1
|
Gonzalez LE, Snyder DT, Casey H, Hu Y, Wang DM, Guetzloff M, Huckaby N, Dziekonski ET, Wells JM, Cooks RG. Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry. Anal Chem 2023; 95:17082-17088. [PMID: 37937965 DOI: 10.1021/acs.analchem.3c04016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Biothreat detection has continued to gain attention. Samples suspected to fall into any of the CDC's biothreat categories require identification by processes that require specialized expertise and facilities. Recent developments in analytical instrumentation and machine learning algorithms offer rapid and accurate classification of Gram-positive and Gram-negative bacterial species. This is achieved by analyzing the negative ions generated from bacterial cell extracts with a modified linear quadrupole ion-trap mass spectrometer fitted with two-dimensional tandem mass spectrometry capabilities (2D MS/MS). The 2D MS/MS data domain of a bacterial cell extract is recorded within five s using a five-scan average after sample preparation by a simple extraction. Bacteria were classified at the species level by their lipid profiles using the random forest, k-nearest neighbor, and multilayer perceptron machine learning models. 2D MS/MS data can also be treated as image data for use with image recognition algorithms such as convolutional neural networks. The classification accuracy of all models tested was greater than 99%. Adding to previously published work on the 2D MS/MS analysis of bacterial growth and the profiling of sporulating bacteria, this study demonstrates the utility and information-rich nature of 2D MS/MS in the identification of bacterial pathogens at the species level when coupled with machine learning.
Collapse
Affiliation(s)
- L Edwin Gonzalez
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Dalton T Snyder
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Harman Casey
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Yanyang Hu
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Donna M Wang
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - Megan Guetzloff
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Nicole Huckaby
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - Eric T Dziekonski
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| | - J Mitchell Wells
- Teledyne FLIR Detection, West Lafayette, Indiana 47907, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette , Indiana 47907, United States
| |
Collapse
|
2
|
Bajaj AO, Slechta ES, Barker AP. Rapid and Accurate Differentiation of Mycobacteroides abscessus Complex Species by Liquid Chromatography-Ultra-High-Resolution Orbitrap™ Mass Spectrometry. Front Cell Infect Microbiol 2022; 12:809348. [PMID: 35356534 PMCID: PMC8959847 DOI: 10.3389/fcimb.2022.809348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
In this study, a Liquid Chromatography-Mass Spectrometry (LC-MS) method for the identification of clinically relevant Mycobacteroides abscessus (Mabs) complex organisms is tested using a set of microbial Type strains. This methodology is based on profiling proteins derived from Mycobacteroides abscessus complex isolates. These protein profiles are then used as markers of species differentiation. To test the resolving power, speed, and accuracy of this assay four ATCC type strains and 32 recent clinical isolates of closely related Mabs species collected at ARUP laboratories (10 clinical isolate strains of M. abscessus subsp. abscessus, 10 M. abscessus subsp. massiliense, 2 M. abscessus subsp. bolletii and 10 M. chelonae) were subjected to this approach. Using multiple deconvolution algorithms, we identified hundreds of individual proteins, with subpopulations of these used as species-specific markers. This assay identified 150, 130, 140 and 110 proteoforms with isocratic elution and 230, 180, 200 and 190 proteoforms with gradient elution for M. abscessus (ATCC 19977), M. massiliense (DSM 45103), M. bolletii (DSM 45149) and M. chelonae (ATCC 35752) respectively. Taxonomic species were identified correctly down to the species level with 100% accuracy. The ability to differentiate Mycobacteroides abscessus complex at sub-species level can in-turn be helpful for patient management. Data analysis showed ~7-17 proteoforms potentially able to differentiate between subspecies. Here, we present a proof-of-principle study employing a rapid mass spectrometry-based method to identify the clinically most common species within the Mabs species complex.
Collapse
Affiliation(s)
- Amol O. Bajaj
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- *Correspondence: Adam P. Barker, ; Amol O. Bajaj,
| | - E. Susan Slechta
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
| | - Adam P. Barker
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, United States
- Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, United States
- *Correspondence: Adam P. Barker, ; Amol O. Bajaj,
| |
Collapse
|
3
|
Use of MALDI-TOF MS (Bruker Daltonics) for identification of Mycobacterium species isolated directly from liquid medium. Enferm Infecc Microbiol Clin 2021; 39:241-243. [DOI: 10.1016/j.eimc.2020.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 02/07/2023]
|
4
|
Mule SN, Costa-Martins AG, Rosa-Fernandes L, de Oliveira GS, Rodrigues CMF, Quina D, Rosein GE, Teixeira MMG, Palmisano G. PhyloQuant approach provides insights into Trypanosoma cruzi evolution using a systems-wide mass spectrometry-based quantitative protein profile. Commun Biol 2021; 4:324. [PMID: 33707618 PMCID: PMC7952728 DOI: 10.1038/s42003-021-01762-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 01/24/2021] [Indexed: 01/31/2023] Open
Abstract
The etiological agent of Chagas disease, Trypanosoma cruzi, is a complex of seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution requires understanding the parasite origin and population structure. In this study, we introduce the PhyloQuant approach to infer the evolutionary relationships between organisms based on differential mass spectrometry-based quantitative features. In particular, large scale quantitative bottom-up proteomics features (MS1, iBAQ and LFQ) were analyzed using maximum parsimony, showing a correlation between T. cruzi DTUs and closely related trypanosomes' protein expression and sequence-based clustering. Character mapping enabled the identification of synapomorphies, herein the proteins and their respective expression profiles that differentiate T. cruzi DTUs and trypanosome species. The distance matrices based on phylogenetics and PhyloQuant clustering showed statistically significant correlation highlighting the complementarity between the two strategies. Moreover, PhyloQuant allows the identification of differentially regulated and strain/DTU/species-specific proteins, and has potential application in the identification of specific biomarkers and candidate therapeutic targets.
Collapse
Affiliation(s)
- Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Carla Monadeli F Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Daniel Quina
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Graziella E Rosein
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | | | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
5
|
Guindo CO, Drancourt M, Grine G. Digestive tract methanodrome: Physiological roles of human microbiota-associated methanogens. Microb Pathog 2020; 149:104425. [PMID: 32745665 DOI: 10.1016/j.micpath.2020.104425] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/21/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Methanogens are the archaea most commonly found in humans, in particular in the digestive tract and are an integral part of the digestive microbiota. They are present in humans from the earliest moments of life and represent the only known source of methane production to date. They are notably detected in humans by microscopy, fluorescent in situ hybridization, molecular biology including PCR-sequencing, metagenomics, matrix-assisted laser desorption ionization time-of-flight mass spectrometry and culture. Methanogens present in the human digestive tract play major roles, in particular the use of hydrogen from the fermentation products of bacteria, thus promoting digestion. They are also involved in the transformation of heavy metals and in the use of trimethylamine produced by intestinal bacteria, thus preventing major health problems, in particular cardiovascular diseases. Several pieces of evidence suggest their close physical contacts with bacteria support symbiotic metabolism. Their imbalance during dysbiosis is associated with many pathologies in humans, particularly digestive tract diseases such as Crohn's disease, ulcerative colitis, diverticulosis, inflammatory bowel disease, irritable bowel syndrome, colonic polyposis, and colorectal cancer. There is a huge deficit of knowledge and partially contradictory information concerning human methanogens, so much remains to be done to fully understand their physiological role in humans. It is necessary to develop new methods for the identification and culture of methanogens from clinical samples. This will permit to isolate new methanogens species as well as their phenotypic characterization, to explore their genome by sequencing and to study the population dynamics of methanogens by specifying in particular their exact role within the complex flora associated with the mucous microbiota of human.
Collapse
Affiliation(s)
- C O Guindo
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - M Drancourt
- IHU Méditerranée Infection, Marseille, France
| | - G Grine
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, UFR Odontologie, Marseille, France.
| |
Collapse
|
6
|
O’Connor JA, O’Reilly B, Corcoran GD, O’Mahony J, Lucey B. A comparison of the HAIN Genotype CM reverse hybridisation assay with the Bruker MicroFlex LT MALDI-TOF mass spectrometer for identification of clinically relevant mycobacterial species. Br J Biomed Sci 2020; 77:152-155. [DOI: 10.1080/09674845.2020.1732639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- JA O’Connor
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - B O’Reilly
- Laboratory Medicine, Diagnostic Directorate, Cork University Hospital, Cork, Ireland
| | - GD Corcoran
- Laboratory Medicine, Diagnostic Directorate, Cork University Hospital, Cork, Ireland
| | - J O’Mahony
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - B Lucey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| |
Collapse
|
7
|
Brown-Elliott BA, Fritsche TR, Olson BJ, Vasireddy S, Vasireddy R, Iakhiaeva E, Alame D, Wallace RJ, Branda JA. Comparison of Two Commercial Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of Nontuberculous Mycobacteria. Am J Clin Pathol 2019; 152:527-536. [PMID: 31314059 PMCID: PMC6733354 DOI: 10.1093/ajcp/aqz073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES This multicenter study's aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM). METHODS NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database. RESULTS Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system. CONCLUSIONS Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.
Collapse
Affiliation(s)
| | - Thomas R Fritsche
- Marshfield Clinic Health System, Marshfield, WI
- University of Wisconsin, La Crosse
| | | | | | | | | | - Diana Alame
- Thomas Jefferson University, Philadelphia, PA
| | | | - John A Branda
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, MA
| |
Collapse
|
8
|
Rotcheewaphan S, Lemon JK, Desai UU, Henderson CM, Zelazny AM. Rapid one-step protein extraction method for the identification of mycobacteria using MALDI-TOF MS. Diagn Microbiol Infect Dis 2019; 94:355-360. [PMID: 31053254 DOI: 10.1016/j.diagmicrobio.2019.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 11/19/2022]
Abstract
Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry is a quick and accurate method for mycobacterial identification from protein extracts. Our new one-step extraction method successfully reduced routine multistep extraction procedure time from over 60 min to under 10 min and used only 1 μL loopful of mycobacteria while providing clinically acceptable identification scores (≥1.8). Overall, 86.8% and 4.4% of mycobacteria isolates (n = 68) were identified to the species/complex and genus levels, respectively, by one-step loop extraction method, comparable to the routine extraction method. Viability studies confirmed killing of mycobacterial isolates after 5 min in the extraction solution replacing lengthy heat killing step. Retrospective 7-month data analysis showed 100% of rapidly and slowly growing mycobacterial isolates were identified to the species/complex level by rapid extraction methods. Our rapid extraction methods substantially reduced processing time and microbial biomass required for testing without sacrificing quality and accuracy of mycobacterial identification.
Collapse
Affiliation(s)
- Suwatchareeporn Rotcheewaphan
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA; Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jamie K Lemon
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Uma U Desai
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Christina M Henderson
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Adrian M Zelazny
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
9
|
Neumann AC, Bauer D, Hoelscher M, Haisch C, Wieser A. Identifying Dormant Growth State of Mycobacteria by Orthogonal Analytical Approaches on a Single Cell and Ensemble Basis. Anal Chem 2018; 91:881-887. [DOI: 10.1021/acs.analchem.8b03646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- A.-C. Neumann
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| | - D. Bauer
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - M. Hoelscher
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| | - C. Haisch
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Munich, Germany
| | - A. Wieser
- German Center for Infection Research (DZIF), Partner Site Munich, 80802 Munich, Germany
| |
Collapse
|
10
|
Di Gaudio F, Indelicato S, Indelicato S, Tricoli MR, Stampone G, Bongiorno D. Improvement of a rapid direct blood culture microbial identification protocol using MALDI-TOF MS and performance comparison with SepsiTyper kit. J Microbiol Methods 2018; 155:1-7. [DOI: 10.1016/j.mimet.2018.10.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 12/18/2022]
|
11
|
Pellegrino FLPC, Chagas TPG, Alves MS, Carvalho-Assef APD, Chapeaurouge A, Asensi MD. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Applications in Bacteriology: brazilian contributions. HU REVISTA 2018. [DOI: 10.34019/1982-8047.2017.v43.2859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.
Collapse
|
12
|
Golichenari B, Velonia K, Nosrati R, Nezami A, Farokhi-Fard A, Abnous K, Behravan J, Tsatsakis AM. Label-free nano-biosensing on the road to tuberculosis detection. Biosens Bioelectron 2018; 113:124-135. [DOI: 10.1016/j.bios.2018.04.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/14/2018] [Accepted: 04/28/2018] [Indexed: 12/16/2022]
|
13
|
Florio W, Tavanti A, Barnini S, Ghelardi E, Lupetti A. Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:1097. [PMID: 29896172 PMCID: PMC5986882 DOI: 10.3389/fmicb.2018.01097] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. A rapid diagnosis also allows for early streamlining of empirical antimicrobial therapies, thus contributing to limit the emergence and spread of antimicrobial resistance. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. Compared to currently used identification methods, MALDI-TOF MS has the advantage of identifying bacteria and yeasts directly from colonies grown on culture plates for primary isolation in a few minutes and with considerable material and labor savings. The reliability and accuracy of MALDI-TOF MS in identification of clinically relevant bacteria and yeasts has been demonstrated by several studies showing that the performance of MALDI-TOF MS is comparable or superior to phenotypic methods currently in use in clinical microbiology laboratories, and can be further improved by database updates and analysis software upgrades. Besides microbial identification from isolated colonies, new perspectives are being explored for MALDI-TOF MS, such as identification of pathogens directly from positive blood cultures, sub-species typing, and detection of drug resistance determinants. In this review, we summarize the state of the art in routine identification of microbial pathogens by MALDI-TOF MS, and highlight recent advancements of this technology in special applications, such as strain typing, assessment of drug susceptibility, and detection of virulence factors.
Collapse
Affiliation(s)
- Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | | | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| |
Collapse
|
14
|
Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species. J Clin Microbiol 2018; 56:JCM.00237-18. [PMID: 29643203 DOI: 10.1128/jcm.00237-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/08/2018] [Indexed: 11/20/2022] Open
Abstract
This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.
Collapse
|
15
|
Murugaiyan J, Lewin A, Kamal E, Bakuła Z, van Ingen J, Ulmann V, Unzaga Barañano MJ, Humięcka J, Safianowska A, Roesler UH, Jagielski T. MALDI Spectra Database for Rapid Discrimination and Subtyping of Mycobacterium kansasii. Front Microbiol 2018; 9:587. [PMID: 29670585 PMCID: PMC5893902 DOI: 10.3389/fmicb.2018.00587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium kansasii is an emerging non-tuberculous mycobacterial (NTM) pathogen capable of causing severe lung disease. Of the seven currently recognized M. kansasii genotypes (I-VII), genotypes I and II are most prevalent and have been associated with human disease, whereas the other five (III-VII) genotypes are predominantly of environmental origin and are believed to be non-pathogenic. Subtyping of M. kansasii serves as a valuable tool to guide clinicians in pursuing diagnosis and to initiate the proper timely treatment. Most of the previous rapid diagnostic tests for mycobacteria employing the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technology focused on species-level identification. The purpose of this study was to establish MALDI-TOF MS reference spectra database for discrimination of M. kansasii at the genotype level. A panel of 32 strains, representatives of M. kansasii genotypes I-VI were selected, whole cell proteins extracted and measured with MALDI-TOF MS. A unique main spectra (MSP) library was created using MALDI Biotyper Compass Explorer software. The spectra reproducibility was assessed by computing composite correlation index and MSPs cross-matching. One hundred clinical M. kansasii isolates used for testing of the database resulted in 90% identification at genus-level, 7% identification at species-level and 2% identification was below the threshold of log score value 1.7, of which all were correct at genotype level. One strain could not be identified. On the other hand, 37% of strains were identified at species level, 40% at genus level and 23% was not identified with the manufacturer's database. The MALDI-TOF MS was proven a rapid and robust tool to detect and differentiate between M. kansasii genotypes. It is concluded that MALDI-TOF MS has a potential to be incorporated into the routine diagnostic workflow of M. kansasii and possibly other NTM species.
Collapse
Affiliation(s)
- Jayaseelan Murugaiyan
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Astrid Lewin
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Elisabeth Kamal
- Division 16, Mycotic and Parasitic Agents and Mycobacteria, Robert Koch Institute, Berlin, Germany
| | - Zofia Bakuła
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Vit Ulmann
- Institute of Public Health, Ostrava, Czechia
| | | | - Joanna Humięcka
- Hospital for Infectious Diseases in Warsaw, Medical University of Warsaw, Warsaw, Poland
| | - Aleksandra Safianowska
- Department of Internal Medicine, Pulmonology, and Allergology, Medical University of Warsaw, Warsaw, Poland
| | - Uwe H Roesler
- Centre for Infectious Medicine, Institute of Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Jagielski
- Department of Applied Microbiology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Warsaw, Poland
| |
Collapse
|
16
|
Sriram R, Sahni A, Dudhat VL, Pujahari A. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid identification of Mycobacterium abscessus. Med J Armed Forces India 2018; 74:22-27. [PMID: 29386727 PMCID: PMC5771778 DOI: 10.1016/j.mjafi.2017.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 02/12/2017] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacteria are increasingly being implicated in infections and have become an important cause of health care associated infections. Mycobacterium abscessus, a rapidly growing mycobacteria, is of particular concern as it tends to be resistant to commonly used therapeutic options. Conventional phenotypic methods for speciation of mycobacteria are time consuming, labor intensive and not always reliable. Molecular methods require expertise and are expensive. The study was used to evaluate the use of matrix associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as a means of rapid identification of M. abscessus. METHODS 35 isolates of rapidly growing Mycobacterium from an outbreak of surgical site infections at a tertiary care hospital were identified using phenotypic methods. The mycobacterial isolates were inactivated and an extraction protocol was followed. These isolates were then analyzed by MALDI biotyper (Bruker Daltonics) using biotyper software 4.0 and the mycobacterial reference database v 2.0. RESULTS All 35 isolates were identified as M. abscessus by MALDI biotyper but the scores obtained according to guidelines of the company were lower than previous studies with only 23 out of the 35 isolates having scores of greater 1.8 which was described as the minimum score to be achieved for reliable identification. CONCLUSION MALDI-TOF MS offers a rapid and inexpensive method for identification of Mycobacteria; however, the scores obtained in our study were lower than reported in other studies.
Collapse
Affiliation(s)
- Raghu Sriram
- Assistant Professor, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - A.K. Sahni
- Brig Med, HQ 15 Corps, C/o 56 APO, India
| | - Vaibhav L. Dudhat
- Resident, Dept of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - A.K. Pujahari
- Ex-Professor & Head, Department of Surgery, Armed Forces Medical College, Pune 411040, India
| |
Collapse
|
17
|
Haworth CS, Banks J, Capstick T, Fisher AJ, Gorsuch T, Laurenson IF, Leitch A, Loebinger MR, Milburn HJ, Nightingale M, Ormerod P, Shingadia D, Smith D, Whitehead N, Wilson R, Floto RA. British Thoracic Society guidelines for the management of non-tuberculous mycobacterial pulmonary disease (NTM-PD). Thorax 2017; 72:ii1-ii64. [DOI: 10.1136/thoraxjnl-2017-210927] [Citation(s) in RCA: 351] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2017] [Indexed: 01/18/2023]
|
18
|
|
19
|
Ravva SV, Harden LA, Sarreal CZ. Characterization and Differentiation of Mycobacterium avium subsp. paratuberculosis from Other Mycobacteria Using Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. Front Cell Infect Microbiol 2017; 7:297. [PMID: 28713782 PMCID: PMC5491938 DOI: 10.3389/fcimb.2017.00297] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease in cattle, is responsible for significant economic losses to the US dairy industry. The pathogen has also been associated with chronic human diseases like Crohn's disease, type 1 diabetes and multiple sclerosis. Determining causation requires rapid characterization and source tracking the pathogen. Here, we used matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry to characterize and differentiate strains of MAP from 14 other species of Mycobacterium from bovine, human, and environmental sources. Lysates from cells disrupted by bead beating in TFA-acetonitrile solution were analyzed by MALDI-TOF. MAP strains were differentiated by mass spectral profiles that are distinct from each other and from other Mycobacterium species. Cluster analysis of spectral profiles indicates two distinct clusters, one dominated by the members of avium complex and a second group dominated by members of fortuitum and parafortuitum complexes. We believe that MALDI-TOF methods can be used to differentiate and source-track MAP strains.
Collapse
Affiliation(s)
- Subbarao V Ravva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
| | - Leslie A Harden
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
| | - Chester Z Sarreal
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agricultural Research Service, United States Department of AgricultureAlbany, CA, United States
| |
Collapse
|
20
|
Comparison of Saramis 4.12 and IVD 3.0 Vitek MS Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria from Solid and Liquid Culture Media. J Clin Microbiol 2017; 55:2045-2054. [PMID: 28424252 DOI: 10.1128/jcm.00006-17] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/04/2017] [Indexed: 01/25/2023] Open
Abstract
During the last decade, many investigators have studied matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identification of mycobacteria. Diverse and contradictory results indicated that optimal level for routine testing has not been reached yet. This work aimed to assess Vitek MS through two distinct versions, Saramis v4.12 RUO and the IVD v3.0, under conditions close to routine laboratory practice. Overall, 111 mycobacterial isolates were subjected to protein extraction and same spectra were matched against both databases. The IVD v3.0 database proved to be superior to Saramis v4.12 and its identification rates remarkably increased, from 67% to 94% for isolates grown on Middlebrook 7H10 solid medium and from 62% to 91% for isolates grown on mycobacterial growth indicator tube (MGIT) liquid medium. With this new version, IVD v3.0, MALDI-TOF MS might be integrated into routine clinical diagnostics, although molecular techniques remain mandatory in some cases.
Collapse
|
21
|
López-Hernández Y, Patiño-Rodríguez O, García-Orta ST, Pinos-Rodríguez JM. Mass spectrometry applied to the identification of Mycobacterium tuberculosis and biomarker discovery. J Appl Microbiol 2017; 121:1485-1497. [PMID: 27718305 DOI: 10.1111/jam.13323] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/28/2016] [Accepted: 08/08/2016] [Indexed: 12/31/2022]
Abstract
An adequate and effective tuberculosis (TB) diagnosis system has been identified by the World Health Organization as a priority in the fight against this disease. Over the years, several methods have been developed to identify the bacillus, but bacterial culture remains one of the most affordable methods for most countries. For rapid and accurate identification, however, it is more feasible to implement molecular techniques, taking advantage of the availability of public databases containing protein sequences. Mass spectrometry (MS) has become an interesting technique for the identification of TB. Here, we review some of the most widely employed methods for identifying Mycobacterium tuberculosis and present an update on MS applied for the identification of mycobacterial species.
Collapse
Affiliation(s)
| | - O Patiño-Rodríguez
- CONACyT, Centro de Desarrollo de Productos Bióticos del Instituto Politécnico Nacional, Morelos, México
| | - S T García-Orta
- Centro de Biociencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J M Pinos-Rodríguez
- Centro de Biociencias, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| |
Collapse
|
22
|
Abstract
ABSTRACT
The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of
Mycobacterium tuberculosis
. Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR. The widespread use of the Xpert MTB/RIF (Cepheid) assay, which detects both
M. tuberculosis
and key genetic determinants of rifampin resistance, is important for the early detection of multidrug-resistant strains. Culture, using both broth and solid media, remains the standard for establishing the laboratory-based diagnosis of tuberculosis. Cultured isolates are identified far less commonly by traditional biochemical profiling and more commonly by molecular methods, such as DNA probes and broad-range PCR with DNA sequencing. Non-nucleic acid-based methods of identification, such as high-performance liquid chromatography and, more recently, matrix-assisted laser desorption/ionization–time of flight mass spectrometry, may also be used for identification. Cultured isolates of
M. tuberculosis
should be submitted for susceptibility testing according to standard guidelines. The use of broth-based susceptibility testing is recommended to significantly decrease the time to result. Cultured isolates may also be submitted for strain typing for epidemiologic purposes. The use of massive parallel sequencing, also known as next-generation sequencing, promises to continue to this molecular revolution in mycobacteriology, as whole-genome sequencing provides identification, susceptibility, and typing information simultaneously.
Collapse
|
23
|
Ntuli V, Njage P, Buys E. Characterization of Escherichia coli and other Enterobacteriaceae in producer-distributor bulk milk. J Dairy Sci 2016; 99:9534-9549. [DOI: 10.3168/jds.2016-11403] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
|
24
|
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
|
25
|
Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria. Clin Microbiol Rev 2016; 29:239-90. [PMID: 26912567 DOI: 10.1128/cmr.00055-15] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.
Collapse
|
26
|
Park JS, Choi SH, Hwang SM, Hong YJ, Kim TS, Park KU, Song J, Kim EC. The impact of protein extraction protocols on the performance of currently available MALDI-TOF mass spectrometry for identification of mycobacterial clinical isolates cultured in liquid media. Clin Chim Acta 2016; 460:190-5. [DOI: 10.1016/j.cca.2016.06.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/24/2016] [Accepted: 06/29/2016] [Indexed: 11/15/2022]
|
27
|
Girard V, Mailler S, Welker M, Arsac M, Cellière B, Cotte-Pattat PJ, Chatellier S, Durand G, Béni AM, Schrenzel J, Miller E, Dussoulier R, Dunne WM, Butler-Wu S, Saubolle MA, Sussland D, Bell M, van Belkum A, Deol P. Identification of mycobacterium spp. and nocardia spp. from solid and liquid cultures by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Diagn Microbiol Infect Dis 2016; 86:277-283. [PMID: 27567285 DOI: 10.1016/j.diagmicrobio.2016.07.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/20/2016] [Accepted: 07/26/2016] [Indexed: 01/15/2023]
Abstract
Identification of microorganisms by MALDI-TOF MS has been widely accepted in clinical microbiology. However, for Mycobacterium spp. and Nocardia spp. such identification has not yet reached the optimal level of routine testing. Here we describe the development of an identification tool for 49 and 15 species of Mycobacterium spp. and Nocardia spp., respectively. During database construction, a number of ambiguous reference identifications were revealed and corrected via molecular analyses. Eventually, more than 2000 individual mass spectra acquired from 494 strains were included in a reference database and subjected to bio-statistical analyses. This led to correct species identification and correct combination of species into several complexes or groups, such as the Mycobacterium tuberculosis complex. With the Advanced Spectrum Classifier algorithm, class-specific bin weights were determined and tested by cross-validation experiments with good results. When challenged with independent isolates, overall identification performance was 90% for identification of Mycobacterium spp. and 88% for Nocardia spp. However, for a number of Mycobacterium sp. isolates, no identification could be achieved and in most cases, this could be attributed to the production of polymers that masked the species-specific protein peak patterns. For the species where >20 isolates were tested, correct identification reached 95% or higher. With the current spectral database, the identification of Mycobacterium spp. and Nocardia spp. by MALDI-TOF MS can be performed in routine clinical diagnostics although in some complicated cases verification by sequencing remains mandatory.
Collapse
Affiliation(s)
- Victoria Girard
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Sandrine Mailler
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Martin Welker
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Maud Arsac
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Béatrice Cellière
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | | | - Sonia Chatellier
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Géraldine Durand
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France
| | - Anne-Marie Béni
- Hôpitaux Universitaires de Genève, Laboratoire de Bactériologie, Rue Gabrielle Perret Gentil 4, 1211, Geneva 14, Switzerland
| | - Jacques Schrenzel
- Hôpitaux Universitaires de Genève, Laboratoire de Bactériologie, Rue Gabrielle Perret Gentil 4, 1211, Geneva 14, Switzerland
| | - Elizabeth Miller
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - Rahima Dussoulier
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - W Michael Dunne
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| | - Susan Butler-Wu
- Clinical Microbiology Laboratory, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA, 90033, USA
| | - Michael A Saubolle
- Banner University Medical Center, 1111 E. McDowell Rd., Phoenix, AZ, 85006, USA
| | - Den Sussland
- Banner University Medical Center, 1111 E. McDowell Rd., Phoenix, AZ, 85006, USA
| | - Melissa Bell
- Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329-4027, USA
| | - Alex van Belkum
- bioMérieux, Microbiology R&D, Route de Port Michaud, 38390, La Balme, Les Grottes, France.
| | - Parampal Deol
- bioMérieux Inc., Microbiology R&D, 100 Rodolphe St, Durham, NC, 27712, USA
| |
Collapse
|
28
|
Elbehiry A, Al-Dubaib M, Marzouk E, Osman S, Edrees H. Performance of MALDI biotyper compared with Vitek ™ 2 compact system for fast identification and discrimination of Staphylococcus species isolated from bovine mastitis. Microbiologyopen 2016; 5:1061-1070. [PMID: 27364641 PMCID: PMC5221440 DOI: 10.1002/mbo3.389] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/23/2016] [Accepted: 05/28/2016] [Indexed: 12/19/2022] Open
Abstract
This study was designed to evaluate the ability of MALDI Biotyper (MBT) compared with Vitek™ 2 compact system for accurate identification of Staphylococcus aureus (S. aureus) and coagulase‐negative staphylococci (CNS) strains and discriminate methicillin‐sensitive S. aureus (MSSA) from methicillin‐resistant S. aureus (MRSA). Throughout Al‐Qassim region, Saudi Arabia, a total of 198 isolates of S. aureus (132 MSSA and 66 MRSA) and 44 CNS were collected from five dairy farms where the prevalence of staphylococcal mastitis was reported. The results produced by Vitek™ 2 compact system demonstrated that 123/132 MSSA isolates (93.18%), 61/66 MRSA (92.42%), and 37/44 CNS species (84.09%) were correctly identified. However; 130/132 MSSA (98.48%), 64/66 MRSA (96.96%), and 44/44 CNS (100%) were correctly identified by MBT with score ≥2. 00. The principal component analysis (PCA) dendrogram generated by MBT illustrated that the tested isolates were classified into two groups of Staphylococcus species at the distance level of 600. S. aureus isolates were found to be closely related with higher peak intensities in the mass of 3,993 Da, 4,121 Da and 5,845 Da were detected in MRSA, whereas, that were lost in MSSA. Conclusion: This study verified that MBT is an alternative powerful tool for precise identification and discrimination of Staphylococcus species.
Collapse
Affiliation(s)
- Ayman Elbehiry
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Sadat City University, Sadat, Egypt.,Department of Public Health, Microbiology Unit, College of Public Health and Health Informatics, Qassim University, Buraidah, Saudi Arabia
| | - Musaad Al-Dubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Eman Marzouk
- Department of Medical laboratories, College of Applied Medical Science, Qassim University, Buraidah, Saudi Arabia
| | - Salama Osman
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia.,Department of Animal Medicine, Faculty of Veterinary Medicine, Kafrelsheikh University, Buraidah, Egypt
| | - Husam Edrees
- Department of Physiology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| |
Collapse
|
29
|
Adams LL, Dionne K, Fisher S, Parrish N. A rapid, standardized protein extraction method using adaptive focused acoustics for identification of mycobacteria by MALDI-ToF MS. Diagn Microbiol Infect Dis 2016; 86:284-288. [PMID: 27575460 DOI: 10.1016/j.diagmicrobio.2016.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 04/18/2016] [Accepted: 06/01/2016] [Indexed: 11/26/2022]
Abstract
Mycobacterial identification using MALDI-ToF MS (MALDI) has been hindered by inadequate extraction methods. Adaptive Focused Acoustics™ uses concentrated ultrasonic energy to achieve cellular disruption. Using this technology, we developed a rapid mycobacterial inactivation/protein extraction method for MALDI-based identification. Agreement for identification to the species level versus conventional identification was stratified by log confidence cut-offs of ≥2.0, ≥ 1.8, or ≥1.7. A total of 182 mycobacterial isolates were tested. Complete inactivation of all species/strains was achieved after 2min. Using a log confidence cut-off of ≥2.0, overall agreement for the commercial method (CM) was 41.7% versus 66.7% for the novel method (NM). For the CM, agreement increased to 66.7% and 83.3% using log confidence cut-offs of ≥1.8 and ≥1.7, respectively; for the NM, agreement was 100% for both cut-offs with all isolates. With no alteration to the existing database, overall agreement for the NM was 83.4%, largely due to low scores for clinical isolates of M. chelonae and M. mucogenicum. Addition of spectra from a single clinical strain of each species to the existing database increased overall agreement to 93.1%.
Collapse
Affiliation(s)
- La'Tonzia L Adams
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Kim Dionne
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Stephanie Fisher
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Nicole Parrish
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA.
| |
Collapse
|
30
|
Floto RA, Olivier KN, Saiman L, Daley CL, Herrmann JL, Nick JA, Noone PG, Bilton D, Corris P, Gibson RL, Hempstead SE, Koetz K, Sabadosa KA, Sermet-Gaudelus I, Smyth AR, van Ingen J, Wallace RJ, Winthrop KL, Marshall BC, Haworth CS. US Cystic Fibrosis Foundation and European Cystic Fibrosis Society consensus recommendations for the management of non-tuberculous mycobacteria in individuals with cystic fibrosis. Thorax 2016; 71 Suppl 1:i1-22. [PMID: 26666259 PMCID: PMC4717371 DOI: 10.1136/thoraxjnl-2015-207360] [Citation(s) in RCA: 284] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms that can cause chronic pulmonary infection, particularly in individuals with pre-existing inflammatory lung disease such as cystic fibrosis (CF). Pulmonary disease caused by NTM has emerged as a major threat to the health of individuals with CF but remains difficult to diagnose and problematic to treat. In response to this challenge, the US Cystic Fibrosis Foundation (CFF) and the European Cystic Fibrosis Society (ECFS) convened an expert panel of specialists to develop consensus recommendations for the screening, investigation, diagnosis and management of NTM pulmonary disease in individuals with CF. Nineteen experts were invited to participate in the recommendation development process. Population, Intervention, Comparison, Outcome (PICO) methodology and systematic literature reviews were employed to inform draft recommendations. An anonymous voting process was used by the committee to reach consensus. All committee members were asked to rate each statement on a scale of: 0, completely disagree, to 9, completely agree; with 80% or more of scores between 7 and 9 being considered ‘good’ agreement. Additionally, the committee solicited feedback from the CF communities in the USA and Europe and considered the feedback in the development of the final recommendation statements. Three rounds of voting were conducted to achieve 80% consensus for each recommendation statement. Through this process, we have generated a series of pragmatic, evidence-based recommendations for the screening, investigation, diagnosis and treatment of NTM infection in individuals with CF as an initial step in optimising management for this challenging condition.
Collapse
Affiliation(s)
- R Andres Floto
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | - Kenneth N Olivier
- Cardiovascular and Pulmonary Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland, USA
| | - Lisa Saiman
- Department of Pediatrics, Columbia University Medical Center, Pediatric Infectious Diseases, New York, New York, USA
| | - Charles L Daley
- Division of Mycobacterial and Respiratory Infections, National Jewish Health, Denver, Colorado, USA
| | - Jean-Louis Herrmann
- INSERM U1173, UFR Simone Veil, Versailles-Saint-Quentin University, Saint-Quentin en Yvelines, France AP-HP, Service de Microbiologie, Hôpital Raymond Poincaré, Garches, France
| | - Jerry A Nick
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Peadar G Noone
- The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Diana Bilton
- Department of Respiratory Medicine, Royal Brompton Hospital, London, UK
| | - Paul Corris
- Department of Respiratory Medicine, Freeman Hospital, High Heaton, Newcastle, UK
| | - Ronald L Gibson
- Department of Pediatrics University of Washington School of Medicine, Seattle, Washington, USA
| | - Sarah E Hempstead
- The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Karsten Koetz
- Department of Pediatrics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kathryn A Sabadosa
- The Dartmouth Institute for Health Policy and Clinical Practice, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Isabelle Sermet-Gaudelus
- Service de Pneumo-Pédiatrie, Université René Descartes, Hôpital Necker-Enfants Malades, Paris, France
| | - Alan R Smyth
- Division of Child Health, Obstetrics & Gynaecology, University of Nottingham, Nottingham, UK
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard J Wallace
- Department of Microbiology, University of Texas Health Science Center, Tyler, Texas, USA
| | | | | | - Charles S Haworth
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
| | | |
Collapse
|
31
|
Kehrmann J, Wessel S, Murali R, Hampel A, Bange FC, Buer J, Mosel F. Principal component analysis of MALDI TOF MS mass spectra separates M. abscessus (sensu stricto) from M. massiliense isolates. BMC Microbiol 2016; 16:24. [PMID: 26926762 PMCID: PMC4772520 DOI: 10.1186/s12866-016-0636-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/03/2016] [Indexed: 11/10/2022] Open
Abstract
Background The discrimination of the members of the Mycobacterium abscessus complex is of clinical interest because one of the subspecies, M. massiliense, exhibits higher rates of response to antibiotic treatment for lung infection than do the other members of that complex. M. abscessus complex contains three subspecies that are laborious to identify; therefore, a routine diagnostic tool would be worthwhile. Results We used principal component analysis, hierarchical cluster analysis, and single-peak analysis to examine peak lists derived from matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) mass spectra of 50 clinical M. abscessus complex isolates, including 28 M. abscessus (sensu stricto), 19 M. massiliense, and 3 M. bolletii isolates grown in mycobacterium growth indicator tube liquid medium and prepared with a bead-based protocol. Principal component analysis but not hierarchical cluster analysis separated M. abscessus (sensu stricto) isolates and M. massiliense isolates into two clusters. Furthermore, single-peak analysis displayed 4 discriminating peaks that separated M. abscessus (sensu stricto) from M. massiliense isolates. M. bolletii isolates did not exhibit specific peaks but resembled the M. abscessus (sensu stricto) peak profile and also grouped within this principal component analysis cluster. Principal component analysis of all peak lists with the exclusion of the four discriminating peaks again separated M. abscessus (sensu stricto) from M. massiliense isolates, thus relativizing the importance of these peaks for subspecies identification. Conclusions Principal component analysis of peak lists derived from MALDI TOF mass spectra is a robust and convenient method of discriminating M. massiliense isolates from the other members of the M. abscessus complex.
Collapse
Affiliation(s)
- Jan Kehrmann
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
| | - Sarah Wessel
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Roshni Murali
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Annegret Hampel
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Franz-Christoph Bange
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Frank Mosel
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| |
Collapse
|
32
|
Kehrmann J, Schoerding AK, Murali R, Wessel S, Koehling HL, Mosel F, Buer J. Performance of Vitek MS in identifying nontuberculous mycobacteria from MGIT liquid medium and Lowenstein–Jensen solid medium. Diagn Microbiol Infect Dis 2016; 84:43-47. [DOI: 10.1016/j.diagmicrobio.2015.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
|
33
|
Hoshino Y, Suzuki K. Differential diagnostic assays for discriminating mycobacteria, especially for nontuberculous mycobacteria: what does the future hold? Future Microbiol 2015; 10:205-16. [PMID: 25689533 DOI: 10.2217/fmb.14.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mycobacteria infections are an important medical problem, and many are regarded as emerging and re-emerging diseases. Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading cause of human morbidity and mortality worldwide, with approximately 8.6 million cases and 1.3 million deaths in 2012. In addition, the incidence of nontuberculous Mycobacterium infection has significantly increased, especially among developed countries. Although phenotypical appearances such as culture characteristics and/or susceptibility to anti-Mycobacterium drugs are variable between different mycobacterial species, early diagnosis is crucial in terms of patient treatment and clinical outcome. In this manuscript, we describe the development of diagnostic techniques, from the classical/conventional to the most recent advances, and provide an overview of the future direction of discrimination procedures.
Collapse
Affiliation(s)
- Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba, Higashi-Murayama, Tokyo, Japan
| | | |
Collapse
|
34
|
Evaluation of MALDI-ToF as a method for the identification of bacteria in the veterinary diagnostic laboratory. Res Vet Sci 2015; 101:42-9. [DOI: 10.1016/j.rvsc.2015.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/30/2015] [Accepted: 05/30/2015] [Indexed: 11/23/2022]
|
35
|
O'Connor JA, O'Reilly B, Corcoran GD, O'Mahony J, Lucey B. Mycobacterium diagnostics: from the primitive to the promising. Br J Biomed Sci 2015; 72:32-41. [PMID: 25906489 DOI: 10.1080/09674845.2015.11666793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.
Collapse
|
36
|
Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
Collapse
|
37
|
Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Nontuberculous Mycobacteria from Clinical Isolates. J Clin Microbiol 2015; 53:2737-40. [PMID: 26063855 DOI: 10.1128/jcm.01380-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 06/01/2015] [Indexed: 11/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of nontuberculous mycobacterial (NTM) isolates was evaluated in this study. Overall, 125 NTM isolates were analyzed by MALDI-TOF and GenoType CM/AS. Identification by 16S rRNA/hsp65 sequencing was considered the gold standard. Agreements between MALDI-TOF and GenoType CM/AS with the reference method were, respectively, 94.4% and 84.0%. In 17 cases (13.6%), results provided by GenoType and MALDI-TOF were discordant; however, the reference method agreed with MALDI-TOF in 16/17 cases (94.1%; P = 0.002).
Collapse
|
38
|
Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. J Clin Microbiol 2015; 53:2355-8. [PMID: 25948607 PMCID: PMC4473197 DOI: 10.1128/jcm.00494-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 04/19/2015] [Indexed: 11/20/2022] Open
Abstract
We determined that the Vitek MS Plus matrix-assisted laser desorption ionization–time of flight mass spectrometry using research-use-only (RUO) v.4.12 and in vitro-diagnostic (IVD) v.3.0 databases accurately identified 41 Mycobacterium abscessus subsp. abscessus and 13 M. abscessus subsp. massiliense isolates identified by whole-genome sequencing to the species but not the subspecies level, from Middlebrook 7H11 and Burkholderia cepacia selective agars. Peak analysis revealed three peaks potentially able to differentiate between subspecies.
Collapse
|
39
|
Implementation of MALDI-TOF MS technology for the identification of clinical isolates of Mycobacterium spp. in mycobacterial diagnosis. Eur J Clin Microbiol Infect Dis 2015; 34:1527-32. [DOI: 10.1007/s10096-015-2381-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/31/2015] [Indexed: 11/25/2022]
|
40
|
Hernández-Toloza JE, Rincón-Serrano MDP, Celis-Bustos YA, Aguillón CI. [Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia]. Enferm Infecc Microbiol Clin 2015; 34:17-22. [PMID: 25888362 DOI: 10.1016/j.eimc.2015.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM. OBJECTIVE To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period. MATERIALS AND METHODS A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis. RESULTS Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study. CONCLUSION Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control.
Collapse
|
41
|
Lin CS, Su CC, Hsieh SC, Lu CC, Wu TL, Jia JH, Wu TS, Han CC, Tsai WC, Lu JJ, Lai HC. Rapid identification of Mycobacterium avium clinical isolates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2015; 48:205-12. [DOI: 10.1016/j.jmii.2013.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 08/07/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
|
42
|
Comparison of the detection characteristics of trace species using laser-induced breakdown spectroscopy and laser breakdown time-of-flight mass spectrometry. SENSORS 2015; 15:5982-6008. [PMID: 25769051 PMCID: PMC4435158 DOI: 10.3390/s150305982] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/27/2015] [Accepted: 02/28/2015] [Indexed: 12/23/2022]
Abstract
The rapid and precise element measurement of trace species, such as mercury, iodine, strontium, cesium, etc. is imperative for various applications, especially for industrial needs. The elements mercury and iodine were measured by two detection methods for comparison of the corresponding detection features. A laser beam was focused to induce plasma. Emission and ion signals were detected using laser-induced breakdown spectroscopy (LIBS) and laser breakdown time-of-flight mass spectrometry (LB-TOFMS). Multi-photon ionization and electron impact ionization in the plasma generation process can be controlled by the pressure and pulse width. The effect of electron impact ionization on continuum emission, coexisting molecular and atomic emissions became weakened in low pressure condition. When the pressure was less than 1 Pa, the plasma was induced by laser dissociation and multi-photon ionization in LB-TOFMS. According to the experimental results, the detection limits of mercury and iodine in N2 were 3.5 ppb and 60 ppb using low pressure LIBS. The mercury and iodine detection limits using LB-TOFMS were 1.2 ppb and 9.0 ppb, which were enhanced due to different detection features. The detection systems of LIBS and LB-TOFMS can be selected depending on the condition of each application.
Collapse
|
43
|
MALDI-TOF mass spectrometry for rapid identification of clinical fungal isolates based on ribosomal protein biomarkers. J Microbiol Methods 2015; 109:93-105. [DOI: 10.1016/j.mimet.2014.12.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 12/23/2022]
|
44
|
Bourassa L, Butler-Wu SM. MALDI-TOF Mass Spectrometry for Microorganism Identification. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
45
|
Loucif L, Bendjama E, Gacemi-Kirane D, Rolain JM. Rapid identification of Streptomyces isolates by MALDI-TOF MS. Microbiol Res 2014; 169:940-7. [DOI: 10.1016/j.micres.2014.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/25/2014] [Accepted: 04/27/2014] [Indexed: 11/17/2022]
|
46
|
Panda A, Kurapati S, Samantaray JC, Srinivasan A, Khalil S. MALDI-TOF mass spectrometry proteomic based identification of clinical bacterial isolates. Indian J Med Res 2014; 140:770-7. [PMID: 25758576 PMCID: PMC4365351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND & OBJECTIVES Pathogenic bacteria often cause life threatening infections especially in immunocompromised individuals. Therefore, rapid and reliable species identification is essential for a successful treatment and disease management. We evaluated a rapid, proteomic based technique for identification of clinical bacterial isolates by protein profiling using matrix-assisted laser desorption-ionization time - of - flight mass spectrometry (MALDI-TOF MS). METHODS Freshly grown bacterial isolates were selected from culture plates. Ethanol/formic acid extraction procedure was carried out, followed by charging of MALDI target plate with the extract and overlaying with α-cyano-4 hydroxy-cinnamic acid matrix solution. Identification was performed using the MALDI BioTyper 1.1, software for microbial identification (Bruker Daltonik GmbH, Bremen, Germany). RESULTS A comparative analysis of 82 clinical bacterial isolates using MALDI -TOF MS and conventional techniques was carried out. Amongst the clinical isolates, the accuracy at the species level for clinical isolates was 98.78%. One out of 82 isolates was not in accordance with the conventional assays because MALDI-TOF MS established it as Streptococcus pneumoniae and conventional methods as Streptococcus viridans. INTERPRETATION & CONCLUSIONS MALDI - TOF MS was found to be an accurate, rapid, cost-effective and robust system for identification of clinical bacterial isolates. This innovative approach holds promise for earlier therapeutic intervention leading to better patient care.
Collapse
Affiliation(s)
- Ashutosh Panda
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Sravya Kurapati
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotish C. Samantaray
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India,Reprint requests: Dr J.C. Samantaray, Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110 029, India e-mail:
| | - Alagiri Srinivasan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Shehla Khalil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
47
|
Larrouy-Maumus G, Puzo G. Mycobacterial envelope lipids fingerprint from direct MALDI-TOF MS analysis of intact bacilli. Tuberculosis (Edinb) 2014; 95:75-85. [PMID: 25488848 DOI: 10.1016/j.tube.2014.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 11/05/2014] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (Mtb) lipids including glycolipids and lipoglycans play a crucial role in the modulation of the host immune response by targeting the innate receptors C-type lectins, TLRs and the CD1 proteins of class 1. Glycolipids have been shown to be biomarkers of M. tuberculosis strains and also of opportunistic mycobacteria called non-tuberculous mycobacteria. Most of the structural and functional work of the Mtb lipids has been done using lipids arising from M. tuberculosis cell growth in vitro. However it is likely that lipid structures can change during infection or among the M. tuberculosis or opportunistic clinical strains. Here we describe a new, rapid and sensitive analysis of lipids directly on whole mycobacteria which can be done in few minutes and on less than 1000 mycobacteria by direct matrix-assisted laser desorption/ionization mass spectrometry using an unusual solvent matrix. By this new methodology, which does not require extraction or purification steps, we are able to discriminate mycobacteria belonging to the Mtb complex as well as opportunistic and non-pathogenic mycobacteria. This method was also found to be successful for identification of an envelope lipid mutant. This work opens a new analytical route for in vivo analysis of mycobacterial lipids.
Collapse
Affiliation(s)
- Gérald Larrouy-Maumus
- Tuberculosis and Infection Biology CNRS, Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, F-31077 Toulouse, France; UPS, Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France.
| | - Germain Puzo
- Tuberculosis and Infection Biology CNRS, Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, F-31077 Toulouse, France; UPS, Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France.
| |
Collapse
|
48
|
Boyle DP, Zembower TR, Qi C. Evaluation of Vitek MS for rapid classification of clinical isolates belonging to Mycobacterium avium complex. Diagn Microbiol Infect Dis 2014; 81:41-3. [PMID: 25445119 DOI: 10.1016/j.diagmicrobio.2014.09.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/16/2014] [Accepted: 09/26/2014] [Indexed: 01/15/2023]
Abstract
We evaluated the ability of the Vitek MS system to classify clinical pulmonary Mycobacterium avium complex isolates compared to multilocus sequence analysis. Vitek MS accurately identified 55% of the isolates as M. avium and 18% as M. intracellulare, but misidentified 24 (27%) Mycobacterium chimaera isolates as Mycobacterium intracellulare.
Collapse
Affiliation(s)
- Daniel P Boyle
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Teresa R Zembower
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
49
|
Rapid inactivation of Mycobacterium and nocardia species before identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2014; 52:3654-9. [PMID: 25078917 DOI: 10.1128/jcm.01728-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The identification of mycobacteria outside biocontainment facilities requires that the organisms first be rendered inactive. Exposure to 70% ethanol (EtOH) either before or after mechanical disruption was evaluated in order to establish a safe, effective, and rapid inactivation protocol that is compatible with identification of Mycobacterium and Nocardia species using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). A combination of 5 min of bead beating in 70% EtOH followed by a 10-min room temperature incubation period was found to be rapidly bactericidal and provided high-quality spectra compared to spectra obtained directly from growth on solid media. The age of the culture, the stability of the refrigerated or frozen lysates, and freeze-thaw cycles did not adversely impact the quality of the spectra or the identification obtained.
Collapse
|
50
|
Gray TJ, Kong F, Jelfs P, Sintchenko V, Chen SCA. Improved identification of rapidly growing mycobacteria by a 16S-23S internal transcribed spacer region PCR and capillary gel electrophoresis. PLoS One 2014; 9:e102290. [PMID: 25013955 PMCID: PMC4094492 DOI: 10.1371/journal.pone.0102290] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 06/17/2014] [Indexed: 01/04/2023] Open
Abstract
The identification of rapidly growing mycobacteria (RGM) remains problematic because of evolving taxonomy, limitations of current phenotypic methods and absence of a universal gene target for reliable speciation. This study evaluated a novel method of identification of RGM by amplification of the mycobacterial 16S–23S rRNA internal transcribed spacer (ITS) followed by resolution of amplified fragments by capillary gel electrophoresis (CGE). Nineteen American Type Culture Collection (ATCC) Mycobacterium strains and 178 clinical isolates of RGM (12 species) were studied. All RGM ATCC strains generated unique electropherograms with no overlap with slowly growing mycobacteria species, including M. tuberculosis. A total of 47 electropherograms for the 178 clinical isolates were observed allowing the speciation of 175/178 (98.3%) isolates, including the differentiation of the closely related species, M. massiliense (M. abscessus subspecies bolletii) and M. abscessus (M. abscessus sensu stricto). ITS fragment size ranged from 332 to 534 bp and 33.7% of clinical isolates generated electropherograms with two distinct peaks, while the remainder where characterized with a single peak. Unique peaks (fragment lengths) were identified for 11/12 (92%) RGM species with only M. moriokaense having an indistinguishable electropherogram from a rarely encountered CGE subtype of M. fortuitum. We conclude that amplification of the 16S–23S ITS gene region followed by resolution of fragments by CGE is a simple, rapid, accurate and reproducible method for species identification and characterization of the RGM.
Collapse
Affiliation(s)
- Timothy J. Gray
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- * E-mail:
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Peter Jelfs
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Marie Bashir Institute for Emerging Infections and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharon C-A. Chen
- Centre for Infectious Diseases and Microbiology, Institute of Clinical Pathology and Medical Research, Westmead, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology – Public Health, Westmead Hospital, Westmead, New South Wales, Australia
- Marie Bashir Institute for Emerging Infections and Biosecurity, Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| |
Collapse
|