Analisis Bioinformatika GenblaCTX-M Pengkode β-Laktamase Spektrum Luas pada Klebsiella pneumoniae Menggunakan Data GenBank NCBI
DOI:
https://doi.org/10.29303/6805v662Keywords:
Klebsiella pneumoniae, blaCTX-M, genetic variation, phylogenetic analysis, antibiotic resistanceAbstract
Klebsiella pneumoniae is a short rod-shaped Gram-negative bacterium capable of fermenting lactose and various other carbohydrates, producing acid and gas. The blaCTX-M gene is one of the major genes responsible for β-lactam resistance in K. pneumoniae. This study aimed to analyze the genetic variation and phylogenetic relationships of the blaCTX-M gene in K. pneumoniae using nucleotide sequence data retrieved from the NCBI GenBank database. A total of 19 sequences representing isolates from different countries were aligned to identify nucleotide variations. The alignment results revealed genetic variation among the isolates, with most forming a closely related cluster indicating high sequence similarity. Eighteen isolates showed identical characteristics with minor variations, while one isolate, NG_048898, exhibited the highest number of nucleotide variations. A total of 168 nucleotide variations were identified, predominantly nonsynonymous substitutions, distributed throughout the nucleotide sequence. Phylogenetic analysis using the Neighbor-Joining method with the Kimura 2-parameter model supported the alignment results, showing a distinct branch for isolate NG_048898, suggesting a different evolutionary origin. These findings highlight the genetic diversity of the blaCTX-M gene in K. pneumoniae isolates and provide important insights into the distribution of β-lactamase genes, which are essential for understanding antibiotic resistance patterns.
References
Alzohairy, A. M. (2011). BioEdit: An important software for molecular biology. GERF Bulletin of Biosciences, 2(1), 60-61.
Baron, S. A., Mediannikov, O., Abdallah, R., Yimagou, E. K., Medkour, H., Dubourg, G., Elamire, Y., dan Raoult, D., (2021). Multidrug-resistant Klebsiella pneumoniae clones from wild chimpanzees and termites in Senegal. Clinical Microbiology and Antimicrobials, 17 August 2021
Becker, L., Fuchs, S., Pfeifer, Y., Semmler, T., Eckmanns, T., Korr, G., Sissolak, D., Friedrichs, M., Zill, E., Tung, M.-L., Dohle, C., Kaase, M., Gatermann, S., Rüssmann, H., Steglich, M., Haller, S., dan Werner, G. (2018). Whole genome sequence analysis of CTX-M-15 producing Klebsiella isolates allowed dissecting a polyclonal outbreak scenario. Frontiers in Microbiology, 9, 322.
Huang, W., Wang, G., Sebra, R., Zhuge, J., Yin, C., Aguero-Rosenfeld, M. E., Schuetz, A. N., Dimitrova, N., dan Fallon, J. T. (2017). Emergence and evolution of multidrug-resistant Klebsiella pneumoniae with both blaKPC and blaCTX-M integrated in the chromosome. Antimicrobial Agents and Chemotherapy, 61(7), 1-11.
Jamal, A., Hermawan, D., dan Nugraha, M. (2014). Pengembangan database Genbank UAI- Bioinformatics menggunakan sistem terdistribusi. Al-Azhar Indonesia Seri Sains dan Teknologi, 2(3), 170-177.
Kumar, S., Ryan, S., dan Hall, T. (2016). Building evolutionary trees using MEGA software: A hands- on approach for students. The American Biology Teacher, 78(7), 608–612
Kumar, S., Stecher, G., Li, M., Knyaz, C., dan Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549.
Lenchenko, E., Blumenkrants, D., Sachivkina, N., Shadrova, N., dan Ibragimova, A. (2020). Morphological and adhesive properties of Klebsiella pneumoniae biofilms. Veterinary World, 13(1), 197.
Makatita, F. A. (2020). Riset in silico dalam pengembangan sains di bidang pendidikan, studi kasus: analisis potensi cendana sebagai agen anti- aging. Jurnal ABDI (Sosial, Budaya dan Sains), 2(1).
Mardhia, M., Liana, D. F., Mahyarudin, M., dan Ih, H. (2025). The first report of antibiotic resistance and virulence factor profiles in multidrug‑resistant clinical isolates of Klebsiella pneumoniae from Pontianak, Indonesia. Osong Public Health and Research Perspectives, 16(2), 160-16.
Mastra, N., S., K. M., Sundari, C. D. W. H., S., K.M., Jirna, I. N., S., K. M., dan Ashari, D. (2025).Bakteriologi klinik. CV Rey Media Grafika.
Palzkill, T. (2018). Structural and mechanistic basis for extended-spectrum drug-resistance mutations in altering the specificity of TEM, CTX-M, and KPC β-lactamases. Frontiers in Molecular Biosciences, 5, 16.
Patel, M. P., Hu, L., Brown, C. A., Sun, Z., Adamski, C. J., Stojanoski, V., Sankaran, B., Prasad, B. V. V., dan Palzkill, T. (2018). Synergistic effects of functionally distinct substitutions in β-lactamase variants shed light on the evolution of bacterial drug resistance. The Journal of biological chemistry 293(46): 17971-17984.
Patil, S., Chen, X., dan Wen, F. (2019). Exploring the phenotype and genotype of multi-drug resistant Klebsiella pneumoniae harbouring blaCTX-M group extended-spectrum β-lactamases recovered from paediatric clinical cases in Shenzhen, China. Annals of Clinical Microbiology and Antimicrobials, 18, 2.
Poirel, L., Naas, T., Le Thomas, I., Karim, A., Bingen, E., dan Nordmann, P. (2001). CTX-M-type extended-spectrum β-lactamase that hydrolyzes ceftazidime through a single amino acid substitution in the omega loop. Antimicrobial Agents and Chemotherapy, 45(12), 3355-3361.
Pratiwi, R. H. (2017). Mekanisme pertahanan bakteri patogen terhadap antibiotik. Pro-Life, 4(3), 418-429.
Qin, X., dan Zhang, Z. (2023). Emergence of a Hybrid IncI1-Iα Plasmid-Encoded blaCTX-M-101 Conferring Resistance to Cephalosporins in Salmonella enterica Serovar Enteritidis. Microorganisms, 11(5), 1275.
Ribeiro, A., Golicz, A., Hackett, C. A., Milne, I., Stephen, G., Marshall, D., Flavell, A. J., & Bayer, M. (2015), An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome, BMC Bioinformatics, 16, 382.
Rodríguez, M. M., Power, P., Naas, T., dan Gutkind, G. (2021). Redefining the origin and evolution of chromosomally encoded blaCTX-M/KLU in the context of a revised taxonomy of genus Kluyvera. Antimicrobial Agents and Chemotherapy, 65(7), 1-6.
Saeed, M. A., Khan, A. U., Ehtisham-ul-Haque, S., Waheed, U., Qamar, M. F., Rehman, A. u., Nasir, A., Zaman, M. A., Kashif, M., Gonzalez, J.P., dan Hosny El-Adawy, H. (2023). Detection and phylogenetic analysis of extended-spectrum β-lactamase (ESBL)-genetic determinants in Gram-negative fecal-microbiota of wild birds and chicken originated at Trimmu Barrage. Antibiotics, 12(1376).
Sharma, S., dan Kumar, S. (2021). Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps. Nature Computational Science, 1(9), 573–577.
Sudeep, K. C., Khanal, S., Han, Z., Joshi, T. P., Zhang, Y., Yang, M., dan Joshi, D. R. (2025). Genomic insights into the extended‑spectrum β‑lactamase-producing Escherichia coli and Klebsiella pneumoniae isolated from hospital wastewater in Nepal. Total Environment Microbiology, 1(4), 1-7.
Tarina, N. T. I., dan Kusuma, S. A. F. (2017). Deteksi bakteri Klebsiella pneumoniae. Farmaka, 15(2), 119–126.
Tongsima, S., Assawamakin, A., Piriyapongsa, J., and Shaw, P.J., 2011, Comparative View of In Silico DNA Sequencing Analysis Tools, Methods in Molecular Biology,790: 207-221.
Tu, I. F., Lin, T. L., Yang, F. L., Lee, I. M., Tu, W. L., Liao, J. H., dan Wu, S. H. (2022). Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: Implications for clinical use. Journal of Biomedical Science, 29(1), 9.
Wyres, K. L., Hawkey, J., Hetland, M. A. K., Fostervold, A., Wick, R. R., Judd, L. M., Hamidian, M., Howden, B. P., Löhr, I. H., dan Holt, K. E. (2019). Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. Journal of Antimicrobial Chemotherapy, 74(3), 577-581.
Zhang, C., Wang, Q., Li, Y., Teng, A., Hu, G., Wuyun, Q., dan Zheng, W. (2024). The Historical Evolution and Significance of Multiple Sequence Alignment in Molecular Structure and Function Prediction. Biomolecules, 14 (12), 1531.
Zhang, D., Kan, X., Huss, S. E., Jiang, L., Chen, L. Q., dan Hu, Y. (2018). Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin. Journal of visualize experiments : JOVE, (138), 56684.
Zhang, J., Xu, Y., Wang, M., Li, X., Liu, Z., Kuang, D., Deng, Z., Ou, H.-Y., dan Qu, J. (2023).Mobilizable plasmids drive the spread of antimicrobial resistance genes and virulence genes in Klebsiella pneumoniae. Genome Medicine, 15, 106.
Downloads
Published
Issue
Section
License
Copyright (c) 2026 Dwi Sakila Ulfa, Gusti Ayu Niscari Dewi, Ira Firati Fionita, Faturrahman, Sarkono
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
