Detection of Class I Integrons and Insertion Sites in Bacteriophage Genomes: Evidence of Shared Genetic Material with Multidrug-Resistant Klebsiella pneumoniae and Acinetobacter species
Date
2025-08-23
Authors
Qais Mohammed Saif El Din AmAli
قيس محمد سيف الدين عم علي
Journal Title
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Publisher
Al-Quds University
Abstract
Ever since the emergence of antibiotic resistance, it has introduced a significant inevitable
challenge in clinical administration and treatment of bacterial infections. During the year of 2021,
health records have demonstrated a total of 4.71 million deaths due to antimicrobial resistance
health consequences, with nearly 25% of them being directly attributable to resistant pathogenic
bacteria. Data-based projections estimate the annual death toll to reach 8.2 million within 2025
2050. These concerning clinical records illustrate the necessity for continuous research efforts for
developing approaches towards allocating this topic and limiting its health consequences. Ascribed
to the latter, we introduce this innovative research, inspired by worldwide publications and
implemented here in Palestine to address the yet to be allocated research gap. We designed a study
approach that aims to investigate the significant incorporation of bacteriophages in mediating the
transfer of antimicrobial resistance-related genetic material across different bacterial species.
Furthermore, we focused on unravelling the molecular entities and constitutes involved in this
integrational process characterized by Integrons, specific insertion sites and resistance-acquiring
genes. In order to achieve this, we retrieved samples from clinically-relevant environments that
represent a reservoir for such bacteriophages, samples were taken from both a sewage-water
treating facility based in Al-Tireh, Ramallah & an oil mill located in Aroura village where the
liquid by-product was collected. These samples exhibited a thorough well-structured process of
laboratory work to eventually retrieve the extracted DNA material, two different specific primer
sets were designed for an accurate investigation approach. The 1st pair being intCiF3a & intCiiiR3a
which were utilized for the purpose of amplifying Class I Integrons that have been documented to
harbor MDR genes, while the 2nd pair was designed for amplification of specific insertion sites
where integration of resistance-affiliated genetic material takes place IS-F & IS-R. Eventually, we
successfully managed to confirm and validate the presence of both Class I Integrons and insertion
sites in our phage samples. Moreover, we further investigated the clinical relevance of our findings
as we aligned them against already annotated genomes where we discovered a 100% similarity of
a 200bp insertion site with MDR-resistant pathogenic Klebseilla pneumoniae. We also discovered
another identical alignment of a 240bp sequence representing a Class I Integron with pathogen
inducing Acinetobacter harboring antibiotic-resistant characteristics. Finally, a 40bp identical
alignment of few of our amplicons with E. coli plasmid “pV139-a” was highlighted. This
highlights the incorporation of Class I Integrons, insertion sites and mobility-facilitating
constituents taking part in transfer of MDR genes and the corresponding health consequences.
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Citation
AmAli، Qais Mohammed. (2025). Detection of Class I Integrons and Insertion Sites in Bacteriophage Genomes: Evidence of Shared Genetic Material with Multidrug-Resistant Klebsiella pneumoniae and Acinetobacter species Unpublished Master,s Thesis Al-Quds University, Palestine