The Prevalence and Automated Identification of Microorganisms Isolated from Clinical Samples in Kalar City
DOI:
https://doi.org/10.24086/cuesj.v10n1y2026.pp12-17Keywords:
Prevalence, isolation, microbial identification, VITEK 2, clinical samplesAbstract
Effective isolation and accurate identification are two critical steps in diagnosing the causes of microbial infections. The ability to effectively analyze and identify isolates using manual isolation and automated instruments in identification is vital to the process. This study investigated the prevalence and distribution of bacterial and fungal isolates from various clinical samples. Laboratory experiments and surveys were conducted among patients who attended Zanko Medical Lab in Kalar City from August 2022 to March 2024. A total of 691 bacterial strains were isolated, with a high identification rate of 94.9%, using the automated VITEK 2 Compact system for microbial identification. Gram-negative bacteria constituted the majority (59.04%), followed by Gram-positive bacteria (34.15%) and yeasts (1.75%). Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa were the most common gram-negative isolates from urine, with Escherichia coli and Klebsiella pneumoniae being more frequent in females and Pseudomonas aeruginosa more frequent in males, particularly those undergoing endoscopic surgery. Among gram-positive isolates, Staphylococcus hemolyticus, Enterococcus faecalis, Streptococcus agalactiae, Staphylococcus aureus, and Staphylococcus saprophyticus were commonly identified, primarily from urine specimens. Urine samples constitute (84.2 %) of the isolates, high vaginal swabs (7.9 %), sputum samples (2.9 %) and other samples. The VITEK 2 Compact system is crucial for accurately identifying most isolates of gram-negative and gram-positive bacteria. Some are too difficult to identify using other methods, such as semi-automated approaches.
Downloads
References
[1] A. I. Bagudo, G. A. Obande, A. Harun, and K. K. B. Singh, “Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex,” Oct. 01, 2020, Sciendo. doi: 10.1515/abm-2020-0026. DOI: https://doi.org/10.1515/abm-2020-0026
[2] M. J. Gharavi, J. Zarei, P. Roshani-Asl, Z. Yazdanyar, M. Sharif, and N. Rashidi, “Comprehensive study of antimicrobial susceptibility pattern and extended spectrum beta-lactamase (ESBL) prevalence in bacteria isolated from urine samples,” Sci Rep, vol. 11, no. 1, Dec. 2021, doi: 10.1038/s41598-020-79791-0. DOI: https://doi.org/10.1038/s41598-020-79791-0
[3] P. J. Van Camp, V. B. S. Prasath, D. B. Haslam, and A. Porollo, “MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile,” Microbiome, vol. 11, no. 1, Dec. 2023, doi: 10.1186/s40168-023-01674-z. DOI: https://doi.org/10.1186/s40168-023-01674-z
[4] D. S. Kim and J. W. Lee, “Urinary Tract Infection and Microbiome,” Jun. 01, 2023, Multidisciplinary Digital Publishing Institute (MDPI). doi: 10.3390/diagnostics13111921. DOI: https://doi.org/10.3390/diagnostics13111921
[5] B. Chaban et al., “Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle,” Microbiome, vol. 2, no. 1, Dec. 2014, doi: 10.1186/2049-2618-2-23. DOI: https://doi.org/10.1186/2049-2618-2-23
[6] N. Romaní et al., “Impact of the MALDI-TOF as a tool for bacterial identification in the frequency of isolation of Aerococcus spp and Actinotignum schaalii in urinary tract infection,” Medicina Clínica Práctica, vol. 2, no. 2, pp. 17–21, Mar. 2019, doi: 10.1016/J.MCPSP.2018.12.004. DOI: https://doi.org/10.1016/j.mcpsp.2018.12.004
[7] S. H. Haji, S. T. H. Aka, and F. A. Ali, “Prevalence and characterisation of carbapenemase encoding genes in multidrug-resistant Gram-negative bacilli,” PLoS One, vol. 16, no. November, Nov. 2021, doi: 10.1371/journal.pone.0259005. DOI: https://doi.org/10.1371/journal.pone.0259005
[8] G. Rajivgandhi, M. Maruthupandy, G. Ramachandran, M. Priyanga, and N. Manoharan, “Detection of ESBL genes from ciprofloxacin resistant Gram negative bacteria isolated from urinary tract infections (UTIs),” Frontiers in Laboratory Medicine, vol. 2, no. 1, pp. 5–13, Mar. 2018, doi: 0.1016/j.flm.2018.01.001. DOI: https://doi.org/10.1016/j.flm.2018.01.001
[9] S. T. Altheide, “Biochemical and Culture-Based Approaches to Identification in the Diagnostic Microbiology Laboratory. Clin Lab Sci, vol. 32, no. 4, pp. 166-175, Oct 2019, doi.org/10.29074/ascls.2019001875. DOI: https://doi.org/10.29074/ascls.2019001875
[10] R. K. Faraj and M. Maaroof, “Molecular detection and Primer designing of some virulence factors and β-lactamases gene among clinical isolates of uncommon bacterial species. J Garm Uni 4, 563-580, (2017), doi.org/10.24271/garmian.118.
[11] A. M. Thari, K. A. S. Mohammed, and N. M. J. Abu-Mejdad, “Antimicrobial susceptibility of bacterial clinical specimens isolated from Al-Sader Teaching Hospital in Basra-Iraq,” Asia Pac J Mol Biol Biotechnol, vol. 32, no. 1, pp. 76–84, 2024, doi: 10.35118/apjmbb.2024.032.1.08. DOI: https://doi.org/10.35118/apjmbb.2024.032.1.08
[12] M. Okwu, O. Imade, O. A. Akpoka, M. Olley, and B. Ashi-ingwu, “Prevalence of Asymptomatic Bacteriuria among Pregnant Women Attending Antenatal Clinics in Ovia North East Local Government Area, Edo State, Nigeria,” Iranian Journal of Medical Microbiology, vol. 15, no. 2, pp. 227–231, Mar. 2021, doi: 10.30699/ijmm.15.2.227. DOI: https://doi.org/10.30699/ijmm.15.2.227
[13] A. Singh, M. Ranjan, R. K. Sharma, and M. K. Singh, “Bacteriological profile and antibiogram analysis from a tertiary care centre in eastern India: Time to Act / ReAct,” Indian Journal of Microbiology Research, vol. 9, no. 1, pp. 69–74, 2022, doi: 10.18231/j.ijmr.2022.011. DOI: https://doi.org/10.18231/j.ijmr.2022.011
[14] K. M. Sangita, D. Bisht, S. S. Faujdar, and V. Goel, “Antimicrobial susceptibility pattern of gram negative bacilli isolated from Delhi NCR population,” Indian Journal of Microbiology Research, vol. 7, no. 3, pp. 218–221, 2020, doi: 10.18231/j.ijmr.2020.039. DOI: https://doi.org/10.18231/j.ijmr.2020.039
[15] C. Huttenhower et al., “Structure, function and diversity of the healthy human microbiome,” Nature, vol. 486, no. 7402, pp. 207–214, Jun. 2012, doi: 10.1038/nature11234. DOI: https://doi.org/10.1038/nature11234
[16] Y. S. Kim, T. Unno, B. Y. Kim, and M. S. Park, “Sex differences in gut microbiota,” Jan. 01, 2020, Korean Society for Sexual Medicine and Andrology. doi: 10.5534/wjmh.190009. DOI: https://doi.org/10.5534/wjmh.190009
[17] H. R. Barbosaa et al., “Counting of viable cluster-forming and non cluster-forming bacteria: a comparison between the drop and the spread methods,” 1995. DOI: https://doi.org/10.1016/0167-7012(94)00062-C
[18] R. K. Faraj and M. N. Maarof, “Isolation and identification of some uncommon bacterial species isolated from different clinical sample”, doi: 10.24271/garmian. DOI: https://doi.org/10.24271/garmian
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2026 Rahman K. Faraj
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License [CC BY-NC-ND 4.0] that allows others to share the work with an acknowledgment of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgment of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
