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Xie O, Davies MR, Tong SYC. Streptococcus dysgalactiae subsp. equisimilis infection and its intersection with Streptococcus pyogenes. Clin Microbiol Rev 2024:e0017523. [PMID: 38856686 DOI: 10.1128/cmr.00175-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
SUMMARYStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an increasingly recognized cause of disease in humans. Disease manifestations range from non-invasive superficial skin and soft tissue infections to life-threatening streptococcal toxic shock syndrome and necrotizing fasciitis. Invasive disease is usually associated with co-morbidities, immunosuppression, and advancing age. The crude incidence of invasive disease approaches that of the closely related pathogen, Streptococcus pyogenes. Genomic epidemiology using whole-genome sequencing has revealed important insights into global SDSE population dynamics including emerging lineages and spread of anti-microbial resistance. It has also complemented observations of overlapping pathobiology between SDSE and S. pyogenes, including shared virulence factors and mobile gene content, potentially underlying shared pathogen phenotypes. This review provides an overview of the clinical and genomic epidemiology, disease manifestations, treatment, and virulence determinants of human infections with SDSE with a particular focus on its overlap with S. pyogenes. In doing so, we highlight the importance of understanding the overlap of SDSE and S. pyogenes to inform surveillance and disease control strategies.
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Affiliation(s)
- Ouli Xie
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Victorian Infectious Disease Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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Tago H, Maeda Y, Tanaka Y, Kohketsu H, Lim TK, Harada M, Yoshino T, Matsunaga T, Tanaka T. Line image sensor-based colony fingerprinting system for rapid pathogenic bacteria identification. Biosens Bioelectron 2024; 249:116006. [PMID: 38199081 DOI: 10.1016/j.bios.2024.116006] [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: 10/13/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/12/2024]
Abstract
The rapid identification of pathogenic bacteria is crucial across various industries, including food or beverage manufacturing. Bacterial microcolony image-based classification has emerged as a promising approach to expedite identification, automate inspections, and reduce costs. However, conventional imaging methods have significant practical limitations, namely low throughput caused by the limited imaging range and slow imaging speed. To address these challenges, we developed an imaging system based on a line image sensor for rapid and wide-field imaging compared to existing colony imaging methods. This system can image a standard Petri dish (92 mm in diameter) completely within 22 s, successfully acquiring bacterial microcolony images. This process yielded a set of discrimination parameters termed as colony fingerprints, which were employed for machine learning. We demonstrated the performance of our system by identifying Staphylococcus aureus in food products using a machine learning model trained on a colony fingerprint dataset of 15 species from 9 genera, including foodborne pathogens. While conventional mass spectrometry-based methods require 24 h of incubation, our colony fingerprinting approach achieved 96% accuracy in just 10 h of incubation. Line image sensor offer high imaging speeds and scalability, allowing for swift and straightforward microbiological testing, eliminating the need for specialized expertise and overcoming the limitations of conventional methods. This innovation marks a transformative shift in industrial applications.
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Affiliation(s)
- Hikaru Tago
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan; Institute of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hiroya Kohketsu
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tae-Kyu Lim
- Malcom Co., Ltd., 4-15-10, Honmachi, Shibuya-ku, Tokyo, 151-0071, Japan
| | - Manabu Harada
- Malcom Co., Ltd., 4-15-10, Honmachi, Shibuya-ku, Tokyo, 151-0071, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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Pham ML, Van Horn K, Zarate E, Pickering E, Murphy C, Bryant K. A multicenter evaluation of Copan's Colibrí™, an automated instrument for MALDI TOF MS target application for bacterial identification. Diagn Microbiol Infect Dis 2024; 108:116098. [PMID: 37890307 DOI: 10.1016/j.diagmicrobio.2023.116098] [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: 07/20/2023] [Revised: 08/24/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023]
Abstract
The Colibrí™ is a new instrument that automates picking and placement of colonies on target plates for MALDI identification. This study compared the performance of the Colibrí™ to standard manual spotting using the VITEK® MS for bacterial identification. Colonies were selected from cultures of urine, wound, respiratory, and positive blood cultures. The Colibrí™ sampled the colonies, transferred them to a MALDI target slide, and overlayed each spot with matrix. Manual spotting was then performed using the same or similar colonies. A total of 444 bacteria were compared. Identification was achieved with both methods for 432 organisms with only 2 discrepant results, overall agreement of 99.54%. Twelve organisms (2.70%) gave no identification using Colibrí™. The Colibrí™ provides automation to a manual process with a high accuracy. Use of the Colibrí™ instrumentation provides an opportunity to reallocate technologist time to more complicated tasks and provides complete traceability from plating to organism identification.
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Affiliation(s)
- My Lien Pham
- Kaiser Permanente, Southern California Permanente Medical Group, Regional Reference Laboratories, Chino Hills, CA, USA
| | - Kenneth Van Horn
- Kaiser Permanente, Southern California Permanente Medical Group, Regional Reference Laboratories, Chino Hills, CA, USA.
| | | | | | | | - Kendall Bryant
- Kaiser Permanente, Airport Way Regional Laboratory, Portland, OR, USA
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Sulaiman IM, Miranda N, Hook W, Mendoza J, Kumfert Q, Barnes T, Sung K, Khan S, Nawaz M, Banerjee P, Simpson S, Karem K. A Single-Laboratory Performance Evaluation of MALDI-TOF MS in Rapid Identification of Staphylococcus aureus, Cronobacter sakazakii, Vibrio parahaemolyticus, and Some Closely Related Bacterial Species of Public Health Importance. J AOAC Int 2023; 106:1574-1588. [PMID: 37725340 DOI: 10.1093/jaoacint/qsad109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Staphylococcus is a genus of Gram-positive bacteria, known to cause food poisoning and gastrointestinal illness in humans. Additionally, the emergence of methicillin-resistant S. aureus (MRSA) strains has caused a major health care burden worldwide. Cronobacter is a group of Gram-negative bacteria that can survive in extreme dry conditions. Cronobacter sakazakii is known to contaminate powdered infant formula and cause life-threatening infections in neonates. Vibrio is a genus of human-pathogenic Gram-negative bacteria that can cause foodborne illness by consuming undercooked or raw seafood. Vibrio parahaemolyticus can cause serious gastrointestinal disease in humans. Thus, rapid identification of Staphylococcus spp., Cronobacter spp., and Vibrio spp. is crucial for the source tracking of contaminated food, as well as to measure the transmission dynamics of these bacterial pathogens causing foodborne diseases and outbreaks. OBJECTIVE This single-laboratory performance evaluation study used the VITEK MS system to evaluate the potential of MALDI-TOF MS technology for rapid identification of S. aureus-like, C. sakazakii-like, and V. parahaemolyticus-like isolates of public health importance. METHOD A total of 226 isolates recovered from various food, environmental surveillance samples, and other sources were identified by bioMérieux VITEK 2 and VITEK MS systems as Staphylococcus spp., Cronobacter spp., and Vibrio spp. Five American Type Culture Collection (ATCC) reference Gram-positive and Gram-negative bacterial isolates were also tested to complete the study. In addition, for some Staphylococcus spp. isolates, whole genome sequencing (WGS) and DNA sequencing of 16S rRNA partial region were also performed for species identification. RESULTS The VITEK MS system was able to provide species identification to all 96 isolates of Staphylococcus spp. and to all 29 isolates of Vibrio spp. examined with a high confidence value (99.9%). Similarly, species identification was observed for the majority of spots (245 of 303) for the 101 Cronobacter spp. isolates (∼82.0%) with a high confidence value (99.9%), and genus level identification was noticed for the rest of the Cronobacter spp. isolates (18.0%; 58 of the 303 spots) analyzed. Species identification data generated by VITEK 2 system were comparable to data obtained by the VITEK MS system. CONCLUSIONS The VITEK MS system is a reliable high-throughput platform that can rapidly identify Staphylococcus, Vibrio, and Cronobacter to the genus level, as well as S. aureus, C. sakazakii, V. parahaemolyticus, and other closely related foodborne isolates and bacterial isolates from additional sources, in most cases. HIGHLIGHTS The VITEK MS system can be used in the rapid genus and species identification of human-pathogenic Staphylococcus spp., Cronobacter spp., and Vibrio spp. isolates.
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Affiliation(s)
- Irshad M Sulaiman
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Nancy Miranda
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Whitney Hook
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Joseph Mendoza
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Quincy Kumfert
- University of California, 1 Shields Avenue, Davis, CA 95616, USA
| | - Tamayo Barnes
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Kidon Sung
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Saeed Khan
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Mohamed Nawaz
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Pratik Banerjee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302 W. Pennsylvania Avenue, Urbana, IL 61801, USA
| | - Steven Simpson
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
| | - Kevin Karem
- Microbiological Sciences Branch, Atlanta Human and Animal Food Laboratory, Office of Regulatory Science, Office of Regulatory Affairs, U.S. Food and Drug Administration, 60 Eighth Street NE, Atlanta, GA 30309, USA
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Putnam NE, Youn JH, Wallace MA, Luethy PM, Burnham CAD, Butler-Wu S, Dekker JP, Lau AF. Comparative Evaluation of Current Biochemical-, Sequencing-, and Proteomic-Based Identification Methods for the Streptococcus bovis Group. J Clin Microbiol 2023; 61:e0171222. [PMID: 36912659 PMCID: PMC10117079 DOI: 10.1128/jcm.01712-22] [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: 11/18/2022] [Accepted: 02/05/2023] [Indexed: 03/14/2023] Open
Abstract
The Streptococcus bovis group (previously group D streptococci) consists of seven distinct species and subspecies. Definitive identification within the group is important, as certain organisms have been associated with gastrointestinal carcinoma, bacteremia, infective endocarditis, meningitis, biliary tract disease, and carcinoma, among others. Definitive identification, however, remains elusive due to limitations and inconsistencies across commonly used identification platforms in the United States. Here, we compared the performance of standard biochemical (Trek Gram-positive identification [GPID] plate, Vitek 2 GPID), sequencing (16S rDNA, sodA) databases (NCBI, RDP, CDC MicrobeNet), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) platforms (Vitek MS, Bruker Biotyper MS) using a set of eight type strains representing all seven strains within the S. bovis group. Despite the evaluation of contemporary methods, no single platform was able to definitively identify all type strains within the S. bovis group. Vitek MS (85.7%, 7/8) provided the most accurate definitive identifications, followed by sodA sequencing (75%, 6/8). Vitek 2 and Bruker Biotyper RUO platforms performed the next best (62.5%, 5/8). All remaining platforms failed to adequately differentiate type strains within the S. bovis group (range, 0 to 37.5%). Laboratorians and clinicians should be aware of the identification limitations of routine testing algorithms and incorporate reflex testing, when appropriate, to platforms such as Vitek MS and/or sodA sequencing that are more able to definitively identify S. bovis group organisms. Further clinical evaluation was conducted using 65 clinical isolates from three geographically distinct U.S. institutions. Future improvements in identification platforms may reveal new clinical and epidemiological trends for members of the S. bovis group.
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Affiliation(s)
- Nicole E. Putnam
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jung-Ho Youn
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Paul M. Luethy
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Susan Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - John P. Dekker
- Clinical Microbiology, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anna F. Lau
- Sterility Testing Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Zhang XD, Gu B, Usman M, Tang JW, Li ZK, Zhang XQ, Yan JW, Wang L. Recent Progress in the Diagnosis of Staphylococcus in Clinical Settings. Infect Dis (Lond) 2022. [DOI: 10.5772/intechopen.108524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Staphylococci are mainly found on the skin or in the nose. These bacteria are typically friendly, causing no harm to healthy individuals or resulting in only minor issues that can go away on their own. However, under certain circumstances, staphylococcal bacteria could invade the bloodstream, affect the entire body, and lead to life-threatening problems like septic shock. In addition, antibiotic-resistant Staphylococcus is another issue because of its difficulty in the treatment of infections, such as the notorious methicillin-resistant Staphylococcus aureus (MRSA) which is resistant to most of the currently known antibiotics. Therefore, rapid and accurate diagnosis of Staphylococcus and characterization of the antibiotic resistance profiles are essential in clinical settings for efficient prevention, control, and treatment of the bacteria. This chapter highlights recent advances in the diagnosis of Staphylococci in clinical settings with a focus on the advanced technique of surface-enhanced Raman spectroscopy (SERS), which will provide a framework for the real-world applications of novel diagnostic techniques in medical laboratories via bench-top instruments and at the bedside through point-of-care devices.
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Osek J, Lachtara B, Wieczorek K. Listeria monocytogenes in foods-From culture identification to whole-genome characteristics. Food Sci Nutr 2022; 10:2825-2854. [PMID: 36171778 PMCID: PMC9469866 DOI: 10.1002/fsn3.2910] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
Listeria monocytogenes is an important foodborne pathogen, which is able to persist in the food production environments. The presence of these bacteria in different niches makes them a potential threat for public health. In the present review, the current information on the classical and alternative methods used for isolation and identification of L. monocytogenes in food have been described. Although these techniques are usually simple, standardized, inexpensive, and are routinely used in many food testing laboratories, several alternative molecular-based approaches for the bacteria detection in food and food production environments have been developed. They are characterized by the high sample throughput, a short time of analysis, and cost-effectiveness. However, these methods are important for the routine testing toward the presence and number of L. monocytogenes, but are not suitable for characteristics and typing of the bacterial isolates, which are crucial in the study of listeriosis infections. For these purposes, novel approaches, with a high discriminatory power to genetically distinguish the strains during epidemiological studies, have been developed, e.g., whole-genome sequence-based techniques such as NGS which provide an opportunity to perform comparison between strains of the same species. In the present review, we have shown a short description of the principles of microbiological, alternative, and modern methods of detection of L. monocytogenes in foods and characterization of the isolates for epidemiological purposes. According to our knowledge, similar comprehensive papers on such subject have not been recently published, and we hope that the current review may be interesting for research communities.
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Affiliation(s)
- Jacek Osek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Beata Lachtara
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
| | - Kinga Wieczorek
- Department of Hygiene of Food of Animal OriginNational Veterinary Research InstitutePuławyPoland
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Thomas TSM, Thomas J, le Roux K, Duze ST, Mkhwanazi F, Duse A. Diagnostic challenges with accurate identification of Listeria monocytogenes isolates from food and environmental samples in South Africa. Afr J Lab Med 2022; 11:1482. [PMID: 35747557 PMCID: PMC9210167 DOI: 10.4102/ajlm.v11i1.1482] [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: 12/02/2020] [Accepted: 02/11/2022] [Indexed: 11/01/2022] Open
Abstract
Background: The 2017–2018 listeriosis outbreak in South Africa warranted testing for Listeria monocytogenes in food products and processing environments. Diagnostic tests are needed to accurately differentiate L. monocytogenes from other Listeria species.Objective: The study assessed the performance of the commonly used tests in our setting to accurately identify L. monocytogenes.Methods: The study was conducted in a public health laboratory in South Africa. Cultured isolates from food and environmental samples were tested both prospectively and retrospectively between August 2018 and December 2018. Isolates were phenotypically identified using tests for detecting β-haemolysis, Christie-Atkins-Munch-Peterson, alanine arylamidase (AlaA), mannosidase, and xylose fermentation. Listeria monocytogenes isolates were identified using automated systems, Microscan Walkaway Plus 96, Vitek® MS, Vitek® 2 and Surefast Listeria monocytogenes PLUS PCR. All results were compared to whole-genome sequencing results.Results: β-haemolysis and Christie-Atkins-Munch-Peterson tests gave delayed positivity or were negative for L. monocytogenes and falsely positive for one strain of Listeria innocua. The AlaA enzyme and Colorex Listeria agar lacked specificity for L. monocytogenes identification. Based on a few phenotypic test results, an aberrant L. monocytogenes strain and Listeria seeligeri strain were reported. All automated platforms overcalled L. monocytogenes in place of other Listeria species.Conclusion: No test was ideal in differentiating Listeria species. This is an issue in resource-limited settings where these tests are currently used. Newer technologies based on enzyme-linked immunosorbent assay and other molecular techniques specific to L. monocytogenes detection need to be investigated.
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Affiliation(s)
- Teena S M Thomas
- Infection Control Services Laboratory, National Health Laboratory Services, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Disease, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Karren le Roux
- Infection Control Services Laboratory, National Health Laboratory Services, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Disease, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sanelisiwe T Duze
- Department of Clinical Microbiology and Infectious Disease, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Faith Mkhwanazi
- Infection Control Services Laboratory, National Health Laboratory Services, Johannesburg, South Africa
| | - Adriano Duse
- Infection Control Services Laboratory, National Health Laboratory Services, Johannesburg, South Africa
- Department of Clinical Microbiology and Infectious Disease, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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Accurate classification of Listeria species by MALDI-TOF mass spectrometry incorporating denoising autoencoder and machine learning. J Microbiol Methods 2021; 192:106378. [PMID: 34818574 DOI: 10.1016/j.mimet.2021.106378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 11/21/2022]
Abstract
Listeria monocytogenes belongs to the category of facultative anaerobic bacteria, and is the pathogen of listeriosis, potentially lethal disease for humans. There are many similarities between L. monocytogenes and other non-pathogenic Listeria species, which causes great difficulties for their correct identification. The level of L. monocytogenes contamination in food remains high according to statistics from the Food and Drug Administration. This situation leads to food recall and destruction, which has caused huge economic losses to the food industry. Therefore, the identification of Listeria species is very important for clinical treatment and food safety. This work aims to explore an efficient classification algorithm which could easily and reliably distinguish Listeria species. We attempted to classify Listeria species by incorporating denoising autoencoder (DAE) and machine learning algorithms in matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). In addition, convolutional neural networks were used to map the high dimensional original mass spectrometry data to low dimensional core features. By analyzing MALDI-TOF MS data via incorporating DAE and support vector machine (SVM), the identification accuracy of Listeria species was 100%. The proposed classification algorithm is fast (range of seconds), easy to handle, and, more importantly, this method also allows for extending the identification scope of bacteria. The DAE model used in our research is an effective tool for the extraction of MALDI-TOF mass spectrometry features. Despite the fact that the MALDI-TOF MS dataset examined in our research had high dimensionality, the DAE + SVM algorithm was still able to exploit the hidden information embedded in the original MALDI-TOF mass spectra. The experimental results in our work demonstrated that MALDI-TOF mass spectrum combined with DAE + SVM could easily and reliably distinguish Listeria species.
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Pastoshchuk A, Yumyna Y, Zelena P, Nudha V, Yanovska V, Kovalenko M, Taran N, Patyka V, Skivka L. Beneficial traits of grain-residing endophytic communities in wheat with different sensitivity to Pseudomonas syringae. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Deep insight into compositional and functional features of endophytic bacterial communities residing in wheat grains opens the way to the use of their plant growth promoting and biocontrol abilities in agricultural biotechnology. The aim of this work was to compare grain-residing endophytes from winter wheat varieties with different sensitivity to Pseudomonas syringae pv. atrofaciens (McCulloch) and to examine their plant-beneficial traits and antagonistic effects. Grain-residing bacteria were isolated from surface-sterilized grains of three wheat varieties sown in Ukraine following a culture-dependent protocol, and were screened for their plant growth promotion (PGP) and antagonistic properties. Bacterial morphotypes were represented by gram-negative rods, endospore-forming bacilli and gram-positive cocci. Different resistance to phytopathogenic pseudomonads was associated with distinctive quantitative and functional features of grain-residing endophytic communities. High resistance to P. syringae was coupled with the prevalence of gram-negative rods in the endophytic community, the highest proportion of endophytic bacteria possessing three PGP activities (phosphate solubilization, nitrogen fixation and production of indolic compounds) simultaneously, and with the most potent antagonistic activity of grain-residing endospore-forming bacilli. In total, five grain-residing isolates, which were obtained from three wheat varieties (two isolates from varieties with medium and high resistance and one – from a low-resistant variety), demonstrated ability to restrain P. syringae pv. atrofaciens (McCulloch) growth. Two isolates (P6 and P10) which were obtained from the high-resistant wheat variety Podolyanka and were assigned to Paenibacillus and Brevibacillus genera according to their biochemical profiling and MS-DS identification, showed the most potent antagonistic effects as indicated by maximum inhibition zone in agar well diffusion assay. These results shed light on the association of the features of grain-residing endophytic bacteria with wheat resistance to phytopathogenic pseudomonads. Isolates from the high-resistant wheat variety can be recommended for grain dressing as plant growth promoting and biocontrol agents for P. syringae pv. atrofaciens (McCulloch).
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Survey of plant growth promoting and antagonistic traits in winter wheat grain endophytic bacteria. EUREKA: LIFE SCIENCES 2021. [DOI: 10.21303/2504-5695.2021.001978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of this work was to isolate endophytic bacteria from wheat grains and to evaluate their plant growth promoting traits (PGPT) as well as an inhibitory effect on P. syringae pv. atrofaciens (McCulloch) growth. Endophytic bacteria were isolated by a culture-dependent protocol from the grains of winter wheat variety of Ukrainian selection Podolyanka with high resistance to syringae. Totally 2.7±0.09 CFU/1 g of dry wheat grain were isolated, ten cultivable bacterial isolates were obtained. Spore-forming bacilli predominated in the wheat grain endophytic community. Gram-negative fermenting and non-fermenting rod-shaped bacteria and Gram-positive cocci were also present. Seven out of ten isolates possessed numerous plant growth promoting traits including phosphate solubilization, oligonitrotrophy, and indolic compound producing. Two isolates possessed antagoniscic activity against syringae in vitro along with plant growth promoting features. According to biochemical profiling and mass-spectrophotometric identification, these two isolates were assigned to Paenibacillus and Brevibacillus genera. These endophytic bacteria can be considered as promising objects for agrobiotechnology. However, more research is needed to confirm their biotechnological potential in planta experiments
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Chen XF, Hou X, Xiao M, Zhang L, Cheng JW, Zhou ML, Huang JJ, Zhang JJ, Xu YC, Hsueh PR. Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review. Microorganisms 2021; 9:microorganisms9071536. [PMID: 34361971 PMCID: PMC8304613 DOI: 10.3390/microorganisms9071536] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/03/2021] [Accepted: 07/10/2021] [Indexed: 12/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.
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Affiliation(s)
- Xin-Fei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Xin Hou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Wei Cheng
- Center of Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing 100053, China;
| | - Meng-Lan Zhou
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jing Huang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Jing-Jia Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
| | - Ying-Chun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100730, China; (X.-F.C.); (X.H.); (M.X.); (L.Z.); (M.-L.Z.); (J.-J.H.); (J.-J.Z.)
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing 100730, China
- Correspondence: (Y.-C.X.); (P.-R.H.)
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung 40447, Taiwan;
- Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Correspondence: (Y.-C.X.); (P.-R.H.)
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Girard V, Monnin V, Giraud D, Polsinelli S, Caillé M, Procop GW, Tuohy M, Wilson D, Richter SS, Kiss K, Clem K, Tolli N, Bridon L, Bradford C, Blamey S, Li J, Pincus DH. Multicenter evaluation of the VITEK MS matrix-assisted laser desorption/ionization-time of flight mass spectrometry system for identification of bacteria, including Brucella, and yeasts. Eur J Clin Microbiol Infect Dis 2021; 40:1909-1917. [PMID: 33837878 DOI: 10.1007/s10096-021-04242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has proven to be rapid and accurate for the majority of clinical isolates. Some gaps remain concerning rare, emerging, or highly pathogenic species, showing the need to continuously expand the databases. In this multicenter study, we evaluated the accuracy of the VITEK MS v3.2 database in identifying 1172 unique isolates compared to identification by DNA sequence analysis. A total of 93.6% of the isolates were identified to species or group/complex level. A remaining 5.2% of the isolates were identified to the genus level. Forty tests gave a result of no identification (0.9%) and 12 tests (0.3%) gave a discordant identification compared to the reference identification. VITEK MS is also the first MALDI-TOF MS system that is able to delineate the four members of the Acinetobacter baumannii complex at species level without any specific protocol or special analysis method. These findings demonstrate that the VITEK MS v3.2 database is highly accurate for the identification of bacteria and fungi encountered in the clinical laboratory as well as emerging species like Candida auris and the highly pathogenic Brucella species.
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Affiliation(s)
- Victoria Girard
- R&D Microbiology, bioMérieux sa, La Balme les Grottes, France.
| | - Valérie Monnin
- R&D Microbiology, bioMérieux sa, La Balme les Grottes, France
| | - Delphine Giraud
- R&D Microbiology, bioMérieux sa, La Balme les Grottes, France
| | | | - Marion Caillé
- R&D Microbiology, bioMérieux sa, La Balme les Grottes, France.,MSD, Clermont-Ferrand, France
| | - Gary W Procop
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Marion Tuohy
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Deborah Wilson
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Sandra S Richter
- Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.,Medical Affairs, bioMérieux, Inc., Durham, NC, USA
| | | | | | | | | | | | - Sara Blamey
- Clinical Affairs, bioMérieux, Inc., St. Louis, MO, USA
| | - Jay Li
- R&D US Data Science, bioMérieux, Inc., Durham, NC, USA
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15
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Jain D, Torres R, Celli R, Koelmel J, Charkoftaki G, Vasiliou V. Evolution of the liver biopsy and its future. Transl Gastroenterol Hepatol 2021; 6:20. [PMID: 33824924 PMCID: PMC7829074 DOI: 10.21037/tgh.2020.04.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
Liver biopsies are commonly used to evaluate a wide variety of medical disorders, including neoplasms and post-transplant complications. However, its use is being impacted by improved clinical diagnosis of disorders, and non-invasive methods for evaluating liver tissue and as a result the indications of a liver biopsy have undergone major changes in the last decade. The evolution of highly effective treatments for some of the common indications for liver biopsy in the last decade (e.g., viral hepatitis B and C) has led to a decline in the number of liver biopsies in recent years. At the same time, the emergence of better technologies for histologic evaluation, tissue content analysis and genomics are among the many new and exciting developments in the field that hold great promise for the future and are going to shape the indications for a liver biopsy in the future. Recent advances in slide scanners now allow creation of "digital/virtual" slides that have image of the entire tissue section present in a slide [whole slide imaging (WSI)]. WSI can now be done very rapidly and at very high resolution, allowing its use in routine clinical practice. In addition, a variety of technologies have been developed in recent years that use different light sources and/or microscopes allowing visualization of tissues in a completely different way. One such technique that is applicable to liver specimens combines multiphoton microscopy (MPM) with advanced clearing and fluorescent stains known as Clearing Histology with MultiPhoton Microscopy (CHiMP). Although it has not yet been extensively validated, the technique has the potential to decrease inefficiency, reduce artifacts, and increase data while being readily integrable into clinical workflows. Another technology that can provide rapid and in-depth characterization of thousands of molecules in a tissue sample, including liver tissues, is matrix assisted laser desorption/ionization (MALDI) mass spectrometry. MALDI has already been applied in a clinical research setting with promising diagnostic and prognostic capabilities, as well as being able to elucidate mechanisms of liver diseases that may be targeted for the development of new therapies. The logical next step in huge data sets obtained from such advanced analysis of liver tissues is the application of machine learning (ML) algorithms and application of artificial intelligence (AI), for automated generation of diagnoses and prognoses. This review discusses the evolving role of liver biopsies in clinical practice over the decades, and describes newer technologies that are likely to have a significant impact on how they will be used in the future.
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Affiliation(s)
- Dhanpat Jain
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Torres
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Romulo Celli
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeremy Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
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16
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Uchida-Fujii E, Niwa H, Kinoshita Y, Nukada T. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) for Identification of Bacterial Isolates From Horses. J Equine Vet Sci 2020; 95:103276. [PMID: 33276932 DOI: 10.1016/j.jevs.2020.103276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/17/2022]
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is used for bacterial identification by analyzing the spectra of isolates and comparing them against a database of reference spectra; it is known for its rapidity and accuracy. Although MALDI-TOF MS is used for identification of bacterial isolates from animals, not all animal pathogens are identified correctly. In this study, we used a commercial MALDI-TOF MS identification system to examine 3724 bacterial isolates from horses and their environments. Isolates that could not be identified with MALDI-TOF MS were identified by 16S rRNA gene sequence taxonomic analysis. MALDI-TOF MS could identify 86.2% of the isolates from horses to the species level, showing that this method could be successfully applied for bacterial identification in horses. However, some species known to be equine pathogenic agents including Taylorella equigenitalis and Rhodococcus equi were difficult to identify with MALDI-TOF MS, which might be the result of an inadequate reference database. Some Prevotella, Staphylococcus, and Streptococcus isolates, which could not be identified with either MALDI-TOF MS or 16S rRNA gene sequencing analysis, formed clusters in the 16S rRNA phylogenic tree, and might be unknown species isolated from horses. Adding the spectra of isolates identified in this study to an in-house database might make MALDI-TOF MS a more useful tool for identifying equine isolates.
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Affiliation(s)
- Eri Uchida-Fujii
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan.
| | - Hidekazu Niwa
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Yuta Kinoshita
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
| | - Toshio Nukada
- Microbiology Division, Equine Research Institute, Japan Racing Association, Shimotsuke, Tochigi, Japan
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17
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Alnakip MEA, Rhouma NR, Abd-Elfatah EN, Quintela-Baluja M, Böhme K, Fernández-No I, Bayoumi MA, Abdelhafez MM, Taboada-Rodríguez A, Calo-Mata P, Barros-Velázquez J. Discrimination of major and minor streptococci incriminated in bovine mastitis by MALDI-TOF MS fingerprinting and 16S rRNA gene sequencing. Res Vet Sci 2020; 132:426-438. [PMID: 32777539 DOI: 10.1016/j.rvsc.2020.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/13/2020] [Accepted: 07/30/2020] [Indexed: 02/05/2023]
Abstract
The current work investigated the discriminatory potential of MALDI-TOF MS fingerprinting towards most-relevant major (Streptococcus agalactiae, S. dysgalactiae, S. uberis) and minor (S. canis, S. parauberis, S. salivarius, S. equinus and S. gallolyticus) streptococci involved in bovine mastitis (BM), in comparison to 16S rRNA gene sequencing (GS)-based identification. The MALDI-TOF MS-generated spectral fingerprints were recruited for eliciting a detailed proteomic map that demonstrated clear variability for inter- and intra-species-specific biomarkers. Besides, a phyloproteomic dendrogram was evolved and comparatively analyzed against the phylogenetic one obtained from 16S rRNA GS in order to assess the differentiation of streptococci of bovine origin based on variability of protein fingerprints versus the variation of 16S rRNA gene homology. Results showed that the discrimination of BM-implicated streptococci can be obtained by both approaches; however MALDI-TOF MS was superior, achieving more variability at both intra- and sub-species levels. MALDI-TOF MS spectral analytics revealed that Streptococcus spp. exhibited three genus-specific biomarkers (peaks with m/z values at 2112, 4452 and 5955) and all streptococci exhibited spectral variability at both species and subspecies levels. Remarkably, MALDI-TOF MS fingerprinting was found to be at least as robust as 16S rRNA GS-based identification, allowing much cheaper and faster analysis, and additionally exhibiting high reliability for characterization of BM-implicated streptococci, thus proving to be a powerful tool that can be used independently within dairy diagnostics.
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Affiliation(s)
- Mohamed E A Alnakip
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain; Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Nasreddin R Rhouma
- Department of Biology, Faculty of Science, Misurata University, Libya; Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Eman N Abd-Elfatah
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Marcos Quintela-Baluja
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Inmaculada Fernández-No
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - Mohmaed A Bayoumi
- Department of Food Control, Faculty of Veterinary Medicine, Zagazig University, 44519, Egypt
| | - Mostafa M Abdelhafez
- Department of Food science and Technology, Faculty of Agriculture, Misurata University, Libya
| | - Amaury Taboada-Rodríguez
- Food Biotechnology Group, Department of Nutrition and Food Science, Faculty of Veterinary Sciences, Murcia university, Campus Espinardo, 30100 Murcia, Spain
| | - Pillar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain
| | - J Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences/College of Biotechnology, University of Santiago de Compostela, Rúa Carballo Calero s/n, Campus Lugo, E-27002 Lugo, Spain.
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18
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Velichko NV, Pinevich AV. Classification and Identification Tasks in Microbiology: Mass Spectrometric Methods Coming to the Aid. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719050151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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19
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Pinheiro D, Monteiro C, Faria MA, Pinto E. Vitek ® MS v3.0 System in the Identification of Filamentous Fungi. Mycopathologia 2019; 184:645-651. [PMID: 31506883 DOI: 10.1007/s11046-019-00377-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/21/2019] [Indexed: 12/19/2022]
Abstract
Infections caused by filamentous fungi are rising in incidence and became a serious health concern. Their rapid and reliable identification in the clinical laboratory is essential for an early and accurate diagnosis to guide timely therapy. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a rapid and reliable method for identification of bacteria and yeasts isolated from clinical samples. However, it has less used for molds identification. The aim of this study was to evaluate Vitek® MS (a MALDI-TOF MS system) ability to identify molds and differentiate species within a complex. A collection of 90 filamentous fungi, 70 clinical and 20 environmental isolates, was studied by morphological and molecular methods and by Vitek® MS. Seventy-four isolates (82.2%) were identified using Vitek® MS v3.0 at Genus/Complex/Species group level; within these, 47/74 (63.5%) were correctly identified at species level and only one was misidentified. In contrast, 16/90 isolates (17.8%) were not identified, of which 13 were not present in the database. Results here expressed favor Vitek® MS v3.0 as a very useful system for identification of most common clinical isolates of filamentous fungi. Accordingly, it may be an important tool for clinical microbiology laboratories in their task to answer to clinicians, adequately and rapidly, helping in proper patient's management.
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Affiliation(s)
- Dolores Pinheiro
- Laboratory of Microbiology, Service of Clinical Pathology, Centro Hospitalar Universitário de S. João, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal.
| | - Carolina Monteiro
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Miguel A Faria
- LAQV-REQUIMTE, Laboratory of Bromatology and Hydrology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Eugénia Pinto
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
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20
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Brown-Elliott BA, Fritsche TR, Olson BJ, Vasireddy S, Vasireddy R, Iakhiaeva E, Alame D, Wallace RJ, Branda JA. Comparison of Two Commercial Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of Nontuberculous Mycobacteria. Am J Clin Pathol 2019; 152:527-536. [PMID: 31314059 PMCID: PMC6733354 DOI: 10.1093/ajcp/aqz073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES This multicenter study's aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM). METHODS NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database. RESULTS Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system. CONCLUSIONS Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.
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Affiliation(s)
| | - Thomas R Fritsche
- Marshfield Clinic Health System, Marshfield, WI
- University of Wisconsin, La Crosse
| | | | | | | | | | - Diana Alame
- Thomas Jefferson University, Philadelphia, PA
| | | | - John A Branda
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, MA
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21
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Li J, Hu W, Li M, Deng S, Huang Q, Lu W. Evaluation of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for identifying VIM- and SPM-type metallo-β-lactamase-producing Pseudomonas aeruginosa clinical isolates. Infect Drug Resist 2019; 12:2781-2788. [PMID: 31564928 PMCID: PMC6735624 DOI: 10.2147/idr.s211984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/07/2019] [Indexed: 01/25/2023] Open
Abstract
Background Metallo-β-lactamase-producing Pseudomonas aeruginosa (MBL-PA) are important causative agents of nosocomial infections and are associated with significant mortality rates, especially in intensive care units. The timely detection and typing of these strains is essential for surveillance, outbreak prevention and antibiotic therapy optimization. In this study, fifteen VIM-type and fifteen SPM-type MBL-PA strains were selected as strains to establish MALDI-TOF MS SuperSpectra. Methods This study was undertaken to evaluate the utility of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with the VITEK MS plus system in the detection of VIM- and SPM-type MBL-PA isolates. For each species, we increased the reference spectra, and then, a SuperSpectrum was created based on the selection of 39 specific masses. In a second step, we validated the SuperSpectra with the remaining 50 isolates (25 isolates of VIM-type and 25 isolates of SPM-type). Results Fifty MBL-PA strains were used as the validation strains, including twenty-five VIM-type and twenty-five SPM-type MBL-PA strains. Complete antimicrobial susceptibility testing and genotypic characterizations were performed for all isolates, which were subsequently identified using the newly created SuperSpectra databases following a previously reported method. The results showed that there was 92% agreement between the MBL profile generated by MALDI-TOF MS and that obtained using gene sequencing analysis methods. Conclusion MALDI-TOF MS is a promising, rapid and economical method for detecting VIM- or SPM-type MBL-PA that could be successfully introduced into the routine diagnostic workflow of clinical microbiology laboratories.
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Affiliation(s)
- Jin Li
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, People's Republic of China
| | - Weiwei Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, People's Republic of China
| | - Min Li
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, People's Republic of China
| | - Shaoli Deng
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, People's Republic of China
| | - Qing Huang
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, People's Republic of China
| | - Weiping Lu
- Department of Clinical Laboratory Medicine, Institute of Surgery Research, Daping Hospital, Army Medical University, Chongqing 400042, People's Republic of China
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22
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Huber CA, Pflüger V, Reed S, Cottrell K, Sidjabat HE, Ranasinghe A, Zowawi HM, Harris P, Paterson DL. Bacterial identification using a SCIEX 5800 TOF/TOF MALDI research instrument and an external database. J Microbiol Methods 2019; 164:105685. [PMID: 31400360 DOI: 10.1016/j.mimet.2019.105685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/03/2019] [Accepted: 08/03/2019] [Indexed: 10/26/2022]
Abstract
In our current study we were identifying 26 bacterial isolates using a SCIEX 5800 TOF/TOF MALDI instrument and an external database. The results were compared with the results of a Vitek® MS system and in case of discrepancies at the species level 16s rRNA sequencing was performed for further verification.
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Affiliation(s)
- Charlotte A Huber
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia.
| | | | - Sarah Reed
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Kyra Cottrell
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Hanna E Sidjabat
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Ama Ranasinghe
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - Hosam M Zowawi
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia; College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia; World Health Organization Collaborating Centre for Infection Prevention and Control, Riyadh, Saudi Arabia
| | - Patrick Harris
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
| | - David L Paterson
- The University of Queensland, UQ Centre for Clinical Research, Herston, Queensland, Australia
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Efimov B, Chaplin A, Sokolova S, Chernaia Z, Pikina A, Savilova A, Kafarskaya L. Application of culture-based, mass spectrometry and molecular methods to the study of gut microbiota in children. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In recent decades, nucleic acid sequencing technologies used for metagenomic analysis have become the main methods for assessing the composition of microbiota. At the same time, the use of novel methods of cultivation and identification of microorganisms in microbiological research led to the renaissance of culture-based technologies, because facilitated the discovery and isolation of both new strains of well-known microorganisms as well as uncultivated and unexplored bacterial taxa. The aim of this study was to evaluate the potential of using the culture-based method for the assessment of the qualitative and quantitative composition of the intestinal microbiota in healthy children. Eleven growth media were inoculated with serial dilutions of stool samples in order to analyze the profile of dominant anaerobic bacteria, as well as aerobic bacteria and fungi in 20 healthy children aged 2–4 years. The identification of microorganisms was performed using MALDI TOF MS and 16S rRNA gene fragment sequencing were used. 1,819 isolated and identified strains belong to 7 phyla, 13 classes, 18 orders, 33 families, 77 genera and 149 species in the Bacteria domain. The Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria phyla were most abundant and frequent. The greatest species diversity (more than 85 species) was found in the Firmicutes phylum. Ten new previously uncharacterized bacterial strains were isolated.
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Affiliation(s)
- B.A. Efimov
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.V. Chaplin
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - S.R. Sokolova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Z.A. Chernaia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.P. Pikina
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - A.M. Savilova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - L.I. Kafarskaya
- Pirogov Russian National Research Medical University, Moscow, Russia
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24
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Hou TY, Chiang-Ni C, Teng SH. Current status of MALDI-TOF mass spectrometry in clinical microbiology. J Food Drug Anal 2019; 27:404-414. [PMID: 30987712 PMCID: PMC9296205 DOI: 10.1016/j.jfda.2019.01.001] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and-positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance.
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Affiliation(s)
- Tsung-Yun Hou
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei,
Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei,
Taiwan
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei,
Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Shih-Hua Teng
- Bruker Taiwan Co., Ltd., Taipei,
Taiwan
- Corresponding author. 4F, 107 Yanshou Street, Songshan District, Taipei City 105, Taiwan. Fax: +886 2 2761 5335. E-mail address: (S.-H. Teng)
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Evaluation of Vitek MS for Differentiation of Cryptococcus neoformans and Cryptococcus gattii Genotypes. J Clin Microbiol 2019; 57:JCM.01282-18. [PMID: 30429250 DOI: 10.1128/jcm.01282-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Cryptococcus neoformans and Cryptococcus gattii are the main pathogenic species of invasive cryptococcosis among the Cryptococcus species. Taxonomic studies have shown that these two taxa have different genotypes or molecular types with biological and ecoepidemiological peculiarities. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been proposed as an alternative method for labor-intensive methods for C. neoformans and C. gattii genotype differentiation. However, Vitek MS, one of the commercial MALDI-TOF MS instruments, has not been yet been evaluated for this purpose. Thus, we constructed an in-house database with reference strains belonging to the different C. neoformans (VNI, VNII, VNIII, and VNIV) and C. gattii (VGI, VGII, VGIII, and VGIV) major molecular types by using the software Saramis Premium (bioMérieux, Marcy-l'Etoile, France). Then, this new database was evaluated for discrimination of the different genotypes. Our in-house database provided correct identification for all C. neoformans and C. gattii genotypes; however, due to the intergenotypic mass spectral similarities, a careful postanalytic evaluation is necessary to provide correct genotype identification.
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26
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MALDI Profiling and Applications in Medicine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:27-43. [DOI: 10.1007/978-3-030-15950-4_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Hogan PG, Mork RL, Boyle MG, Muenks CE, Morelli JJ, Thompson RM, Sullivan ML, Gehlert SJ, Merlo JR, McKenzie MG, Wardenburg JB, Rzhetsky A, Burnham CAD, Fritz SA. Interplay of personal, pet, and environmental colonization in households affected by community-associated methicillin-resistant Staphylococcus aureus. J Infect 2018; 78:200-207. [PMID: 30503843 DOI: 10.1016/j.jinf.2018.11.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 01/25/2023]
Abstract
OBJECTIVE We sought to determine the prevalence, molecular epidemiology, and factors associated with Staphylococcus aureus environmental surface and pet colonization in households of children with community-associated methicillin-resistant S. aureus (CA-MRSA) infection. METHODS Between 2012 and 2015, 150 children with CA-MRSA infections and their household contacts and pets were enrolled in this cross-sectional study in metropolitan Saint Louis, MO. Cultures to detect S. aureus were collected from 3 anatomic sites of household members, 2 dog/cat sites, and 21 environmental surfaces in each household. Molecular epidemiology of S. aureus isolates was determined via repetitive-sequence PCR. Generalized linear models were developed to identify factors associated with S. aureus/MRSA household contamination. RESULTS MRSA was recovered from environmental surfaces in 69 (46%) households (median 2 surfaces [range 1-18]). The enrollment infecting strain type was the most common strain recovered from the environment in most (64%) households. In generalized linear models, factors associated with a higher proportion of MRSA-contaminated environmental surfaces were household member MRSA colonization burden, MRSA as the dominant S. aureus strain colonizing household members, more strain types per household member, index case African-American race, and renting (vs. owning) the home. Of 132 pets, 14% were colonized with MRSA. Pets whose primary caretaker was MRSA-colonized were more likely to be MRSA-colonized than pets whose primary caretaker was not MRSA-colonized (50% vs. 4%, p < 0.001). CONCLUSIONS Household environments and pet dogs and cats serve as reservoirs of MRSA. Household member MRSA colonization burden predicts environmental MRSA contamination. Longitudinal studies will inform the directionality of household transmission.
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Affiliation(s)
- Patrick G Hogan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan L Mork
- Graduate Program in the Biophysical Sciences, University of Chicago, Chicago, IL, USA; Committee of Microbiology, University of Chicago, Chicago, IL, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Mary G Boyle
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Carol E Muenks
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - John J Morelli
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryley M Thompson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Melanie L Sullivan
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Sarah J Gehlert
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Jessica R Merlo
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Matt G McKenzie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Andrey Rzhetsky
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Carey-Ann D Burnham
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephanie A Fritz
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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Comparison of the Fully Automated FilmArray BCID Assay to a 4-Hour Culture Test Coupled to Mass Spectrometry for Day 0 Identification of Microorganisms in Positive Blood Cultures. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7013470. [PMID: 30584536 PMCID: PMC6280299 DOI: 10.1155/2018/7013470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 11/08/2018] [Indexed: 01/11/2023]
Abstract
Rapid bacterial identification of positive blood culture is important for adapting the antimicrobial therapy in patients with blood stream infection. The aim of this study was to evaluate the performance of the multiplex FilmArray Blood Culture Identification (BCID) assay by comparison to an in-house protocol based on MALDI-TOF MS identification of microcolonies after a 4-hour culture, for identifying on the same day the microorganisms present in positive blood culture bottles. One hundred and fifty-three positive bottles from 123 patients were tested prospectively by the 3 techniques of bacterial identification: 11 bottles yielding negative results by the 3 tests were considered false positive (7.2%). The reference MALDI-TOF MS technique identified 134 monomicrobial (87.6%) and 8 double infections (5.2%), which resulted in a total of 150 microorganisms. Globally, 137 (91.3%) of these 150 pathogens were correctly identified by the fully automated multiplex FilmArray BCID system at the species or genus level on day of growth detection, versus 117 (78.8%) by MALDI-TOF MS identification on nascent microcolonies after a 4-hour culture (P < 0.01). By combining the two approaches, 140 (93.5%) of the positive bottles were identified successfully at day 0. These results confirm the excellent sensitivity of the FilmArray BCID assay, notably in case of multimicrobial infection. Due to the limited number of targets included into the test, it must be coupled to another identification strategy, as that presented in this study relying on MALDI-TOF MS identification of microcolonies obtained after a very short culture period.
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29
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Hung WW, Chen YH, Tseng SP, Jao YT, Teng LJ, Hung WC. Using groEL as the target for identification of Enterococcus faecium clades and 7 clinically relevant Enterococcus species. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2018; 52:255-264. [PMID: 30473144 DOI: 10.1016/j.jmii.2018.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 11/27/2022]
Abstract
BACKGROUND/PURPOSE Accurate identification is important for effective treatment because Enterococcus species have talents to cope with various antibiotics either by intrinsic resistance or by acquisition of mobile genetic elements. The groEL gene is a permissive target in identification of bacteria. We aimed to develop simple assays based on groEL for identification of enterococci. RESULTS We continued our previous work and determined groEL gene sequences of Enterococcus species isolated from clinical specimens. Phylogenetic analysis based on groEL revealed that each strain clustered well with their reference strains (bootstrap value 100%), in which Enterococcusfaecium and Enterococcusgallinarum could be split into two clades. The divergence of E. faecium was coincident with hospital-associated clade, known as clade A, and community-associated clade, known as clade B. A PCR-restriction fragment length polymorphism (PCR-RFLP) assay was therefore designed to differentiate the two E. faecium clades, based on the specific RsaI cutting sites present in the two clades. To differentiate 7 clinical relevant Enterococcus species, the multiplex PCR assay was designed to identify Enterococcusavium, Enterococcuscasseliflavus, Enterococcusfaecalis, E. faecium, E. gallinarum, Enterococcushirae and Enterococcusraffinosus. Specificity was tested with other Enterococcus species including Enterococcuscecorum, Enterococcusdurans and Enterococcusmundtii. None of these bacterial species generated products of similar size to those of the seven Enterococcus species. CONCLUSION The simple PCR-RFLP and multiplex PCR assays on the basis of groEL gene provided an alternative way to identify Enterococcus species.
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Affiliation(s)
- Wei-Wen Hung
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Yen-Hsu Chen
- Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Sung-Pin Tseng
- Department of Medical Laboratory Science and Biotechnology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Ting Jao
- Infection Control Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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Performance of Vitek MS v3.0 for Identification of Mycobacterium Species from Patient Samples by Use of Automated Liquid Medium Systems. J Clin Microbiol 2018; 56:JCM.00219-18. [PMID: 29875193 DOI: 10.1128/jcm.00219-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/31/2018] [Indexed: 12/27/2022] Open
Abstract
The accuracy and robustness of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) system was evaluated by identifying mycobacteria from automated liquid-medium systems using patient samples. This is the first report to demonstrate that proteins within the liquid medium, its supplements, and decontamination reagents for nonsterile patient samples do not generate misidentification or false-positive results by use of the Vitek MS v3.0 system. Prior to testing with patient samples, a seeded-culture study was conducted to challenge the accuracy of the Vitek MS system at identifying mycobacteria from liquid medium by mimicking a clinical workflow. Seventy-seven Mycobacterium strains representing 21 species, seeded in simulated sputum, were decontaminated, inoculated into BacT/Alert MP liquid culture medium, incubated until positivity, and identified using the Vitek MS system. A total of 383 liquid cultures were tested, of which 379 (99%) were identified correctly to the species/complex/group level, 4 (1%) gave a "no-identification" result, and no misidentifications were observed. Following the simulated-sputum study, a total of 73 smear-positive liquid-medium cultures detected using BD BBL MGIT and VersaTREK Myco liquid media were identified by the Vitek MS system. Sixty-four cultures (87.7%) were correctly identified to the species/complex/group level; 7 (9.6%) resulted in no identification; and 2 (2.7%) were misidentified at the species level. These results indicate that the Vitek MS v3.0 system is an accurate tool for routine diagnostics of Mycobacterium species isolated from liquid cultures.
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Evaluation of the Vitek MS v3.0 Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry System for Identification of Mycobacterium and Nocardia Species. J Clin Microbiol 2018; 56:JCM.00237-18. [PMID: 29643203 DOI: 10.1128/jcm.00237-18] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/08/2018] [Indexed: 11/20/2022] Open
Abstract
This multicenter study was designed to assess the accuracy and reproducibility of the Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system for identification of Mycobacterium and Nocardia species compared to DNA sequencing. A total of 963 clinical isolates representing 51 taxa were evaluated. In all, 663 isolates were correctly identified to the species level (69%), with another 231 (24%) correctly identified to the complex or group level. Fifty-five isolates (6%) could not be identified despite repeat testing. All of the tuberculous mycobacteria (45/45; 100%) and most of the nontuberculous mycobacteria (569/606; 94%) were correctly identified at least to the group or complex level. However, not all species or subspecies within the M. tuberculosis, M. abscessus, and M. avium complexes and within the M. fortuitum and M. mucogenicum groups could be differentiated. Among the 312 Nocardia isolates tested, 236 (76%) were correctly identified to the species level, with an additional 44 (14%) correctly identified to the complex level. Species within the N. nova and N. transvalensis complexes could not always be differentiated. Eleven percent of the isolates (103/963) underwent repeat testing in order to get a final result. Identification of a representative set of Mycobacterium and Nocardia species was highly reproducible, with 297 of 300 (99%) replicates correctly identified using multiple kit lots, instruments, analysts, and sites. These findings demonstrate that the system is robust and has utility for the routine identification of mycobacteria and Nocardia in clinical practice.
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Stingu CS, Eschrich K, Thiel J, Borgmann T, Schaumann R, Rodloff AC. Identification of viridans streptococci With Matrix-Assisted Laser Desorption & Ionization Time-of-flight Mass Spectrometry by an In-house Method and a Commercially Available System. Ann Lab Med 2018. [PMID: 28643493 PMCID: PMC5500743 DOI: 10.3343/alm.2017.37.5.434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Two matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based methods were compared for their ability to identify viridans streptococci. One approach employed a reference database and software developed in-house. All inhouse measurements were performed using an Autoflex II Instrument (Bruker Daltonics GmbH, Germany). The other system, a VITEK-MS (BioMérieux, France) was operated on the commercially available V2.0 Knowledge Base for Clinical Use database. Clinical isolates of viridans streptococci (n=184) were examined. Discrepant results were resolved by 16S rDNA sequencing. Species-level identification percentages were compared by a chi-square test. The in-house method correctly identified 179 (97%) and 175 (95%) isolates to the group and species level respectively. In comparison, the VITEK-MS system correctly identified 145 (79%) isolates to the group and species level. The difference between the two methods was statistically significant at both group and species levels. Using the Autoflex II instrument combined with an extraction method instead of whole cell analysis resulted in more reliable viridans streptococci identification. Our results suggest that combining extraction with powerful analysis software and the careful choice of well-identified strains included into the database was useful for identifying viridans streptococci species.
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Affiliation(s)
- Catalina Suzana Stingu
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany.
| | - Klaus Eschrich
- Rudolf-Schoenheimer-Institute for Biochemistry, University of Leipzig, Leipzig, Germany
| | - Juliane Thiel
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany
| | - Toralf Borgmann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany
| | - Reiner Schaumann
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany
| | - Arne C Rodloff
- Institute for Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany
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Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis. Sci Rep 2018. [PMID: 29515167 PMCID: PMC5841357 DOI: 10.1038/s41598-018-22642-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.
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Multicenter Evaluation of the Vitek MS v3.0 System for the Identification of Filamentous Fungi. J Clin Microbiol 2018; 56:JCM.01353-17. [PMID: 29142047 DOI: 10.1128/jcm.01353-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 12/21/2022] Open
Abstract
Invasive fungal infections are an important cause of morbidity and mortality affecting primarily immunocompromised patients. While fungal identification to the species level is critical to providing appropriate therapy, it can be slow and laborious and often relies on subjective morphological criteria. The use of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry has the potential to speed up and improve the accuracy of identification. In this multicenter study, we evaluated the accuracy of the Vitek MS v3.0 system in identifying 1,601 clinical mold isolates compared to identification by DNA sequence analysis and supported by morphological and phenotypic testing. Among the 1,519 isolates representing organisms in the v3.0 database, 91% (n = 1,387) were correctly identified to the species level. An additional 27 isolates (2%) were correctly identified to the genus level. Fifteen isolates were incorrectly identified, due to either a single incorrect identification (n = 13) or multiple identifications from different genera (n = 2). In those cases, when a single identification was provided that was not correct, the misidentification was within the same genus. The Vitek MS v3.0 was unable to identify 91 (6%) isolates, despite repeat testing. These isolates were distributed among all the genera. When considering all isolates tested, even those that were not represented in the database, the Vitek MS v3.0 provided a single correct identification 98% of the time. These findings demonstrate that the Vitek MS v3.0 system is highly accurate for the identification of common molds encountered in the clinical mycology laboratory.
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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New Technologies for the Diagnosis of Infection. DIAGNOSTIC PATHOLOGY OF INFECTIOUS DISEASE 2018. [PMCID: PMC7152403 DOI: 10.1016/b978-0-323-44585-6.00006-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Thouvenot P, Vales G, Bracq-Dieye H, Tessaud-Rita N, Maury MM, Moura A, Lecuit M, Leclercq A. MALDI-TOF mass spectrometry-based identification of Listeria species in surveillance: A prospective study. J Microbiol Methods 2017; 144:29-32. [PMID: 29066314 DOI: 10.1016/j.mimet.2017.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 10/18/2022]
Abstract
This study aimed to evaluate MALDI-TOF MS for species discrimination of Listeria in the context of routine surveillance. MALDI-TOF MS yielded 100% accuracy for the identification of L. monocytogenes, L. innocua, L. ivanovii, L. fleischmannii, L. grayi, L. seeligeri, L. weihenstephanensis and L. welshimeri, as confirmed by whole genome sequence analyses.
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Affiliation(s)
- Pierre Thouvenot
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Guillaume Vales
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Hélène Bracq-Dieye
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Nathalie Tessaud-Rita
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Mylène M Maury
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Alexandra Moura
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France; Inserm U1117, Paris, France; Paris Descartes University, Necker-Enfants Malades University Hospital, Department of Infectious Diseases and Tropical Medicine, Institut Imagine, APHP, Paris, France.
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, National Reference Centre and WHO Collaborating Centre for Listeria, Paris, France.
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Bao R, Gao X, Hu B, Zhou Z. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a powerful tool for identification of Corynebacterium species. J Thorac Dis 2017; 9:3239-3245. [PMID: 29221301 DOI: 10.21037/jtd.2017.09.69] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool that has initiated a revolution in the clinical microbiology laboratory for identification of nosocomial pathogens. The efficacy of MALDI-TOF MS produced by bioMerieux, Marcy l'Etoile, France (VITEK MS) for detecting Corynebacterium remains unknown. Methods Corynebacterium isolates were isolated from clinical specimen in a tertial teaching hospital from 2012 to 2013. All strains confirmed by rpoB sequencing were identified by API Coryne (bioMerieux), Phoenix (BD) and VITEK MS, respectively. The coincidence rate was used to evaluate the consistency and accuracy across three methods. Results In all, 75 Corynebacterium isolates were collected in this study. The dominant isolates were Corynebacterium striatum (58.7%), Corynebacterium jeikeium (16.0%), Corynebacterium amycolatum (5.3%), Corynebacterium urealyticum (5.3%), Corynebacterium glucuronolyticum (2.7%) and Corynebacterium minutissimum (2.7%). We found that there was no significant difference in the identification of corynebacterium to genus level by MS (100%, 75/75) or Phoenix (93.3%, 70/75) (P=0.058). However, 92.0% (69/75) strains were successfully identified to species by MS while which by Phoenix and API was 78.7% and 65.3% respectively. Compared with gene sequencing, the coincidence rate of identification by MS was significantly higher than Phoenix (P=0.036) and API (P<0.001). Compared with API Coryne (bioMerieux) and Phoenix, VITEK MS shown significant shorter detecting period and less cost. Conclusions VITEK MS was a powerful tool, which could be applied in clinical laboratory, improving the diagnosis for Corynebacterium infection.
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Affiliation(s)
- Rong Bao
- Department of Clinical Microbiology Laboratory, Respiratory, Zhongshan Hospital, Fudan University, Shanghai 20032, China
| | | | | | - Zhaoyan Zhou
- Department of Clinical Microbiology Laboratory, Respiratory, Zhongshan Hospital, Fudan University, Shanghai 20032, China
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources. FOOD SCIENCE AND HUMAN WELLNESS 2017. [DOI: 10.1016/j.fshw.2017.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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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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Utility of strain typing of Propionibacterium acnes in central nervous system and prosthetic joint infections to differentiate contamination from infection: a retrospective cohort. Eur J Clin Microbiol Infect Dis 2017; 36:2483-2489. [PMID: 28842758 DOI: 10.1007/s10096-017-3090-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/09/2017] [Indexed: 02/07/2023]
Abstract
The study aimed to retrospectively assess if strain typing of Propionibacterium acnes could help to distinguish between infection and contamination in isolates recovered from the central nervous system (CNS) and prosthetic joints (PJs). This was a retrospective cohort of all Propionibacterium species isolates from the Barnes-Jewish Hospital (St Louis, MO, USA) clinical microbiology laboratory from 2011 to 2014. Available frozen isolates were recovered, and strain type (IA-1, IA-2, IB, II, III, or nontypeable class A or B) was determined via polymerase chain reaction (PCR)-based methods. For CNS isolates, P. acnes was considered pathogenic if treating physicians administered ≥7 days of directed antibiotic therapy against P. acnes. During the study period, Propionibacterium species was isolated from clinical cultures 411 times. 152 isolates were available for analysis. Of the 152 isolates, 140 were confirmed to be P. acnes, 61 of which were from the CNS (45 contaminants, 16 infections). Strain type IA-1 was more common (50.0%, 8 out of 16) among CNS infections than among contaminants (22.2%, 10 out of 45). For PJ isolates 61.3% (19 out of 31) met the criteria for infection. The predominant strain type for CNS infection was IA-1 and for PJ isolates, IB. Strain type IA-1 was isolated more often in patients with CNS infections, which may indicate a predilection of this strain type to cause CNS infection. Future research should prospectively evaluate strain typing as a means of assisting in the diagnosis of CNS infections and confirm our findings.
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Impact of Organism Identification Method on Central Line-Associated Bloodstream Infection Designation. Infect Control Hosp Epidemiol 2017. [PMID: 28633680 DOI: 10.1017/ice.2017.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hatcher SM, Rhodes SM, Stewart JR, Silbergeld E, Pisanic N, Larsen J, Jiang S, Krosche A, Hall D, Carroll KC, Heaney CD. The Prevalence of Antibiotic-Resistant Staphylococcus aureus Nasal Carriage among Industrial Hog Operation Workers, Community Residents, and Children Living in Their Households: North Carolina, USA. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:560-569. [PMID: 28362266 PMCID: PMC5381988 DOI: 10.1289/ehp35] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 05/14/2023]
Abstract
BACKGROUND Antibiotic use in industrial hog operations (IHOs) can support the emergence of antibiotic-resistant (ABR) Staphylococcus aureus. The extent of ABR S. aureus exposure in IHO workers and children living in their households remains unclear. OBJECTIVE We investigated ABR S. aureus nasal carriage prevalence among adults with versus without occupational exposure to IHOs and among children living in their households. METHODS In total, 198 IHO worker-child household pairs and 202 community referent (CR) adult-child household pairs completed a questionnaire and provided a nasal swab which was analyzed for S. aureus, methicillin-resistant S. aureus (MRSA), multidrug-resistant S. aureus (MDRSA), absence of scn (putative marker of livestock association), and spa type. RESULTS S. aureus nasal carriage prevalence was higher among IHO (53%) compared with CR (31%) adults [adjusted prevalence ratio (aPR): 1.40; 95% confidence interval (CI): 1.07, 1.83], but MRSA nasal carriage prevalence was uncommon (2-3%) in IHO and CR adults. MDRSA nasal carriage prevalence was similar among IHO workers and CR adults (12% vs. 8%; aPR: 1.14; 95% CI: 0.56, 2.29). Nasal carriage prevalence was higher among IHO compared with CR children for S. aureus (49% vs. 31%; aPR: 1.50; 95% CI: 1.13, 1.99), MRSA (14% vs. 6%; aPR: 2.37; 95% CI: 1.14, 4.92), and MDRSA (23% vs. 8%; aPR: 2.64; 95% CI: 1.47, 4.75). We also found suggestive evidence of a higher prevalence of S. aureus, MRSA, and MDRSA among children living with an IHO worker who did versus did not report taking personal protective equipment (PPE) home from the IHO. Livestock-associated S. aureus nasal carriage predominated among IHO workers. CONCLUSION Our findings support the importance of further research on the prevalence and potential sources of exposure to ABR S. aureus among children living with IHO workers.
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Affiliation(s)
- Sarah M. Hatcher
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Sarah M. Rhodes
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Jill R. Stewart
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Ellen Silbergeld
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nora Pisanic
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jesper Larsen
- Microbiology and Infection Control, Statens Serum Institute, Copenhagen, Denmark
| | - Sharon Jiang
- Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, North Carolina, USA
| | - Amanda Krosche
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Devon Hall
- Rural Empowerment Association for Community Help, Warsaw, North Carolina, USA
| | - Karen C. Carroll
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher D. Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Address correspondence to C.D. Heaney, Departments of Environmental Health and Engineering and Epidemiology, Johns Hopkins Bloomberg School of Public Health, Room W7033B, 615 North Wolfe St., Baltimore, MD 21205 USA. Phone: (443) 287-4989. E-mail:
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Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol 2017; 13:922. [PMID: 28348067 PMCID: PMC5371729 DOI: 10.15252/msb.20167062] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.
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Affiliation(s)
- Pierre M Jean Beltran
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
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Performance of the matrix-assisted laser desorption ionization time-of-flight mass spectrometry system for rapid identification of streptococci: a review. Eur J Clin Microbiol Infect Dis 2017; 36:1005-1012. [DOI: 10.1007/s10096-016-2879-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/13/2016] [Indexed: 11/30/2022]
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Sandalakis V, Goniotakis I, Vranakis I, Chochlakis D, Psaroulaki A. Use of MALDI-TOF mass spectrometry in the battle against bacterial infectious diseases: recent achievements and future perspectives. Expert Rev Proteomics 2017; 14:253-267. [PMID: 28092721 DOI: 10.1080/14789450.2017.1282825] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Advancements in microbial identification occur increasingly faster as more laboratories explore, refine and extend the use of mass spectrometry in the field of microbiology. Areas covered: This review covers the latest knowledge found in the literature for quick identification of various classes of bacterial pathogens known to cause human infection by the use of MALDI-TOF MS technology. Except for identification of bacterial strains, more researchers try to 'battle time' in favor of the patient. These novel approaches to identify bacteria directly from clinical samples and even determine antibiotic resistance are extensively revised and discussed. Expert commentary: Mass spectrometry is the future of bacterial identification and creates a new era in modern microbiology. Its incorporation in routine practice seems to be not too far, providing a valuable alternative, especially in terms of time, to conventional techniques. If the technology further advances, quick bacterial identification and probable identification of common antibiotic resistance might guide patient decision-making regarding bacterial infectious diseases in the near future.
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Affiliation(s)
- Vassilios Sandalakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Ioannis Goniotakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Iosif Vranakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Dimosthenis Chochlakis
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
| | - Anna Psaroulaki
- a Laboratory of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, School of Medicine , University of Crete , Heraklion , Greece
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Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm. J Clin Microbiol 2017; 55:914-922. [PMID: 28053215 DOI: 10.1128/jcm.01990-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/27/2016] [Indexed: 12/21/2022] Open
Abstract
Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcusmitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae, whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper.
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Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults. Antimicrob Agents Chemother 2016; 60:7303-7312. [PMID: 27671074 DOI: 10.1128/aac.01289-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n = 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n = 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the community-dwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P = 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P = 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota.
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Abstract
Although mass spectrometry has been used clinically for decades, the advent of immunoassay technology moved the clinical laboratory to more labor saving automated platforms requiring little if any sample preparation. It became clear, however, that immunoassays lacked sufficient sensitivity and specificity necessary for measurement of certain analytes or for measurement of analytes in specific patient populations. This limitation prompted clinical laboratories to revisit mass spectrometry which could additionally be used to develop assays for which there was no commercial source. In this chapter, the clinical applications of mass spectrometry in therapeutic drug monitoring, toxicology, and steroid hormone analysis will be reviewed. Technologic advances and new clinical applications will also be discussed.
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Affiliation(s)
- D French
- University of California San Francisco, San Francisco, CA, United States.
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50
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Non LR, Santos CAQ. The occurrence of infective endocarditis with Staphylococcus lugdunensis bacteremia: A retrospective cohort study and systematic review. J Infect 2016; 74:179-186. [PMID: 27777118 DOI: 10.1016/j.jinf.2016.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/11/2016] [Accepted: 10/17/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Staphylococcus lugdunensis is a coagulase-negative staphylococcus with similar virulence characteristics as Staphylococcus aureus. Whether S. lugdunensis causes infective endocarditis (IE) in a similar proportion of cases as S. aureus (reported to be 12.6% in a definitive multicenter prospective study) is unclear. METHODS We conducted a retrospective cohort study of adult patients with at least one blood culture positive for S. lugdunensis at our institution from January 2006 to December 2014. We examined microbiology data, ascertained disease severity and determined the proportion of patients with definite or possible IE based on the 2000 Modified Duke Criteria. Because coagulase-negative staphylococci were routinely identified to the species level at our institution from 2012 onwards, we determined the proportion of patients with definite or possible IE before and after implementation of routine speciation. We also compared our results with reported proportions of IE among patients with S. lugdunensis bacteremia (SLB) in other institutions by conducting a systematic review of the scientific literature. Nonparametric bootstrapping methods were performed to determine 95% confidence intervals (CI) for proportions of IE in patients with SLB. RESULTS Seventy-four patients with SLB were identified, of whom 64% (47/74) had sepsis by SIRS criteria, and 18% (13/74) had severe illness by Pittsburgh bacteremia score (PBS). Kaplan-Meier survival analysis showed that one-year survival among patients with severe illness was worse than patients with non-severe illness (p = 0.02). Fifteen percent (11/74) of patients had definite or possible IE (95% CI 6.8-23.0%). The proportion of SLB patients with definite or possible IE was 15.8% (6/38, 95% CI 5.3-28.9%) prior to routine speciation and 13.9% (5/36, 95% CI 2.8-27.8%) after routine speciation (p = 0.71). Among patients with at least two positive blood cultures for S. lugdunensis, 25% (10/40, 95% CI 12.5-40.0%) had IE. Systematic review of the literature yielded eight relevant retrospective studies. Of studies that included patients with one or more positive blood cultures for S. lugdunensis, the proportion of IE ranged from 6.3% to 27.0%. CONCLUSION The proportion of definite or possible IE among patients with SLB is similar to the proportion of IE among patients with S. aureus bacteremia. The proportions of IE among patients with SLB at other institutions fall within the 95% CI yielded by bootstrapping. Our findings suggest that growth of S. lugdunensis in two separate blood cultures should prompt consideration of workup for IE.
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Affiliation(s)
- Lemuel R Non
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA.
| | - Carlos A Q Santos
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, USA
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