IN-DEPTH

Research on emerging zoonotic RNA viruses and antibiotic-resistant bacteria

IN-DEPTH

Research on emerging zoonotic RNA viruses and antibiotic-resistant bacteria
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Research Area

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Viruses
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Mycobacteria
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Gram-negative
bacteria

Project Status

From the beginning of the Project period (July 14th, 2020), a total of 190 pools of mosquitoes, 249 homogenized rat tissue samples, 60 bat blood samples, 321 carbapenem-resistant Acinetobacter baumannii (CRAB) and Pseudomonas aeruginosa (CRPA) isolates, and 12 multidrug-resistant (MDR) Mycobacterium tuberculosis isolates have been collected. Information on animal and mosquito demographics (time and location of sampling and taxonomic classification) as well as demographic, epidemiological, and clinical data of all patients diagnosed with infections caused by collected CRAB, CRPA, and MDR M. tuberculosis isolates were also obtained. All protocols for the planned molecular procedures were designed and optimized following manufacturers’ instructions and in-house testing.

All collected CRPA and CRAB isolates were screened for the presence of the beta-lactamases class B and D. The blaOXA-23 and blaOXA-24 genes were found in genomes of the CRAB isolates, whereas the blaNDM-1 gene was found among both CRPA and CRAB isolates. All CRPA isolates harboring the gene encoding metallo-ß-lactamases were genotyped by using Multilocus sequence typing (MLST; acsA, aroE, guaA, mutL, nuoD, ppsA, and trpE genes sequenced). A total of 30 CRAB isolate has been subjected to whole-genome sequencing (WGS) by Illumina technology in order to reveal phylogenetic characteristics and molecular markers of antibiotic resistance.

DNAs of 9 MDR M. tuberculosis strains have been extracted with a high-quality range (>600 ng/ml) and subjected to whole-genome sequencing (WGS) by Illumina technology in order to reveal phylogenetic characteristics and molecular markers of resistance to antituberculosis drugs.

Pathogen DNA sequences generated during the Project period are being uploaded to the NCBI Genbank database. Also, the sequences are submitted to the Sequence database, which is available on our Project website, together with sequences obtained by previous related research, including the SARS-CoV-2 sequences generated during the project “National study of seroprevalence and molecular characterization of SARS-CoV-2 during an epidemic in the population of Serbia (EPI-COVID-SERBIA)”. This database is the first digital repository of genes and genomes of emerging bacteria and viruses in Serbia.

PROJECT IN NUMBERS

3/5
PUBLISHED PAPERS
87
GENERATED SEQUENCES
832
TESTED SAMPLES
22/24
PROJECT COUNTDOWN

Project activities

Phylogenetic, philodynamic and phylogeographic analyses
Workshops