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Iglesies-Torrent J, Garrido M, Morales J, Pitart C, Vergara A, Fernández-Pittol M. Enhancing pneumococcal bacteraemia diagnosis: A comparative assessment of culture-independent assays (MALDI-TOF-MS Sepsityper® module and a lateral flow inmunochromatography test). ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2024:S2529-993X(24)00114-X. [PMID: 38705749 DOI: 10.1016/j.eimce.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/12/2024] [Indexed: 05/07/2024]
Abstract
INTRODUCTION Pneumococcal bacteraemia is a major contributor to global morbidity and mortality. Traditional culture-based methods lack sensitivity and are time-consuming. This study aimed to assess the effectiveness of two culture-independent assays, the MALDI-TOF-MS Sepsityper® module and the lateral flow inmunochromatography test (LFICT) with the Standard F® Streptococcus pneumoniae, directly from positive blood culture (BC) bottles. METHODS A prospective study was conducted from December 2021 to July 2022. For all BC positives for S. pneumoniae a double centrifugation protocol was implemented. The resulting pellet was subsequently processed using both techniques. RESULTS The LFICT showed exceptional performance with 100% sensitivity and specificity, outperforming the MALDI-TOF-MS Sepsityper® module, which achieved 85.2% sensitivity and 100% specificity. Nevertheless, the combination of these assays offers a robust and comprehensive approach to diagnosis. CONCLUSIONS The simultaneous use of both techniques offers a promising alternative that can be integrated into routine practices directly from BC samples.
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Affiliation(s)
| | - Míriam Garrido
- Department of Microbiology, Hospital Clínic, Barcelona, Spain
| | - Javier Morales
- Department of Microbiology, Hospital Clínic, Barcelona, Spain
| | - Cristina Pitart
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Andrea Vergara
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain; University of Barcelona, Barcelona, Spain
| | - Mariana Fernández-Pittol
- Department of Microbiology, Hospital Clínic, Barcelona, Spain; Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
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Fernandez-Pittol M, Bosch J, Ballesté-Delpierre C, Gonzalez C, Vasilakopoulou A, Berbel D, Riccobono E, Gatermann S, Kamotsay K, Reissier S, Szabo D, Aszalos AZ, Francius L, Volland H, Stankov-Pugès M, Rosenmöller M, Naas T, Vila J. Multicenter study to assess the use of BL-DetecTool for the detection of CTX-M-type ESBLs and carbapenemases directly from clinical specimens. J Clin Microbiol 2024; 62:e0113623. [PMID: 38319119 PMCID: PMC10935652 DOI: 10.1128/jcm.01136-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major public health problems worldwide. Multiple strategies have been put in place to address this problem. One of them is the rapid detection of the mechanisms of resistance, such as extended-spectrum beta-lactamases (ESBLs) and/or carbapenemases. We conducted a multicenter study that included nine European centers for the assessment of prototypes of a novel lateral flow immunoassay-based device (BL-DetecTool) for a rapid detection of ESBL (NG-Test CTX-M-MULTI DetecTool) and/or carbapenemases (NG-Test CARBA 5 DetecTool) from Enterobacterales and Pseudomonas aeruginosa in positive urine, positive blood cultures, and rectal swabs. We performed a prospective analysis between January 2021 and June 2022, including overall 22,010 samples. Based on each hospital information, the sensitivity to detect CTX-M was 84%-100%, 90.9%-100%, and 75%-100% for urine, positive blood cultures, and enriched rectal swabs, respectively. On the other hand, the sensitivity to detect carbapenemases was 42.8%-100%, 75%-100%, and 66.6%-100% for urine, positive blood cultures, and enriched rectal swab, respectively. BL-DetecTool allows a rapid and reliable detection of ESBL and carbapenemases directly from urine, positive blood cultures, or enriched rectal swabs, being an easy technique to implement in the workflow of clinical microbiology laboratories. IMPORTANCE The assessed rapid assay to detect CTX-M beta-lactamases and carbapenemases directly from clinical samples can favor in the rapid detection of these mechanisms of resistance and hence the administration of a more adequate antimicrobial treatment.
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Affiliation(s)
- Mariana Fernandez-Pittol
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Jordi Bosch
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | | | - Camille Gonzalez
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Alexandra Vasilakopoulou
- Laboratory of Clinical Microbiology, Attikon University General Hospital, Medical School, National Kapodistrian University Athens (Greece), Athens, Greece
| | - Dàmaris Berbel
- Microbiology Department, Hospital de Bellvitge. IDIBELL. UB. CIBERES, Barcelona, Spain
| | - Eleonora Riccobono
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sören Gatermann
- German National Reference Laboratory for Multidrug-Resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Germany - (Germany), Bochum, Germany
| | - Katalin Kamotsay
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Sophie Reissier
- Department of Bacteriology, Amiens University Hospital, Amiens, France
| | - Dora Szabo
- Semmelweis University, Institute of Medical Microbiology, Budapest, Hungary
| | - Albert Zoltan Aszalos
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
| | | | - Hervé Volland
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, Gif-sur-Yvette, France
| | | | | | - Thierry Naas
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Jordi Vila
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
- Department of Clinical Microbiology - CDB, University of Barcelona, Hospital Clínic, Barcelona, Spain
- CIBER de Enfermedades Infecciosas , Barcelona, Spain
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Sánchez D, Torres I, Padrón C, Giménez E, Colomina J, Carretero D, Buesa J, Navarro D, Albert E. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and lateral flow immunochromatography for rapid identification of β-lactamase-gene-harboring Enterobacterales in urine specimens: Performance and cost-benefit analyses. Diagn Microbiol Infect Dis 2024; 108:116127. [PMID: 37988931 DOI: 10.1016/j.diagmicrobio.2023.116127] [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: 05/31/2023] [Revised: 09/29/2023] [Accepted: 10/28/2023] [Indexed: 11/23/2023]
Abstract
In this single-center prospective study, we evaluated the performance to the MALDI-ToF MS based method in conjunction with lateral flow immunochromatographic (LFIC) in urine specimens for rapid diagnosis of bacterial Urinary Tract Infection (UTI) and detection of carbapenemase and/or extended-spectrum β- lactamase (ESBL) enzymes produced by the involved bacteria, compared to standard culture, and antimicrobial susceptibility testing/genotypic resistance markers characterization performed on culture-grown colonies. In addition, a cost-benefit analysis comparing this approach against standard procedures was conducted. A total of 324 urines were included in the study, of which 288 (88.9 %) yielded concordant results by the MALDI-ToF MS and conventional culture (Kappa agreement, 0.82; P<0.001). Direct LFIC testing could be carried out in 249/324 urines. Bacterial species carrying β-lactam genotypic resistance markers were identified in 35 urines (35 CTX-M and 2 OXA-48). Two ESBL-producing Escherichia coli were missed by LFIC (Kappa agreement with standard procedures of 0.96; P<0.001). The cost-benefit analysis indicated that our novel approach resulted in an improvement of clinical outcomes (less need of outpatient care) with a marginal incremental cost (€2.59).
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Affiliation(s)
- David Sánchez
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Carmelo Padrón
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Javier Colomina
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Diego Carretero
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain
| | - Javier Buesa
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain; Department of Microbiology, School of Medicine, University of Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, INCLIVA Research institute, Valencia, Spain.
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Grey B, Upton M, Joshi LT. Urinary tract infections: a review of the current diagnostics landscape. J Med Microbiol 2023; 72. [PMID: 37966174 DOI: 10.1099/jmm.0.001780] [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] [Indexed: 11/16/2023] Open
Abstract
Urinary tract infections are the most common bacterial infections worldwide. Infections can range from mild, recurrent (rUTI) to complicated (cUTIs), and are predominantly caused by uropathogenic Escherichia coli (UPEC). Antibiotic therapy is important to tackle infection; however, with the continued emergence of antibiotic resistance there is an urgent need to monitor the use of effective antibiotics through better stewardship measures. Currently, clinical diagnosis of UTIs relies on empiric methods supported by laboratory testing including cellular analysis (of both human and bacterial cells), dipstick analysis and phenotypic culture. Therefore, development of novel, sensitive and specific diagnostics is an important means to rationalise antibiotic therapy in patients. This review discusses the current diagnostic landscape and highlights promising novel diagnostic technologies in development that could aid in treatment and management of antibiotic-resistant UTIs.
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Affiliation(s)
- Braith Grey
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
| | - Mathew Upton
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
| | - Lovleen Tina Joshi
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, Devon, UK
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Jover-García J, López-Millán C, Gil-Tomás JJ, Callejón-Fernández M, Lecuona-Fernández M. Identification and antibiogram of Enterobacterales from direct urine samples using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) technology and disk-plate diffusion technique. Indian J Med Microbiol 2023; 46:100457. [PMID: 37945131 DOI: 10.1016/j.ijmmb.2023.100457] [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: 12/05/2022] [Revised: 07/23/2023] [Accepted: 07/31/2023] [Indexed: 11/12/2023]
Abstract
Identification and antibiogram of uropathogenic microorganisms from direct urine samples present a great clinical impact. Here, we present a combined procedure to determine identification (IDd) of bacteria through MALDI-TOF-MS technology and antibiogram (ATBd) using disk-plate diffusion technique, of UTI-producing Enterobacterales against the most used antibiotics. Ninety-four urine samples with presence of pyuria and Gram-negative bacilli were selected. The IDd showed a high success rate (90%). ATBd procedure showed a high correlation for tested antibiotics. This simplified, low cost and reduced work time two-step procedure significantly reduces results turnaround time and benefit the clinical management of patients with UTI.
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Affiliation(s)
- Jorge Jover-García
- Microbiology Service, Hospital Universitario de Canarias, Carretera Ofra s/n, 38320, La Cuesta, Santa Cruz de Tenerife, Canary Islands, Spain.
| | - Celia López-Millán
- Microbiology Service, Hospital Universitario de Canarias, Carretera Ofra s/n, 38320, La Cuesta, Santa Cruz de Tenerife, Canary Islands, Spain.
| | - Jesús J Gil-Tomás
- Laboratory Clinical Management Unit, Hospital La Inmaculada, Av. Dra. Ana Parra s/n, 04600, Huércal-Overa, Almería, Spain.
| | - Manuel Callejón-Fernández
- Microbiology Service, Hospital Universitario de Canarias, Carretera Ofra s/n, 38320, La Cuesta, Santa Cruz de Tenerife, Canary Islands, Spain.
| | - María Lecuona-Fernández
- Microbiology Service, Hospital Universitario de Canarias, Carretera Ofra s/n, 38320, La Cuesta, Santa Cruz de Tenerife, Canary Islands, Spain.
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Abbott IJ, Peel TN, Cairns KA, Stewardson AJ. Antibiotic management of urinary tract infections in the post-antibiotic era: a narrative review highlighting diagnostic and antimicrobial stewardship. Clin Microbiol Infect 2023; 29:1254-1266. [PMID: 35640839 DOI: 10.1016/j.cmi.2022.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 12/22/2022]
Abstract
BACKGROUND As one of the most common indications for antimicrobial prescription in the community, the management of urinary tract infections (UTIs) is both complicated by, and a driver of, antimicrobial resistance. OBJECTIVES To highlight the key clinical decisions involved in the diagnosis and treatment of UTIs in adult women, focusing on clinical effectiveness and both diagnostic and antimicrobial stewardship as we approach the post-antimicrobial era. SOURCES Literature reviewed via directed PubMed searches and manual searching of the reference list for included studies to identify key references to respond to the objectives. A strict time limit was not applied. We prioritised recent publications, randomised trials, and systematic reviews (with or without meta-analyses) where available. Searches were limited to English language articles. A formal quality assessment was not performed; however, the strengths and limitations of each paper were reviewed by the authors throughout the preparation of this manuscript. CONTENT We discuss the management of UTIs in ambulatory adult women, with particular focus on uncomplicated infections. We address the diagnosis of UTIs, including the following: definition and categorisation; bedside assessments and point-of-care tests; and the indications for, and use of, laboratory tests. We then discuss the treatment of UTIs, including the following: indications for treatment, antimicrobial sparing approaches, key considerations when selecting a specific antimicrobial agent, specific treatment scenarios, and duration of treatment. We finally outline emerging areas of interest in this field. IMPLICATIONS The steady increase in antimicrobial resistance among common uropathogens has had a substantial affect on the management of UTIs. Regarding both diagnosis and treatment, the clinician must consider both the patient (clinical effectiveness and adverse effects, including collateral damage) and the community more broadly (population-level antimicrobial selection pressure).
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Affiliation(s)
- Iain J Abbott
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia; Microbiology Unit, Alfred Health, Melbourne, Victoria, Australia.
| | - Trisha N Peel
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Kelly A Cairns
- Pharmacy Department, Alfred Health, Melbourne, Victoria, Australia
| | - Andrew J Stewardson
- Department of Infectious Diseases, Alfred Hospital and Central Clinical School, Monash University, Melbourne, Victoria, Australia
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Neuenschwander FR, Groß B, Schubert S. Rapid Antibiotic Susceptibility Testing of Gram-Negative Bacteria Directly from Urine Samples of UTI Patients Using MALDI-TOF MS. Antibiotics (Basel) 2023; 12:1042. [PMID: 37370361 DOI: 10.3390/antibiotics12061042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common human infections and are most often caused by Gram-negative bacteria such as Escherichia coli. In view of the increasing number of antibiotic-resistant isolates, rapidly initiating effective antibiotic therapy is essential. Therefore, a faster antibiotic susceptibility test (AST) is desirable. The MALDI-TOF MS-based phenotypic antibiotic susceptibility test (MALDI AST) has been used in blood culture diagnostics to rapidly detect antibiotic susceptibility. This study demonstrates for the first time that MALDI AST can be used to rapidly determine antibiotic susceptibility in UTIs directly from patients' urine samples. MALDI-TOF MS enables the rapid identification and AST of Gram-negative UTIs within 4.5 h of receiving urine samples. Six urinary tract infection antibiotics, including ciprofloxacin, cotrimoxazole, fosfomycin, meropenem, cefuroxime, and nitrofurantoin, were analyzed and compared with conventional culture-based AST methods. A total of 105 urine samples from UTI patients contained bacterial isolates for MALDI AST. The combination of ID and AST by MALDI-TOF allowed us to interpret the result according to EUCAST guidelines. An overall agreement of 94.7% was found between MALDI AST and conventional AST for the urinary tract pathogens tested.
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Affiliation(s)
- Felix R Neuenschwander
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Birgit Groß
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
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Zubair M, Wang J, Yu Y, Faisal M, Qi M, Shah AU, Feng Z, Shao G, Wang Y, Xiong Q. Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases. Front Vet Sci 2022; 9:1079359. [PMID: 36601329 PMCID: PMC9806867 DOI: 10.3389/fvets.2022.1079359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Proteomics is playing an increasingly important role in identifying pathogens, emerging and re-emerging infectious agents, understanding pathogenesis, and diagnosis of diseases. Recently, more advanced and sophisticated proteomics technologies have transformed disease diagnostics and vaccines development. The detection of pathogens is made possible by more accurate and time-constrained technologies, resulting in an early diagnosis. More detailed and comprehensive information regarding the proteome of any noxious agent is made possible by combining mass spectrometry with various gel-based or short-gun proteomics approaches recently. MALDI-ToF has been proved quite useful in identifying and distinguishing bacterial pathogens. Other quantitative approaches are doing their best to investigate bacterial virulent factors, diagnostic markers and vaccine candidates. Proteomics is also helping in the identification of secreted proteins and their virulence-related functions. This review aims to highlight the role of cutting-edge proteomics approaches in better understanding the functional genomics of pathogens. This also underlines the limitations of proteomics in bacterial secretome research.
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Affiliation(s)
- Muhammad Zubair
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jia Wang
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yanfei Yu
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Faisal
- Division of Hematology, Department of Medicine, The Ohio State University College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Mingpu Qi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Abid Ullah Shah
- National Research Centre of Engineering and Technology for Veterinary Biologicals, Institute of Veterinary Immunology and Engineering, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhixin Feng
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Guoqing Shao
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yu Wang
- China Pharmaceutical University, Nanjing, China,*Correspondence: Yu Wang
| | - Qiyan Xiong
- Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China,College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China,School of Life Sciences, Jiangsu University, Zhenjiang, China,Qiyan Xiong
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Anwer R, Darami H, Almarri FK, Albogami MA, Alahaydib F. MALDI-TOF MS for Rapid Analysis of Bacterial Pathogens Causing Urinary Tract Infections in the Riyadh Region. Diseases 2022; 10:diseases10040078. [PMID: 36278577 PMCID: PMC9590002 DOI: 10.3390/diseases10040078] [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: 08/20/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
The successful treatment of bacterial disease is relied on selecting a suitable drug based on the type of bacteria and antimicrobial susceptibility testing. The study’s objective was to identify bacterial isolates from urine samples of patients from the community, followed by antimicrobial susceptibility testing of the isolated bacteria. A total of seventy urine samples were received in the clinical microbiology laboratory; out of which 18 culture-positive cultures and by direct identification using MALDI-TOF MS (Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry) were identified. Of 18 identified bacteria, 17 (94%) were pathogenic. The culture demonstrated that the major species detected in urine samples were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecalis, and Aeromonas caviae. E. coli (72.2%) was the most common bacterium retrieved from urine samples followed by K. pneumoniae (16.6%). Interestingly, all the isolates, except Enterococcus faecalis, were resistant to erythromycin. The isolates 8 of 13 (61.5%) were resistant to both of the cotrimoxazole and tetracycline. We performed MLST (Multi-locus Sequence Typing) typing of 13 E. coli isolates to study their genetic relatedness and diversity. MLST typing of E. coli showed a total of nine different STs (Sequence Types), which showed the diversity among them. ST 129 was the most common ST found in three E. coli isolates. In our study, two isolates with ST 1126 and ST 1432 represented the global clonal complex 155. MALDI-TOF MS provided dependable results for identifying the bacteria up to species level from urine samples by indirect culture methods. Such local surveillances are highly recommended for empirical therapy awareness and determining isolates’ level of resistance.
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Affiliation(s)
- Razique Anwer
- Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
- Correspondence:
| | - Hassan Darami
- Department of OB & Gyne, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
| | - Firas K. Almarri
- College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
| | - Mazen A. Albogami
- College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
| | - Faisal Alahaydib
- Medical Center, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13317-4233, Saudi Arabia
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Legaria M, Barberis C, Famiglietti A, De Gregorio S, Stecher D, Rodriguez C, Vay C. Urinary tract infection caused by anaerobic bacteria. Utility of anaerobic urine culture. Anaerobe 2022; 78:102636. [DOI: 10.1016/j.anaerobe.2022.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 08/30/2022] [Indexed: 11/01/2022]
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Implementation of a New Protocol for Direct Identification from Urine in the Routine Microbiological Diagnosis. Antibiotics (Basel) 2022; 11:antibiotics11050582. [PMID: 35625226 PMCID: PMC9137483 DOI: 10.3390/antibiotics11050582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/14/2022] [Accepted: 04/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background: The direct identification of uropathogens from urine samples, in combination with the rapid detection of resistance, would allow early adjustment of empirical antimicrobial treatment. Methods: Two hundred and ninety-eight urine samples processed between 1 June and 31 December 2020, selected with flow cytometry, with direct identification by MALDI-TOF mass spectrometry, and rapid detection of extended-spectrum beta-lactamase (ESBL) and carbapenemases-producing strains by lateral flow were analyzed. Results: The positive predictive value of the direct identification of the 86 samples that met the flow cytometry criterion (>5000 bacteria/µL) was 96.4%. Reliable direct identification was obtained in 14 of the 27 (51.8%) urinary source bacteraemias. There was 100% agreement between the lateral flow and antibiogram in the detection of ESBL and carbapenemases. Conclusion: the protocol for the direct identification and rapid detection of ESBL and carbapenemases-producing strains from urine samples is a reliable and useful tool.
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Liu Z, Tang H, Xu H, Lu G, Yang W, Xia Z, Zhu Y, Ni S, Men W, Shen J. Rapid Identification and Drug Sensitivity Test to Urinary Tract Infection Pathogens by DOT-MGA. Infect Drug Resist 2022; 15:1391-1397. [PMID: 35392368 PMCID: PMC8980293 DOI: 10.2147/idr.s356045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/17/2022] [Indexed: 11/25/2022] Open
Abstract
Aim To reduce the inspection time for urinary tract pathogens and provide a rapid and effective therapeutic plan for clinical anti-infection treatment, this study developed a rapid identification (ID) and antimicrobial sensitivity test (AST) method by DOT-MGA. Methods We grouped midstream urine samples with single bacteria according to the number of bacteria (≤5/5–15/≥ 15) under per oil microscope after Gram staining. Then we adopted differential centrifugation to process the grouped samples to collect precipitate. MALDI-TOF MS was performed using precipitate directly or after short-term culture. If succeed, we resuspended the precipitate into droplets with or without antibiotics at a MALDI target. Four hours later, mass spectrometer (MS) was used to identify the culture on the target and to analyse AST. Results Samples (count ≥ 15), which precipitate can be directly identified by MS; otherwise, the precipitate need a short-term cultured for 3–6 h before ID. The consistency of the ID results between conventional culture and the precipitate is 100%. Compared with broth microdilution method, DOT-MGA for predicting AST had a high consistency. EA and CA for IPM, LEV, CAZ, NIT, and FOT were 100%/100%, 98%/90%, 98%/92%, 100%/90%, 98%/94%, respectively. No VME was observed in all tests. Besides, MIC50 for the five antibiotics by DOT-MGA and broth microdilution method were ≤1/≤0.5,>2/2,≤4/≤2,≤32/≤16,≤64/≤32 and MIC90 were ≤1/≤0.5, >2/>4, 16/16, 128/128, 128/64. Conclusion This study can shorten the ID time (minimum 0.5h) and AST (minimum 4h) of the main pathogens of urinary tract infection to 5–10 hours, which greatly reduce the inspection time and provide substantial help for the rapid diagnosis and treatment of patients with urinary tract infection.
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Affiliation(s)
- Zhen Liu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Hao Tang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Huaming Xu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Guoping Lu
- Laboratory Department of Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, 236000, People’s Republic of China
| | - Wensu Yang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Zhaoxin Xia
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Yi Zhu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Shenwang Ni
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Wanqi Men
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
| | - Jilu Shen
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People’s Republic of China
- Correspondence: Jilu Shen, The Fourth Affiliated Hospital of Anhui Medical University Laboratory, No. 100 Huaihai Avenue, Xinzhan District, Hefei, Anhui Province, 230012, People’s Republic of China, Tel +86 151 5515 2963, Email
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Applying Diagnostic Stewardship to Proactively Optimize the Management of Urinary Tract Infections. Antibiotics (Basel) 2022; 11:antibiotics11030308. [PMID: 35326771 PMCID: PMC8944608 DOI: 10.3390/antibiotics11030308] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/05/2022] [Accepted: 02/17/2022] [Indexed: 02/06/2023] Open
Abstract
A urinary tract infection is amongst the most common bacterial infections in the community and hospital setting and accounts for an estimated 1.6 to 2.14 billion in national healthcare expenditure. Despite its financial impact, the diagnosis is challenging with urine cultures and antibiotics often inappropriately ordered for non-specific symptoms or asymptomatic bacteriuria. In an attempt to limit unnecessary laboratory testing and antibiotic overutilization, several diagnostic stewardship initiatives have been described in the literature. We conducted a systematic review with a focus on the application of molecular and microbiological diagnostics, clinical decision support, and implementation of diagnostic stewardship initiatives for urinary tract infections. The most successful strategies utilized a bundled, multidisciplinary, and multimodal approach involving nursing and physician education and feedback, indication requirements for urine culture orders, reflex urine culture programs, cascade reporting, and urinary antibiograms. Implementation of antibiotic stewardship initiatives across the various phases of laboratory testing (i.e., pre-analytic, analytic, post-analytic) can effectively decrease the rate of inappropriate ordering of urine cultures and antibiotic prescribing in patients with clinically ambiguous symptoms that are unlikely to be a urinary tract infection.
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14
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Microbial Identification in the Clinical Microbiology Laboratory Using MALDI-TOF-MS. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:207-216. [PMID: 34905176 DOI: 10.1007/978-1-0716-1936-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MALDI-TOF mass spectrometry has been applied with huge success to the identification of cultured microorganisms in clinical microbiology laboratories where it has become the reference method because it is simple, fast, and highly reproducible. We describe the different procedures used in the routine for pathogen identification using the Bruker MALDI Biotyper® system.
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15
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Legaria MC, Nastro M, Camporro J, Heger F, Barberis C, Stecher D, Rodriguez CH, Vay CA. Peptostreptococcus anaerobius: Pathogenicity, identification, and antimicrobial susceptibility. Review of monobacterial infections and addition of a case of urinary tract infection directly identified from a urine sample by MALDI-TOF MS. Anaerobe 2021; 72:102461. [PMID: 34626800 DOI: 10.1016/j.anaerobe.2021.102461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/17/2022]
Abstract
Peptostreptococcus anaerobius is a gram-positive anaerobic coccus (GPAC) found in the gastrointestinal and vaginal microbiota. The organism is mainly found in polymicrobial and scarcely in monobacterial infections such as prosthetic and native endocarditis. Anaerobic bacteria have rarely been reported as the cause of urinary tract infection (UTI). Although GPAC are susceptible to most antimicrobials used against anaerobic infections, P. anaerobius has shown to be more resistant. Herein, we report a case of UTI caused by P. anaerobius from a 62-year-old man with a history of urological disease. Surprisingly, the microorganism was directly identified by Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) from the urine sample. The isolate was successfully identified by phenotypic methods, MALDI-TOF MS, and 16S rRNA gene sequencing. P. anaerobius showed no β-lactamase-producing activity, was resistant to penicillin, ampicillin, ciprofloxacin and levofloxacin, and displayed intermediate susceptibility to ampicillin-sulbactam and amoxicillin-clavulanic acid. Successful treatment was achieved with oral amoxicillin-clavulanic acid. Antimicrobial susceptibility testing (AST) should be performed on P. anaerobius isolates due to their unpredictable AST patterns and because empirically administered antimicrobial agents may not be active. This report shows that MALDI-TOF MS, directly used in urine specimens, may be a quick option to diagnose UTI caused by P. anaerobius or other anaerobic bacteria. This review is a compilation of monobacterial infections caused by P. anaerobius published in the literature, their pathogenicity, identification, and data about the antimicrobial susceptibility of P. anaerobius.
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Affiliation(s)
- M C Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina.
| | - M Nastro
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, INFIBIOC, Buenos Aires, Argentina
| | - J Camporro
- Universidad de Buenos Aires. Facultad de Medicina, Hospital de Clínicas José de San Martín, Servicio de Infectología, Buenos Aires, Argentina
| | - F Heger
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina
| | - C Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, INFIBIOC, Buenos Aires, Argentina
| | - D Stecher
- Universidad de Buenos Aires. Facultad de Medicina, Hospital de Clínicas José de San Martín, Servicio de Infectología, Buenos Aires, Argentina
| | - C H Rodriguez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, INFIBIOC, Buenos Aires, Argentina
| | - C A Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Laboratorio de Bacteriología, INFIBIOC, Buenos Aires, Argentina
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16
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Gilboe HM, Reiakvam OM, Aasen L, Tjade T, Bjerner J, Ranheim TE, Gaustad P. Rapid diagnosis and reduced workload for urinary tract infection using flowcytometry combined with direct antibiotic susceptibility testing. PLoS One 2021; 16:e0254064. [PMID: 34228764 PMCID: PMC8259986 DOI: 10.1371/journal.pone.0254064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/19/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND We evaluated if flowcytometry, using Sysmex UF-5000, could improve diagnosis of urinary tract infections by rapid identification of culture negative and contaminated samples prior to culture plating, thus reducing culture plating workload and response time. We also evaluated if it is possible to reduce the response time for antibiotic susceptibility profiles using the bacteria information flag on Sysmex UF-5000 to differentiate between Gram positive and negative bacteria, followed by direct Antibiotic Susceptibility Testing (dAST) on the positive urine samples. METHODS One thousand urine samples were analyzed for bacteria, white blood cells and squamous cells by flowcytometry before culture plating. Results from flowcytometric analysis at different cut-off values were compared to results of culture plating. We evaluated dAST on 100 urine samples that were analyzed as positive by flowcytometry, containing either Gram positive or Gram negative bacteria. RESULTS Using a cut-off value with bacterial count ≥100.000/mL and WBCs ≥10/μL, flowcytometry predicted 42,1% of samples with non-significant growth. We found that most contaminated samples contain few squamous cells. For 52/56 positive samples containing Gram negative bacteria dAST was identical to routine testing. Overall, there was concordance in 555/560 tested antibiotic combinations. CONCLUSION Flowcytometry offers advantages for diagnosis of urinary tract infections. Screening for negative urine samples on the day of arrival reduces culture plating and workload, and results in shorter response time for the negative samples. The bacteria information flag predicts positive samples containing Gram negative bacteria for dAST with high accuracy, thus Antibiotic Susceptibility Profile can be reported the day after arrival. For the positive samples containing Gram negative bacteria the concordance was very good between dAST and Antibiotic Susceptibility Testing in routine. For positive samples containing Gram positive bacteria the results were not convincing. We did not find any correlation between epithelial cells and contamination.
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Affiliation(s)
| | | | - Linda Aasen
- Department of Microbiology, Fürst Medical Laboratory, Oslo, Norway
| | - Trygve Tjade
- Department of Microbiology, Fürst Medical Laboratory, Oslo, Norway
| | - Johan Bjerner
- Department of Microbiology, Fürst Medical Laboratory, Oslo, Norway
| | | | - Peter Gaustad
- Department of Microbiology, Fürst Medical Laboratory, Oslo, Norway
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Ying J, Gao W, Huang D, Ding C, Ling L, Pan T, Yu S. Application of MALDI-TOF MS Profiling Coupled With Functionalized Magnetic Enrichment for Rapid Identification of Pathogens in a Patient With Open Fracture. Front Chem 2021; 9:672744. [PMID: 33996766 PMCID: PMC8120279 DOI: 10.3389/fchem.2021.672744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 01/17/2023] Open
Abstract
Posttraumatic infections can occur in orthopedic trauma patients, especially in open fractures. Rapid and accurate identification of pathogens in orthopedic trauma is important for clinical diagnosis and antimicrobial treatment. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been successfully used for first-line identification of pathogens grown on culture plates. However, for direct analysis of liquid clinical specimens, pre-purification of the sample is necessary. Herein, we investigated the feasibility of coupling Fc-MBL@Fe3O4 enrichment with MALDI-TOF MS profiling in the identification of pathogens in liquid-cultured samples. This method is successfully used for the identification of pathogens in a patient with an open-leg fracture obtained at sea. Pathogens were enriched by Fc-MBL@Fe3O4 from briefly pre-cultured liquid media and identified by MALDI-TOF MS. We identified an opportunistic pathogen, Vibrio alginolyticus, which is uncommon in clinical orthopedic trauma infection but exists widely in the sea. Therefore, combining Fc-MBL@Fe3O4 enrichment and MALDI-TOF MS profiling has great potential for direct identification of microbes in clinical samples.
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Affiliation(s)
| | - Wenjing Gao
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | | | - Chuanfan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Ling Ling
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
| | - Tao Pan
- Department of Breast Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shaoning Yu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, China
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18
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Sun B, Wang W, Ma P, Gu B. Accuracy of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for direct bacterial identification from culture-positive urine samples. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:647. [PMID: 33987345 PMCID: PMC8106043 DOI: 10.21037/atm-20-7310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Background Urinary tract infection (UTI) is one of the most frequent reasons for antimicrobial therapy. In typical clinical setting, 18–48 h is needed to identify pathogens by urine culture. A rapid method for pathogenic UTI diagnosis by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed in recent years. Methods This meta-analysis systematically evaluated the accuracy of MALDI-TOF MS for direct identification of bacteria from culture-positive urine samples. We queried the electronic database of Medline and Web of Science to obtain relevant articles. Results Nineteen articles involving 4,579 isolates were included after final selection in the meta-analysis. The random-effects pooled identification accuracy of MALDI-TOF MS was 0.82 with 95% confidence interval of 0.79 to 0.86 at the species level. For Gram-negative isolates, the correct identification performance of the species ranged from 0.54 to 0.98, with a cumulative rate of 0.87 (95% CI: 0.83 to 0.91). For Gram-positive isolates, the correct identification rate ranged from 0.32 to 0.80, with a cumulative rate of 0.59 (95% CI: 0.49 to 0.68). Conclusions MALDI-TOF MS provides a reliable direct identification of bacteria, particularly in cases of Gram-negative isolates, from clinical urine specimens. Nevertheless, the identification accuracy of this method is moderate for Gram-positive bacteria.
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Affiliation(s)
- Bin Sun
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Ping Ma
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou, China
| | - Bing Gu
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Medical Technology School of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China
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Riedel S, Halls J, Dutta S, Toraskar N, Lemon J, Carter K, Sinclair W, Lopansri BK, Styer AM, Wolk DM, Walker GT. Clinical evaluation of the acuitas® AMR gene panel for rapid detection of bacteria and genotypic antibiotic resistance determinants. Diagn Microbiol Infect Dis 2021; 100:115383. [PMID: 33894657 DOI: 10.1016/j.diagmicrobio.2021.115383] [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: 01/19/2021] [Revised: 03/13/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Urinary tract infections are leading causes of hospital admissions. Accurate and timely diagnosis is important due to increasing morbidity and mortality from antimicrobial resistance. We evaluated a polymerase chain reaction test (Acuitas AMR Gene Panel with the Acuitas Lighthouse Software) for detection of 5 common uropathogens (Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Enterococcus faecalis) and antibiotic resistance genes directly from urine for prediction of phenotypic resistance. Overall percent agreement was 97% for semiquantitative detection of uropathogens versus urine culture using a cut-off of 104 colony forming units per mL urine. Overall accuracy was 91% to 93% for genotypic prediction of common antibiotic resistance harbored by E. coli, K. pneumoniae, and P. mirabilis.
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Affiliation(s)
- Stefan Riedel
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Justin Halls
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Sanjucta Dutta
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | | | | | - Kendra Carter
- Intermountain Medical Center, Central Microbiology Laboratory, Murray, UT, USA
| | - Will Sinclair
- Intermountain Medical Center, Central Microbiology Laboratory, Murray, UT, USA
| | - Bert K Lopansri
- Intermountain Medical Center, Central Microbiology Laboratory, Murray, UT, USA; University of Utah, Department of Internal Medicine, Salt Lake City, UT, USA
| | - Amanda M Styer
- Geisinger Health System, Diagnostic Medical Institute, Danville, PA, USA
| | - Donna M Wolk
- Geisinger Health System, Diagnostic Medical Institute, Danville, PA, USA
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20
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LEI DERU, CHEN PEIYING, CHEN XUETING, ZONG YUJIE, LI XIANGYANG. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry for Identification of Microorganisms in Clinical Urine Specimens after Two Pretreatments. Pol J Microbiol 2021; 70:1-7. [PMID: 34131429 PMCID: PMC8196241 DOI: 10.33073/pjm-2021-018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/29/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023] Open
Abstract
Rapid identification of microorganisms in urine is essential for patients with urinary tract infections (UTIs). Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been proposed as a method for the direct identification of urinary pathogens. Our purpose was to compare centrifugation-based MALDI-TOF MS and short-term culture combined with MALDI-TOF MS for the direct identification of pathogens in urine specimens. We collected 965 urine specimens from patients with suspected UTIs, 211/965 isolates were identified as positive by conventional urine culture. Compared with the conventional method, the results of centrifugation-based MALDI-TOF MS were consistent in 159/211 cases (75.4%), of which 135/159 (84.9%) had scores ≥ 2.00; 182/211 cases (86.3%) were detected using short-term culture combined with MALDI-TOF MS, of which 153/182 (84.1%) had scores ≥ 2.00. There were no apparent differences among the three methods (p = 0.135). MALDI-TOF MS appears to accelerate the microbial identification speed in urine and saves at least 24 to 48 hours compared with the routine urine culture. Centrifugation-based MALDI-TOF MS is characterized by faster identification speed; however, it is substantially affected by the number of bacterial colonies. In contrast, short-term culture combined with MALDI-TOF MS has a higher detection rate but a relatively slow identification speed. Combining these characteristics, the two methods may be effective and reliable alternatives to traditional urine culture.
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Affiliation(s)
- DERU LEI
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - PEIYING CHEN
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - XUETING CHEN
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - YUJIE ZONG
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - XIANGYANG LI
- The Center of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
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Rapid Detection and Antibiotic Susceptibility of Uropathogenic Escherichia coli by Flow Cytometry. Microorganisms 2020; 8:microorganisms8081233. [PMID: 32823555 PMCID: PMC7463773 DOI: 10.3390/microorganisms8081233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 01/24/2023] Open
Abstract
Background: Early preliminary data on antibiotic resistance patterns available before starting the empiric therapy of urinary tract infections (UTIs) in patients with risk factors for acquiring antibiotic resistance could improve both clinical and epidemiological outcomes. The aim of the present study was two-fold: (i) to assess the antibiotic susceptibility of uropathogenic Escherichia coli isolates, exhibiting different antibiotic resistance phenotypes, directly in artificially contaminated urine samples using a flow cytometry (FC) based protocol; (ii) to optimize the protocol on urine samples deliberately contaminated with bacterial suspensions prepared from uropathogenic E. coli strains. Results: The results of the FC based antimicrobial susceptibility testing (AST) protocol were compared with the reference AST methods results (disk diffusion and broth microdilution) for establishing the sensitivity and specificity. The proposed FC protocol allowed the detection and quantification of uropathogenic E. coli strains susceptibility to nitrofurantoin, trimethoprim–sulfamethoxazole, ciprofloxacin, and ceftriaxone within 4 h after the inoculation of urine specimens. The early availability of preliminary antibiotic susceptibility results provided by direct analysis of clinical specimens could essentially contribute to a more targeted emergency therapy of UTIs in the anticipation of AST results obtained by reference methodology. Conclusions: This method will increase the therapeutic success rate and help to prevent the emergence and dissemination of drug resistant pathogens.
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22
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Ho ML, Liu WF, Tseng HY, Yeh YT, Tseng WT, Chou YY, Huang XR, Hsu HC, Ho LI, Pan SW. Quantitative determination of leukocyte esterase with a paper-based device. RSC Adv 2020; 10:27042-27049. [PMID: 35515798 PMCID: PMC9055505 DOI: 10.1039/d0ra03306e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/09/2020] [Indexed: 11/21/2022] Open
Abstract
The commercially-available colorimetric urine dipstic for the early detection of urinary tract infection (UTI) has several limitations. The quantitative determination of urinary leukocyte esterase (LE) for predicting UTI remains uncertain. This study presents a paper-based analytical device to detect LE (LE-PAD) as a point-of-care quantitative test for UTI. The LE-PAD is composed of a coating of mixed 3-(N-tosyl-L-alaninyloxy)-5-phenylpyrrole (PE) and 1-diazo-2-naphthol-4-sulfonic acid (DAS) deposited onto a silver conducting film (Ag film). The LE/urine reacts with the PE and DAS, and the resulting products in turn react with the silver coating, causing a change in resistivity. The quantitative calibration curve was established in this study and has been used to analyse urine samples from inpatients with urinary catheters (n = 21). The results revealed that the level of LE determined by LE-PADs was predictive of UTI diagnosis with an area under the receiver operating characteristic curve of 0.875 (95% confidence interval, 0.704-1.000). Using an appropriate cut-off value, the sensitivity and specificity of UTI diagnosis by LE-PAD were 87.5% and 92.3%, while the LE-positivities of urine dipstics were 62.5% and 76.9%, respectively. For UTI diagnosis, the LE-PAD demonstrated positive and negative likelihood ratios of 11.38 and 0.14, suggesting that the novel LE-PAD is a reliable test.
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Affiliation(s)
- Mei-Lin Ho
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Wei-Fang Liu
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Hsin-Yi Tseng
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Yu-Tzu Yeh
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Wei-Ting Tseng
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Yin-Yu Chou
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Xin-Ru Huang
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Hung-Cheng Hsu
- Department of Chemistry, Soochow University Taipei 111 Taiwan +886 2 2881 1053 +886 2 2881 9471 ext. 6827
| | - Li-Ing Ho
- Department of Chest Medicine, Taipei Veterans General Hospital Taipei 11217 Taiwan
- School of Medicine, National Yang-Ming University Taipei 11221 Taiwan
| | - Sheng-Wei Pan
- Department of Chest Medicine, Taipei Veterans General Hospital Taipei 11217 Taiwan
- School of Medicine, National Yang-Ming University Taipei 11221 Taiwan
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Oros D, Ceprnja M, Zucko J, Cindric M, Hozic A, Skrlin J, Barisic K, Melvan E, Uroic K, Kos B, Starcevic A. Identification of pathogens from native urine samples by MALDI-TOF/TOF tandem mass spectrometry. Clin Proteomics 2020; 17:25. [PMID: 32581661 PMCID: PMC7310424 DOI: 10.1186/s12014-020-09289-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
Background Reliable high-throughput microbial pathogen identification in human urine samples is crucial for patients with cystitis symptoms. Currently employed methods are time-consuming and could lead to unnecessary or inadequate antibiotic treatment. Purpose of this study was to assess the potential of mass spectrometry for uropathogen identification from a native urine sample. Methods In total, 16 urine samples having more than 105 CFU/mL were collected from clinical outpatients. These samples were analysed using standard urine culture methods, followed by 16S rRNA gene sequencing serving as control and here described culture-independent MALDI-TOF/TOF MS method being tested. Results Here we present advantages and disadvantages of bottom-up proteomics, using MALDI-TOF/TOF tandem mass spectrometry, for culture-independent identification of uropathogens (e.g. directly from urine samples). The direct approach provided reliable identification of bacteria at the genus level in monobacterial samples. Taxonomic identifications obtained by proteomics were compared both to standard urine culture test used in clinics and genomic test based on 16S rRNA sequencing. Conclusions Our findings indicate that mass spectrometry has great potential as a reliable high-throughput tool for microbial pathogen identification in human urine samples. In this case, the MALDI-TOF/TOF, was used as an analytical tool for the determination of bacteria in urine samples, and the results obtained emphasize high importance of storage conditions and sample preparation method impacting reliability of MS2 data analysis. The proposed method is simple enough to be utilized in existing clinical settings and is highly suitable for suspected single organism infectious etiologies. Further research is required in order to identify pathogens in polymicrobial urine samples.
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Affiliation(s)
- Damir Oros
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Marina Ceprnja
- Biochemical Laboratory, Special Hospital Agram, Polyclinic Zagreb, 10000 Zagreb, Croatia
| | - Jurica Zucko
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Mario Cindric
- Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Amela Hozic
- Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Jasenka Skrlin
- Department for Clinical Microbiology and Hospital Infection, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Karmela Barisic
- Faculty of Pharmacy and Biochemistry, Zagreb University, Zagreb, Croatia
| | - Ena Melvan
- Department of Biological Science, Faculty of Science, Macquarie University, Sydney, Australia
| | - Ksenija Uroic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Blazenka Kos
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
| | - Antonio Starcevic
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, Zagreb University, 10000 Zagreb, Croatia
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Tang M, Yang J, Li Y, Zhang L, Peng Y, Chen W, Liu J. Diagnostic Accuracy of MALDI-TOF Mass Spectrometry for the Direct Identification of Clinical Pathogens from Urine. Open Med (Wars) 2020; 15:266-273. [PMID: 32292823 PMCID: PMC7147288 DOI: 10.1515/med-2020-0038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/28/2019] [Indexed: 12/20/2022] Open
Abstract
Matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) has become one of the most popular methods for the rapid and cost-effective detection of clinical pathogenic microorganisms. This study aimed to evaluate and compare the diagnostic performance of MALDI-TOF MS with that of conventional approaches for the direct identification of pathogens from urine samples. A systematic review was conducted based on a literature search of relevant databases. The pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR) and area under the summary receiver operating characteristic (SROC) curve of the combined studies were estimated. Nine studies with a total of 3920 subjects were considered eligible and included in the meta-analysis. The pooled sensitivity was 0.85 (95% CI 0.79-0.90), and the pooled specificity was 0.93 (95% CI 0.82-0.97). The PLR and NLR were 11.51 (95% CI 4.53-29.26) and 0.16 (95% CI 0.11-0.24), respectively. The area under the SROC curve was 0.93 (95% CI 0.91-0.95). Sensitivity analysis showed that the results of this meta-analysis were stable. MALDI-TOF MS could directly identify microorganisms from urine samples with high sensitivity and specificity.
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Affiliation(s)
- Min Tang
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Jia Yang
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Ying Li
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Luhua Zhang
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Ying Peng
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
| | - Wenbi Chen
- Department of Pathogenic Biology, College of Preclinical Medicine, Southwest Medical University, Luzhou city, Sichuan Province, China
| | - Jinbo Liu
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou City, Sichuan Province, China
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25
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Rubio E, Zboromyrska Y, Bosch J, Fernandez-Pittol MJ, Fidalgo BI, Fasanella A, Mons A, Román A, Casals-Pascual C, Vila J. Evaluation of flow cytometry for the detection of bacteria in biological fluids. PLoS One 2019; 14:e0220307. [PMID: 31390352 PMCID: PMC6685611 DOI: 10.1371/journal.pone.0220307] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/12/2019] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVES Conventional microbiological procedures for the isolation of bacteria from biological fluids consist of culture on solid media and enrichment broth. However, these methods can delay the microbiological identification for up to 4 days. The aim of this study was to evaluate the analytical performance of Sysmex UF500i (Sysmex, Kobe, Japan) as a screening method for the detection of bacteria in different biological fluids in comparison with direct Gram staining and the conventional culture on solid media and enrichment broth. METHODS A total of 479 biological fluid samples were included in the study (180 ascitic, 131 amniotic, 56 synovial, 40 cerebrospinal, 36 pleural, 24 peritoneal, 9 bile and 3 pericardial fluids). All samples were processed by conventional culture methods and analyzed by flow cytometry. Direct Gram staining was performed in 339 samples. The amount of growth on culture was recorded for positive samples. RESULTS Bacterial and white blood cell count by flow cytometry was significantly higher among culture positive samples and samples with a positive direct Gram stain compared to culture negative samples. Bacterial count directly correlated with the amount of growth on culture (Kruskall-Wallis H χ2(3) = 11.577, p = 0.009). The best specificity (95%) for bacterial count to predict culture positivity was achieved applying a cut-off value of 240 bacteria/μL. CONCLUSIONS Bacterial and white blood cell counts obtained with flow cytometry correlate with culture results in biological fluids. Bacterial count can be used as a complementary method along with the direct Gram stain to promptly detect positive samples and perform other diagnostic techniques in order to accelerate the bacterial detection and identification.
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Affiliation(s)
- Elisa Rubio
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
- * E-mail:
| | - Yuliya Zboromyrska
- Consorci del Laboratori Intercomarcal de l´Alt Penedès, l´Anoia i el Garraf, Vilafranca del Penedès, Barcelona, Spain
| | - Jordi Bosch
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal, Barcelona, Institute for Global Health, Barcelona, Spain
| | - Mariana J. Fernandez-Pittol
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Berta I. Fidalgo
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Assumpta Fasanella
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Anna Mons
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Angely Román
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Climent Casals-Pascual
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal, Barcelona, Institute for Global Health, Barcelona, Spain
| | - Jordi Vila
- Department of Microbiology, Biomedical Diagnostic Center (BDC), Hospital Clinic, University of Barcelona, Barcelona, Spain
- ISGlobal, Barcelona, Institute for Global Health, Barcelona, Spain
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Bryson AL, Hill EM, Doern CD. Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress. Clin Lab Med 2019; 39:391-404. [PMID: 31383264 DOI: 10.1016/j.cll.2019.05.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This article summarizes recent advances in the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to new areas of infectious diseases diagnostics. We discuss progress toward routine identification of mycobacteria and filamentous fungi and direct identification of pathogens from clinical specimens. Of greatest interest is the use of MALDI-TOF MS for identifying organisms from positive blood cultures and from clinical specimens such as urine. Last, We highlight some exciting new possibilities for MALDI-TOF MS phenotypic susceptibility testing for bacteria and yeast.
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Affiliation(s)
- Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA
| | - Emily M Hill
- Pathology & Laboratory Medicine, Hunter Holmes McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23224, USA
| | - Christopher D Doern
- Department of Pathology, Virginia Commonwealth University Health System, 403 North 13th Street, Richmond, VA 23298, USA.
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Li W, Sun E, Wang Y, Pan H, Zhang Y, Li Y, Zhang X, Li C, Du L, Wang C. Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol. Front Microbiol 2019; 10:1182. [PMID: 31231323 PMCID: PMC6560049 DOI: 10.3389/fmicb.2019.01182] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
Usually, 18–48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18–24 h. Rapid identification and AST of the pathogens allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6–24 h for AST; noteworthily, only 6–8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.
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Affiliation(s)
- Wei Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Enhua Sun
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Ying Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Hongwei Pan
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Yong Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Chen Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
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Idelevich EA, Becker K. How to accelerate antimicrobial susceptibility testing. Clin Microbiol Infect 2019; 25:1347-1355. [PMID: 31055166 DOI: 10.1016/j.cmi.2019.04.025] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/27/2019] [Accepted: 04/18/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) results are crucial for timely administration of effective antimicrobial treatment, and, thus, should be made available to clinicians as fast as possible. In particular, increasing rates of multidrug-resistant organisms emphasize the need for rapid AST (rAST). OBJECTIVES This article aims to provide microbiologists and clinicians with a critical overview of the current state of possibilities to accelerate AST. We also intend to discuss technical and strategic aspects of rAST, which may be helpful to academic researchers and assay developers in the industry. SOURCES We have reviewed literature on rAST methods and their implementation in routine diagnostics. CONTENT Phenotypic rAST is universal, mechanism-independent and allows exact categorization, but it demands time for the microorganisms to start the growth and to express the response to antibiotics. Detection of selected resistance mechanisms is more rapid, but the interpretation of its clinical impact is limited. Technical challenges of phenotypic rAST include inoculum effect, delayed expression of resistance, lag phase and initial biomass increase in susceptible isolates. Criteria for a successful rAST assay are ease of use, random access, capacity for simultaneous testing of multiple specimens, affordability and financial attractiveness for industry. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based AST seems to be particularly promising, as it can optimally be combined with MALDI-TOF MS identification. Direct testing from clinical specimens provides particularly early findings, with positive blood cultures being the most suitable specimen type. Polymicrobial samples and inoculum effect are serious obstacles for direct AST from other clinical specimens. Next to the technology improvement, optimization of pre-analytics and laboratory organization is essential. IMPLICATIONS It appears feasible to generate an AST report within the same working shift; however, only affordable and easy-to-use rAST technologies have a chance to enter broad diagnostic routine. Efforts should be made by industry, authorities and academia to enable wide dissemination of rAST in clinical diagnostics.
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Affiliation(s)
- E A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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Direct Identification of Pathogens in Urine by Use of a Specific Matrix-Assisted Laser Desorption Ionization-Time of Flight Spectrum Database. J Clin Microbiol 2019; 57:JCM.01678-18. [PMID: 30700506 DOI: 10.1128/jcm.01678-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/24/2019] [Indexed: 11/20/2022] Open
Abstract
Urinary tract infections are among the most common reasons for antimicrobial treatment, and early diagnosis could have a significant impact by enabling rapid administration of the adapted antibiotic and preventing complications. The current delay between sample receipt and pathogen identification is about 24 to 48 h, which could be significantly shortened by use of an accurate direct method. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is already used for the identification of pathogens in clinical laboratories and constitutes a promising tool for direct diagnosis. A simple preparation protocol was established for the processing of urine samples prior to MS analysis. MALDI-TOF spectra collected directly from 1,000 infected urine samples were used to create a specific reference database (named Urinf). A prospective study was then carried out to evaluate the Urinf database and compare the results obtained with the standard database provided by Bruker on the Biotyper Real Time Classification software. Seven hundred eighty urine specimens were processed and analyzed according to our method. Among them, almost 90% of 500 infected monobacterial samples could be correctly diagnosed with the Urinf database, compared to 50% using the standard database. The identification of Enterobacteriaceae, Staphylococcus aureus, Staphylococcus saprophyticus, Pseudomonas aeruginosa, Enterococcus faecalis, and Enterococcus faecium was greatly improved but not for Staphylococcus epidermidis The creation of a database adapted to a particular type of clinical sample has great potential to increase both the rate and rapidity of pathogen identification. Sensitivity still remains to be improved for bacterial species that exhibit few specific peaks on mass spectra.
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Guzmán-Puche J, Gracia-Ahufinger I, Causse M, Tejero-García R, Rodríguez-López FC, Casal-Román M. Combination of Coral UTI Screen TM system, gram-stain and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for diagnosis of urinary tract infections directly from urine samples. J Chemother 2019; 31:74-80. [PMID: 30784363 DOI: 10.1080/1120009x.2019.1573284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
This study proposes an algorithm for microbiological diagnosis of urinary tract infections based on screening by luminometry and Gram-stain, followed by identification by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Positive urine samples detected with the luminometry screening Coral UTI ScreenTM system underwent Gram staining and identification of the causative organism was performed by MALDI-TOF Microflex LT mass spectrometer (Bruker Daltonics, Germany). Subsequently, the results were compared with those of conventional culture identification using WIDER MIC/id system (Francisco Soria Melguizo SA, Spain). Considering the conventional approach as the gold standard, the proposed algorithm presented both a high specificity (98.1%) and a positive likelihood ratio of 37.42. The implementation of this algorithm would allow diagnosis of urinary tract infection in less than an hour in 92.4% of positive samples. This combination of techniques would be useful particularly for patients with severe UTI, pyelonephritis or urinary sepsis.
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Affiliation(s)
- Julia Guzmán-Puche
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain
| | - Irene Gracia-Ahufinger
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Manuel Causse
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Rocío Tejero-García
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Fernando Carlos Rodríguez-López
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain.,c Spanish Network for Infectious Disease Research (REIPI RD12/0015) , Instituto de Salud Carlos III , Madrid , Spain
| | - Manuel Casal-Román
- a UGC Microbiology , Reina Sofía University Hospital , Córdoba , Spain.,b Maimónides Institute for Research in Biomedicine of Córdoba (IMIBIC) , Universidad de Córdoba , Córdoba , Spain
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Zboromyrska Y, Bosch J, Aramburu J, Cuadros J, García-Riestra C, Guzmán-Puche J, Liébana Martos C, Loza E, Muñoz-Algarra M, Ruiz de Alegría C, Sánchez-Hellín V, Vila J. A multicentre study investigating parameters which influence direct bacterial identification from urine. PLoS One 2018; 13:e0207822. [PMID: 30533050 PMCID: PMC6289437 DOI: 10.1371/journal.pone.0207822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/05/2018] [Indexed: 01/12/2023] Open
Abstract
Rapid diagnosis is one of the best ways to improve patient management and prognosis as well as to combat the development of bacterial resistance. The aim of this study was to study parameters that impact the achievement of reliable identification using a combination of flow cytometry and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF-MS).The study was carried out in nine hospitals in Spain and included 1,050 urine samples with bacterial counts of 5x106 bacteria/ml. MALDI-ToF-MS-based identification was performed according to a previously described protocol. Valid identification by direct MALDI-ToF-MS was obtained in 72.8% of samples, in 80.3% of samples found to be positive by culture, 32.2% of contaminated samples, and 19.7% of negative samples. Among the positives samples with a valid identification the concordance at the species level was 97.2%. The parameters related to success of direct identification were: high bacterial count, the presence of Escherichia coli as a pathogen and rod-bacteria morphology provided by flow cytometry. The parameters related to failure were a high epithelial cell (EC) count, a high white blood cell (WBC) count and urine samples obtained from in-patients. In summary, this multicentre study confirms previously published data on the usefulness and accuracy of direct MALDI-ToF-MS-based identification of bacteria from urine samples. It seems important to evaluate not only the bacterial count, but also other parameters, such as EC and WBC counts, bacterial species and morphology, and the health care setting, to decide whether the sample is suitable for direct identification.
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Affiliation(s)
- Yuliya Zboromyrska
- Consorci del Laboratori Intercomarcal, Vilafranca del Penedès, Spain
- * E-mail:
| | - Jordi Bosch
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
- ISGlobal, Instituto de Salud Global de Barcelona, Barcelona, Spain
| | - Jesus Aramburu
- Microbiology Unit, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Juan Cuadros
- Microbiology Department, Hospital Príncipe de Asturias, Alcalá de Henares, Spain
| | - Carlos García-Riestra
- Microbiology Department, Complejo Hospitalario Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Julia Guzmán-Puche
- Microbiology Unit, Hospital Reina Sofía, IMIBIC-Reina Sofía University Hospital-University of Córdoba, Córdoba, Spain
| | - Carmen Liébana Martos
- Infectious Diseases and Clinical Microbiology Unit, Complejo Hospitalario de Jaén, Jaén, Spain
| | - Elena Loza
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - María Muñoz-Algarra
- Department of Clinical Microbiology, Hospital Universitario Puerta de Hierro, Majadahonda, Spain
| | | | | | - Jordi Vila
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
- ISGlobal, Instituto de Salud Global de Barcelona, Barcelona, Spain
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Esposito S, Rinaldi VE, Argentiero A, Farinelli E, Cofini M, D'Alonzo R, Mencacci A, Principi N. Approach to Neonates and Young Infants with Fever without a Source Who Are at Risk for Severe Bacterial Infection. Mediators Inflamm 2018; 2018:4869329. [PMID: 30581369 PMCID: PMC6287153 DOI: 10.1155/2018/4869329] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/07/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Among neonates and infants <3 months of age with fever without a source (FWS), 5% to 15% of cases are patients with fever caused by a serious bacterial infection (SBI). To favour the differentiation between low- and high-risk infants, several algorithms based on analytical and clinical parameters have been developed. The aim of this review is to describe the management of young infants with FWS and to discuss the impact of recent knowledge regarding FWS management on clinical practice. MATERIALS AND METHODS PubMed was used to search for all of the studies published over the last 35 years using the keywords: "fever without source" or "fever of unknown origin" or "meningitis" or "sepsis" or "urinary tract infection" and "neonate" or "newborn" or "infant <90 days of life" or "infant <3 months". RESULTS AND DISCUSSION The selection of neonates and young infants who are <3 months old with FWS who are at risk for SBI remains a problem without a definitive solution. The old Rochester criteria remain effective for identifying young infants between 29 and 60 days old who do not have severe bacterial infections (SBIs). However, the addition of laboratory tests such as C-reactive protein (CRP) and procalcitonin (PCT) can significantly improve the identification of children with SBI. The approach in evaluating neonates is significantly more complicated, as their risk of SBIs, including bacteremia and meningitis, remains relevant and none of the suggested approaches can reduce the risk of dramatic mistakes. In both groups, the best antibiotic must be carefully selected considering the clinical findings, the laboratory data, the changing epidemiology, and increasing antibiotic resistance of the most common infectious bacteria.
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Affiliation(s)
- Susanna Esposito
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Victoria Elisa Rinaldi
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Alberto Argentiero
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Edoardo Farinelli
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Marta Cofini
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Renato D'Alonzo
- Pediatric Clinic, Department of Surgical and Biomedical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Antonella Mencacci
- Microbiology Unit, Department of Medicine, Università degli Studi di Perugia, Perugia, Italy
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Oyaert M, Delanghe J. Progress in Automated Urinalysis. Ann Lab Med 2018; 39:15-22. [PMID: 30215225 PMCID: PMC6143458 DOI: 10.3343/alm.2019.39.1.15] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/13/2018] [Accepted: 08/29/2018] [Indexed: 12/17/2022] Open
Abstract
New technological advances have paved the way for significant progress in automated urinalysis. Quantitative reading of urinary test strips using reflectometry has become possible, while complementary metal oxide semiconductor (CMOS) technology has enhanced analytical sensitivity and shown promise in microalbuminuria testing. Microscopy-based urine particle analysis has greatly progressed over the past decades, enabling high throughput in clinical laboratories. Urinary flow cytometry is an alternative for automated microscopy, and more thorough analysis of flow cytometric data has enabled rapid differentiation of urinary microorganisms. Integration of dilution parameters (e.g., creatinine, specific gravity, and conductivity) in urine test strip readers and urine particle flow cytometers enables correction for urinary dilution, which improves result interpretation. Automated urinalysis can be used for urinary tract screening and for diagnosing and monitoring a broad variety of nephrological and urological conditions; newer applications show promising results for early detection of urothelial cancer. Concomitantly, the introduction of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has enabled fast identification of urinary pathogens. Automation and workflow simplification have led to mechanical integration of test strip readers and particle analysis in urinalysis. As the information obtained by urinalysis is complex, the introduction of expert systems may further reduce analytical errors and improve the quality of sediment and test strip analysis. With the introduction of laboratory-on-a-chip approaches and the use of microfluidics, new affordable applications for quantitative urinalysis and readout on cell phones may become available. In this review, we present the main recent developments in automated urinalysis and future perspectives.
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Affiliation(s)
- Matthijs Oyaert
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium.
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Périllaud-Dubois C, Pilmis B, Diep J, de Ponfilly GP, Perreau S, Ruffier d'Epenoux L, Mizrahi A, Couzigou C, Vidal B, Le Monnier A, Nguyen Van JC. Performance of rapid antimicrobial susceptibility testing by disk diffusion on MHR-SIR agar directly on urine specimens. Eur J Clin Microbiol Infect Dis 2018; 38:185-189. [PMID: 30386946 DOI: 10.1007/s10096-018-3413-5] [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] [Received: 08/09/2018] [Accepted: 10/24/2018] [Indexed: 01/21/2023]
Abstract
The standard method for the diagnosis of urinary tract infections is urine culture that requires 18-48 h for the identification of the bacteria and an additional 24 h until the results of antimicrobial susceptibility testing (AST) are available. We evaluated here a rapid AST method by disc diffusion performed directly on urine samples with a delay of 8 h. A total of 245 urine samples with monobacterial Gram negative observed on microscopy were tested in parallel by two AST methods. Rapid AST method was performed directly on urine samples using Rapid Mueller-Hinton (MHR-SIR) with 8-h incubation before reading and standard method was performed as usual. We compared the categorical agreement and the correlation between the diameters obtained by standard method and by MHR-SIR directly on urine samples. Over the 5285 tested combinations, we observed 5172 (97.9%) categorical agreement, 82 (1.5%) minor errors, 17 (0.3%) major errors, and 14 (0.3%) very major errors. Our results showed an excellent categorical agreement and correlations between diameters for MHR-SIR and standard methods. MHR-SIR performed directly on urine samples with monomicrobial Enterobacteriacae can predict the result of overall AST profile in 8 h with reliable results. The main advantage of MHR-SIR is that it offers the possibility of obtaining results 40 h earlier than conventional AST. The cost is estimated for less than 6 USD for 16 antibiotics, chosen by the microbiologist.
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Affiliation(s)
| | - Benoît Pilmis
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Julien Diep
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | | | - Simon Perreau
- Laboratoire de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | | | - Assaf Mizrahi
- Laboratoire de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Carine Couzigou
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France.,Equipe opérationnel d'hygiène, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Barbara Vidal
- Unité Mobile de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France.,Equipe opérationnel d'hygiène, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Alban Le Monnier
- Laboratoire de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - Jean-Claude Nguyen Van
- Laboratoire de Microbiologie Clinique, Groupe Hospitalier Paris Saint-Joseph, Paris, France.
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Ghosh PN, Fisher MC, Bates KA. Diagnosing Emerging Fungal Threats: A One Health Perspective. Front Genet 2018; 9:376. [PMID: 30254662 PMCID: PMC6141620 DOI: 10.3389/fgene.2018.00376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 11/17/2022] Open
Abstract
Emerging fungal pathogens are a growing threat to global health, ecosystems, food security, and the world economy. Over the last century, environmental change and globalized transport, twinned with the increasing application of antifungal chemical drugs have led to increases in outbreaks of fungal diseases with sometimes catastrophic effects. In order to tackle contemporary epidemics and predemic threats, there is a pressing need for a unified approach in identification and monitoring of fungal pathogens. In this paper, we discuss current high throughput technologies, as well as new platforms capable of combining diverse data types to inform practical epidemiological strategies with a focus on emerging fungal pathogens of wildlife.
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Affiliation(s)
- Pria N. Ghosh
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Matthew C. Fisher
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Kieran A. Bates
- Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
- Institute of Zoology, Zoological Society of London, London, United Kingdom
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36
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Váradi L, Luo JL, Hibbs DE, Perry JD, Anderson RJ, Orenga S, Groundwater PW. Methods for the detection and identification of pathogenic bacteria: past, present, and future. Chem Soc Rev 2018. [PMID: 28644499 DOI: 10.1039/c6cs00693k] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In order to retard the rate of development of antibacterial resistance, the causative agent must be identified as rapidly as possible, so that directed patient treatment and/or contact precautions can be initiated. This review highlights the challenges associated with the detection and identification of pathogenic bacteria, by providing an introduction to the techniques currently used, as well as newer techniques that are in development. Focusing on the chemical basis for these techniques, the review also provides a comparison of their advantages and disadvantages.
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Affiliation(s)
- Linda Váradi
- Faculty of Pharmacy, The University of Sydney, Sydney, NSW 2006, Australia.
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Oviaño M, Ramírez CDLL, Barbeyto LP, Bou G. Rapid direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples by MALDI-TOF MS analysis. J Antimicrob Chemother 2018; 72:1350-1354. [PMID: 28119478 DOI: 10.1093/jac/dkw579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/15/2016] [Indexed: 11/12/2022] Open
Abstract
Objectives Development of an automated MALDI-TOF MS-based method for the rapid, direct detection of carbapenemase-producing Enterobacteriaceae in clinical urine samples within 90 min of sample reception. Methods A total of 3041 urine samples were processed by flow cytometry, and a cut-off value of ≥1.5 × 10 5 bacteria/mL was used to select samples for the study. Following these criteria, 608 samples were selected for direct bacterial identification. Detection of carbapenemase activity by MALDI-TOF MS analysis was only performed after reliable direct identification of Gram-negative bacilli. A novel protocol was developed for extracting bacteria from urine samples by using the Sepsityper Kit (Bruker Daltonik, Germany). Carbapenem resistance was detected with imipenem as an antibiotic marker and the results were automatically interpreted using the STAR-BL module of MALDI-TOF Biotyper Compass software (Bruker Daltonik, Germany). Results The MALDI-TOF MS-based assay yielded direct reliable identification of 91% (503/553) of the samples. The assay showed 100% sensitivity (30/30) and specificity (454/454) for detecting carbapenemase activity within 90 min of sample reception. Isolates included in the study were further characterized by PCR and sequencing, and bla OXA-48 was detected from all isolates that tested positive in the MALDI-TOF MS-based resistance assay. Conclusions The proposed protocol for the direct analysis of urine samples by MALDI-TOF MS is suitable for use in clinical laboratories to identify bacteria and detect carbapenemase activity, thus saving at least 24-48 h relative to current routine methods.
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38
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Oviaño M, Rodríguez-Sánchez B, Gómara M, Alcalá L, Zvezdanova E, Ruíz A, Velasco D, Gude MJ, Bouza E, Bou G. Direct identification of clinical pathogens from liquid culture media by MALDI-TOF MS analysis. Clin Microbiol Infect 2017; 24:624-629. [PMID: 28962998 DOI: 10.1016/j.cmi.2017.09.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVES We propose using MALDI-TOF MS as a tool for identifying microorganisms directly from liquid cultures after enrichment of the clinical sample in the media, to obtain a rapid microbiological diagnosis and an adequate administration of the antibiotic therapy in a clinical setting. METHODS To evaluate this approach, a series of quality control isolates were grown in thioglycollate (TG) broth and brain heart infusion (BHI) broth and extracted under four different protocols before finally being identified by MALDI-TOF MS. After establishing the best extraction protocol, we validated the method in a total of 300 liquid cultures (150 in TG broth and 150 in BHI broth) of different types of clinical samples obtained from two tertiary Spanish hospitals. RESULTS The initial evaluation showed that the extraction protocol including a 5 minute sonication step yielded 100% valid identifications, with an average score value of 2.305. In the clinical validation of the procedure, 98% of the microorganisms identified from the TG broth were correctly identified relative to 97% of those identified from the BHI broth. In 24% of the samples analysed, growth by direct sowing was only successful in the liquid medium, and no growth was observed in the direct solid agar cultures. CONCLUSIONS Use of MALDI-TOF MS plus the sonication-based extraction method enabled direct and accurate identification of microorganisms in liquid culture media in 15 minutes, in contrast to the 24 hours of subculture required for conventional identification, allowing the administration of a targeted antimicrobial therapy.
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Affiliation(s)
- M Oviaño
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - B Rodríguez-Sánchez
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - M Gómara
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - L Alcalá
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - E Zvezdanova
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - A Ruíz
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - D Velasco
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - M J Gude
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain
| | - E Bouza
- Servicio de Microbiología, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - G Bou
- Servicio de Microbiología, Complejo Hospitalario Universitario A Coruña, La Coruña, Spain.
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Integrated microfluidic platform for rapid antimicrobial susceptibility testing and bacterial growth analysis using bead-based biosensor via fluorescence imaging. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2492-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Davenport M, Mach KE, Shortliffe LMD, Banaei N, Wang TH, Liao JC. New and developing diagnostic technologies for urinary tract infections. Nat Rev Urol 2017; 14:296-310. [PMID: 28248946 PMCID: PMC5473291 DOI: 10.1038/nrurol.2017.20] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Timely and accurate identification and determination of the antimicrobial susceptibility of uropathogens is central to the management of UTIs. Urine dipsticks are fast and amenable to point-of-care testing, but do not have adequate diagnostic accuracy or provide microbiological diagnosis. Urine culture with antimicrobial susceptibility testing takes 2-3 days and requires a clinical laboratory. The common use of empirical antibiotics has contributed to the rise of multidrug-resistant organisms, reducing treatment options and increasing costs. In addition to improved antimicrobial stewardship and the development of new antimicrobials, novel diagnostics are needed for timely microbial identification and determination of antimicrobial susceptibilities. New diagnostic platforms, including nucleic acid tests and mass spectrometry, have been approved for clinical use and have improved the speed and accuracy of pathogen identification from primary cultures. Optimization for direct urine testing would reduce the time to diagnosis, yet these technologies do not provide comprehensive information on antimicrobial susceptibility. Emerging technologies including biosensors, microfluidics, and other integrated platforms could improve UTI diagnosis via direct pathogen detection from urine samples, rapid antimicrobial susceptibility testing, and point-of-care testing. Successful development and implementation of these technologies has the potential to usher in an era of precision medicine to improve patient care and public health.
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Affiliation(s)
- Michael Davenport
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Linda M Dairiki Shortliffe
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
| | - Niaz Banaei
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, California 94304 USA
| | - Tza-Huei Wang
- Departments of Mechanical and Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, 300 Pasteur Drive S-287, Stanford, California 94305 USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304 USA
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Direct Detection and Identification of Bacterial Pathogens from Urine with Optimized Specimen Processing and Enhanced Testing Algorithm. J Clin Microbiol 2017; 55:1488-1495. [PMID: 28249997 DOI: 10.1128/jcm.02549-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 02/17/2017] [Indexed: 11/20/2022] Open
Abstract
Rapid and accurate detection and identification of microbial pathogens causing urinary tract infections allow prompt and specific treatment. We optimized specimen processing to maximize the limit of detection (LOD) by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and evaluated the capacity of combination of MALDI-TOF MS and urine analysis (UA) for direct detection and identification of bacterial pathogens from urine samples. The optimal volumes of processed urine, formic acid/acetonitrile, and supernatant spotted onto the target plate were 15 ml, 3 μl, and 3 μl, respectively, yielding a LOD of 1.0 × 105 CFU/ml. Among a total of 1,167 urine specimens collected from three hospital centers, 612 (52.4%) and 351 (30.1%) were, respectively, positive by UA and urine culture. Compared with a reference method comprised of urine culture and 16S rRNA gene sequencing, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MALDI-TOF MS alone and MALDI-TOF MS coupled with UA were 86.6% versus 93.4% (χ2 = 8.93; P < 0.01), 91.5% versus 96.3% (χ2 = 7.06; P < 0.01), 81.5% versus 96.4% (χ2 = 37.32; P < 0.01), and 94.1% versus 93.1% (χ2 = 0.40; P > 0.05), respectively. No significant performance differences were revealed among the three sites, while specificity and NPV of MALDI-TOF MS for males were significantly higher than those for females (specificity, 94.3% versus 77.3%, χ2 = 44.90, P < 0.01; NPV, 95.5% versus 86.1%, χ2 = 18.85, P < 0.01). Our results indicated that the optimization of specimen processing significantly enhanced analytical sensitivity and that the combination of UA and MALDI-TOF MS provided an accurate and rapid detection and identification of bacterial pathogens directly from urine.
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Siller-Ruiz M, Hernández-Egido S, Sánchez-Juanes F, González-Buitrago JM, Muñoz-Bellido JL. Fast methods of fungal and bacterial identification. MALDI-TOF mass spectrometry, chromogenic media. Enferm Infecc Microbiol Clin 2017; 35:303-313. [PMID: 28108122 DOI: 10.1016/j.eimc.2016.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/16/2022]
Abstract
MALDI-TOF mass spectrometry is now a routine resource in Clinical Microbiology, because of its speed and reliability in the identification of microorganisms. Its performance in the identification of bacteria and yeasts is perfectly contrasted. The identification of mycobacteria and moulds is more complex, due to the heterogeneity of spectra within each species. The methodology is somewhat more complex, and expanding the size of species libraries, and the number of spectra of each species, will be crucial to achieve greater efficiency. Direct identification from blood cultures has been implemented, since its contribution to the management of severe patients is evident, but its application to other samples is more complex. Chromogenic media have also contributed to the rapid diagnosis in both bacteria and yeast, since they accelerate the diagnosis, facilitate the detection of mixed cultures and allow rapid diagnosis of resistant species.
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Affiliation(s)
- María Siller-Ruiz
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - Sara Hernández-Egido
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España
| | - José Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España; Servicio de Bioquímica Clínica, Complejo Asistencial Universitario de Salamanca, Salamanca, España; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, España
| | - Juan Luis Muñoz-Bellido
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Complejo Asistencial Universitario de Salamanca, Universidad de Salamanca, CSIC, Salamanca, España; Servicio de Microbiología, Complejo Asistencial Universitario de Salamanca, Salamanca, España; Departamento de Ciencias Biomédicas y del Diagnóstico, Universidad de Salamanca, Salamanca, España.
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Proteomics progresses in microbial physiology and clinical antimicrobial therapy. Eur J Clin Microbiol Infect Dis 2016; 36:403-413. [PMID: 27812806 PMCID: PMC5309286 DOI: 10.1007/s10096-016-2816-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/16/2016] [Indexed: 02/05/2023]
Abstract
Clinical microbial identification plays an important role in optimizing the management of infectious diseases and provides diagnostic and therapeutic support for clinical management. Microbial proteomic research is aimed at identifying proteins associated with microbial activity, which has facilitated the discovery of microbial physiology changes and host–pathogen interactions during bacterial infection and antimicrobial therapy. Here, we summarize proteomic-driven progresses of host–microbial pathogen interactions at multiple levels, mass spectrometry-based microbial proteome identification for clinical diagnosis, and antimicrobial therapy. Proteomic technique progresses pave new ways towards effective prevention and drug discovery for microbial-induced infectious diseases.
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Cimmino T, Le Page S, Raoult D, Rolain JM. Contemporary challenges and opportunities in the diagnosis and outbreak detection of multidrug-resistant infectious disease. Expert Rev Mol Diagn 2016; 16:1163-1175. [PMID: 27690721 DOI: 10.1080/14737159.2016.1244005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The dissemination of multi-drug resistant bacteria (MDRB) has become a major public health concern worldwide because of the increase in infections caused by MDRB, the difficulty in treating them, and expenditures in patient care. Areas covered: We have reviewed challenges and contemporary opportunities for rapidly confronting infections caused by MDRB in the 21st century, including surveillance, detection, identification of resistance mechanisms, and action steps. Expert commentary: In this context, the first critical point for clinical microbiologists is to be able to rapidly detect an abnormal event, an outbreak and/or the spread of a MDRB with surveillance tools so that healthcare policies and therapies adapted to a new stochastic event that will certainly occur again in the future can be implemented.
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Affiliation(s)
- Teresa Cimmino
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Stéphanie Le Page
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Didier Raoult
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
| | - Jean-Marc Rolain
- a URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille University , Marseille , France
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