scholarly journals COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control

2021 ◽  
Vol 9 (4) ◽  
pp. 708
Author(s):  
Jéssica Costa ◽  
Eugénio C. Ferreira ◽  
Cledir Santos
Keyword(s):  
Ir Spectroscopy ◽  
Clinical Symptoms ◽  
Cost Effective ◽  
Accurate Diagnosis ◽  
Adequate Treatment ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Epidemiologic Profile ◽  
Effective Diagnosis ◽  
Tof Ms

COVID-19 and arboviruses (ARBOD) epidemics co-occurrence is a great concern. In tropical and subtropical regions, ARBOD diseases such as chikungunya, dengue, and Zika are frequent. In both COVID-19 and ARBOD cases, an accurate diagnosis of infected patients is crucial to promote adequate treatment and isolation measures in COVID-19 cases. Overlap of clinical symptoms and laboratory parameters between COVID-19 and ARBOD present themselves as an extra challenge during diagnosis. COVID-19 diagnosis is mainly performed by quantitative reverse polymerase chain reaction (RT-qPCR), while ARBOD diagnosis is performed by serology, detection of antigen or antibody, and molecular diagnosis. In this review, the epidemiologic profile of arboviruses and SARS-CoV-2 is analyzed, and potential risks of symptom overlap is addressed. The implementation of an analytical platform based on infrared (IR) spectroscopy, MALDI-TOF mass spectrometry, and RT-qPCR is discussed as an efficient strategy for a fast, robust, reliable, and cost-effective diagnosis system even during the co-occurrence of virus outbreaks. The spectral data of IR spectroscopy and MALDI-TOF MS obtained from COVID-19 infected and recovered patients can be used to build up an integrated spectral database. This approach can enable us to determine quickly the groups that have been exposed and have recovered from COVID-19 or ARBOD, avoiding misdiagnoses.

scholarly journals A diagnostic challenge in clinical laboratory: Misidentification of Neisseria subflava as Neisseria meningitidis by MALDI-TOF MS

2020 ◽  
pp. 1-3
Author(s):  
Tugce Unalan-Altintop ◽  
Alper Karagoz ◽  
Gulsen Hazirolan
Keyword(s):  
Neisseria Meningitidis ◽  
Clinical Laboratory ◽  
Cost Effective ◽  
Diagnostic Challenge ◽  
Accurate Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Neisseria Subflava ◽  
Effective Diagnosis ◽  
Tof Ms

Abstract MALDI-TOF MS provides fast, easy to perform and cost-effective diagnosis in clinical microbiology laboratories, however in some cases results of MALDI-TOF MS should be confirmed with additional tests. This confirmation is especially important for causes of life-threatening infections like Neisseria meningitidis. In our laboratory, three isolates were identified as N. meningitidis by Bruker MALDI Biotyper (BD, USA) between April 2018 and March 2019 from clinical specimens of blood, sputum, and urine. 16S rRNA sequencing was performed for further investigation. Two of the isolates were identified as Neisseria subflava and only one was confirmed as N. meningitidis by sequencing. These results show that MALDI-TOF MS is not always reliable in the diagnosis of N. meningitidis and clinical microbiologists should confirm these results with additional tests. Also, clinical correlations should be determined. Accurate identification of this microorganism is very important because of the necessity of prophylactic antimicrobial usage and biosafety precautions. Enlarged databases of Neisseria species are needed to overcome this problem.

scholarly journals Detection of Carbapenemase-Producing Enterobacteriaceae in the Baltic Countries and St. Petersburg Area

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Anastasia Pavelkovich ◽  
Arta Balode ◽  
Petra Edquist ◽  
Svetlana Egorova ◽  
Marina Ivanova ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Cost Effective ◽  
Maldi Tof Ms ◽  
E Coli ◽  
Maldi Tof ◽  
Baltic Countries ◽  
Exact Data ◽  
Cost Effective Method ◽  
The Baltic ◽  
Tof Ms

The spread of carbapenemase-producing Enterobacteriaceae is a global problem; however, no exact data on the epidemiology of carbapenemase in the Baltic countries and St. Petersburg area is available. We aimed to evaluate the epidemiology of carbapenemase-producingEscherichia coliandKlebsiella pneumoniaein the Baltic States and St. Petersburg, Russia, and to compare the different methods for carbapenemase detection. From January to May 2012, allK. pneumoniae  n=1983andE. coli  n=7774clinical isolates from 20 institutions in Estonia, Latvia, Lithuania, and St. Petersburg, Russia were screened for carbapenem susceptibility. The IMP, VIM, GIM, NDM, KPC, and OXA-48 genes were detected using real-time PCR and the ability to hydrolyze ertapenem was determined using MALDI-TOF MS. Seventy-seven strains were found to be carbapenem nonsusceptible. From these, 15K. pneumoniaestrains hydrolyzed ertapenem and carried theblaNDMgene. All of these strains carried integron 1 and most carried integron 3 as well as genes of the CTX-M-1 group. No carbapenemase-producingE. coliorK. pneumoniaestrains were found in Estonia, Latvia, or Lithuania; however, NDM-positiveK. pneumoniaewas present in the hospital in St. Petersburg, Russia. A MALDI-TOF MS-based assay is a suitable and cost-effective method for the initial confirmation of carbapenemase production.

scholarly journals Rapid and cost-effective identification of Bartonella species using mass spectrometry

2009 ◽  
Vol 58 (9) ◽  
pp. 1154-1159 ◽  
Author(s):  
Pierre-Edouard Fournier ◽  
Carine Couderc ◽  
Sylvain Buffet ◽  
Christophe Flaudrops ◽  
Didier Raoult
Keyword(s):  
Mass Spectrometry ◽  
Species Identification ◽  
Chemical Reactivity ◽  
Bacterial Species ◽  
Cost Effective ◽  
Molecular Techniques ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Bacteria of the genus Bartonella are emerging zoonotic bacteria recognized in a variety of human diseases. Due to their poor chemical reactivity, these fastidious bacteria are poorly characterized using routine phenotypic laboratory tests. Identification is usually achieved using molecular techniques that are time-consuming, expensive and technically demanding. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a new technique for bacterial species identification. This study evaluated the use of MALDI-TOF MS for rapid genus and species identification of Bartonella species. Reference strains representing 17 recognized Bartonella species were studied. For each species, MS spectra for four colonies were analysed. The consensus spectrum obtained for each species was unique among spectra obtained for 2843 bacteria within the Bruker database, including 109 alphaproteobacteria. Thirty-nine additional blind-coded Bartonella strains were correctly identified at the species level, including 36 with a significant score. Altogether, these data demonstrate that MS is an accurate and reproducible tool for rapid and inexpensive identification of Bartonella species.

scholarly journals An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures

2017 ◽  
Vol 8 ◽  
Author(s):  
Menglan Zhou ◽  
Qiwen Yang ◽  
Timothy Kudinha ◽  
Liying Sun ◽  
Rui Zhang ◽  
...  
Keyword(s):  
Direct Cost ◽  
Cost Effective ◽  
Blood Cultures ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

scholarly journals Applications of MALDI Mass Spectrometry in Clinical Chemistry

2016 ◽  
Vol 62 (1) ◽  
pp. 134-143 ◽  
Author(s):  
Mark W Duncan ◽  
Dobrin Nedelkov ◽  
Ryan Walsh ◽  
Stephen J Hattan
Keyword(s):  
Mass Spectrometry ◽  
Clinical Chemistry ◽  
Cost Effective ◽  
Maldi Mass Spectrometry ◽  
Ease Of Use ◽  
Mass Detection ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Abstract BACKGROUND MALDI-TOF mass spectrometry (MS) is set to make inroads into clinical chemistry because it offers advantages over other analytical platforms. These advantages include low acquisition and operating costs, ease of use, ruggedness, and high throughput. When coupled with innovative front-end strategies and applied to important clinical problems, it can deliver rapid, sensitive, and cost-effective assays. CONTENT This review describes the general principles of MALDI-TOF MS, highlights the unique features of the platform, and discusses some practical methods based upon it. There is substantial potential for MALDI-TOF MS to make further inroads into clinical chemistry because of the selectivity of mass detection and its ability to independently quantify proteoforms. SUMMARY MALDI-TOF MS has already transformed the practice of clinical microbiology and this review illustrates how and why it is now set to play an increasingly important role in in vitro diagnostics in particular, and clinical chemistry in general.

scholarly journals Detection of Colistin Resistance in Escherichia coli by Use of the MALDI Biotyper Sirius Mass Spectrometry System

2019 ◽  
Vol 57 (12) ◽  
Author(s):  
R. Christopher D. Furniss ◽  
Laurent Dortet ◽  
William Bolland ◽  
Oliver Drews ◽  
Katrin Sparbier ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Escherichia Coli ◽  
Cost Effective ◽  
Colistin Resistance ◽  
Content Type ◽  
Maldi Tof Ms ◽  
E Coli ◽  
Maldi Tof ◽  
Maldi Biotyper ◽  
Tof Ms

ABSTRACT Polymyxin antibiotics are a last-line treatment for multidrug-resistant Gram-negative bacteria. However, the emergence of colistin resistance, including the spread of mobile mcr genes, necessitates the development of improved diagnostics for the detection of colistin-resistant organisms in hospital settings. The recently developed MALDIxin test enables detection of colistin resistance by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) in less than 15 min but is not optimized for the mass spectrometers commonly found in clinical microbiology laboratories. In this study, we adapted the MALDIxin test for the MALDI Biotyper Sirius MALDI-TOF MS system (Bruker Daltonics). We optimized the sample preparation protocol by using a set of 6 mobile colistin resistance (MCR) protein-expressing Escherichia coli clones and validated the assay with a collection of 40 E. coli clinical isolates, including 19 confirmed MCR protein producers, 12 colistin-resistant isolates that tested negative for commonly encountered mcr genes (i.e., likely chromosomally resistant isolates), and 9 polymyxin-susceptible isolates. We calculated polymyxin resistance ratio (PRR) values from the acquired spectra; PRR values of 0, indicating polymyxin susceptibility, were obtained for all colistin-susceptible E. coli isolates, whereas positive PRR values, indicating resistance to polymyxins, were obtained for all resistant strains, independent of the genetic basis of resistance. Thus, we report a preliminary feasibility study showing that an optimized version of the MALDIxin test adapted for the routine MALDI Biotyper Sirius system provides an unbiased, fast, reliable, cost-effective, and high-throughput way of detecting colistin resistance in clinical E. coli isolates.

scholarly journals Evaluation of Microarray and Lysis Filtration Combined MALDI TOF MS Procedures for the Identification of Gram Negative Bacteremia

2021 ◽  
Author(s):  
Mehmet Soylu ◽  
Ayşe Arslan ◽  
Şöhret Aydemir ◽  
Alper Tünger
Keyword(s):  
Cost Effective ◽  
Common Species ◽  
Cohen’S Kappa ◽  
Filtration Method ◽  
Gram Negative ◽  
Maldi Tof Ms ◽  
Identification Time ◽  
Maldi Tof ◽  
Cohen's Kappa ◽  
Tof Ms

Objective: Each hour of delay in antibiotics administration increases mortality in sepsis. The aim of this study was to decrease the bacteria identification time to initiate appropriate antibiotic treatment as early as possible. Method: Tests were applied to 39 Gram negative bacteria isolated from blood cultures sent to our laboratory from intensive care units between November 2015- February 2016. The results of bacterial identification tested on both microarray and LFM methods were compared. Results: In the comparison of MALDI-TOF MS after sub-culture, MALDI-TOF after lysis centrifugation and microarray methods, sensitivity was determined as 82% (32/39) in LFM and as 87.1% (34/39) in the microarray method. All three methods had a concordance of 76.9% (30/39). Most common species identified in this study were Acinetobacter spp., Klebsiella spp. and Escherichia spp., and their Cohen’s Kappa coefficients for LFM and post-subculture MALDI were calculated as 0.715, 0.843, and 0.938, respectively. In addition, their BC-GN microarray and post-subculture MALDI concordance rates calculated with Cohen’s Kappa were 0.935, 0.753 and 0.938, respectively. Both methods showed good correlations with the post-culture MALDI method. Conclusion: Lysis centrifugation and microarray platforms decrease the identification time in blood culture processing successfully. Results of this study suggest that for the laboratories with MALDI-TOF mass spectrophotometer, the lysis filtration method is a fast and cost-effective method that may be suitable for routine procedures.

Clinical Validation of a 106-SNV MALDI-ToF MS Pharmacogenomic Panel

2020 ◽  
Vol 5 (3) ◽  
pp. 454-466
Author(s):  
Grace R Williams ◽  
Leanne Cook ◽  
Lionel D Lewis ◽  
Gregory J Tsongalis ◽  
Robert D Nerenz
Keyword(s):  
Drug Response ◽  
Clinical Laboratory ◽  
Cost Effective ◽  
Accurate Method ◽  
Care Providers ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Assay Precision ◽  
Custom Panel ◽  
Tof Ms

Abstract Background Laboratorians have the opportunity to help minimize the frequency of adverse drug reactions by implementing pharmacogenomic testing and alerting care providers to possible patient/drug incompatibilities before drug treatment is initiated. Methods combining PCR with MALDI-ToF MS have allowed for sensitive, economical, and multiplexed pharmacogenomic testing results to be delivered in a timely fashion. Method This study evaluated the analytical performance of the Agena Biosciences iPLEX® PGx 74 panel and a custom iPLEX panel on a MassARRAY MALDI-TOF MS instrument in a clinical laboratory setting. Collectively, these panels evaluate 112 SNVs across 34 genes implicated in drug response. Using commercially available samples (Coriell Biorepository) and in-house extracted DNA, we determined ideal reaction conditions and assessed accuracy, precision, and robustness. Results Following protocol optimization, the Agena PGx74 and custom panels demonstrated 100% concordance with the 1000 Genomes Project Database and clinically validated hydrolysis probe genotyping assays. 100% concordance was also observed in all assessments of assay precision when appropriate QC metrics were applied. Conclusions Significant development time was required to optimize sample preparation and instrumental analysis and 3 assays were removed due to inconsistent performance. Following modification of the manufacturer’s protocol and instituting manual review of each assay plate, the Agena PGx74 and custom panel constitute a cost-effective, robust, and accurate method for clinical identification of 106 SNVs involved in drug response.

scholarly journals Clostridium ramosum rapidly identified by MALDI-TOF MS. A rare gram-variable agent of bacteraemia.

2020 ◽  
Vol 2 (8) ◽  
Author(s):  
M.C. Legaria ◽  
S.D. García ◽  
V. Tudanca ◽  
C. Barberis ◽  
L. Cipolla ◽  
...  
Keyword(s):  
Type Species ◽  
Clinical Symptoms ◽  
Gc Content ◽  
Ionization Time ◽  
Content Type ◽  
Maldi Tof Ms ◽  
Link Type ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Tof Ms

Clostridium ramosum is an enteric anaerobic, endospore-forming, gram-positive rod with a low GC content that is rarely associated with disease in humans. We present a case of C. ramosum bacteraemia. To the best of our knowledge, this is the second case of C. ramosum bacteraemia in an elderly patient presenting with fever, abdominal pain and bilious emesis. We highlight the Gram stain variability, the lack of visualization of spores and the atypical morphology of the colonies that showed C. ramosum in a polymicrobial presentation that initially appeared to show monomicrobial bacteraemia. The microorganism was rapidly identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We present a comprehensive literature review of 32 cases of clinical infections by C. ramosum in which we describe, if available, sex, age, clinical symptoms, predisposing conditions, other organisms present in the blood culture, other samples with C. ramosum , identification methodology, treatment and outcome.

scholarly journals Isolation and Identification of Optochin-Resistant Viridans Group Streptococci from the Sputum Samples of Adult Patients in Jakarta, Indonesia

2021 ◽  
Vol 2021 ◽  
pp. 1-5
Author(s):  
Wisiva Tofriska Paramaiswari ◽  
Nurma Sumar Sidik ◽  
Miftahuddin Majid Khoeri ◽  
Wisnu Tafroji ◽  
Wahyu Finasari Said ◽  
...  
Keyword(s):  
Clinical Symptoms ◽  
Sputum Sample ◽  
Common Species ◽  
Species Level ◽  
Adult Patients ◽  
Isolation And Identification ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Viridans Group Streptococci ◽  
Tof Ms

Aim. To investigate optochin-resistant viridans group streptococci (VGS) strains isolated from the sputum sample of adult patients with different clinical symptoms. Materials and Methods. Optochin-resistant VGS isolates were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). recA sequencing was used to confirm identified isolates at the genus level by MALDI-TOF MS. Finding. We identified 79% of tested isolates (148/187) at the species-level identification using the MALDI-TOF MS tool. We identified that the most common species isolated from sputum specimens were S. oralis (44.9%) followed by S. mitis (25.7%), S. infantis (9.1%), S. parasanguinis (7.5%), S. peroris (3.7%), S. anginosus (2.7%), and S. sanguinis (2.1%). Discussion. The S. oralis strains were majority of optochin-resistant VGS isolates obtained from sputum of adult patients in Jakarta, Indonesia. MALDI-TOF MS showed potential for the rapid identification tool to identify optochin-resistant VGS isolates. Although there were discrepancies in identifying isolates at the genus/species level, the performance could be improved by expanding its database.

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