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Karisa J, Ominde K, Tuwei M, Bartilol B, Ondieki Z, Musani H, Wanjiku C, Mwikali K, Babu L, Rono M, Eminov M, Mbogo C, Bejon P, Mwangangi J, Laroche M, Maia M. Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast. Wellcome Open Res 2024; 8:151. [PMID: 38957296 PMCID: PMC11217722 DOI: 10.12688/wellcomeopenres.18982.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Background Protein analysis using matrix-assisted laser desorption/ionisation time-of-flight mass-spectrometry (MALDI-TOF MS) represents a promising tool for entomological surveillance. In this study we tested the discriminative power of this tool for measuring species and blood meal source of main Afrotropical malaria vectors on the Kenyan coast. Methods Mosquito collections were conducted along the coastal region of Kenya. MALDI-TOF MS spectra were obtained from each individual mosquito's cephalothorax as well as the abdomens of blood-engorged mosquitoes. The same mosquitoes were also processed using gold standard tests: polymerase chain reaction (PCR) for species identification and enzyme linked immunosorbent assay (ELISA) for blood meal source identification. Results Of the 2,332 mosquitoes subjected to MALDI-TOF MS, 85% (1,971/2,332) were considered for database creation and validation. There was an overall accuracy of 97.5% in the identification of members of the An. gambiae ( An. gambiae, 100%; An. arabiensis, 91.9%; An. merus, 97.5%; and An. quadriannulatus, 90.2%) and An. funestus ( An. funestus, 94.2%; An. rivulorum, 99.4%; and An. leesoni, 94.1%) complexes. Furthermore, MALDI-TOF MS also provided accurate (94.5% accuracy) identification of blood host sources across all mosquito species. Conclusions This study provides further evidence of the discriminative power of MALDI-TOF MS to identify sibling species and blood meal source of Afrotropical malaria vectors, further supporting its utility in entomological surveillance. The low cost per sample (<0.2USD) and high throughput nature of the method represents a cost-effective alternative to molecular methods and could enable programs to increase the number of samples analysed and therefore improve the data generated from surveillance activities.
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Affiliation(s)
- Jonathan Karisa
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- The Open University, Milton Keynes, United Kingdom, Walton Hall, Kents Hill, Milton Keynes MK7 6AA, UK
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | - Kelly Ominde
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Mercy Tuwei
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | - Brian Bartilol
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Zedekiah Ondieki
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Harun Musani
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Caroline Wanjiku
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Kioko Mwikali
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Lawrence Babu
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Martin Rono
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- Pwani University, Kilifi, Kenya, 195-80108, Kenya
| | | | - Charles Mbogo
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Philip Bejon
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- University of Oxford, Centre for Global Health and Tropical Medicine, Oxford, UK, Oxford, UK
| | - Joseph Mwangangi
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
| | - Maureen Laroche
- The University of Texas Medical Branch -, Galveston National Laboratory 301 University Blvd, Texas, Galveston TX 77555-1019, USA
| | - Marta Maia
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Kilifi, Kenya, 230-80108, Kenya
- University of Oxford, Centre for Global Health and Tropical Medicine, Oxford, UK, Oxford, UK
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Wan TW, Lee TF, Chen XJ, Hunag YT, Teng LJ, Hsueh PR, Chiu HC. Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci. J Clin Microbiol 2023; 61:e0114323. [PMID: 38038480 PMCID: PMC10729738 DOI: 10.1128/jcm.01143-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Differentiating Streptococcus pneumoniae among nonpneumococcal viridans group streptococci (VGS) is challenging in conventional laboratories. Therefore, we aimed to evaluate the performance of the latest Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system in identifying VGS by comparing the results to those of the specific gene sequencing approach. Clinical isolates were initially identified using the BD Phoenix system to identify Streptococcus species. The optochin test was used to distinguish nonpneumococcal VGS from S. pneumoniae. The species of individual reference strains and clinical isolates were determined by comparing the sequences of the 16S rDNA, gyrB, sodA, groESL, or coaE genes with those in the GenBank sequence databases. We evaluated the performance of the Bruker Biotyper MALDI-TOF MS in VGS identification using two different machines with three databases. We collected a total of 103 nonpneumococcal VGS and 29 S. pneumoniae blood isolates at a medical center in northern Taiwan. Among these isolates, only seven could not be identified at the species level by the specific gene sequencing approach. We found that none of the nonpneumococcal VGS isolates were misidentified as pneumococci by the latest Biotyper system, and vice versa. However, certain strains, especially those in the mitis and bovis groups, could still not be correctly identified. The latest Bruker Biotyper 4.1 (DB_10833) showed significant improvement in identifying VGS strains. However, a specific gene sequencing test is still needed to precisely differentiate the species of strains in the mitis and bovis groups.
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Affiliation(s)
- Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xiang-Jun Chen
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Tsung Hunag
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Infectious Diseases, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Smith RD, Johnson JK, Ernst RK. Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles. Diagn Microbiol Infect Dis 2023; 107:116018. [PMID: 37478505 DOI: 10.1016/j.diagmicrobio.2023.116018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.
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Affiliation(s)
- Richard D Smith
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA; Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA.
| | - J Kristie Johnson
- Department of Pathology, School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Robert K Ernst
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, USA
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Karisa J, Ominde K, Tuwei M, Bartilol B, Ondieki Z, Musani H, Wanjiku C, Mwikali K, Babu L, Rono M, Eminov M, Mbogo C, Bejon P, Mwangangi J, Laroche M, Maia M. Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18982.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Background: Protein analysis using matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) represents a promising tool for entomological surveillance. In this study we tested the discriminative power of this tool for measuring species and blood meal source of main Afrotropical malaria vectors on the Kenyan coast. Methods: Mosquito collections were conducted along the coastal region of Kenya. MALDI-TOF MS spectra were obtained from each individual mosquito’s cephalothorax as well as the abdomens of blood-engorged mosquitoes. The same mosquitoes were also processed using gold standard tests: polymerase chain reaction (PCR) for species identification and enzyme linked immunosorbent assay (ELISA) for blood meal source identification. Results: Of the 2,332 mosquitoes subjected to MALDI-TOF MS, 85% (1,971/2,332) were considered for database creation and validation. There was an overall accuracy of 97.5% in the identification of members of the An. gambiae (An. gambiae, 100%; An. arabiensis, 91.9%; An. merus, 97.5%; and An. quadriannulatus, 90.2%) and An. funestus (An. funestus, 94.2%; An. rivulorum, 99.4%; and An. leesoni, 94.1%) complexes. Furthermore, MALDI-TOF MS also provided accurate (94.5% accuracy) identification of blood host sources across all mosquito species. Conclusions: This study provides further evidence of the discriminative power of MALDI-TOF MS to identify sibling species and blood meal source of Afrotropical malaria vectors, further supporting its utility in entomological surveillance. The low cost per sample (<0.2USD) and high throughput nature of the method represents a cost-effective alternative to molecular methods and could enable programs to increase the number of samples analysed and therefore improve the data generated from surveillance activities.
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Xiong L, Long X, Ni L, Wang L, Zhang Y, Cui L, Guo J, Yang C. Comparison of Autof Ms1000 and EXS3000 MALDI-TOF MS Platforms for Routine Identification of Microorganisms. Infect Drug Resist 2023; 16:913-921. [PMID: 36814830 PMCID: PMC9939805 DOI: 10.2147/idr.s352307] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/20/2022] [Indexed: 02/16/2023] Open
Abstract
Purpose Matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF) has recently been widely used in clinical microbiology laboratories, with the advantages of being reliable, rapid, and cost-effective. Here, we reported the performance of two MALDI-TOF MS instruments, EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China), which are commonly used in clinical microbiology field. Methods A total of 209 common clinical common isolates, including 70 gram-negative bacteria strains, 58 gram-positive bacteria strains, 33 yeast strains, 15 anaerobic bacteria strains, and 33 mold strains, and 19 mycobacterial strains were tested. All strains were identified by EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China). Sequence analysis of 16S rRNA or ITS regions was used to verify all strains. Results Current study found that species-level discrimination was found to be 191 (91.39%) and 190 (90.91%) by EXS3000 and Autof ms1000, respectively. Genus-level discrimination was 205 (98.09%) by the EXS3000 and 205 (98.09%) by the Autof ms1000, respectively. The correct results at species level of the EXS3000 were 91.43% (64/70) for gram-negative bacteria, 93.1% (54/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 81.82% (27/33) for filamentous fungi. The correct results at species level of the Autof ms1000 were 92.86% (65/70) for gram-negative bacteria, 91.38% (53/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 78.79% (26/33) for filamentous fungi. Conclusion Although the results show that the EXS3000 and Autof ms1000 systems are equally good choices in terms of analytical efficiency for routine procedures, the test result of EXS3000 is slightly better than Autof ms1000. It's worth mentioning that the target plate of the EXS 3000 instrument is reusable, but the target plate of the Autof ms1000 is disposable, making the EXS3000 more effective in reducing costs.
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Affiliation(s)
- Lijuan Xiong
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Xu Long
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Lijun Ni
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lili Wang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Yang Zhang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Lili Cui
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China,Correspondence: Jian Guo, Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, No. 1800 Yuntai Road, Pudong New Area, Shanghai, People’s Republic of China, Tel +86-17701810639, Email
| | - Chunying Yang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China,Chunying Yang, Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 83 Feishan Street, Yunyan District, Guiyang City, Guizhou Province, People’s Republic of China, Tel +86-13658504875, Email
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Pan F, Zhao N, Zhao W, Wang C, Sun Y, Zhang H, Qin J, Liu Q, Zhang H. Performance of Two Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of the Viridans Group Streptococci. Infect Drug Resist 2023; 16:2901-2909. [PMID: 37193297 PMCID: PMC10183192 DOI: 10.2147/idr.s407667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 05/18/2023] Open
Abstract
Background Due to similar colony morphology among viridans group streptococci (VGS), the differentiation of VGS species remains difficult in routine clinical microbiology. Recently, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been described as a fast method for identifying various bacteria at species level, and also for the VGS strains. Methods A total of 277 VGS isolates were identified with the two MALDI-TOF MS systems (VITEK MS and Bruker Biotyper). The tuf and rpoB gene sequencing was used as the reference identification method for comparison. Results Based on tuf and rpoB gene sequencing, 84 isolates were S. pneumoniae and 193 strains were other VGS isolates including S. anginosus group (n=91, 47.2%), S. mitis group (n=80, 41.5%), S. bovis group (n=11, 5.7%), S. salivarius group (n=10, 5.2%), and S. mutans group (n=1, 0.5%). VITEK MS and Bruker Biotyper accurately identified 94.6% and 89.9% of all VGS isolates, respectively. VITEK MS showed better identification results than Bruker Biotyper for S. mitis group including S. pneumoniae and S. bovis group, but for other VGS isolates, two MALDI-TOF MS systems showed comparable identification performance. However, VITEK MS was able to identify S. gallolyticus to the subspecies level with high-confidence (S. gallolyticus ssp. pasteurianus), while the Bruker Biotyper system could not. While Bruker Biotyper system could be able to correctly differentiate the subspecies of S. salivarius from S. vestibularis, VITEK MS poorly identify. Conclusion This study demonstrated that two MALDI-TOF MS systems allowed discrimination for most VGS isolates with different identification performance, but Bruker Biotyper could produce more misidentifications and VITEK MS system. It is crucial to be familiar with the performance of MALDI-TOF MS systems used in clinical microbiology.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Wantong Zhao
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Sun
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Haomin Zhang
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Juanxiu Qin
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
- Qian Liu, Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China, Email
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
- Correspondence: Hong Zhang, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, Tel +86 189 1712 8200, Email
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Elbehiry A, Aldubaib M, Abalkhail A, Marzouk E, ALbeloushi A, Moussa I, Ibrahem M, Albazie H, Alqarni A, Anagreyyah S, Alghamdi S, Rawway M. How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings. Vaccines (Basel) 2022; 10:1881. [PMID: 36366389 PMCID: PMC9699604 DOI: 10.3390/vaccines10111881] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 08/01/2023] Open
Abstract
Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Musaad Aldubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ahmad ALbeloushi
- Al Bukayriyah General Hospital, Qassim, Al Bukayriyah 52725, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Hamad Albazie
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Abdullah Alqarni
- Department of Support Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Sulaiman Anagreyyah
- Department of Preventive Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Saleh Alghamdi
- Department of Biomedical Engineering, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, Sakaka 42421, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt
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Evangelista AJ, Ferreira TL. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the diagnosis of microorganisms. Future Microbiol 2022; 17:1409-1419. [PMID: 36169347 DOI: 10.2217/fmb-2022-0067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Microbiology culture is the gold standard method for identifying microorganisms. This identification protocol takes several days to complete. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can identify different microorganisms quickly and accurately. The objective of this work was to evaluate the use of MALDI-TOF MS in the routine of clinical laboratories to identify microorganisms and to identify their resistance to antimicrobials. This study evaluated the relevance of the MALDI-TOF MS technique for microbiological diagnosis through a literature review. The authors found that MALDI-TOF MS can identify bacteria, fungi, viruses and parasites, even in blood cultures, and also serves to assess antimicrobial resistance. Thus, MALDI-TOF MS can become an indispensable tool in laboratory diagnosis.
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Dahms M, Eiserloh S, Rödel J, Makarewicz O, Bocklitz T, Popp J, Neugebauer U. Raman Spectroscopic Differentiation of Streptococcus pneumoniae From Other Streptococci Using Laboratory Strains and Clinical Isolates. Front Cell Infect Microbiol 2022; 12:930011. [PMID: 35937698 PMCID: PMC9353136 DOI: 10.3389/fcimb.2022.930011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/15/2022] [Indexed: 12/03/2022] Open
Abstract
Streptococcus pneumoniae, commonly referred to as pneumococci, can cause severe and invasive infections, which are major causes of communicable disease morbidity and mortality in Europe and globally. The differentiation of S. pneumoniae from other Streptococcus species, especially from other oral streptococci, has proved to be particularly difficult and tedious. In this work, we evaluate if Raman spectroscopy holds potential for a reliable differentiation of S. pneumoniae from other streptococci. Raman spectra of eight different S. pneumoniae strains and four other Streptococcus species (S. sanguinis, S. thermophilus, S. dysgalactiae, S. pyogenes) were recorded and their spectral features analyzed. Together with Raman spectra of 59 Streptococcus patient isolates, they were used to train and optimize binary classification models (PLS-DA). The effect of normalization on the model accuracy was compared, as one example for optimization potential for future modelling. Optimized models were used to identify S. pneumoniae from other streptococci in an independent, previously unknown data set of 28 patient isolates. For this small data set balanced accuracy of around 70% could be achieved. Improvement of the classification rate is expected with optimized model parameters and algorithms as well as with a larger spectral data base for training.
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Affiliation(s)
- Marcel Dahms
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies), Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
| | - Simone Eiserloh
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies), Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
| | - Jürgen Rödel
- Institute for Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Oliwia Makarewicz
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Jena, Germany
| | - Thomas Bocklitz
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies), Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies), Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
| | - Ute Neugebauer
- Leibniz Institute of Photonic Technology Jena (a member of Leibniz Health Technologies), Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital, Jena, Germany
- *Correspondence: Ute Neugebauer,
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Ikegami H, Noguchi S, Fukuda K, Akata K, Yamasaki K, Kawanami T, Mukae H, Yatera K. Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing. Sci Rep 2021; 11:19534. [PMID: 34599245 PMCID: PMC8486753 DOI: 10.1038/s41598-021-98985-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.
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Affiliation(s)
- Hiroaki Ikegami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Kazumasa Fukuda
- Department of Microbiology, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Kentaro Akata
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Kei Yamasaki
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Toshinori Kawanami
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, Japan, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu-city, Fukuoka, 807-8555, Japan.
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11
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Nix ID, Idelevich EA, Schlattmann A, Sparbier K, Kostrzewa M, Becker K. MALDI-TOF Mass Spectrometry-Based Optochin Susceptibility Testing for Differentiation of Streptococcus pneumoniae from other Streptococcus mitis Group Streptococci. Microorganisms 2021; 9:microorganisms9102010. [PMID: 34683331 PMCID: PMC8537049 DOI: 10.3390/microorganisms9102010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/15/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Discrimination of Streptococcus pneumoniae from other Streptococcus mitis group (SMG) species is still challenging but very important due to their different pathogenic potential. In this study, we aimed to develop a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based optochin susceptibility test with an objective read-out. Optimal test performance was established and evaluated by testing consecutively collected respiratory isolates. Optochin in different concentrations as a potential breakpoint concentration was added to a standardized inoculum. Droplets of 6 µL with optochin and, as growth control, without optochin were spotted onto a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard. Spectra were acquired, and results were interpreted as S. pneumoniae in the case of optochin susceptibility (no growth), or as non-S. pneumoniae in the case of optochin non-susceptibility (growth). Highest test accuracy was achieved after 20 h incubation time (95.7%). Rapid testing after 12 h incubation time (optochin breakpoint 2 µg/mL; correct classification 100%, validity 62.5%) requires improvement by optimization of assay conditions. The feasibility of the MALDI-TOF MS-based optochin susceptibility test was demonstrated in this proof-of-principle study; however, confirmation and further improvements are warranted.
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Affiliation(s)
- Ilka D. Nix
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Evgeny A. Idelevich
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Andreas Schlattmann
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
| | - Katrin Sparbier
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Markus Kostrzewa
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (M.K.)
| | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (E.A.I.); (A.S.)
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
- Correspondence: ; Tel.: +49-3834-86-5560
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12
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Lee OJ, Ko YJ, Lee SB, Kim CM, Jang SJ, Kook JK, Lim YK, Shin JH, Shin MG, Kee SJ, Jeong SH, Kang SH, Park G. Performance assessment of ASTA MicroIDSys, a new matrix assisted laser desorption ionization-time of flight mass spectrometry system, for identification of viridans group streptococci. Microbiol Immunol 2021; 65:566-574. [PMID: 34516008 DOI: 10.1111/1348-0421.12942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/30/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
The performance of the ASTA MicroIDSys system (ASTA, Suwon, South Korea), a new matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) system, was evaluated for the identification of viridans group streptococci (VGS) and compared with the results obtained with the Bruker Biotyper system (Bruker Daltonics, Hamburg, Germany). A total of 106 Streptococcus reference strains belonging to 24 species from the bacterial strain bank was analyzed using the two MALDI-TOF MS systems. Of the 106 reference strains tested, ASTA MicroIDSys and Bruker Biotyper correctly identified 84.9% and 81.1% at the species level, 100% and 97.2% at the group level and 100% and 98.1% at the genus level, respectively. The difference between the two systems was not statistically significant (P = 0.289). Out of 24 species, 13 species were accurately identified to the species level with 100% accurate identification rates with both systems. The accurate identification rates at the species level of ASTA MicroIDSys and Bruker Biotyper were 100% and 87.5% for the S. anginosus group; 78.4% and 73.5% for the S. mitis group; 91.7% and 91.7% for the S. mutans group; and 100% and 100% for the S. salivarius group, respectively. The ASTA MicroIDSys showed an identification performance equivalent to that of the Bruker Biotyper for VGS. Therefore, it would be useful for the identification of VGS strains in clinical microbiology laboratories. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- O-Jin Lee
- Department of Laboratory Medicine, Green Cross Laboratories, Yongin, Republic of Korea
| | - Young Jin Ko
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Seul-Bi Lee
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Choon Mee Kim
- Premedical Science, College of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Sook-Jin Jang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Yun Kyong Lim
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, College of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Jong Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Myung Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Republic of Korea
| | - Seung Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Republic of Korea
| | - Seong-Ho Kang
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
| | - Geon Park
- Department of Laboratory Medicine, School of Medicine, Chosun University, Gwangju, Republic of Korea
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Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia. Int J Microbiol 2021; 2021:6646925. [PMID: 34335780 PMCID: PMC8294987 DOI: 10.1155/2021/6646925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/20/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Aim To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. Materials and Methods Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.
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14
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Jensen CS, Dargis R, Shewmaker P, Nielsen XC, Christensen JJ. Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry. Diagn Microbiol Infect Dis 2021; 101:115487. [PMID: 34339919 DOI: 10.1016/j.diagmicrobio.2021.115487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022]
Abstract
This study evaluated the ability of the MALDI-ToF MS from Bruker Daltonics to identify clinical Mitis-Group-Streptococcus isolates with a focus on Streptococcus pseudopneumoniae. The results were analyzed using the standard log(score) and the previously published list(score). Importantly, using the log(score) no misidentifications occurred and 27 of 29 (93%) S. pneumoniae and 27 of 30 (90%) S. oralis strains were identified, but only 1 of 31 (3%) S. pseudopneumoniae and 1 of 13 (8%) S. mitis strains were identified. However, our results show that 30 of 31 S. pseudopneumoniae strains had a S. pseudopneumoniae Main Spectral Profiles within the 3 best matches. Using the list(score) all S. oralis and S. pneumoniae strains were identified correctly, but list(score) misidentified 10 S. pseudopneumoniae and 5 S. mitis. We propose to use the log(score) for identification of S. pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis, but for some strains additional testing may be needed.
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Affiliation(s)
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | | | | | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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15
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MALDI-TOF mass spectrometry in the 21st century clinical microbiology laboratory. Enferm Infecc Microbiol Clin 2021; 39:192-200. [DOI: 10.1016/j.eimc.2020.02.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
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16
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Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods. J Clin Microbiol 2021; 59:JCM.02503-20. [PMID: 33208473 DOI: 10.1128/jcm.02503-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
A correct identification of Streptococcus pseudopneumoniae is a prerequisite for investigating the clinical impact of the bacterium. The identification has traditionally relied on phenotypic methods. However, these phenotypic traits have been shown to be unreliable, with some S. pseudopneumoniae strains giving conflicting results. Therefore, sequence-based identification methods have increasingly been used for identification of S. pseudopneumoniae In this study, we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify S. pseudopneumoniae Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to their respective species. It was not possible to identify all S. pseudopneumoniae strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, which could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae, and fastANI differentiated between S. pseudopneumoniae and S. pneumoniae using an ANI cutoff of 96%.
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Rapid direct detection of pathogens for diagnosis of joint infections by MALDI-TOF MS after liquid enrichment in the BacT/Alert blood culture system. PLoS One 2020; 15:e0243790. [PMID: 33306699 PMCID: PMC7732097 DOI: 10.1371/journal.pone.0243790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/25/2020] [Indexed: 11/19/2022] Open
Abstract
Pathogen identification is a critical step during diagnosis of infectious diseases. Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight mass spectrometry (MALDI-TOF-MS) has become the gold standard for identification of microorganisms cultured on solid media in microbiology laboratories. Direct identification of microbes from liquid specimen, circumventing the need for the additional overnight cultivation step, has been successfully established for blood culture, urine and liquor. Here, we evaluate the ability of MALDI-TOF MS for direct identification of pathogens in synovial fluid after liquid enrichment in BacT/Alert blood culture bottles. Influence of synovial specimen quality on direct species identification with the MALDI BioTyper/Sepsityper was tested with samples inoculated from pretested native synovia with concomitant inoculation of blood or pus, or highly viscous fluid. Here, we achieved >90% concordance with culture on solid medium, and only mixed-species samples posed significant problems. Performance in routine diagnostics was tested prospectively on bottles inoculated by treating physicians on ward. There, we achieved >70% concordance with culture on solid media. The major contributors to test failure were the absence of a measurable mass signal and mixed-specimen samples. The Sepsityper workflow worked well on samples derived from BacT/Alert blood culture bottles inoculated with synovial fluid, giving concordant results to identification from solid media. Host remnant material in the inoculum, such as blood or pus, had no detrimental effect on identification score values of the BioTyper system after processing with the Sepsityper workflow, and neither had the initial viscosity of the synovial sample.
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18
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Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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19
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Kosecka-Strojek M, Wolska M, Żabicka D, Sadowy E, Międzobrodzki J. Identification of Clinically Relevant Streptococcus and Enterococcus Species Based on Biochemical Methods and 16S rRNA, sodA, tuf, rpoB, and recA Gene Sequencing. Pathogens 2020; 9:pathogens9110939. [PMID: 33187333 PMCID: PMC7696602 DOI: 10.3390/pathogens9110939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococci and enterococci are significant opportunistic pathogens in epidemiology and infectious medicine. High genetic and taxonomic similarities and several reclassifications within genera are the most challenging in species identification. The aim of this study was to identify Streptococcus and Enterococcus species using genetic and phenotypic methods and to determine the most discriminatory identification method. Thirty strains recovered from clinical samples representing 15 streptococcal species, five enterococcal species, and four nonstreptococcal species were subjected to bacterial identification by the Vitek® 2 system and Sanger-based sequencing methods targeting the 16S rRNA, sodA, tuf, rpoB, and recA genes. Phenotypic methods allowed the identification of 10 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains (Leuconostoc, Granulicatella, and Globicatella genera). The combination of sequencing methods allowed the identification of 21 streptococcal strains, five enterococcal strains, and four nonstreptococcal strains. The 16S rRNA and rpoB genes had the highest identification potential. Only a combination of several molecular methods was sufficient for unambiguous confirmation of species identity. This study will be useful for comparison of several identification methods, both those used as a first choice in routine microbiology and those used for final confirmation.
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Affiliation(s)
- Maja Kosecka-Strojek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
- Correspondence: ; Tel.: +48-12-664-6365
| | - Mariola Wolska
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
| | - Dorota Żabicka
- Department of Molecular Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Ewa Sadowy
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, 00-725 Warsaw, Poland;
| | - Jacek Międzobrodzki
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland; (M.W.); (J.M.)
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Nybakken EJ, Oppegaard O, Gilhuus M, Jensen CS, Mylvaganam H. Identification of Streptococcus dysgalactiae using matrix-assisted laser desorption/ionization-time of flight mass spectrometry; refining the database for improved identification. Diagn Microbiol Infect Dis 2020; 99:115207. [PMID: 33069003 DOI: 10.1016/j.diagmicrobio.2020.115207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/05/2020] [Accepted: 09/05/2020] [Indexed: 10/23/2022]
Abstract
Matrix-assisted laser desorption/ionization time of flight (MALDI-ToF) has revolutionized bacterial identification. However, the phylogenetic resolution is still insufficient for discerning several β-haemolytic streptococcal species. We aimed to improve the diagnostic performance of MALDI-ToF through manual curation of the reference spectra in Brukers Compass Library DB-7854. Before intervention, only 133 out of 217 (62%) Streptococcus dysgalactiae isolates were successfully identified to the species level, 83 isolates were identified to the genus level as either S. dysgalactiae, S. pyogenes or S. canis, and one S. dysgalactiae isolate was wrongly identified as S. canis. All 109 S. canis isolates were successfully identified to the species level. Removal of three reference spectra from the database significantly improved the identification of S. dysgalactiae to 94%, without compromising identification of S. canis. This illustrates the advantage of refinement of the reference database in order to improve the analytic precision of MALDI-ToF.
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Affiliation(s)
- Eirik Jovall Nybakken
- Department of Microbiology, P.b. 1400, Haukeland University Hospital, 5021, Bergen, Norway.
| | - Oddvar Oppegaard
- Department of Medicine, Haukeland University Hospital, 5021, Bergen, Norway
| | | | | | - Haima Mylvaganam
- Department of Microbiology, Haukeland University Hospital, 5021, Bergen, Norway
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21
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Diagnostic tools for bacterial infections in travellers: Current and future options. Travel Med Infect Dis 2020; 37:101856. [PMID: 32841728 DOI: 10.1016/j.tmaid.2020.101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022]
Abstract
International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.
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Rodríguez-Sánchez B, Cercenado E, Coste AT, Greub G. Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696525 PMCID: PMC6351997 DOI: 10.2807/1560-7917.es.2019.24.4.1800193] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction MALDI-TOF MS represents a new technological era for microbiology laboratories. Improved sample processing and expanded databases have facilitated rapid and direct identification of microorganisms from some clinical samples. Automated analysis of protein spectra from different microbial populations is emerging as a potential tool for epidemiological studies and is expected to impact public health. Aim To demonstrate how implementation of MALDI-TOF MS has changed the way microorganisms are identified, how its applications keep increasing and its impact on public health and hospital hygiene. Methods A review of the available literature in PubMED, published between 2009 and 2018, was carried out. Results Of 9,709 articles retrieved, 108 were included in the review. They show that rapid identification of a growing number of microorganisms using MALDI-TOF MS has allowed for optimisation of patient management through prompt initiation of directed antimicrobial treatment. The diagnosis of Gram-negative bacteraemia directly from blood culture pellets has positively impacted antibiotic streamlining, length of hospital stay and costs per patient. The flexibility of MALDI-TOF MS has encouraged new forms of use, such as detecting antibiotic resistance mechanisms (e.g. carbapenemases), which provides valuable information in a reduced turnaround time. MALDI-TOF MS has also been successfully applied to bacterial typing. Conclusions MALDI-TOF MS is a powerful method for protein analysis. The increase in speed of pathogen detection enables improvement of antimicrobial therapy, infection prevention and control measures leading to positive impact on public health. For antibiotic susceptibility testing and bacterial typing, it represents a rapid alternative to time-consuming conventional techniques.
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Affiliation(s)
- Belén Rodríguez-Sánchez
- These authors contributed equally to this work.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alix T Coste
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland.,Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.,These authors contributed equally to this work
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23
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Hahn A, Podbielski A, Meyer T, Zautner AE, Loderstädt U, Schwarz NG, Krüger A, Cadar D, Frickmann H. On detection thresholds-a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results. Acta Trop 2020; 205:105377. [PMID: 32007448 DOI: 10.1016/j.actatropica.2020.105377] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/18/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023]
Abstract
Diagnostic testing in the infectious disease laboratory facilitates decision-making by physicians at the bedside as well as epidemiological assessments and surveillance at study level. Problems may arise if test results are uncritically considered as being the same as the unknown true value. To allow a better understanding, the influence of external factors on the interpretation of test results is introduced with the example of prevalence, followed by the presentation of strengths and weaknesses of important techniques in the infectious disease laboratory like microscopy, cultural diagnostics, serology, mass spectrometry, nucleic acid amplification and hypothesis-free metagenomic sequencing with focus on basic, high-technology and potential future approaches. Special problems like multiplex testing as well as uncertainty of test evaluations, if no gold standard is available, are also stressed with a final glimpse on emerging future technologies for the infectious disease laboratory. In the conclusions, suitability for point-of-care-testing and field laboratory applications is summarized. The aim is to illustrate the limitations of diagnostic accuracy to both clinicians and study planners and to stress the importance of close cooperation with experts in laboratory disciplines so as to avoid potentially critical misunderstandings due to inappropriate interpretation of diagnostic test results.
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Affiliation(s)
- Andreas Hahn
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Andreas Podbielski
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany
| | - Thomas Meyer
- Department of Dermatology, St. Josef Hospital, Bochum, Germany
| | - Andreas Erich Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ulrike Loderstädt
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | | | - Andreas Krüger
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany
| | - Daniel Cadar
- Bernhard Nocht Institute for Tropical Medicine Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, Rostock, Germany; Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany.
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24
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Imai K, Nemoto R, Kodana M, Tarumoto N, Sakai J, Kawamura T, Ikebuchi K, Mitsutake K, Murakami T, Maesaki S, Fujiwara T, Hayakawa S, Hoshino T, Seki M, Maeda T. Rapid and Accurate Species Identification of Mitis Group Streptococci Using the MinION Nanopore Sequencer. Front Cell Infect Microbiol 2020; 10:11. [PMID: 32083020 PMCID: PMC7002467 DOI: 10.3389/fcimb.2020.00011] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
Differentiation between mitis group streptococci (MGS) bacteria in routine laboratory tests has become important for obtaining accurate epidemiological information on the characteristics of MGS and understanding their clinical significance. The most reliable method of MGS species identification is multilocus sequence analysis (MLSA) with seven house-keeping genes; however, because this method is time-consuming, it is deemed unsuitable for use in most clinical laboratories. In this study, we established a scheme for identifying 12 species of MGS (S. pneumoniae, S. pseudopneumoniae, S. mitis, S. oralis, S. peroris, S. infantis, S. australis, S. parasanguinis, S. sinensis, S. sanguinis, S. gordonii, and S. cristatus) using the MinION nanopore sequencer (Oxford Nanopore Technologies, Oxford, UK) with the taxonomic aligner "What's in My Pot?" (WIMP; Oxford Nanopore's cloud-based analysis platform) and Kraken2 pipeline with the custom database adjusted for MGS species identification. The identities of the species in reference genomes (n = 514), clinical isolates (n = 31), and reference strains (n = 4) were confirmed via MLSA. The nanopore simulation reads were generated from reference genomes, and the optimal cut-off values for MGS species identification were determined. For 31 clinical isolates (S. pneumoniae = 8, S. mitis = 17 and S. oralis = 6) and 4 reference strains (S. pneumoniae = 1, S. mitis = 1, S. oralis = 1, and S. pseudopneumoniae = 1), a sequence library was constructed via a Rapid Barcoding Sequencing Kit for multiplex and real-time MinION sequencing. The optimal cut-off values for the identification of MGS species for analysis by WIMP and Kraken2 pipeline were determined. The workflow using Kraken2 pipeline with a custom database identified all 12 species of MGS, and WIMP identified 8 MGS bacteria except S. infantis, S. australis, S. peroris, and S. sinensis. The results obtained by MinION with WIMP and Kraken2 pipeline were consistent with the MGS species identified by MLSA analysis. The practical advantage of whole genome analysis using the MinION nanopore sequencer is that it can aid in MGS surveillance. We concluded that MinION sequencing with the taxonomic aligner enables accurate MGS species identification and could contribute to further epidemiological surveys.
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Affiliation(s)
- Kazuo Imai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Rina Nemoto
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Toru Kawamura
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kenji Ikebuchi
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Takashi Murakami
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Taku Fujiwara
- Department of Pediatric Dentistry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Tomonori Hoshino
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Mitsuko Seki
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Division of Pediatric Dentistry, Meikai University School of Dentistry, Sakado, Japan
| | - Takuya Maeda
- Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
- Department of Laboratory Medicine, Saitama Medical University, Saitama, Japan
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25
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Farfour E, Degand N, Muggeo A, Marcelino P, Vasse M, Guillard T. Accurate identification of S. pneumoniae using MALDI-TOF mass spectrometry, still a challenge for clinical laboratories? Eur J Clin Microbiol Infect Dis 2020; 39:209-211. [DOI: 10.1007/s10096-019-03716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
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26
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Ling J, Wang H, Li G, Feng Z, Song Y, Wang P, Shao H, Zhou H, Chen G. A novel short-term high-lactose culture approach combined with a matrix-assisted laser desorption ionization-time of flight mass spectrometry assay for differentiating Escherichia coli and Shigella species using artificial neural networks. PLoS One 2019; 14:e0222636. [PMID: 31593573 PMCID: PMC6782097 DOI: 10.1371/journal.pone.0222636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/04/2019] [Indexed: 11/29/2022] Open
Abstract
Background Escherichia coli is currently unable to be reliably differentiated from Shigella species by routine matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, a reliable and rapid identification method was established for Escherichia coli and Shigella species based on a short-term high-lactose culture using MALDI-TOF MS and artificial neural networks (ANN). Materials and methods The Escherichia coli and Shigella species colonies, treated with (Condition 1)/without (Condition 2) a short-term culture with an in-house developed high-lactose fluid medium, were prepared for MALDI-TOF MS assays. The MS spectra were acquired in linear positive mode, with a mass range from 2000 to 12000 Da and were then compared to discover new biomarkers for identification. Finally, MS spectra data sets 1 and 2, extracted from the two conditions, were used for ANN training to investigate the benefit on bacterial classification produced by the new biomarkers. Results Twenty-seven characteristic MS peaks from the Escherichia coli and Shigella species were summarized. Seven unreported MS peaks, with m/z 2330.745, m/z 2341.299, m/z 2371.581, m/z 2401.038, m/z 3794.851, m/z 3824.839 and m/z 3852.548, were discovered in only the spectra from the E. coli strains after a short-term high-lactose culture and were identified as belonging to acid shock protein. The prediction accuracies of the ANN models, based on data set 1 and 2, were 97.71±0.16% and 74.39±0.34% (n = 5), with an extremely remarkable difference (p < 0.001), and the areas under the curve of the receiver operating characteristic curve were 0.72 and 0.99, respectively. Conclusions In summary, adding a short-term high-lactose culture approach before the analysis enabled a reliable and easy differentiation of Escherichia coli from the Shigella species using MALDI-TOF MS and ANN.
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Affiliation(s)
- Jin Ling
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
- Department of Pharmacy, Zhejiang Jinhua Guangfu Hospital, Jinhua, China
| | - Hong Wang
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Gaomin Li
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Zhen Feng
- Department of Antibiotics and Microbiology, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Yufei Song
- Department of Gastroenterology, Lihuili Hospital of Ningbo Medical Center, Ningbo, China
| | - Peng Wang
- Shanghai Key Laboratory of Intelligent Information Processing, School of Computer Science, Fudan University, Shanghai, China
| | - Hong Shao
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Hu Zhou
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Gang Chen
- Department of Biochemical Drugs and Biological Products, Shanghai Institute for Food and Drug Control, Shanghai, China
- NMPA Key Laboratory for Quality Control of Therapeutic Monoclonal Antibodies, Shanghai Institute for Food and Drug Control, Shanghai, China
- * E-mail:
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27
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Marquart ME, Benton AH, Galloway RC, Stempak LM. Antibiotic susceptibility, cytotoxicity, and protease activity of viridans group streptococci causing endophthalmitis. PLoS One 2018; 13:e0209849. [PMID: 30576393 PMCID: PMC6303072 DOI: 10.1371/journal.pone.0209849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/12/2018] [Indexed: 12/14/2022] Open
Abstract
The viridans group streptococci comprise multiple species and have gained more recognition in recent years as common etiologic agents of bacterial endophthalmitis. The purpose of this study was to identify the species of human endophthalmitis isolates of viridans streptococci and to characterize their potential virulence attributes. The species of 22 endophthalmitis strains of viridans streptococci were identified by Matrix Assisted Laser Desorption Ionization Time-of-Flight. Susceptibilities to 3 antibiotics commonly used for bacterial endophthalmitis were determined. The extracellular milieu of each strain was tested for cytotoxicity of retinal pigmented epithelial cells, hemolysis of sheep erythrocytes, and protease activity using gelatin zymography. Identified species were Streptococcus mitis/oralis, S. salivarius, S. vestibularis, S. parasanguinis, S. mutans, S. constellatus, and S. gordonii. One strain of S. pseudoporcinus was also identified. All strains were sensitive to vancomycin, 77% were resistant to amikacin, and 27% had intermediate resistance to ceftazidime. Extracellular milieu from all strains except one (S. pseudoporcinus) were largely devoid of toxicity to retinal pigmented epithelial cells and sheep erythrocytes. Twelve strains, 10 of which were S. mitis/oralis, produced protease activity. Interestingly, not all of the S. mitis/oralis strains were proteolytic. These findings highlight the diversity of virulence factor production in ocular strains of the viridans streptococci not only at the group level but also at the species level.
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Affiliation(s)
- Mary E. Marquart
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Angela H. Benton
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Regina C. Galloway
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Lisa M. Stempak
- Department of Pathology, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
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28
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Su TY, Lee MH, Huang CT, Liu TP, Lu JJ. The clinical impact of patients with bloodstream infection with different groups of Viridans group streptococci by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Medicine (Baltimore) 2018; 97:e13607. [PMID: 30558035 PMCID: PMC6320099 DOI: 10.1097/md.0000000000013607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identifying viridans group streptococcus (VGS) was improving. However, the clinical impact of identifying VGS had not been well recognized. Our study had comprehensively studied the clinical manifestations and outcome of VGS blood stream infection by using MALDI-TOF MS for identification.This retrospective study enrolled 312 adult patients with a monomicrobial blood culture positive for VGS. Blood culture was examined through MALDI-TOF MS.The most common VGS species were the Streptococcus anginosus group (38.8%) and Streptococcus mitis group (22.8%). Most species showed resistance to erythromycin (35.6%), followed by clindamycin (25.3%) and penicillin (12.5%). Skin and soft tissue infection and biliary tract infection were significantly related to S. anginosus group bacteremia (P = .001 and P = .005, respectively). S. mitis group bacteremia was related to infective endocarditis and bacteremia with febrile neutropenia (P = .005 and P < .001, respectively). Infective endocarditis was also more likely associated with S. sanguinis group bacteremia (P = .009). S. anginosus group had less resistance rate to ampicillin, erythromycin, clindamycin, and ceftriaxone (P = .019, <.001, .001, and .046, respectively). A more staying in intensive care unit, underlying solid organ malignancy, and a shorter treatment duration were independent risk factors for 30-day mortality. This study comprehensively evaluated different VGS group and their clinical manifestations, infection sources, concomitant diseases, treatments, and outcomes. Categorizing VGS into different groups by MALDI-TOF MS could help clinical physicians well understand their clinical presentations.
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Affiliation(s)
- Ting-Yi Su
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Ming-Hsun Lee
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Ching-Tai Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Tsui-Ping Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
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29
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A Case of Recurrent Erysipelas Caused by Streptococcus mitis Group. Case Rep Infect Dis 2018; 2018:5156085. [PMID: 30018832 PMCID: PMC6029475 DOI: 10.1155/2018/5156085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/31/2018] [Indexed: 12/15/2022] Open
Abstract
The aetiology of erysipelas remains poorly defined though beta-haemolytic streptococci are considered as the main causative pathogens. We describe a case of a 70-year-old woman with recurrent erysipelas in her left arm due to infection with streptococci of the mitis group. Her past medical history includes lymphoedema of the left arm secondary to lymph node dissection due to breast cancer surgery. On seven different occasions during a decade, she has presented a clinical picture of erysipelas and in three of them with Streptococcus mitis group bacteraemia. The results indicate that two cases were caused by Streptococcus mitis and one case was caused by Streptococcus oralis. This is, to our knowledge, the first reported cases of S. mitis and of S. oralis as the causative agents of erysipelas.
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30
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External Quality Assurance for Laboratory Identification and Capsular Typing of Streptococcus pneumoniae. Sci Rep 2017; 7:13280. [PMID: 29038446 PMCID: PMC5643306 DOI: 10.1038/s41598-017-13605-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/26/2017] [Indexed: 12/20/2022] Open
Abstract
An external quality assessment (EQA) scheme for pneumococcal serotype identification has been performed over a period of 11 years, by a network of European pneumococcal reference laboratories. We report the results from the EQA, and present an assessment of the acceptability and utility of the EQA scheme. Reports from 22 EQA panels distributed in 2005-2016 were analysed. Each EQA panel consisted of seven isolates. A questionnaire including seven questions related to the acceptability and utility of the EQA scheme was distributed to all participating laboratories. Altogether, 154 pneumococcal isolates were tested. Of the 92 serologically distinct serotypes currently defined, 49 serotypes were included in the rounds. Discrepant results were observed in eight EQA rounds, involving 11 isolates (7.1%, 95% CI: 4% to 12%). All participating laboratories reported that the EQA scheme was useful for quality assurance purposes. Our results show that comparable serotyping data can be obtained in different laboratories. The EQA participation helps to keep the typing procedures at a high standard and provides data for accreditation purposes. The EQA is helpful when new technologies are introduced, and reveal limitations of both genotypic and phenotypic methods. Continuation of the presented EQA scheme is planned.
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31
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization. J Clin Microbiol 2017; 55:3328-3338. [PMID: 28855303 DOI: 10.1128/jcm.00868-17] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation.
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32
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Slotved HC, Facklam RR, Fuursted K. Assessment of a novel bile solubility test and MALDI-TOF for the differentiation of Streptococcus pneumoniae from other mitis group streptococci. Sci Rep 2017; 7:7167. [PMID: 28769078 PMCID: PMC5540920 DOI: 10.1038/s41598-017-07772-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/03/2017] [Indexed: 01/25/2023] Open
Abstract
This study assesses a novel bile solubility test and MALDI-TOF for the differentiation of Streptococcus pneumoniae from other mitis group streptococci, including differentiation of S. pneumoniae from Streptococcus pseudopneumoniae. Eighty-four species verified mitis group isolates were subjected to our bile solubility test (which measures and calculates the differences of absorbance in the test tube containing 10% sodium deoxycholate versus a blank control tube, after incubation for 10 minutes at 36 °C using a spectrophotometer) and MALDI-TOF MS (both the standard result output and by visual spectra evaluation). Applying a calculated optimal cut-off absorbance-value of 2.1, differentiated S. pneumoniae from all but one other mitis group streptococci (one S. mitis isolate generated an OD-value above 2.1). MALDI-TOF score value identification identified correctly 46 S. pneumoniae and 4 S. pseudopneumoniae but misidentified 16 other mitis group strains. Visual spectra evaluation correctly identified all S. pneumoniae and S. pseudopneumoniae strains but misidentified 13 other mitis group strains. The bile solubility test based on spectrophotometric reading described in this study can differentiate S. pneumoniae from other Streptococcus species. Combining the bile solubility test and the MALDI-TOF spectra results provide a correct identification of all S. pneumoniae and S. pseudopneumoniae isolates.
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Affiliation(s)
- Hans-Christian Slotved
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Richard R Facklam
- Retired, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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33
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Marín M, Cercenado E, Sánchez-Carrillo C, Ruiz A, Gómez González Á, Rodríguez-Sánchez B, Bouza E. Accurate Differentiation of Streptococcus pneumoniae from other Species within the Streptococcus mitis Group by Peak Analysis Using MALDI-TOF MS. Front Microbiol 2017; 8:698. [PMID: 28487677 PMCID: PMC5403922 DOI: 10.3389/fmicb.2017.00698] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 11/13/2022] Open
Abstract
Despite the benefits of MALDI-TOF MS technology (Matrix-Assisted Laser Desorption-Ionization Time-Of-Flight Mass Spectrometry) reported worldwide and the continuous improving of the available databases, discrimination between Streptococcus pneumoniae and closely related species within the Streptococcus mitis group (SMG) using this methodology has been suboptimal. However, the accurate identification at the species level of this group of microorganisms is important for the appropriate management of infected patients. In this study, 216 SMG isolates -101 S. pneumoniae and 115 corresponding to 7 non-pneumococcal species within this group- were analyzed. All the isolates had been previously identified by conventional methods (optochin and bile solubility tests) and non-pneumococcal isolates were confirmed by sequence analysis (sodA and plys genes) when required. The isolates were also identified with the MALDI Biotyper 3.1 (Bruker Daltonics, Bremen, Germany) using an updated library containing 6,903 Main Spectra Profiles (MSPs). All the analyzed S. pneumoniae were correctly identified with MALDI-TOF MS at species level using the most updated database and all the non-pneumococcal SMG isolates were also identified at the group level. Several peaks (4,964.32, 6,888.90, and 9,516.46 m/z) have been found to be specific of S. pneumoniae, whilst a different set of peaks have proved to be present only in S. mitis (6,839.07 m/z) and S. oralis (5,297.61, 5822.53, and 6,839.07 m/z). Peak analysis allowed correct species assignment of 101/101 S. pneumoniae isolates (100%) and 102/105 S. mitis/oralis isolates (97.1%). Thus, the implementation of MALDI-TOF MS plus peak analysis for the identification of this group of microorganisms may provide precise species-level information that will allow the early implementation of directed antibiotic therapy.
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Affiliation(s)
- Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
| | - Emilia Cercenado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain
| | | | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
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