An in-house technique for direct identification of bacteria from positive blood cultures using MALDI-TOF MS
DOI:
https://doi.org/10.61529/idjp.v35i1.480Abstract
Background: Rapid identification of pathogens from positive blood cultures is crucial for timely antibiotic therapy and effective antimicrobial stewardship. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) enables early organism identification when applied directly to blood culture broth. This study evaluated a simplified, low-cost, in-house direct MALDI-TOF method and compared its diagnostic performance with the standard colony-based approach.
Materials and Methods: This prospective study was conducted at the Microbiology Section of Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, from February to July 2025. One hundred positive blood cultures detected by the BACT/ALERT VIRTUO® system were included. Each specimen underwent both conventional post-culture MALDI-TOF MS identification and an in-house direct method using separator-gel tube centrifugation followed by saline washing. Genus- and species-level concordance between the two methods was calculated.
Results: Overall species-level and genus-level concordance were 60% and 66%, respectively. Gram-negative rods demonstrated the highest species-level accuracy (77.2%), whereas Gram-positive rods showed no species-level identification. Anaerobic bottles achieved higher accuracy (species: 67.3%, genus: 72.7%) than aerobic bottles (species: 51.1%, genus: 57.8%). Excellent agreement was observed for Klebsiella pneumoniae, Pseudomonas aeruginosa, Proteus mirabilis, and Acinetobacter baumannii, while coagulase-negative staphylococci and Enterococcus species exhibited lower identification rates.
Conclusion: The in-house MALDI-TOF method gave rapid, reliable, and cost-effective identification of Gram-negative bacteria, reducing turnaround time. Enhanced performance for Gram-positive identification can be achieved by incorporating detergent-assisted extraction. Integration of direct MALDI-TOF into routine workflows may support quick reporting and targeted therapy.
Keywords: Antimicrobial stewardship, Blood culture, MALDI-TOF MS, Rapid bacterial identification
References
Wang Y, Jin Y, Bai Y, Song Z, Chu W, Zhao M, et al. Rapid method for direct identification of positive blood cultures by MALDI-TOF MS. Exp Ther Med. 2020; 20(6): 235. DOI: https://doi.org/10.3892/etm.2020.9365
Zengin Canalp H, Bayraktar B. Direct rapid identification from positive blood cultures by MALDI-TOF MS: Specific focus on turnaround times. Microbiol Spectr 2021; 9(3): e01103-21. DOI: https://doi.org/10.1128/spectrum.01103-21
Calderaro A, Chezzi C. MALDI-TOF MS: A reliable tool in the real life of the clinical microbiology laboratory. Microorganisms. 2024; 12(2): 322. DOI: https://doi.org/10.3390/microorganisms12020322
Pérez-López A, Elamin N, Nabor R, Dumindin S, Roscoe D, Hasan MR, et al. Performance and impact on initial antibiotic choice of direct identification of pathogens from pediatric blood culture bottles using an in-house MALDI-TOF MS protocol. Microbiol Spectr. 2021; 9(3): e01905-21. DOI: https://doi.org/10.1128/spectrum.01905-21
Nomura F, Tsuchida S, Murata S, Satoh M, Matsushita K. Mass spectrometry-based microbiological testing for bloodstream infection. Clin Proteomics. 2020;17(1):14. DOI: https://doi.org/10.1186/s12014-020-09278-7
Haider A, Ringer M, Kotroczó Z, Mohácsi-Farkas C, Kocsis T. The current level of MALDI-TOF MS applications in the detection of microorganisms: a short review of benefits and limitations. Microbiol Res. 2023; 14(1): 80-90.
DOI: https://doi.org/10.3390/microbiolres14010008
Ko YJ, Kook J-K, Lee CK. In-house method for direct bacterial identification in positive blood culture broths using microfiltration, bead beating, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Microbiol Methods. 2021; 180: 106065. DOI: https://doi.org/10.1016/j.mimet.2020.106065
Hamilton F, Evans R, MacGowan A. The value of MALDI-TOF failure to provide an identification of Staphylococcal species direct from blood cultures and rule out Staphylococcus aureus bacteraemia: A post-hoc analysis of the RAPIDO trial. Access Microbiol. 2021; 3(2): 000192. DOI: https://doi.org/10.1099/acmi.0.000192
Yoo IY, Ha SI, Huh HJ, Kim TY, Shim HJ, Lee H, et al. Evaluation of a Modified Protocol for the SepsiPrep kit for direct identification and antimicrobial susceptibility testing from positive blood culture using BACTEC plus and BacT/Alert blood culture bottles. Ann Lab Med. 2024; 44(2): 183-7. DOI: https://doi.org/10.3343/alm.2023.0294
Watanabe N, Koyama S, Maeda T, Karaushi H, Taji Y, Kawasaki Y, et al. Direct Species identification in positive blood culture bottles from patients with hematologic malignancies. Cureus. 2024; 16(4): e59043. DOI: https://doi.org/10.7759/cureus.59043
Puckett LM, Rajkotia P, Coppola L, Baumgartner L, Roberts AL, Maldonado Y, et al. Impact of direct from blood culture identification of pathogens paired with antimicrobial stewardship interventions in a pediatric hospital. J Pediatr Pharmacol Ther. 2021; 26(8): 802-8. DOI: https://doi.org/10.5863/1551-6776-26.8.802
Dai Y, Xu X, Yan X, Li D, Cao W, Tang L, et al. Evaluation of a rapid and simplified protocol for direct identification of microorganisms from positive blood cultures by using Matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Front Cell Infect Microbiol. 2021; 11: 632679. DOI: https://doi.org/10.3389/fcimb.2021.632679
Karadağ D, Ergon MC. Investigation of different methods in rapid microbial identification directly from positive blood culture bottles by MALDI-TOF MS. Microbiol Spectr. 2024; 12(8): e0063824. DOI: https://doi.org/10.1128/spectrum.00638-24
Almuhayawi MS, Wong AY, Kynning M, Lüthje P, Ullberg M, Özenci V. Identification of microorganisms directly from blood culture bottles with polymicrobial growth: Comparison of film array and direct MALDI-TOF MS. APMIS. 2021; 129(4): 178-85. DOI: https://doi.org/10.1111/apm.13107
Gray TJ, Thomas L, Olma T, Mitchell DH, Iredell JR, Chen SC. Rapid identification of gram-negative bacteria from blood culture broth using MALDI-TOF mass spectrometry. J Vis Exp. 2014; 28(87):51663. DOI: https://doi.org/10.3791/51663
Kuo F-C, Chien C-C, Lee MS, Wang J-W, Lin P-C, Lee C-H. Rapid diagnosis of periprosthetic joint infection from synovial fluid in blood culture bottles by direct matrix-assisted laser desorption ionization time-of-flight mass spectrometry. PLoS One. 2020; 15(9): e0239290. DOI: https://doi.org/10.1371/journal.pone.0239290
Noll C, Nasruddin-Yekta A, Sternisek P, Weig M, Groß U, Schilling AF, et al. Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system. PLoS One. 2020; 15(12): e0243790. DOI: https://doi.org/10.1371/journal.pone.0243790
Assi F, Melalka L, Jabri B, Sekhsokh Y, Zouhdi M. Improving septicemia diagnostics: A comparative analysis of direct and post-culture MALDI-TOF MS* methods for bacterial identification. Tunis Med. 2024; 102(12): 1000-3. DOI: https://doi.org/10.62438/tunismed.v102i12.5221
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