Comparison of microarray and lysis filtration combined with MALDI-TOF MS methods for rapid diagnosis of gram-positive bacteria
Abstract
Aim: Early diagnosis of sepsis is crucial for patients’ prognosis. The primary objective of this study is to compare three methods for identifying bacteria in blood cultures: MALDI-TOF MS post-culture, MALDI-TOF MS after lysis filtration (LFM), and the Verigene System BC-GP microarray. Furthermore, the study evaluates the resistance profiles using the microarray method.
Materials and Methods: A total of 40 blood culture bottles positive for Gram-positive bacteria were collected from adult patients in the intensive care unit (ICU) of a university hospital. After detecting positive signals, we applied three identification methods: MALDI-TOF MS from subcultures, MALDI-TOF MS after lysis filtration directly from the liquid sample, and the Verigene System BC-GP microarray (Nanosphere Inc. Northbrook, USA) test.
Results: The consistency of LFM identification and the microarray method compared to post-culture MALDI-TOF MS was 75% (30/40) and 90% (36/40), respectively. The agreement between LFM and the microarray method was 83.3% (30/36). All three methods were consistent in 67.5% (27/40) of the bottles.
Conclusion: The study indicates that both lysis filtration and microarray methods are effective for rapid diagnosis in sepsis patients. Each method has its own advantages and limitations. Lysis filtration combined with MALDI-TOF MS offers a cost-efficient, fast, and broad-database approach, providing results in approximately 9-10 hours instead of the conventional 48-72 hours when combined with automatic susceptibility testing.
Keywords
Sepsis matrix-assisted laser desorption-Ionization mass spectrometry lysis filtration microarray analysis
Supporting Institution
Ege Üniversitesi Bilimsel Araştırmalar Etik Kurulu
References
- Wang W, Ma L, Liu, B, Ouyang L. The role of trained immunity in sepsis. Frontiers in Immunology. 2024;15:1449986.
- La Via L, Sangiorgio G, Stefani S, Marino A, Nunnari G, Cocuzza S, et al. The global burden of sepsis and septic shock. Epidemiologia. 2024;5(3):456-478.
- Nofal MA, Shitawi J, Altarawneh HB, Alrosan S, Alqaisi Y, Al-Harazneh AM, et al. Recent trends in septic shock management: a narrative review of current evidence and recommendations. Annals of Medicine and Surgery. 2024;86(8):4532-4540.
- Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, et al. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis for the identification of pathogenic microorganisms: a review. Microorganisms. 2021;9(7):1536.
- Howard AK, Claeys K, Biggs JM, Parbuoni KA, Johnson K, Luneburg P, et al. Performance of Verigene rapid diagnostic testing for detection of inpatient pediatric bacteremia. The Journal of Pediatric Pharmacology and Therapeutics. 2021;26(5):472-477.
- Fothergill A, Kasinathan V, Hyman J, Walsh J, Drake T, Wang YF. Rapid identification of bacteria and yeasts from positive-blood-culture bottles by using a lysis-filtration method and matrix-assisted laser desorption ionization-time of flight mass spectrum analysis with the SARAMIS database. J Clin Microbiol. 2013;51(3):805-9.
- Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas. 1960;20(1):37-46.
- Landis JR, Koch GG. The measurement of observer agreement for categorical data. Biometrics. 1977;33(1):159-74.
- Pan F, Zhao N, Zhao W, Wang C, Sun Y, Zhang H, et al. Performance of Two Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of the Viridans Group Streptococci. Infect Drug Resist. 2023;2901-9.
- Calderaro A, Chezzi C. MALDI-TOF MS: a reliable tool in the real life of the clinical microbiology laboratory. Microorganisms. 2024;12(2):322.
- Zhang Z, Xing E, Zhao W, Song M, Zhang C, Liu H, et al. Rapid identification of pathogenic bacteria from clinical positive blood cultures via virus-like magnetic bead enrichment and MALDI-TOF MS profiling. Analyst. 2025;150:827-840
- Peri AM, Chatfield MD, Ling W, Furuya-Kanamori L, Harris PN, Paterson DL. Rapid diagnostic tests and antimicrobial stewardship programs for the management of bloodstream infection: what is their relative contribution to improving clinical outcomes? A systematic review and network meta-analysis. Clinical Infectious Diseases. 2024;79(2):502-515.
- Liborio MP, Harris PN, Ravi C, Irwin AD. Getting up to speed: rapid pathogen and antimicrobial resistance diagnostics in sepsis. Microorganisms. 2024;12(9):1824.
- Özdemir L, Özdemir B, Gegin S, Aksu EA. Rare Pathogenic Lower Respiratory Tract Factors and Antibiotic Sensitivity Situations in Respiratory Intensive Care. Hitit Medical Journal. 2024;6(2):200-207.
- Dursun ZB, Aydın S, Çelik İ. Microorganisms Caused of Bacteremia in the Intensive Care Unit and Their Antibiotic Susceptibilities. Flora. 2019;24(3):183-189.
- Ulusoy TU, Hekimoglu CH, Parlayan HNK, Altin N, Senturk GC, Sencan I. Comparison of the Distribution of Healthcare-Associated Infections and Causative Agents Between Intensive Care Units and Other Clinics. Clinics. 2024;2849:100-0.
- Sandu AM, Chifiriuc MC, Vrancianu CO, Cristian RE, Alistar CF, Constantin M, t al. Healthcare-Associated Infections: The Role of Microbial and Environmental Factors in Infection Control—A Narrative Review. Infectious Diseases and Therapy. 2025;1-39.
- Aggarwal A, Abhishek KS, Tak V, Mehrotra S, Nag VG, Jain V. A Day Saved is a Life Saved: Direct Antimicrobial Susceptibility Testing from Positively Flagged Blood Culture Bottles and their Concordance with the Routine Method. Infectious Disorders. 2024;24(8):72-78.
- Umemura H, Nishiyama H, Tanimichi Y, Seino K, Nakajima M, Tsuchida S, et al. Impact of direct identification of bacteria in blood culture–positive specimens by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry on physician selection of antimicrobial therapy. Journal of Infection and Chemotherapy. 2025;31(2):102548.
- Tian PP, Su SS, Zhu LS, Wang T, Yang H, Du MY, et al. Short-term culture for rapid identification by mass spectrometry and automated antimicrobial susceptibility testing from positive bottles. BMC Infectious Diseases. 2024;24(1);566.
- Becker K, Lupetti A. MALDI-TOF MS in microbiological diagnostics: future applications beyond identification. Frontiers in microbiology. 2023;14:204452.
- Lapin JS, Smith RD, Hornback KM, Johnson JK, Claeys KC. From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. 2023;43(8):847-863.
- Guevara R, Davis MG, Davis MA, Ahmed S, Shah S, Cuaron K, et al. Efficacy of VERIGENE® Blood Culture Assays in accurately and rapidly detecting Gram-negative and Gram-positive pathogens. Infectious Disorders. 2022;22(5):71-76.
- Wang Y, Lindsley K, Bleak TC, Jiudice S, Uyei J, Gu Y, et al. Performance of molecular tests for diagnosis of bloodstream infections in the clinical setting: a systematic literature review and meta-analysis. Clinical Microbiology and Infection. 2024;31:360-372
- Watanabe R, Asai K, Kuroda M, Kujiraoka M, Sekizuka T, Katagiri M, et al. Quick detection of causative bacteria in cases of acute cholangitis and cholecystitis using a multichannel gene autoanalyzer. Surgery Today. 2021;51:1938-1945.
- Dunbar SA, Gardner C, Das S. Diagnosis and management of bloodstream infections with rapid, multiplexed molecular assays. Frontiers in Cellular and Infection Microbiology. 2022;12: 859935.
- Haider A, Ringe 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. Microbiology Research. 2023;14(1):80-90.
Gram-pozitif bakterilerin hızlı tanısında mikroarray ve lizis filtrasyon sonrası MALDI-TOF MS yöntemlerinin karşılaştırılması
Abstract
Amaç: Sepsisin erken tanısı hastanın prognozu açısından çok önemlidir. Bu nedenle, etken mikroorganizmanın hızlı bir şekilde belirlenmesi ve uygun tedaviye başlanması kritik öneme sahiptir. Bu çalışmanın amacı, kan kültürlerinde üreyen Gram-pozitif bakterilerin tanımlanmasında kullanılan üç yöntemi karşılaştırmaktır: kültür sonrası MALDI-TOF MS tanımlama yöntemi, lizis filtrasyon sonrası MALDI-TOF MS (LFM) tanımlama yöntemi ve mikroarray yöntemi. Ayrıca, mikroarray yöntemi ile etkenlerin direnç profillerinin belirlenmesi hedeflenmiştir.
Gereç ve Yöntem: Çalışmaya, bir üniversite hastanesinin erişkin yoğun bakım ünitelerinden alınan ve Gram-pozitif bakteri üremesi saptanan 40 kan kültürü şişesi dahil edilmiştir.
Kan kültürü şişesinin pozitif sinyal vermesinden sonra, üç farklı tanımlama yöntemi uygulanmıştır: Subkültür yapıldıktan sonra kültür kolonisinden MALDI-TOF MS ile tanımlama, şişeden alınan örneğe lizis filtrasyon uygulandıktan sonra MALDI-TOF MS ile tanımlama ve Nanosphere Verigene System BC-GP mikroarray (Nanosphere Inc. Northbrook, USA) test yöntemi. Elde edilen sonuçlar karşılaştırılmıştır.
Bulgular: Kültür sonrası MALDI TOF MS ile LFM tanımlaması arasındaki uyum oranı %75 (30/40) olarak hesaplanmıştır. Kültür sonrası MALDI TOF MS ile mikroarray sonuçları arasındaki uyum %90 (36/40) bulunmuştur. LFM ile mikroarray yöntemleri arasındaki benzerlik ise %83,3 (30/36) olarak belirlenmiştir. Üç yöntemin de tutarlı sonuç verdiği örneklerin oranı %67,5 (27/40) olarak hesaplanmıştır.
Sonuç: Çalışma bulguları, sepsisli olgularda hem lizis filtrasyon hem de mikroarray test yöntemlerinin hızlı tanı açısından etkili olabileceğini ortaya koymuştur. Her iki yöntemin de avantajları ve sınırlılıkları mevcuttur. Lizis filtrasyon sonrası uygulanan MALDI-TOF MS yöntemi; düşük maliyeti, kısa sürede sonuç vermesi, geniş veri tabanı desteği ve Gram boyama gerektirmemesi gibi özellikleriyle, kütle spektrometrisi altyapısına sahip laboratuvarlar için uygun bir seçenek olarak değerlendirilmiştir. Ayrıca, lizis filtrasyon ile elde edilen süspansiyondan otomatik duyarlılık testlerinin yapılabilmesi sayesinde, yaklaşık 9–10 saat içinde tanı ve duyarlılık sonuçlarına ulaşılabileceği ve bu sürenin konvansiyonel yöntemlerle karşılaştırıldığında belirgin ölçüde daha kısa olduğu sonucuna varılmıştır.
Keywords
Sepsis matrix-destekli laser desorpsiyon-ionizasyon kütle spektrometrisi lizis filtrasyon mikroarray analizi
Supporting Institution
ege Üniversitesi Klinik Araştırmalar Etik Kurulu
References
- Wang W, Ma L, Liu, B, Ouyang L. The role of trained immunity in sepsis. Frontiers in Immunology. 2024;15:1449986.
- La Via L, Sangiorgio G, Stefani S, Marino A, Nunnari G, Cocuzza S, et al. The global burden of sepsis and septic shock. Epidemiologia. 2024;5(3):456-478.
- Nofal MA, Shitawi J, Altarawneh HB, Alrosan S, Alqaisi Y, Al-Harazneh AM, et al. Recent trends in septic shock management: a narrative review of current evidence and recommendations. Annals of Medicine and Surgery. 2024;86(8):4532-4540.
- Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, et al. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analysis for the identification of pathogenic microorganisms: a review. Microorganisms. 2021;9(7):1536.
- Howard AK, Claeys K, Biggs JM, Parbuoni KA, Johnson K, Luneburg P, et al. Performance of Verigene rapid diagnostic testing for detection of inpatient pediatric bacteremia. The Journal of Pediatric Pharmacology and Therapeutics. 2021;26(5):472-477.
- Fothergill A, Kasinathan V, Hyman J, Walsh J, Drake T, Wang YF. Rapid identification of bacteria and yeasts from positive-blood-culture bottles by using a lysis-filtration method and matrix-assisted laser desorption ionization-time of flight mass spectrum analysis with the SARAMIS database. J Clin Microbiol. 2013;51(3):805-9.
- Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas. 1960;20(1):37-46.
- Landis JR, Koch GG. The measurement of observer agreement for categorical data. Biometrics. 1977;33(1):159-74.
- Pan F, Zhao N, Zhao W, Wang C, Sun Y, Zhang H, et al. Performance of Two Matrix-Assisted Laser Desorption Ionization–Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of the Viridans Group Streptococci. Infect Drug Resist. 2023;2901-9.
- Calderaro A, Chezzi C. MALDI-TOF MS: a reliable tool in the real life of the clinical microbiology laboratory. Microorganisms. 2024;12(2):322.
- Zhang Z, Xing E, Zhao W, Song M, Zhang C, Liu H, et al. Rapid identification of pathogenic bacteria from clinical positive blood cultures via virus-like magnetic bead enrichment and MALDI-TOF MS profiling. Analyst. 2025;150:827-840
- Peri AM, Chatfield MD, Ling W, Furuya-Kanamori L, Harris PN, Paterson DL. Rapid diagnostic tests and antimicrobial stewardship programs for the management of bloodstream infection: what is their relative contribution to improving clinical outcomes? A systematic review and network meta-analysis. Clinical Infectious Diseases. 2024;79(2):502-515.
- Liborio MP, Harris PN, Ravi C, Irwin AD. Getting up to speed: rapid pathogen and antimicrobial resistance diagnostics in sepsis. Microorganisms. 2024;12(9):1824.
- Özdemir L, Özdemir B, Gegin S, Aksu EA. Rare Pathogenic Lower Respiratory Tract Factors and Antibiotic Sensitivity Situations in Respiratory Intensive Care. Hitit Medical Journal. 2024;6(2):200-207.
- Dursun ZB, Aydın S, Çelik İ. Microorganisms Caused of Bacteremia in the Intensive Care Unit and Their Antibiotic Susceptibilities. Flora. 2019;24(3):183-189.
- Ulusoy TU, Hekimoglu CH, Parlayan HNK, Altin N, Senturk GC, Sencan I. Comparison of the Distribution of Healthcare-Associated Infections and Causative Agents Between Intensive Care Units and Other Clinics. Clinics. 2024;2849:100-0.
- Sandu AM, Chifiriuc MC, Vrancianu CO, Cristian RE, Alistar CF, Constantin M, t al. Healthcare-Associated Infections: The Role of Microbial and Environmental Factors in Infection Control—A Narrative Review. Infectious Diseases and Therapy. 2025;1-39.
- Aggarwal A, Abhishek KS, Tak V, Mehrotra S, Nag VG, Jain V. A Day Saved is a Life Saved: Direct Antimicrobial Susceptibility Testing from Positively Flagged Blood Culture Bottles and their Concordance with the Routine Method. Infectious Disorders. 2024;24(8):72-78.
- Umemura H, Nishiyama H, Tanimichi Y, Seino K, Nakajima M, Tsuchida S, et al. Impact of direct identification of bacteria in blood culture–positive specimens by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry on physician selection of antimicrobial therapy. Journal of Infection and Chemotherapy. 2025;31(2):102548.
- Tian PP, Su SS, Zhu LS, Wang T, Yang H, Du MY, et al. Short-term culture for rapid identification by mass spectrometry and automated antimicrobial susceptibility testing from positive bottles. BMC Infectious Diseases. 2024;24(1);566.
- Becker K, Lupetti A. MALDI-TOF MS in microbiological diagnostics: future applications beyond identification. Frontiers in microbiology. 2023;14:204452.
- Lapin JS, Smith RD, Hornback KM, Johnson JK, Claeys KC. From bottle to bedside: Implementation considerations and antimicrobial stewardship considerations for bloodstream infection rapid diagnostic testing. Pharmacotherapy: The Journal of Human Pharmacology and Drug Therapy. 2023;43(8):847-863.
- Guevara R, Davis MG, Davis MA, Ahmed S, Shah S, Cuaron K, et al. Efficacy of VERIGENE® Blood Culture Assays in accurately and rapidly detecting Gram-negative and Gram-positive pathogens. Infectious Disorders. 2022;22(5):71-76.
- Wang Y, Lindsley K, Bleak TC, Jiudice S, Uyei J, Gu Y, et al. Performance of molecular tests for diagnosis of bloodstream infections in the clinical setting: a systematic literature review and meta-analysis. Clinical Microbiology and Infection. 2024;31:360-372
- Watanabe R, Asai K, Kuroda M, Kujiraoka M, Sekizuka T, Katagiri M, et al. Quick detection of causative bacteria in cases of acute cholangitis and cholecystitis using a multichannel gene autoanalyzer. Surgery Today. 2021;51:1938-1945.
- Dunbar SA, Gardner C, Das S. Diagnosis and management of bloodstream infections with rapid, multiplexed molecular assays. Frontiers in Cellular and Infection Microbiology. 2022;12: 859935.
- Haider A, Ringe 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. Microbiology Research. 2023;14(1):80-90.
Details
| Primary Language | English |
|---|---|
| Subjects | Medical Bacteriology |
| Journal Section | Research Articles |
| Authors | |
| Publication Date | September 8, 2025 |
| Submission Date | February 19, 2025 |
| Acceptance Date | May 6, 2025 |
| Published in Issue | Year 2025 Volume: 64 Issue: 3 |
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