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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Mappa C, Alpha-Bazin B, Pible O, Armengaud J. Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics. Microorganisms 2023; 11:1170. [PMCID: PMC10223342 DOI: 10.3390/microorganisms11051170] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 06/01/2023] Open
Abstract
Shotgun proteomics has proven to be an attractive alternative for identifying a pathogen and characterizing the antimicrobial resistance genes it produces. Because of its performance, proteotyping of microorganisms by tandem mass spectrometry is expected to become an essential tool in modern healthcare. Proteotyping microorganisms that have been isolated from the environment by culturomics is also a cornerstone for the development of new biotechnological applications. Phylopeptidomics is a new strategy that estimates the phylogenetic distances between the organisms present in the sample and calculates the ratio of their shared peptides, thus improving the quantification of their contributions to the biomass. Here, we established the limit of detection of tandem mass spectrometry proteotyping based on MS/MS data recorded for several bacteria. The limit of detection for Salmonella bongori with our experimental set-up is 4 × 104 colony-forming units from a sample volume of 1 mL. This limit of detection is directly related to the amount of protein per cell and therefore depends on the shape and size of the microorganism. We have demonstrated that identification of bacteria by phylopeptidomics is independent of their growth stage and that the limit of detection of the method is not degraded in presence of additional bacteria in the same proportion.
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Affiliation(s)
- Charlotte Mappa
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, 30207 Bagnols-sur-Cèze, France
| | - Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
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Svetličić E, Dončević L, Ozdanovac L, Janeš A, Tustonić T, Štajduhar A, Brkić AL, Čeprnja M, Cindrić M. Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing. Molecules 2022; 27:molecules27175461. [PMID: 36080229 PMCID: PMC9457756 DOI: 10.3390/molecules27175461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
For mass spectrometry-based diagnostics of microorganisms, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used to identify urinary tract pathogens. However, it requires a lengthy culture step for accurate pathogen identification, and is limited by a relatively small number of available species in peptide spectral libraries (≤3329). Here, we propose a method for pathogen identification that overcomes the above limitations, and utilizes the MALDI-TOF/TOF MS instrument. Tandem mass spectra of the analyzed peptides were obtained by chemically activated fragmentation, which allowed mass spectrometry analysis in negative and positive ion modes. Peptide sequences were elucidated de novo, and aligned with the non-redundant National Center for Biotechnology Information Reference Sequence Database (NCBInr). For data analysis, we developed a custom program package that predicted peptide sequences from the negative and positive MS/MS spectra. The main advantage of this method over a conventional MALDI-TOF MS peptide analysis is identification in less than 24 h without a cultivation step. Compared to the limited identification with peptide spectra libraries, the NCBI database derived from genome sequencing currently contains 20,917 bacterial species, and is constantly expanding. This paper presents an accurate method that is used to identify pathogens grown on agar plates, and those isolated directly from urine samples, with high accuracy.
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Affiliation(s)
- Ema Svetličić
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lucija Dončević
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Luka Ozdanovac
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Andrea Janeš
- Clinical Department of Laboratory Diagnostics, University Hospital Dubrava, Avenija Gojka Šuška 6, 10000 Zagreb, Croatia
| | | | - Andrija Štajduhar
- Division for Medical Statistics, Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10000 Zagreb, Croatia
| | | | - Marina Čeprnja
- Special Hospital Agram, Agram EEIG, Trnjanska cesta 108, 10000 Zagreb, Croatia
| | - Mario Cindrić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-16384422
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Liu Z, Tang H, Xu H, Lu G, Yang W, Xia Z, Zhu Y, Ni S, Men W, Shen J. Rapid Identification and Drug Sensitivity Test to Urinary Tract Infection Pathogens by DOT-MGA. Infect Drug Resist 2022; 15:1391-1397. [PMID: 35392368 PMCID: PMC8980293 DOI: 10.2147/idr.s356045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/17/2022] [Indexed: 11/25/2022] Open
Abstract
Aim To reduce the inspection time for urinary tract pathogens and provide a rapid and effective therapeutic plan for clinical anti-infection treatment, this study developed a rapid identification (ID) and antimicrobial sensitivity test (AST) method by DOT-MGA. Methods We grouped midstream urine samples with single bacteria according to the number of bacteria (≤5/5–15/≥ 15) under per oil microscope after Gram staining. Then we adopted differential centrifugation to process the grouped samples to collect precipitate. MALDI-TOF MS was performed using precipitate directly or after short-term culture. If succeed, we resuspended the precipitate into droplets with or without antibiotics at a MALDI target. Four hours later, mass spectrometer (MS) was used to identify the culture on the target and to analyse AST. Results Samples (count ≥ 15), which precipitate can be directly identified by MS; otherwise, the precipitate need a short-term cultured for 3–6 h before ID. The consistency of the ID results between conventional culture and the precipitate is 100%. Compared with broth microdilution method, DOT-MGA for predicting AST had a high consistency. EA and CA for IPM, LEV, CAZ, NIT, and FOT were 100%/100%, 98%/90%, 98%/92%, 100%/90%, 98%/94%, respectively. No VME was observed in all tests. Besides, MIC50 for the five antibiotics by DOT-MGA and broth microdilution method were ≤1/≤0.5,>2/2,≤4/≤2,≤32/≤16,≤64/≤32 and MIC90 were ≤1/≤0.5, >2/>4, 16/16, 128/128, 128/64. Conclusion This study can shorten the ID time (minimum 0.5h) and AST (minimum 4h) of the main pathogens of urinary tract infection to 5–10 hours, which greatly reduce the inspection time and provide substantial help for the rapid diagnosis and treatment of patients with urinary tract infection.
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Affiliation(s)
- Zhen Liu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Hao Tang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Huaming Xu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Guoping Lu
- Laboratory Department of Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, 236000, People’s Republic of China
| | - Wensu Yang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Zhaoxin Xia
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Yi Zhu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Shenwang Ni
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Wanqi Men
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Jilu Shen
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
- Correspondence: Jilu Shen, The Fourth Affiliated Hospital of Anhui Medical University Laboratory, No. 100 Huaihai Avenue, Xinzhan District, Hefei, Anhui Province, 230012, People’s Republic of China, Tel +86 151 5515 2963, Email
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Das S, Roychoudhury S, Roychoudhury S, Agarwal A, Henkel R. Role of Infection and Leukocytes in Male Infertility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1358:115-140. [DOI: 10.1007/978-3-030-89340-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Yoon EJ, Jeong SH. MALDI-TOF Mass Spectrometry Technology as a Tool for the Rapid Diagnosis of Antimicrobial Resistance in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10080982. [PMID: 34439032 PMCID: PMC8388893 DOI: 10.3390/antibiotics10080982] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the antimicrobial resistance (AMR) in microorganisms. Primarily, antimicrobial susceptibility testing is able to be carried out either by comparing the area under curve of MALDI spectra of bacteria grown in media with antimicrobial drugs or by identifying the shift peaks of bacteria grown in media including 13C isotope with antimicrobial drugs. Secondly, the antimicrobial resistance is able to be determined through identifying (i) the antimicrobial-resistant clonal groups based on the fingerprints of the clone, (ii) the shift peak of the modified antimicrobial drug, which is inactivated by the resistance determinant, (iii) the shift peak of the modified antimicrobial target, (iv) the peak specific for the antimicrobial determinant, and (v) the biomarkers that are coproduced proteins with AMR determinants. This review aims to present the current usage of the MALDI-TOF MS technique for diagnosing antimicrobial resistance in bacteria, varied approaches for AMR diagnostics using the methodology, and the future applications of the methods for the accurate and rapid identification of AMR in infection-causing bacterial pathogens.
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Affiliation(s)
- Eun-Jeong Yoon
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Korea;
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
- Correspondence:
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Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. Microorganisms 2021; 9:microorganisms9071539. [PMID: 34361974 PMCID: PMC8307939 DOI: 10.3390/microorganisms9071539] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/06/2021] [Accepted: 07/18/2021] [Indexed: 12/11/2022] Open
Abstract
Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. 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:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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Sun B, Wang W, Ma P, Gu B. Accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for direct bacterial identification from culture-positive urine samples. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:647. [PMID: 33987345 PMCID: PMC8106043 DOI: 10.21037/atm-20-7310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background Urinary tract infection (UTI) is one of the most frequent reasons for antimicrobial therapy. In typical clinical setting, 18–48 h is needed to identify pathogens by urine culture. A rapid method for pathogenic UTI diagnosis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed in recent years. Methods This meta-analysis systematically evaluated the accuracy of MALDI-TOF MS for direct identification of bacteria from culture-positive urine samples. We queried the electronic database of Medline and Web of Science to obtain relevant articles. Results Nineteen articles involving 4,579 isolates were included after final selection in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS was 0.82 with 95% confidence interval of 0.79 to 0.86 at the species level. For Gram-negative isolates, the correct identification performance of the species ranged from 0.54 to 0.98, with a cumulative rate of 0.87 (95% CI: 0.83 to 0.91). For Gram-positive isolates, the correct identification rate ranged from 0.32 to 0.80, with a cumulative rate of 0.59 (95% CI: 0.49 to 0.68). Conclusions MALDI-TOF MS provides a reliable direct identification of bacteria, particularly in cases of Gram-negative isolates, from clinical urine specimens. Nevertheless, the identification accuracy of this method is moderate for Gram-positive bacteria.
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Affiliation(s)
- Bin Sun
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Ping Ma
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Bing Gu
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China
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Miller C, Bates ST, Gielda LM, Creighton JC. The role of parental care in the establishment of the offspring digestive tract microbiome in Nicrophorus defodiens. Anim Behav 2021. [DOI: 10.1016/j.anbehav.2020.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Rentschler S, Kaiser L, Deigner HP. Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance. Int J Mol Sci 2021; 22:E456. [PMID: 33466437 PMCID: PMC7796476 DOI: 10.3390/ijms22010456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.
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Affiliation(s)
- Simone Rentschler
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057 Rostock, Germany
- Faculty of Science, Tuebingen University, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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Rapid identification of uropathogens by combining Alfred 60 system with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry technology. Eur J Clin Microbiol Infect Dis 2020; 39:1855-1863. [PMID: 32388696 DOI: 10.1007/s10096-020-03919-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/28/2020] [Indexed: 10/23/2022]
Abstract
Rapid identification of uropathogens is needed to determine appropriate antimicrobial therapy. This study evaluated performance of the Alfred 60 system combined with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) technology for rapid identification of uropathogens. The Alfred 60 system was used to screen urine cultures, followed by identifying the microbial pathogen in positive cultures using MALDI-TOF MS. The Alfred 60 detected positive cultures by measuring the turbidity of urine samples, which were transferred automatically to vials containing liquid medium and incubated for 3.5 h at 35 °C in the Alfred 60 system. Vials that showed growth were removed and centrifuged. The pellet was subjected to MALDI-TOF MS identification. In parallel, positive urine samples were inoculated onto agar plates for identification by conventional culture. The time required to detect positive urine cultures with Alfred 60 and identify the uropathogens with MALDI-TOF MS ranged from 15 min to 3.5 h. Among 146 positive urine samples tested, conventional cultures showed three culture groups: group 1 included 101 samples with growth of a single type of microorganism; group 2 included 34 samples with 2 types of microorganisms; and group 3 included 11 samples with ≥ 3 types of microorganisms. Direct identification by MALDI-TOF MS was concordant with 95% of the samples in group 1, 100% of the principal microorganism in group 2, but could not identify microorganisms in group 3. This combination of methods provides rapid, reliable microbial identification for most positive urine cultures.
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Mohan B, Gautam N, Sethuraman N, Kaur H, Taneja N. Evaluation of matrix assisted laser desorption ionisation-time of flight mass spectrometry in direct identification of bacteriuria from urine samples. Indian J Med Microbiol 2020; 38:293-298. [PMID: 33154238 DOI: 10.4103/ijmm.ijmm_20_206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Objective The use of matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI) directly on urine can significantly improve turnaround time for diagnosing urinary tract infection (UTI). The present study was planned to compare the performance of MALDI directly on urine samples with conventional urine culture and evaluate an algorithm using a combination of significant pyuria and MALDI directly on urine samples as a screening method for diagnosing UTI. Materials and Methods A total of 1000 urine samples from patients with symptoms suggestive of UTIs were analysed. Urine microscopy, urine culture and MALDI were performed simultaneously on all the samples. Results MALDI correctly identified the microorganisms in 73.83% monomicrobial samples. In culture showing a mixed growth of two and more than three organisms, MALDI was able to identify one microorganism in 27.58% and 15.78% of samples, respectively. There were no peaks by MALDI in 93.53% of 464 sterile samples. The sequential algorithm using urine microscopy and MALDI could correctly identify UTI in 66.23% cases. Conclusion MALDI can be utilised to rule out bacteriuria in >93% of sterile urine samples. The combination of significant pyuria and direct MALDI as screening method to diagnose UTI (whether monomicrobial or polymicrobial) was not found to be superior than using direct MALDI on urine samples alone.
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Affiliation(s)
- Balvinder Mohan
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Neha Gautam
- Department of Microbiology, Dr YSPGMC, Nahan, Himachal Pradesh, India
| | - Nandini Sethuraman
- Department of Microbiology, Apollo Hospitals, Chennai, Tamil Nadu, India
| | - Harsimran Kaur
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Neelam Taneja
- Department of Medical Microbiology, PGIMER, Chandigarh, India
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15
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Holmes DT, Romney MG, Angel P, DeMarco ML. Proteomic applications in pathology and laboratory medicine: Present state and future prospects. Clin Biochem 2020; 82:12-20. [PMID: 32442429 DOI: 10.1016/j.clinbiochem.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/13/2020] [Accepted: 05/13/2020] [Indexed: 12/11/2022]
Abstract
Clinical mass spectrometry applications have traditionally focused on small molecules, particularly in the areas of therapeutic drug monitoring, toxicology, and measurement of endogenous and exogenous steroids. More recently, the use of matrix assisted laser desorption/ionization time of flight mass spectrometry for the identification of microbial pathogens has been widely implemented. Following this evolution, there has been an expanding role for the measurement of peptides and proteins in pathology and laboratory medicine. This review explores the current state of protein measurement by clinical mass spectrometry and the analytical strategies employed, as well as emerging applications in clinical chemistry, clinical microbiology and anatomical pathology.
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Affiliation(s)
- Daniel T Holmes
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, 1081 Burrard St, Vancouver, BC V6Z 1Y6, Canada; University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC V6T 2B5 Canada.
| | - Marc G Romney
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, 1081 Burrard St, Vancouver, BC V6Z 1Y6, Canada; University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC V6T 2B5 Canada.
| | - Peggi Angel
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charelston, SC 29425 Canada.
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, 1081 Burrard St, Vancouver, BC V6Z 1Y6, Canada; University of British Columbia Department of Pathology and Laboratory Medicine, Vancouver, BC V6T 2B5 Canada.
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16
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Sun C, Zhang X, Wang J, Cheng C, Kang H, Gu B, Ma P. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry combined with UF-5000i urine flow cytometry to directly identify pathogens in clinical urine specimens within 1 hour. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:602. [PMID: 32566628 PMCID: PMC7290531 DOI: 10.21037/atm.2019.10.73] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Urinary tract infection (UTI) is one of the most common hospital-associated infectious. The traditional laboratory diagnosis method for UTI requires at least 24 hours, and it cannot provide the etiology basis for the clinic in time. The aim of our study is to develop a new method for pathogenic diagnosis of UTI by combining matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and UF-5000i from urine samples directly within 1 hour. Methods A total of 1,503 urine samples were collected from patients suggesting symptoms of UTI from August 2018 to January 2019. Each of these samples was divided into three aliquots. The first aliquot was used for conventional cleaning mid-stream urine culture; the second one for UF-5000i analysis to screen out the bacterial counts, which were more than 1×105 bacteria/mL. The third one was processed to bacterial purification and directly identified by the MALDI-TOF MS. Results In our study, 296 of 1,503 urine specimens were screened out by UF-5000i (bacterial pellets counts ≥105/mL). Compared the conventional culture-dependent method, the results of our methods were consistent in 249 of 263 (94.7%) cases, and they were both single-microorganism. Among 249 credible results, species-level identification (score ≥2.0) was contained 233 (233/249. 93.6%), 16 (16/249, 6.4%) samples scored between 1.7 and 1.99, and 14 (14/249, 5.6%) samples scored <1.7 or no peaks found. When there were 2 different kinds of bacteria in the urine, the result of MALDI-TOF MS was unreliable. Conclusions MALDI-TOF MS combined with UF-5000i to identify the pathogenic bacteria in urine directly is a novel and reliable method and saves at least 23 hours relative to the current routine conventional method. Thus its rapid and accurate detection may provide the basis of etiology for clinical diagnosis of UTIs efficiently.
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Affiliation(s)
- Chuang Sun
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China
| | - Xiao Zhang
- Department of Laboratory Medicine, Suzhou Ninth People's Hospital, Suzhou 215200, China
| | - Jingqiao Wang
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China
| | - Chen Cheng
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China
| | - Haiquan Kang
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Bing Gu
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
| | - Ping Ma
- Medical Technology School of Xuzhou Medical University, Xuzhou 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, China
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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18
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Mörtelmaier C, Panda S, Robertson I, Krell M, Christodoulou M, Reichardt N, Mulder I. Identification performance of MALDI-ToF-MS upon mono- and bi-microbial cultures is cell number and culture proportion dependent. Anal Bioanal Chem 2019; 411:7027-7038. [PMID: 31486868 PMCID: PMC6834929 DOI: 10.1007/s00216-019-02080-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/31/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023]
Abstract
Biotyping using matrix-assisted laser desorption ionization-time of flight (MALDI-ToF) mass spectroscopy (MS) has revolutionized microbiology by allowing clinicians and scientists to rapidly identify microbes at genus and species levels. The present study extensively assesses the suitability and reliability of MALDI-ToF biotyping of 14 different aerobic and anaerobic bacterial species as pure and mixed cultures. Reliable identification at species level was possible from biomaterial of older colonies and even frozen biomaterial, although this was species dependent. Using standard instrument settings and direct application of biomaterial onto the MALDI-ToF target plates, it was determined that the cell densities necessary for completely reliable identification of pure cultures varied between 2.40 × 108 and 1.10 × 1010 viable cell counts (VCCs) per mL, depending on the species. Evaluation of the mixed culture algorithm of the Bruker Biotyper® software showed that the performance of the algorithm depends greatly on the targeted species, on their phylogenetic distance, and on their ratio of VCC per mL in the mixed culture. Hence, the use of MALDI-ToF-MS with incorporation of the mixed culture algorithm of the software is a useful pre-screening tool for early identification of contaminants, but due to the great variability in performance between different species and the usually unknown percentage of the possible contaminant in the mixture, it is advisable to combine this method with other microbiology methods.
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Affiliation(s)
| | - Suchita Panda
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | - Iain Robertson
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | - Mareike Krell
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
| | | | | | - Imke Mulder
- 4D Pharma Research Ltd., Cornhill Road, Aberdeen, AB25 2ZS, UK
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Bryson AL, Hill EM, Doern CD. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress. Clin Lab Med 2019; 39:391-404. [PMID: 31383264 DOI: 10.1016/j.cll.2019.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This article summarizes recent advances in the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to new areas of infectious diseases diagnostics. We discuss progress toward routine identification of mycobacteria and filamentous fungi and direct identification of pathogens from clinical specimens. Of greatest interest is the use of MALDI-TOF MS for identifying organisms from positive blood cultures and from clinical specimens such as urine. Last, We highlight some exciting new possibilities for MALDI-TOF MS phenotypic susceptibility testing for bacteria and yeast.
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Affiliation(s)
- Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA
| | - Emily M Hill
- Pathology & Laboratory Medicine, Hunter Holmes McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23224, USA
| | - Christopher D Doern
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA.
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20
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Comparison of MALDI-TOF MS Biotyper and 16S rDNA sequencing for the identification of Pseudomonas species isolated from fish. Microb Pathog 2019; 132:313-318. [PMID: 30999019 DOI: 10.1016/j.micpath.2019.04.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/20/2022]
Abstract
Effective and reliable methods of identification of Pseudomonas species are important for the characterization of microorganisms. Freshwater ecosystems are an important source of Pseudomonas species, including those pathogenic to fish and humans. The aim of the present study was to compare the identification conducted with MALDI-TOF MS Biotyper and 16S rDNA sequencing of fish-borne Pseudomonas spp. Altogether, 13 different Pseudomonas spp. were isolated from freshwater fish. Phylogenetic analysis showed a clear taxonomic placement only for 13 out of 15 Pseudomonas isolates. Accordance of identification method was found only in 6 out of 15 isolates. The human pathogenic Pseudomonas spp. were not found in our study, indicating that the fish could be considered as safe for consumption. The present study revealed a high discriminatory power of the mass spectra investigation and 16S rDNA gene sequencing technology for the identification of Pseudomonas spp. associated with freshwater fish.
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Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization-Time of Flight Spectrum Database. J Clin Microbiol 2019; 57:JCM.01678-18. [PMID: 30700506 DOI: 10.1128/jcm.01678-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/24/2019] [Indexed: 11/20/2022] Open
Abstract
Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae, Staphylococcus aureus, Staphylococcus saprophyticus, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra.
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Guzmán-Puche J, Gracia-Ahufinger I, Causse M, Tejero-García R, Rodríguez-López FC, Casal-Román M. Combination of Coral UTI Screen TM system, gram-stain and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for diagnosis of urinary tract infections directly from urine samples. J Chemother 2019; 31:74-80. [PMID: 30784363 DOI: 10.1080/1120009x.2019.1573284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This study proposes an algorithm for microbiological diagnosis of urinary tract infections based on screening by luminometry and Gram-stain, followed by identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Positive urine samples detected with the luminometry screening Coral UTI ScreenTM system underwent Gram staining and identification of the causative organism was performed by MALDI-TOF Microflex LT mass spectrometer (Bruker Daltonics, Germany). Subsequently, the results were compared with those of conventional culture identification using WIDER MIC/id system (Francisco Soria Melguizo SA, Spain). Considering the conventional approach as the gold standard, the proposed algorithm presented both a high specificity (98.1%) and a positive likelihood ratio of 37.42. The implementation of this algorithm would allow diagnosis of urinary tract infection in less than an hour in 92.4% of positive samples. This combination of techniques would be useful particularly for patients with severe UTI, pyelonephritis or urinary sepsis.
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Affiliation(s)
- Julia Guzmán-Puche
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain
| | - Irene Gracia-Ahufinger
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Manuel Causse
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Rocío Tejero-García
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Fernando Carlos Rodríguez-López
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Manuel Casal-Román
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain
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Gu YF, Li Y, Zhang XL, Yu LM, Huang BH, Sun CM. A New Method Aimed to Quickly Identify Pathogen and Drug Susceptibility Test Based on Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry Combined with Flow Cytometry. Surg Infect (Larchmt) 2019; 20:219-224. [PMID: 30657423 DOI: 10.1089/sur.2018.145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
AIM To discuss the significance and applied value in the rapid identification and drug susceptibility test for blood stream infection (BSI) using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) combined with flow cytometry (FCM). METHODS The bacteria were separated from the positive blood culture bottle using the separation gel-adsorption method system, and then applying MALDI-TOF MS combined with FCM to identify pathogen and drug susceptibility test quickly. RESULTS The efficiency of the separation gel-adsorption method for gram-negative bacterium, gram-positive bacteria, and fungi is 71%, 74%, and 88%, respectively. The results of identifying pathogens using MALDI-TOFMS are in agreement with results obtained using VITEK®2 (bioMérieux, Marcy l'Etoile, France); both methods can identify 90% of bacteria to species. For fungi, MALDI-TOF MS can identify 75% fungi to species, which is superior to VITEK2, which identifies 60% fungi to species. The results of drug susceptibility test using FCM are almost identical to VITEK2; additionally, the addition of fluorescein diacetate can identify the heterogenic drug-resistant strains. CONCLUSIONS We can quickly identify pathogen and drug-susceptibility test based on MALDI-TOF MS combined with FCM, which is consistent with traditional methods and can shorten the report time from 36-72 hour to 3 hours. More importantly, these methods are of great significance and clinical importance for the rapid identification of BSI.
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Affiliation(s)
- Yu-Feng Gu
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Yu Li
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Xiao-Lu Zhang
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Li-Mei Yu
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Bao-Hua Huang
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
| | - Cheng-Ming Sun
- Department of Clinical Laboratory Center, Yantai Yuhuangding Hospital, Yantai, Shandong, China
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Liang T, Leung LM, Opene B, Fondrie WE, Lee YI, Chandler CE, Yoon SH, Doi Y, Ernst RK, Goodlett DR. Rapid Microbial Identification and Antibiotic Resistance Detection by Mass Spectrometric Analysis of Membrane Lipids. Anal Chem 2019; 91:1286-1294. [PMID: 30571097 DOI: 10.1021/acs.analchem.8b02611] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Infectious diseases have a substantial global health impact. Clinicians need rapid and accurate diagnoses of infections to direct patient treatment and improve antibiotic stewardship. Current technologies employed in routine diagnostics are based on bacterial culture followed by morphological trait differentiation and biochemical testing, which can be time-consuming and labor-intensive. With advances in mass spectrometry (MS) for clinical diagnostics, the U.S. Food and Drug Administration has approved two microbial identification platforms based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS analysis of microbial proteins. We recently reported a novel and complementary approach by comparing MALDI-TOF mass spectra of microbial membrane lipid fingerprints to identify ESKAPE pathogens. However, this lipid-based approach used a sample preparation method that required more than a working day from sample collection to identification. Here, we report a new method that extracts lipids efficiently and rapidly from microbial membranes using an aqueous sodium acetate (SA) buffer that can be used to identify clinically relevant Gram-positive and -negative pathogens and fungal species in less than an hour. The SA method also has the ability to differentiate antibiotic-susceptible and antibiotic-resistant strains, directly identify microbes from biological specimens, and detect multiple pathogens in a mixed sample. These results should have positive implications for the manner in which bacteria and fungi are identified in general hospital settings and intensive care units.
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Affiliation(s)
- Tao Liang
- Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , Baltimore , Maryland 20742 , United States
| | - Lisa M Leung
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States.,Divisions of Microbiology and Molecular Biology, Laboratories Administration , Maryland Department of Health , Baltimore , Maryland 21215 , United States
| | - Belita Opene
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States
| | - William E Fondrie
- Center for Vascular and Inflammatory Diseases , University of Maryland , Baltimore , Maryland 20742 , United States
| | - Young In Lee
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States
| | - Courtney E Chandler
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States
| | - Sung Hwan Yoon
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States
| | - Yohei Doi
- Division of Infectious Diseases, School of Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry , University of Maryland , Baltimore , Maryland 20742 , United States
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy , University of Maryland , Baltimore , Maryland 20742 , United States
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Oyaert M, Delanghe J. Progress in Automated Urinalysis. Ann Lab Med 2018; 39:15-22. [PMID: 30215225 PMCID: PMC6143458 DOI: 10.3343/alm.2019.39.1.15] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/13/2018] [Accepted: 08/29/2018] [Indexed: 12/17/2022] Open
Abstract
New technological advances have paved the way for significant progress in automated urinalysis. Quantitative reading of urinary test strips using reflectometry has become possible, while complementary metal oxide semiconductor (CMOS) technology has enhanced analytical sensitivity and shown promise in microalbuminuria testing. Microscopy-based urine particle analysis has greatly progressed over the past decades, enabling high throughput in clinical laboratories. Urinary flow cytometry is an alternative for automated microscopy, and more thorough analysis of flow cytometric data has enabled rapid differentiation of urinary microorganisms. Integration of dilution parameters (e.g., creatinine, specific gravity, and conductivity) in urine test strip readers and urine particle flow cytometers enables correction for urinary dilution, which improves result interpretation. Automated urinalysis can be used for urinary tract screening and for diagnosing and monitoring a broad variety of nephrological and urological conditions; newer applications show promising results for early detection of urothelial cancer. Concomitantly, the introduction of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has enabled fast identification of urinary pathogens. Automation and workflow simplification have led to mechanical integration of test strip readers and particle analysis in urinalysis. As the information obtained by urinalysis is complex, the introduction of expert systems may further reduce analytical errors and improve the quality of sediment and test strip analysis. With the introduction of laboratory-on-a-chip approaches and the use of microfluidics, new affordable applications for quantitative urinalysis and readout on cell phones may become available. In this review, we present the main recent developments in automated urinalysis and future perspectives.
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Affiliation(s)
- Matthijs Oyaert
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.
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Vrioni G, Tsiamis C, Oikonomidis G, Theodoridou K, Kapsimali V, Tsakris A. MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:240. [PMID: 30069442 PMCID: PMC6046294 DOI: 10.21037/atm.2018.06.28] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The laboratory diagnosis of infections is based on pathogen identification and antimicrobial susceptibility determination. The gold standard of cultivation, isolation and susceptibility testing is a time-consuming procedure and in some cases this can be threatening for patients' outcome. In the current review the applications of mass spectrometry in pathogen identification and especially in detecting biomarkers of antimicrobial resistance are analyzed. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry is a new technology that has revolutionized pathogen identification and has also proven to accelerate detection of antimicrobial resistance compared to the traditional antibiotic susceptibility tests (AST) as well as DNA amplification methodologies. The technology has incorporated up to know four different methodologies: (I) the detection of differences of mass spectra of susceptible and resistant isolates of a given microorganism using the classical strain typing methodology; (II) the analysis of bacterial induced hydrolysis of β-lactam antibiotics; (III) the detection of stable (non-radioactive) isotope-labeled amino acids; and (IV) the analysis of bacterial growth in the presence and absence of antibiotics using an internal standard. The implementation of MALDI-TOF methodologies has improved detection of resistance in aerobic, Gram-positive and Gram-negative bacteria, mycobacteria, anaerobic bacteria, fungi and viruses. The MALDI-TOF is an easy to use, rapid, reliable, economical, and environmentally friendly methodology. However, this technology needs further development of research protocols that will be validated for routine application.
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Affiliation(s)
- Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Tsiamis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Oikonomidis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kalliopi Theodoridou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Violeta Kapsimali
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Šalplachta J, Horká M, Růžička F, Šlais K. Identification of bacterial uropathogens by preparative isoelectric focusing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J Chromatogr A 2018; 1532:232-237. [DOI: 10.1016/j.chroma.2017.11.072] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/20/2017] [Accepted: 11/30/2017] [Indexed: 01/25/2023]
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Shell WS, Sayed ML, Allah FMG, Gamal FEM, Khedr AA, Samy AA, Ali AHM. Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry as a reliable proteomic method for characterization of Escherichia coli and Salmonella isolates. Vet World 2017; 10:1083-1093. [PMID: 29062198 PMCID: PMC5639107 DOI: 10.14202/vetworld.2017.1083-1093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 08/10/2017] [Indexed: 11/16/2022] Open
Abstract
Aim: Identification of pathogenic clinical bacterial isolates is mainly dependent on
phenotypic and genotypic characteristics of the microorganisms. These conventional
methods are costive, time-consuming, and need special skills and training. An
alternative, mass spectral (proteomics) analysis method for identification of
clinical bacterial isolates has been recognized as a rapid, reliable, and
economical method for identification. This study was aimed to evaluate and compare
the performance, sensitivity and reliability of traditional bacteriology,
phenotypic methods and matrix-assisted laser desorption-ionization-time-of-flight
mass spectrometry (MALDI-TOF MS) in the identification of clinical
Escherichia coli and Salmonella isolates
recovered from chickens. Materials and Methods: A total of 110 samples (cloacal, liver, spleen, and/or gall bladder) were
collected from apparently healthy and diseased chickens showing clinical signs as
white chalky diarrhea, pasty vent, and decrease egg production as well as freshly
dead chickens which showing postmortem lesions as enlarged liver with congestion
and enlarged gall bladder from different poultry farms. Results: Depending on colonial characteristics and morphological characteristics,
E. coli and Salmonella isolates were
recovered and detected in only 42 and 35 samples, respectively. Biochemical
identification using API 20E identification system revealed that the suspected
E. coli isolates were 33 out of 42 of colonial and
morphological identified E. coli isolates where
Salmonella isolates were represented by 26 out of 35 of
colonial and morphological identified Salmonella isolates.
Serological identification of isolates revealed that the most predominant
E. coli serotypes were O1 and O78 while the most predominant
Salmonella serotype of Salmonella was
Salmonella Pullorum. All E. coli and
Salmonella isolates were examined using MALDI-TOF MS. In
agreement with traditional identification, MADI-TOF MS identified all clinical
bacterial samples with valid scores as E. coli and
Salmonella isolates except two E. coli
isolates recovered from apparently healthy and diseased birds, respectively, with
recovery rate of 93.9% and 2 Salmonella isolates recovered
from apparently healthy and dead birds, respectively, with recovery rate of
92.3%. Conclusion: Our study demonstrated that Bruker MALDI-TOF MS Biotyper is a reliable rapid and
economic tool for the identification of Gram-negative bacteria especially
E. coli and Salmonella which could be used as
an alternative diagnostic tool for routine identification and differentiation of
clinical isolates in the bacteriological laboratory. MALDI-TOF MS need more
validation and verification and more study on the performance of direct colony and
extraction methods to detect the most sensitive one and also need using more
samples to detect sensitivity, reliability, and performance of this type of
bacterial identification.
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Affiliation(s)
- Waleed S Shell
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - Mahmoud Lotfy Sayed
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - Fatma Mohamed Gad Allah
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | | | - Afaf Ahmed Khedr
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
| | - A A Samy
- Department of Microbiology and Immunology, National Research Center, Cairo, Egypt
| | - Abdel Hakam M Ali
- Central Laboratory for Evaluation of Veterinary Biologics Abbasaia, Agriculture Research Center, Cairo, Egypt
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Druckenmüller K, Gärtner A, Jäckel U, Klug K, Schiffels J, Günther K, Elbers G. Development of a methodological approach for the characterization of bioaerosols in exhaust air from pig fattening farms with MALDI-TOF mass spectrometry. Int J Hyg Environ Health 2017; 220:974-983. [DOI: 10.1016/j.ijheh.2017.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/06/2017] [Accepted: 05/06/2017] [Indexed: 12/16/2022]
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Abstract
Hospital-associated infection (HAI) in immunocompromised patients can result in high rates of morbidity and mortality. Infections caused by multidrug-resistant organisms (MDROs) are especially worrisome because of the limited choice of remaining antibiotics available when a patient becomes colonized or infected with an MDRO. It is therefore important that immunocompromised patients be cared for in an environment that limits the risk for acquiring infections. However, with healthcare being increasingly delivered in settings other than the traditional inpatient hospital wards, a bigger effort will need to be set forth to prevent or rapidly diagnose HAI. The last few years have seen a significant increase in the number of singleplex and multiplex molecular assays for the detection of many of the organisms responsible for HAI, but more is needed as infections caused by organisms like Legionella pneumophila and Aspergillus species are still diagnosed with methods that have relatively low yield and are slow to provide actionable results. Finally, the use of novel techniques for outbreak investigations will provide new information on transmission of infectious agents in healthcare settings and allow stronger, evidence-based recommendations to be developed for prevention of HAIs in the immunocompromised host.
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Choi JS, Kim J, Kim HS, Kwon CW, Kim MS, Choi SH. NaOH-HCl neutralized urine preparation for direct testing of uropathogens by Bruker MS. J Clin Lab Anal 2017. [PMID: 28649705 DOI: 10.1002/jcla.22280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND We evaluated the analytical performance of a NaOH-HCl neutralization protocol for identifying uropathogens directly from urine samples by a Bruker MS system (Bruker Daltonics, German) and sought to establish a protocol for integrating the method with conventional screening. METHODS Among all urine samples requested for Gram staining, UF-1000i, and urine cultures by physicians, we selected samples that were positive by both Gram staining and UF-1000i testing. Urine was prepared by neutralization using 0.01M NaOH-HCl, and the samples were processed by Bruker MS. For the low detection limit, one strain each of Escherichia coli and Enterococcus faecium was inoculated in sterile deionized water and sterile urine specimens at sequential dilutions. RESULTS In a total of 1270 urine samples, 125 samples (9.8%) were positive by both Gram staining and UF-1000i. Of 94 samples showing a single morphotype on agar plates, 82 samples had colony counts ≥105 CFU/mL and most uropathogens (95.1%, 78 of 82) had UF-1000i counts ≥106 bacteria/mL. Among them, Bruker MS correctly identified 86.6% (71/82) of all isolates, 89.2% (66/74) of Gram-negative bacteria (GNB), and 62.5% (5/8) of Gram-positive cocci (GPC) with higher average scores for GPC (mean score 2.013) and GNB (mean score 2.110). CONCLUSIONS Bruker MS with urine preparation by NaOH-HCl neutralization provides a simple, cost-effective, and accurate method for identifying uropathogens directly from urine. Using Bruker MS when single morphotype Gram staining and the UF-1000i count as ≥106 bacteria/mL may improve the efficiency of bacterial identification in routine practice.
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Affiliation(s)
- Ji Seon Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
- Institute for Integrative Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Jayoung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
- Institute for Integrative Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Han-Soo Kim
- Department of Biomedical Sciences, Catholic Kwandong University, Gangneung, Korea
- Institute for BioMedical Convergence, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Chang-Wan Kwon
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Min-Sung Kim
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
| | - Seong-Hyeok Choi
- Department of Laboratory Medicine, International St. Mary's Hospital, Catholic Kwandong University, Incheon, Korea
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Kollef MH, Burnham CAD. Ventilator-Associated Pneumonia: The Role of Emerging Diagnostic Technologies. Semin Respir Crit Care Med 2017; 38:253-263. [PMID: 28578550 PMCID: PMC7117076 DOI: 10.1055/s-0037-1599224] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance has emerged as a key determinant of outcome in patients with serious infections along with the virulence of the underlying pathogen. Within the intensive care unit (ICU) setting, ventilator-associated pneumonia (VAP) is a common nosocomial infection that is frequently caused by multidrug-resistant bacteria. Antimicrobial resistance is a growing challenge in the care of critically ill patients. Escalating rates of antibiotic resistance add substantially to the morbidity, mortality, and cost related to infection in the ICU. Both gram-positive organisms, such as methicillin-resistant Staphylococcus aureus and vancomycin-intermediate S. aureus, and gram-negative bacteria, including Pseudomonas aeruginosa, Acinetobacter species, carbapenem-resistant Enterobacteriaceae, such as the Klebsiella pneumoniae carbapenemase-producing bacteria, and extended spectrum β-lactamase organisms, have contributed to the escalating rates of resistance seen in VAP and other nosocomial infections. The rising rates of antimicrobial resistance have led to the routine empiric administration of broad-spectrum antibiotics even when bacterial infection is not documented. Moreover, there are several new broader-spectrum antibiotics that have recently become available and others scheduled for approval in the near future. The challenge to ICU clinicians is how to most effectively utilize these agents to maximize patient benefits while minimizing further emergence of resistance. Use of rapid diagnostics may hold the key for achieving this important balance. There is an urgent need for integrating the administration of new and existing antibiotics with the emerging rapid diagnostic technologies in a way that is both cost-effective and sustainable for the long run.
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Affiliation(s)
- Marin H Kollef
- Division of Pulmonary and Critical Care Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
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Prospective Evaluation of Light Scatter Technology Paired with Matrix-Assisted Laser Desorption Ionization -Time of Flight Mass Spectrometry for Rapid Diagnosis of Urinary Tract Infections. J Clin Microbiol 2017; 55:1802-1811. [PMID: 28356414 DOI: 10.1128/jcm.00027-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/20/2017] [Indexed: 01/14/2023] Open
Abstract
Urinary tract infections are one of the most common reasons for health care visits. Diagnosis and optimal treatment often require a urine culture, which takes an average of 1.5 to 2 days from urine collection to results, delaying optimal therapy. Faster, but accurate, alternatives are needed. Light scatter technology has been proposed for several years as a rapid screening tool, whereby negative specimens are excluded from culture. A commercially available light scatter device, BacterioScan 216Dx (BacterioScan, Inc.), has recently been advertised for this application. Paired use of mass spectrometry (MS) for bacterial identification and automated-system-based susceptibility testing straight from the light scatter suspension might provide dramatic improvement in times to a result. The present study prospectively evaluated the BacterioScan device, with culture as the reference standard. Positive light scatter specimens were used for downstream rapid matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS organism identification and automated-system-based antimicrobial susceptibility testing. Prospective evaluation of 439 urine samples showed a sensitivity of 96.5%, a specificity of 71.4%, and positive and negative predictive values of 45.1% and 98.8%, respectively. MALDI-TOF MS analysis of the suspension after density-based selection yielded a sensitivity of 72.1% and a specificity of 96.9%. Antimicrobial susceptibility testing of the samples identified by MALDI-TOF MS produced an overall categorical agreement of 99.2%. Given the high sensitivity and negative predictive value of results obtained, BacterioScan 216Dx is a reasonable approach for urine screening and might produce negative results in as few as 3 h, with no downstream workup. Paired rapid identification and susceptibility testing might be useful when MALDI-TOF MS results in an organism identification, and it might decrease the time to a result by more than 24 h.
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Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm. J Clin Microbiol 2017; 55:1488-1495. [PMID: 28249997 DOI: 10.1128/jcm.02549-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/17/2017] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allow prompt and specific treatment. We optimized specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile, and supernatant spotted onto the target plate were 15 ml, 3 μl, and 3 μl, respectively, yielding a LOD of 1.0 × 105 CFU/ml. Among a total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were, respectively, positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS alone and MALDI-TOF MS coupled with UA were 86.6% versus 93.4% (χ2 = 8.93; P < 0.01), 91.5% versus 96.3% (χ2 = 7.06; P < 0.01), 81.5% versus 96.4% (χ2 = 37.32; P < 0.01), and 94.1% versus 93.1% (χ2 = 0.40; P > 0.05), respectively. No significant performance differences were revealed among the three sites, while specificity and NPV of MALDI-TOF MS for males were significantly higher than those for females (specificity, 94.3% versus 77.3%, χ2 = 44.90, P < 0.01; NPV, 95.5% versus 86.1%, χ2 = 18.85, P < 0.01). Our results indicated that the optimization of specimen processing significantly enhanced analytical sensitivity and that the combination of UA and MALDI-TOF MS provided an accurate and rapid detection and identification of bacterial pathogens directly from urine.
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Susa AC, Xia Z, Williams ER. Small Emitter Tips for Native Mass Spectrometry of Proteins and Protein Complexes from Nonvolatile Buffers That Mimic the Intracellular Environment. Anal Chem 2017; 89:3116-3122. [DOI: 10.1021/acs.analchem.6b04897] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Anna C. Susa
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Zijie Xia
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
| | - Evan R. Williams
- Department of Chemistry, University of California, Berkeley, California 94720-1460, United States
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S. Shell W, L. Sayed M, A. El-Geda A, M. El Sade G, A. Samy A, M.M. Ali A. Identification of Staphylococcus aureus Causing Bovine Mastitis using MALDI-TOF Fingerprinting. ACTA ACUST UNITED AC 2017. [DOI: 10.3923/ijds.2017.105.113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Sandalakis V, Goniotakis I, Vranakis I, Chochlakis D, Psaroulaki A. Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives. Expert Rev Proteomics 2017; 14:253-267. [PMID: 28092721 DOI: 10.1080/14789450.2017.1282825] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to 'battle time' in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed. Expert commentary: Mass spectrometry is the future of bacterial identification and creates a new era in modern microbiology. Its incorporation in routine practice seems to be not too far, providing a valuable alternative, especially in terms of time, to conventional techniques. If the technology further advances, quick bacterial identification and probable identification of common antibiotic resistance might guide patient decision-making regarding bacterial infectious diseases in the near future.
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Affiliation(s)
- Vassilios Sandalakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Ioannis Goniotakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Iosif Vranakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Dimosthenis Chochlakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Anna Psaroulaki
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
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Abstract
Although mass spectrometry has been used clinically for decades, the advent of immunoassay technology moved the clinical laboratory to more labor saving automated platforms requiring little if any sample preparation. It became clear, however, that immunoassays lacked sufficient sensitivity and specificity necessary for measurement of certain analytes or for measurement of analytes in specific patient populations. This limitation prompted clinical laboratories to revisit mass spectrometry which could additionally be used to develop assays for which there was no commercial source. In this chapter, the clinical applications of mass spectrometry in therapeutic drug monitoring, toxicology, and steroid hormone analysis will be reviewed. Technologic advances and new clinical applications will also be discussed.
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Affiliation(s)
- D French
- University of California San Francisco, San Francisco, CA, United States.
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Emerging and Future Applications of Matrix-Assisted Laser Desorption Ionization Time-of-Flight (MALDI-TOF) Mass Spectrometry in the Clinical Microbiology Laboratory. J Mol Diagn 2016; 18:789-802. [DOI: 10.1016/j.jmoldx.2016.07.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/17/2022] Open
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McLellan LK, Hunstad DA. Urinary Tract Infection: Pathogenesis and Outlook. Trends Mol Med 2016; 22:946-957. [PMID: 27692880 DOI: 10.1016/j.molmed.2016.09.003] [Citation(s) in RCA: 180] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 09/10/2016] [Indexed: 02/07/2023]
Abstract
The clinical syndromes comprising urinary tract infection (UTI) continue to exert significant impact on millions of patients worldwide, most of whom are otherwise healthy women. Antibiotic therapy for acute cystitis does not prevent recurrences, which plague up to one fourth of women after an initial UTI. Rising antimicrobial resistance among uropathogenic bacteria further complicates therapeutic decisions, necessitating new approaches based on fundamental biological investigation. In this review, we highlight contemporary advances in the field of UTI pathogenesis and how these might inform both our clinical perspective and future scientific priorities.
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Affiliation(s)
- Lisa K McLellan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - David A Hunstad
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
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Fritzenwanker M, Imirzalioglu C, Chakraborty T, Wagenlehner FM. Modern diagnostic methods for urinary tract infections. Expert Rev Anti Infect Ther 2016; 14:1047-1063. [DOI: 10.1080/14787210.2016.1236685] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Haiko J, Savolainen LE, Hilla R, Pätäri-Sampo A. Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry. J Microbiol Methods 2016; 129:81-84. [PMID: 27503535 DOI: 10.1016/j.mimet.2016.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/04/2016] [Accepted: 08/04/2016] [Indexed: 11/29/2022]
Abstract
Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3h at 35°C with 5% CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5)cfu/ml in culture (n=107), compared with conventional culture method. However, Gram-positive bacteria (n=28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24h to 4-6h.
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Affiliation(s)
- Johanna Haiko
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland.
| | - Laura E Savolainen
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland.
| | - Risto Hilla
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland.
| | - Anu Pätäri-Sampo
- Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, HUSLAB, Helsinki, Finland.
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Challenges in biomarker discovery with MALDI-TOF MS. Clin Chim Acta 2016; 458:84-98. [PMID: 27134187 DOI: 10.1016/j.cca.2016.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Abstract
MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.
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Zboromyrska Y, Rubio E, Alejo I, Vergara A, Mons A, Campo I, Bosch J, Marco F, Vila J. Development of a new protocol for rapid bacterial identification and susceptibility testing directly from urine samples. Clin Microbiol Infect 2016; 22:561.e1-6. [PMID: 26899829 DOI: 10.1016/j.cmi.2016.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/23/2015] [Accepted: 01/28/2016] [Indexed: 01/21/2023]
Abstract
The current gold standard method for the diagnosis of urinary tract infections (UTI) is urine culture that requires 18-48 h for the identification of the causative microorganisms and an additional 24 h until the results of antimicrobial susceptibility testing (AST) are available. The aim of this study was to shorten the time of urine sample processing by a combination of flow cytometry for screening and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for bacterial identification followed by AST directly from urine. The study was divided into two parts. During the first part, 675 urine samples were processed by a flow cytometry device and a cut-off value of bacterial count was determined to select samples for direct identification by MALDI-TOF-MS at ≥5 × 10(6) bacteria/mL. During the second part, 163 of 1029 processed samples reached the cut-off value. The sample preparation protocol for direct identification included two centrifugation and two washing steps. Direct AST was performed by the disc diffusion method if a reliable direct identification was obtained. Direct MALDI-TOF-MS identification was performed in 140 urine samples; 125 of the samples were positive by urine culture, 12 were contaminated and 3 were negative. Reliable direct identification was obtained in 108 (86.4%) of the 125 positive samples. AST was performed in 102 identified samples, and the results were fully concordant with the routine method among 83 monomicrobial infections. In conclusion, the turnaround time of the protocol described to diagnose UTI was about 1 h for microbial identification and 18-24 h for AST.
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Affiliation(s)
- Y Zboromyrska
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - E Rubio
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - I Alejo
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - A Vergara
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - A Mons
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - I Campo
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | - J Bosch
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - F Marco
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - J Vila
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain; ISGlobal, Barcelona Centre for International Health Research (CRESIB), Hospital Clínic, University of Barcelona, Barcelona, Spain.
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Direct Identification of Urinary Tract Pathogens from Urine Samples, Combining Urine Screening Methods and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2016; 54:988-93. [PMID: 26818668 DOI: 10.1128/jcm.02832-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/17/2016] [Indexed: 01/01/2023] Open
Abstract
Early diagnosis of urinary tract infections (UTIs) is essential to avoid inadequate or unnecessary empirical antibiotic therapy. Microbiological confirmation takes 24 to 48 h. The use of screening methods, such as cytometry and automated microscopic analysis of urine sediment, allows the rapid prediction of negative samples. In addition, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a widely established technique in clinical microbiology laboratories used to identify microorganisms. We evaluated the ability of MALDI-TOF MS to identify microorganisms from direct urine samples and the predictive value of automated analyzers for the identification of microorganisms in urine by MALDI-TOF MS. A total of 451 urine samples from patients with suspected UTIs were first analyzed using the Sysmex UF-1000iflow cytometer, an automatic sediment analyzer with microscopy (SediMax), culture, and then processed by MALDI-TOF MS with a simple triple-centrifuged procedure to obtain a pellet that was washed and centrifuged and finally applied directly to the MALDI-TOF MS plate. The organisms in 336 samples were correctly identified, mainly those with Gram-negative bacteria (86.10%). No microorganisms were misidentified, and noCandidaspp. were correctly identified. Regarding the data from autoanalyzers, the best bacteriuria cutoffs were 1,000 and 200 U/μl for UF-1000iand SediMax, respectively. It was concluded that the combination of a urine screening method and MALDI-TOF MS provided a reliable identification from urine samples, especially in those containing Gram-negative bacteria.
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Verification and Validation of Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry-Based Protocols. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Microbial Identification in Clinical Microbiology. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Performances and Reliability of Bruker Microflex LT and VITEK MS MALDI-TOF Mass Spectrometry Systems for the Identification of Clinical Microorganisms. BIOMED RESEARCH INTERNATIONAL 2015; 2015:516410. [PMID: 26793718 PMCID: PMC4697076 DOI: 10.1155/2015/516410] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/14/2015] [Accepted: 11/16/2015] [Indexed: 11/17/2022]
Abstract
In clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) technology has been established as a cost effective, reliable, and faster alternative identification platform. In this study, we evaluated the reliability of the two available MALDI-TOF MS systems for their routine clinical level identification accuracy and efficiency in a clinical microbiology laboratory setting. A total of 1,341 routine phenotypically identified clinical bacterial and fungal isolates were selected and simultaneously analyzed using VITEK MS (bioMérieux, France) and Microflex LT (Bruker Diagnostics, Germany) MALDI-TOF MS systems. For any isolate that could not be identified with either of the systems and for any discordant result, 16S rDNA gene or ITS1/ITS2 sequencing was used. VITEK MS and Microflex LT correctly identified 1,303 (97.17%) and 1,298 (96.79%) isolates to the species level, respectively. In 114 (8.50%) isolates initial phenotypic identification was inaccurate. Both systems showed a similar identification efficiency and workflow robustness, and they were twice as more accurate compared to routine phenotypic identification in our sample pool. MALDITOF systems with their accuracy and robustness offer a good identification platform for routine clinical microbiology laboratories.
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Cassou CA, Williams ER. Desalting protein ions in native mass spectrometry using supercharging reagents. Analyst 2015; 139:4810-9. [PMID: 25133273 DOI: 10.1039/c4an01085j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Effects of the supercharging reagents m-NBA and sulfolane on sodium ion adduction to protein ions formed using native mass spectrometry were investigated. There is extensive sodium adduction on protein ions formed by electrospray ionization from aqueous solutions containing millimolar concentrations of NaCl, which can lower sensitivity by distributing the signal of a given charge state over multiple adducted ions and can reduce mass measuring accuracy for large proteins and non-covalent complexes for which individual adducts cannot be resolved. The average number of sodium ions adducted to the most abundant ion formed from ten small (8.6-29 kDa) proteins for which adducts can be resolved is reduced by 58% or 80% on average, respectively, when 1.5% m-NBA or 2.5% sulfolane are added to aqueous solutions containing sodium compared to without the supercharging reagent. Sulfolane is more effective than m-NBA at reducing sodium ion adduction and at preserving non-covalent protein-ligand and protein-protein interactions. Desalting with 2.5% sulfolane enables detection of several glycosylated forms of 79.7 kDa holo-transferrin and NADH bound to the 146 kDa homotetramer LDH, which are otherwise unresolved due to peak broadening from extensive sodium adduction. Although sulfolane is more effective than m-NBA at protein ion desalting, m-NBA reduces salt clusters at high m/z and can increase the signal-to-noise ratios of protein ions by reducing chemical noise. Desalting is likely a result of these supercharging reagents binding sodium ions in solution, thereby reducing the sodium available to adduct to protein ions.
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Affiliation(s)
- Catherine A Cassou
- Department of Chemistry, University of California, B42 Hildebrand Hall, Berkeley, California 94720-1460, USA.
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