Characterization of Acinetobacter baumannii sushens insulated from Trabzon Fatih State Hospital based on whole genome analysis

Acinetobacter baumannii is an important nosocomial pathogen and poses a major problem for human health. Analysis of the genome of this antibiotic-resistant bacterium is important. In our study, the characterization of Acinetobacter baumannii A24 strain isolated in Trabzon Fatih State Hospital based on whole genome analysis was performed. While the isolate was resistant to imipenem, meropenem, ciprofloxacin, levofloxacin and trimethoprim/sulfamethoxazole, it was sensitive to amikacin, gentamicin, tobramycin and colistin antibiotics. The DNA concentration of the isolated genome for whole genome analysis was found to be 270,9 ng/ul and its purity was 1,87. In bioinformatics analysis, it was determined as 4,978,982 raw reading, 4,972,661 clean reading, efficiency rate 99,87%, error rate 0,03%, GC rate 39,10%. The nucleotide sequence of the genome of the bacteria was submitted to GenBank and the Genbank accessory number was taken as CP051262. AdeFGH efflux pump, Bap, Csu fimbria, PNAG, phospholipase C, phospholipase D, outer membrane protein, capsule, LPS, acinetobactin, using Hem porphyrin, two-component system, BfmRS, penicillin binding protein, katA, manganese transport system, methionine sulfoxide reductase, RecN virulence factors were detected. As a result of MLST analysis, according to the Acinetobacter baumannii # 1 and Acinetobacter baumannii # 2 sequence types 218 and 2 were determined respectively. Also, the sequence type of the isolate was determined as 218 using the PubMLST database. According to plasmidFinder 2.1 analysis, no plasmid was found in the isolate. Through the ISFinder program, insertion sequences; ISAba1, ISAba33, ISA1006, ISAba52, IS1007 were found. Using ResFinder 3.2 and CLC genomics 13 antibiotic resistance genes detected; blaOXA-66, blaOXA-23 partial, blaTEM-1, blaADC-73, GNAT acetyltransferase, Aminoglycoside phosphotransferase (2 genes), aac-3-IIa, aac-(6')-Ian, ant (3'')-II, aph-(3'')-II, aph (3'')-Ib, aph (6)-I family-o transferase. Comparison between A24 and reference genome obtained from BRIG application also showed that the similarity with the reference genome was quite high. As a result of PHAST analysis, 28,6 kb and 17,3 kb prophage regions were found in the genome. The amino acid sequence of ADC-73 detected in Acinetobacter baumannii A24 strain was compared with the amino acid sequences of ADC-1, ADC-7, ADC-68, ampC, MOX-1 and FOX-4 using jalview. Ser66, Lys69 and Try152, which are the catalytic residues of the enzyme, were also found to be protected in seven different β-lactamases. Acinetobacter baumannii ADC-73 predicted secondary structure map was generated using PSIPRED4.0. According to the map, it was seen that there were 11 alpha helix and 9 beta layer secondary structures. 3D dimensional structure of ADC-73 was created with MODELLER program. As the created structure is theoretical, web-based building evaluation programs were used for the validation and improvement of the building. Based on the results obtained from the programs, it was revealed that the created homology model was reliable and structurally similar to natural structures. In this master's thesis, the complete genome of the Acinetobacter baumannii ST218 isolate was reported. Genomic analysis showed the presence of genes in the genome that confer resistance to aminoglycoside, β-lactam, and sulfonamide antibiotics. In addition, the two-dimensional and three-dimensional structure of ADC-73 β-lactamase found in this strain were elucidated.