of Antibiotic Resistance (EDAR6), Gothenburg, Sweden, September 22-27, 2022. (Poster Presentation P1-009)
“Antibiotic And Biocides Resistance Genes In Acinetobacter Baumannii Clinical And Wastewater Strains Before And After The Onset Of COVID-19 Pandemic” (Ilda Czobor Barbu, Irina Gheorghe, Marius Surleac, Simona Paraschiv, Gratiela Gradisteanu Pircalabioru, Dan Otelea, Mariana Carmen Chifiriuc) – 6th Conference on the Environmental Dimension of Antibiotic Resistance (EDAR6), Gothenburg, Sweden, September 22-27, 2022. (Poster Presentation P1-085)
“Wastewater treatment plants at the crossroads of the aquatic and clinical reservoirs of antimicrobial resistance – The radar study” (Mariana Carmen Chifiriuc, Marcela Popa, Luminita Marutescu, Ilda Czobor, Irina Gheorghe, Gratiela Gradisteanu, Dan Otelea, Simona Paraschiv, Marius Surleac, Mircea Ioan Popa, Cerasela Dragomirescu, Alexandru Muntean, Codruta Usein, Mihaela Oprea, Sorin Dinu, Mihai Nita Lazar, Anton Ficai) – Symposium of International Chemical Engineering and Materials (SICHEM), UPB, Bucharest, Romania, 17 – 18 November, 2022. (Oral Presentation)
“Turning the Escherichia coli upside-down – an overview on the pathogenicity and MGE of strains circulating in Romania between 2019-2020” (Marius Surleac, Ilda Czobor Barbu, Simona Paraschiv, Irina Gheorghe-Barbu, Robert Hohan, Carmen Chifiriuc, Dan Otelea) – 18th Edition of The Scientific Days of the National Institute for Infectious Diseases „Prof. Dr. Matei Balș” National Congress, Sinaia, Romania, November 21-24, 2022. (Oral Presentation)
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Scientific Report – Part I
The first stage of this project proposes the following: i) obtaining the reference sequences of the mobile genetic elements (MGE) (e.g. insertion sequences, transposons, integrons, genomic islands, etc.) but also other antibiotic & biocide resistance and virulence determinants, ii) adnotation of over 700 sequences (corresponding to multiresistant strains from ESKAPEE group, isolated from different geographical regions from Romania, having the complete genomes sequenced in our lab), iii) the pangenome analysis of these strains. The MGE sequences have been downloaded from various databases and then organised by various categories, in order to be compared with the sequencing data of the Romanian isolates. Therefore, a set of preliminary analyses has been performed, underlining a high diversity of circulating MGEs in Romania, which will further be analyzed in more detail through the next stages of this project. The adnotations, the pangenome and phylogenetic analyses of the strains belonging to various ESKAPEE pathogen species from the analyzed set, suggest that these pangenomes are open, that they have a set of common genes for all the strains in the same species, but also accessory genes that could show genomic signatures specific to a geographical region or to clinical origins and aquatic environments as well. All these results, together with the ones that will be analyzed in the next stage of the project will provide useful information for a better understanding of the resistome dynamics in the ESKAPEE strains circulating throughout Romania.
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Marius Surleac, PhD – Links & Highlights: Hirsch = 11 (Google Scholar); Cumulative Impact Factor = 130.36; Google Scholar; PubMed.
Carmen Mariana Chifiriuc, Prof., PhD – Links & Highlights: Hirsch = 50 (Google Scholar); Google Scholar; Pubmed.