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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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Abou Chacra L, Drouet H, Ly C, Bretelle F, Fenollar F. Evaluation of Various Diagnostic Strategies for Bacterial Vaginosis, Including a New Approach Based on MALDI-TOF Mass Spectrometry. Microorganisms 2024; 12:111. [PMID: 38257938 PMCID: PMC10821145 DOI: 10.3390/microorganisms12010111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Bacterial vaginosis (BV) is a common dysbiosis of unclear etiology but with potential consequences representing a public health problem. The diagnostic strategies vary widely. The Amsel criteria and Nugent score have obvious limitations, while molecular biology techniques are expensive and not yet widespread. We set out to evaluate different diagnostic strategies from vaginal samples using (1) a combination of abnormal vaginal discharge and vaginal pH > 4.5; (2) the Amsel-like criteria (replacing the "whiff test" with "malodorous discharge"); (3) the Nugent score; (4) the molecular quantification of Fannyhessea vaginae and Gardnerella vaginalis (qPCR); (5) and MALDI-TOF mass spectrometry (we also refer to it as "VAGI-TOF"). Overall, 54/129 patients (42%) were diagnosed with BV using the combination of vaginal discharge and pH, 46/118 (39%) using the Amsel-like criteria, 31/130 (24%) using qPCR, 32/130 (25%) using "VAGI-TOF", and 23/84 (27%) using the Nugent score (not including the 26 (31%) with intermediate flora). Of the 84 women for whom the five diagnostic strategies were performed, the diagnosis of BV was considered for 38% using the combination of vaginal discharge and pH, 34.5% using the Amsel-like criteria, 27% using the Nugent score, 25% using qPCR, and 25% using "VAGI-TOF". When qPCR was considered as the reference, the sensitivity rate for BV was 76.2% for the combination of vaginal discharge and pH, 90.5% for the Amsel-like criteria, 95.2% for the Nugent score, and 90.5% for "VAGI-TOF", while the specificity rates were 74.6%, 84.1%, 95.3%, and 95.3%, respectively. When the Nugent score was considered as the reference, the sensitivity for BV was 69.6% for the combination of vaginal discharge and pH, 82.6% for the Amsel-like criteria, 87% for qPCR, and 78.7% for "VAGI-TOF", while the specificity rates were 80%, 94.3%, 100%, and 97.1%, respectively. Overall, the use of qPCR and "VAGI-TOF" provided a consistent diagnosis of BV, followed by the Nugent score. If qPCR seems tedious and for some costly, "VAGI-TOF" could be an inexpensive, practical, and less time-consuming alternative.
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Affiliation(s)
- Linda Abou Chacra
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Hortense Drouet
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Claudia Ly
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Florence Bretelle
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, MEPHI, 13005 Marseille, France;
- Department of Gynaecology and Obstetrics, Gynépole, La Conception, AP-HM, 13005 Marseille, France
| | - Florence Fenollar
- Campus Santé Timone, Aix-Marseille University, IRD, AP-HM, SSA, VITROME, 13005 Marseille, France; (L.A.C.); (H.D.); (C.L.)
- IHU-Méditerranée Infection, 13005 Marseille, France
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Yacouba A, Bellali S, Haddad G, Mavros N, Fontanini A, Dubourg G, Lagier JC, Raoult D, Bou Khalil J. Use of scanning electron microscopy and energy dispersive X-ray for urine analysis: A preliminary investigation. Microsc Res Tech 2023; 86:1249-1257. [PMID: 36773029 DOI: 10.1002/jemt.24301] [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: 08/17/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/12/2023]
Abstract
Scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) are powerful tools to study the ultrastructure of numerous specimens and to determine their elemental composition, respectively. However, results have not yet been reported on their application to urine samples in routine clinical laboratory practice. Herein we investigate urine sediment by using SEM and EDX to detect and identify different urine components. A total of 206 urine samples from patients with and without urinary tract infections were analyzed using SEM and EDX. Microorganisms, crystals, epithelial cells, leukocytes, and erythrocytes were targeted in urine sediment samples. The identification of urine components was based on their morphology, size, contrast, and elemental composition. SEM-analysis allowed us to identify and classify microorganisms in urine sediments into the categories of gram-negative bacilli, cluster cocci, chain cocci, gram-negative bacilli, gram-positive bacilli, and yeasts. In addition, various types of epithelial cells such as renal, transitional, and squamous epithelial cells were found. Furthermore, leukocytes and erythrocytes were well identified, with the detection of various morphological forms of erythrocytes, such as dysmorphic and isomorphic erythrocytes. Using SEM-EDX analysis, calcium oxalate was the most frequently-identified crystal (92.0%), with prominent peaks of C, O, and Ca elements, followed by struvite (6%), with peaks of Mg, P, O, and N. These preliminary data suggest that the two complementary SEM-EDX analyses can be used to detect and identify microorganisms and crystals in urine samples. Further studies are still needed to apply SEM-EDX to urine sediment analysis. SEM-EDX analyses provided comparative results with the routine results, with accurate identification, high resolution and deep focus compared to the routine urinalysis SEM-analysis allowed us to identify and classify microorganisms in urine sediments into the categories of gram-negative bacilli, cluster cocci, chain cocci, gram-negative bacilli, gram-positive bacilli and yeasts. SEM-EDX analysis enabled the accurate identification of crystals based on both morphology and elemental composition.
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Affiliation(s)
- Abdourahamane Yacouba
- IRD, AP-HM, MEPHI, Aix Marseille University, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
- Université Abdou Moumouni, Niamey, Niger
| | | | - Gabriel Haddad
- IRD, AP-HM, MEPHI, Aix Marseille University, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | | | | | - Grégory Dubourg
- IRD, AP-HM, MEPHI, Aix Marseille University, Marseille, France
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Lila ASA, Rajab AAH, Abdallah MH, Rizvi SMD, Moin A, Khafagy ES, Tabrez S, Hegazy WAH. Biofilm Lifestyle in Recurrent Urinary Tract Infections. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010148. [PMID: 36676100 PMCID: PMC9865985 DOI: 10.3390/life13010148] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023]
Abstract
Urinary tract infections (UTIs) represent one of the most common infections that are frequently encountered in health care facilities. One of the main mechanisms used by bacteria that allows them to survive hostile environments is biofilm formation. Biofilms are closed bacterial communities that offer protection and safe hiding, allowing bacteria to evade host defenses and hide from the reach of antibiotics. Inside biofilm communities, bacteria show an increased rate of horizontal gene transfer and exchange of resistance and virulence genes. Additionally, bacterial communication within the biofilm allows them to orchestrate the expression of virulence genes, which further cements the infestation and increases the invasiveness of the infection. These facts stress the necessity of continuously updating our information and understanding of the etiology, pathogenesis, and eradication methods of this growing public health concern. This review seeks to understand the role of biofilm formation in recurrent urinary tact infections by outlining the mechanisms underlying biofilm formation in different uropathogens, in addition to shedding light on some biofilm eradication strategies.
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Affiliation(s)
- Amr S. Abu Lila
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Correspondence: (A.S.A.L.); (W.A.H.H.)
| | - Azza A. H. Rajab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Marwa H. Abdallah
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Syed Mohd Danish Rizvi
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - Afrasim Moin
- Department of Pharmaceutics, College of Pharmacy, University of Ha’il, Ha’il 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il 81442, Saudi Arabia
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Shams Tabrez
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat 113, Oman
- Correspondence: (A.S.A.L.); (W.A.H.H.)
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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: 6] [Impact Index Per Article: 3.0] [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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Alfhili MA, Ahmad I, Alraey Y, Alangari A, Alqahtani T, Dera AA. Antibacterial and anti-biofilm activity of plumbagin against multi-drug resistant clinical bacterial isolates. Saudi Med J 2022; 43:1224-1233. [PMID: 36379534 PMCID: PMC10043915 DOI: 10.15537/smj.2022.43.11.20220446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023] Open
Abstract
OBJECTIVES To evaluate the antibacterial activity of plumbagin (PGN) against multidrug resistance (MDR) clinical isolates. METHODS This study was carried out at the Department of Clinical Lab Sciences, King Khalid University from October 6, 2021 to December 14, 2021. We investigated the antibacterial and anti-virulence activity of PGN against MDR Gram-negative (Escherichia coli, Klebsiella pneumoniae, Salmonella Typhi, and Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus [S. aureus], Staphylococcus saprophyticus [S. saprophyticus], Streptococcus pyogenes, and Enterococcus faecalis) clinical bacterial isolates. Agar well diffusion, microdilution assay, colony count method, biofilm formation, and time-kill kinetics were employed to probe the MIC, MBC, and anti-virulence activity of PGN. RESULTS Plumbagin inhibited the growth of all tested isolates, with S. saprophyticus exhibiting the highest sensitivity. MIC values ranged from 0.029 to 0.117 µg/mL whereas MBC ranged from 0.235 to 0.94 µg/mL, with 79% to 99% growth inhibition. Moreover, all tested isolates showed a marked decrease in biofilm formation, with S. saprophyticus and S. aureus being the most sensitive. CONCLUSION Plumbagin is a stand-alone, broad spectrum antibacterial with promising potential against the rising threat of antimicrobial resistance.
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Affiliation(s)
- Mohammad A. Alfhili
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
| | - Irfan Ahmad
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
| | - Yasser Alraey
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
| | - Abdulaziz Alangari
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
| | - Taha Alqahtani
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
| | - Ayed A. Dera
- From the Chair of Medical and Molecular Genetics Research (Alfhili), Department of Clinical Laboratory Sciences, from the Department of Clinical Laboratory Sciences (Alangari), College of Applied Medical Sciences, King Saud University, Riyadh; from the Department of Clinical Laboratory Sciences (Ahmad, Alraey, Dera), College of Applied Medical Sciences, and from the Department of Pharmacology (Alqahtani), College of Pharmacy, King Khalid University, Abha, Kingdom of Saudi Arabia.
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Svetličić E, Dončević L, Ozdanovac L, Janeš A, Tustonić T, Štajduhar A, Brkić AL, Čeprnja M, Cindrić M. Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing. Molecules 2022; 27:molecules27175461. [PMID: 36080229 PMCID: PMC9457756 DOI: 10.3390/molecules27175461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/19/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
For mass spectrometry-based diagnostics of microorganisms, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used to identify urinary tract pathogens. However, it requires a lengthy culture step for accurate pathogen identification, and is limited by a relatively small number of available species in peptide spectral libraries (≤3329). Here, we propose a method for pathogen identification that overcomes the above limitations, and utilizes the MALDI-TOF/TOF MS instrument. Tandem mass spectra of the analyzed peptides were obtained by chemically activated fragmentation, which allowed mass spectrometry analysis in negative and positive ion modes. Peptide sequences were elucidated de novo, and aligned with the non-redundant National Center for Biotechnology Information Reference Sequence Database (NCBInr). For data analysis, we developed a custom program package that predicted peptide sequences from the negative and positive MS/MS spectra. The main advantage of this method over a conventional MALDI-TOF MS peptide analysis is identification in less than 24 h without a cultivation step. Compared to the limited identification with peptide spectra libraries, the NCBI database derived from genome sequencing currently contains 20,917 bacterial species, and is constantly expanding. This paper presents an accurate method that is used to identify pathogens grown on agar plates, and those isolated directly from urine samples, with high accuracy.
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Affiliation(s)
- Ema Svetličić
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lucija Dončević
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Luka Ozdanovac
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Andrea Janeš
- Clinical Department of Laboratory Diagnostics, University Hospital Dubrava, Avenija Gojka Šuška 6, 10000 Zagreb, Croatia
| | | | - Andrija Štajduhar
- Division for Medical Statistics, Andrija Štampar Teaching Institute of Public Health, Mirogojska cesta 16, 10000 Zagreb, Croatia
| | | | - Marina Čeprnja
- Special Hospital Agram, Agram EEIG, Trnjanska cesta 108, 10000 Zagreb, Croatia
| | - Mario Cindrić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-16384422
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9
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Cheng W, Shi H, Teng M, Yu M, Feng B, Ding C, Yu S, Yang F. Rapid identification of bacterial mixtures in urine using MALDI-TOF MS-based algorithm profiling coupled with magnetic enrichment. Analyst 2022; 147:443-449. [PMID: 34985055 DOI: 10.1039/d1an02098f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Urinary tract infections (UTIs) are a severe public health problem caused by mono- or poly-bacteria. Culture-based methods are routinely used for the diagnosis of UTIs in clinical practice, but those are time consuming. Rapid and unambiguous identification of each pathogen in UTIs can have a significant impact on timely diagnoses and precise treatment. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an alternative method for the identification of pathogens in clinical laboratories. However, a certain number of pure bacteria are required for MALDI-TOF MS analysis. Here, we explored a strategy combining magnetic enrichment and MALDI-TOF MS for the rapid identification of pathogenic bacterial mixtures in urine. Fragment crystallizable mannose-binding lectin-modified Fe3O4 (Fc-MBL@Fe3O4) was used for rapid enrichment and the individual-peak-based similarity model as the analytical tool. Within 30 min, a mixture of the four most prevalent UTI-causing bacteria, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa, was successfully identified using this method. This rapid MALDI-TOF MS-based strategy has potential applications in the clinical identification of UTI pathogens.
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Affiliation(s)
- Wenmin Cheng
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Mengjing Teng
- Kweichow Moutai Group, Renhuai, Guizhou, 564501, China
| | - Menghuan Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Bin Feng
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Chuanfan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou, 564501, China
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10
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Matarneh A, Ali GA, Goravey W. Pyelonephritis-associated Staphylococcus saprophyticus bacteremia in an immunocompetent host: Case report and review of the literature. Clin Case Rep 2021; 9:e05183. [PMID: 34917380 PMCID: PMC8645171 DOI: 10.1002/ccr3.5183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/21/2021] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus saprophyticus is one of the coagulase-negative staphylococcus species. It is the second most frequent causative microorganism in acute uncomplicated urinary tract infections in young women. However, it is potentially capable of causing more invasive infections including bacteremia, particularly secondary to pyelonephritis. We present a young, previously healthy lady who presented with urinary symptoms and hemodynamic instability and was found to have multiple renal and ureteric calculi with pyelonephritis. Later, blood and urine cultures isolated methicillin-resistant S. saprophyticus. The patient was successfully treated with a course of antibiotics targeting the organism with a favorable outcome. The clinical presentations and management of this rare entity of S. saprophyticus bacteremia-related pyelonephritis are outlined. In addition, the literature on similar cases was reviewed to raise awareness and avoid devastating consequences.
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Affiliation(s)
- Ahmad Matarneh
- Department of Internal MedicineHamad Medical CorporationDohaQatar
| | - Gawahir A. Ali
- Department of Infectious DiseasesCommunicable Diseases CentreHamad Medical CorporationDohaQatar
| | - Wael Goravey
- Department of Infectious DiseasesCommunicable Diseases CentreHamad Medical CorporationDohaQatar
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11
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Saad E, Awadelkarim A, Ali M, Yeddi A. Recurrent renal abscess complicating Staphylococcus saprophyticus infection in an immunocompetent young female patient: A case report and review of literature. IDCases 2021; 26:e01290. [PMID: 34621618 PMCID: PMC8482430 DOI: 10.1016/j.idcr.2021.e01290] [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: 08/01/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 11/25/2022] Open
Abstract
Staphylococcus saprophyticus is second only to Escherichia coli as the most frequent causative organism of uncomplicated urinary tract infections (UTIs) among the sexually active female population. However, it is considered a rare cause of complicated UTIs in immunocompetent hosts with no identifiable risk factors for the occurrence of a complicated urinary tract infection. We report an exceedingly rare case of a 20-year-old otherwise healthy female patient, with no identifiable risk factors for complicated UTIs, who presented with a recurrent renal abscess secondary to S. saprophyticus. Serial cultures from multiple sources were negative, and the culprit organism was identified by a polymerase chain reaction (PCR) analysis of the drained pus that identified the 16 s rDNA sequences of S. saprophyticus on serial occasions. To our current date, similar cases have been rarely reported in the available literature. Our case also highlights the diagnostic value of molecular biology techniques in the identification of causative pathogens in cases of culture-negative infections when conventional microbiologic tests fail to isolate the culprit organisms. Clinical microbiology studies are needed to further explore the exact possible interactions between bacterial-specific characteristics and host-related factors that may explain the occurrence of the complicated UTIs that are associated with S. Saprophyticus among patients who are not considered to have certain risk factors that would usually predispose to complicated UTIs.
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Affiliation(s)
- Eltaib Saad
- Department of Internal Medicine, Saint Francis Presence Hospital, Evanston, IL, USA
| | - Abdelaziz Awadelkarim
- Department of Internal Medicine, Wayne State University/Detroit Medical Center, Detroit, MI, USA
| | - Mohammed Ali
- Department of Internal Medicine, Wayne State University/Detroit Medical Center, Detroit, MI, USA
| | - Ahmed Yeddi
- Department of Internal Medicine, Wayne State University/Detroit Medical Center, Detroit, MI, USA
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12
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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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13
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Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105387] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Pettengill MA. Hindsight Is 2019-the Year in Clinical Microbiology. ACTA ACUST UNITED AC 2020; 42:87-92. [PMID: 32461708 PMCID: PMC7241978 DOI: 10.1016/j.clinmicnews.2020.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Much changed in clinical microbiology in 2019, and, like the organisms, we, as clinical microbiologists, are responsible to detect, characterize, and teach others about our discipline. Also, it is important for us to adapt to changes in the field. In this review, I highlight some of the papers, practices, and regulatory issues that defined 2019 for our field, from my perspective.
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Affiliation(s)
- Matthew A Pettengill
- Thomas Jefferson University, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania
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15
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Arienzo A, Cellitti V, Ferrante V, Losito F, Stalio O, Murgia L, Marino R, Cristofano F, Orrù M, Visca P, Di Somma S, Silvestri L, Ziparo V, Antonini G. A new point-of-care test for the rapid detection of urinary tract infections. Eur J Clin Microbiol Infect Dis 2020; 39:325-332. [PMID: 31707506 PMCID: PMC7010689 DOI: 10.1007/s10096-019-03728-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/01/2019] [Indexed: 01/14/2023]
Abstract
Urinary tract infections (UTIs) are among the most common infections in all age groups. Fast and accurate diagnosis is essential to ensure a timely and effective therapy. Alongside with reference culture-based methods, several point-of-care tests (POCTs) for early detection of UTIs have been developed, but they have not been significantly implemented in current clinical practice. The Micro Biological Survey (MBS) POCT is a simple test developed by MBS Diagnostics Ltd. (London, UK) for the detection and management of UTIs. The present study has been undertaken to investigate the potentials and limits of the MBS POCT. A total of 349 patients were enrolled in two open-label, monocentric, non-interventional clinical trials in collaboration with an Emergency Medicine department and the outpatient clinic of two hospitals in Rome. Results of urine analysis using the MBS POCT were compared with those of the routine culture-based tests for UTI diagnosis performed by the hospital laboratory. The MBS POCT provided fast results revealing high bacterial count UTIs (≥ 105 CFU/ml) with 97% accuracy, 92% sensitivity, 100% specificity, 99% PPV, and 96% NPV within a 5-h analytical time threshold.
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Affiliation(s)
| | - Valentina Cellitti
- Interuniversity Consortium "Istituto Nazionale Biostrutture e Biosistemi" (INBB), Rome, Italy
| | - Valeria Ferrante
- Interuniversity Consortium "Istituto Nazionale Biostrutture e Biosistemi" (INBB), Rome, Italy
| | - Francesca Losito
- Interuniversity Consortium "Istituto Nazionale Biostrutture e Biosistemi" (INBB), Rome, Italy
| | - Ottavia Stalio
- Science Department, Università degli Studi Roma Tre, Rome, Italy
| | - Lorenza Murgia
- Science Department, Università degli Studi Roma Tre, Rome, Italy
| | - Rossella Marino
- Emergency Medicine, Department of Medical-Surgery Sciences and Translational Medicine, Università La Sapienza of Rome, Azienda Ospedaliera Sant'Andrea, Rome, Italy
| | - Flavia Cristofano
- Emergency Medicine, Department of Medical-Surgery Sciences and Translational Medicine, Università La Sapienza of Rome, Azienda Ospedaliera Sant'Andrea, Rome, Italy
| | - Michela Orrù
- Interuniversity Consortium "Istituto Nazionale Biostrutture e Biosistemi" (INBB), Rome, Italy
| | - Paolo Visca
- Science Department, Università degli Studi Roma Tre, Rome, Italy
| | - Salvatore Di Somma
- Emergency Medicine, Department of Medical-Surgery Sciences and Translational Medicine, Università La Sapienza of Rome, Azienda Ospedaliera Sant'Andrea, Rome, Italy
| | | | | | - Giovanni Antonini
- Science Department, Università degli Studi Roma Tre, Rome, Italy.
- Interuniversity Consortium "Istituto Nazionale Biostrutture e Biosistemi" (INBB), Rome, Italy.
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16
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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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