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Inamine E, Carneiro MS, Wilhelm CM, Barth AL. Evaluation of an adapted method of relative growth to determine the susceptibility of Enterobacterales to polymyxin B by MALDI-TOF MS. Braz J Microbiol 2023; 54:1841-1846. [PMID: 37402940 PMCID: PMC10484837 DOI: 10.1007/s42770-023-01014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Polymyxin B resistance is an emerging problem worldwide. The reference method to determine susceptibility to polymyxins is broth microdilution (BMD). As BMD is time consuming, it is necessary to develop new methodologies to provide faster evaluation of polymyxin susceptibility. This study aimed to evaluate polymyxin B susceptibility of Enterobacterales using an adapted methodology of relative growth (RG) by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). A total of 60 isolates of Enterobacterales (22 resistant and 38 susceptible to polymyxin B by BMD) were evaluated. The adapted RG technique presented categorical agreement of 96.7% with only 2 major errors (3.3%) in comparison to BMD. Our findings demonstrate a high agreement between BMD and adapted RG, indicating that this methodology is promising for differentiating polymyxin B-susceptible isolates from polymyxin B-resistant isolates and could be implemented routinely in microbiology laboratories that already use the MALDI-TOF MS to identify bacteria.
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Affiliation(s)
- E Inamine
- PPGCM - Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, Porto Alegre, RS, 2350, Brazil
- ISCMPA - Complexo Hospitalar Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - M S Carneiro
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, Porto Alegre, RS, 2350, Brazil.
- PPGCF - Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - C M Wilhelm
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, Porto Alegre, RS, 2350, Brazil
- PPGCF - Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - A L Barth
- PPGCM - Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- LABRESIS - Laboratório de Pesquisa em Resistência Bacteriana, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos, Porto Alegre, RS, 2350, Brazil
- PPGCF - Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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2
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Dadwal R, Paul S, Gupta P, Yadav R, Sood S, Ghosh AK, Shivaprakash MR, Gainder S, Sethi S. Stable isotope labeling as a promising tool for rapid drug susceptibility testing in Neisseria gonorrhoeae. Braz J Microbiol 2023; 54:1819-1825. [PMID: 37258877 PMCID: PMC10485193 DOI: 10.1007/s42770-023-00996-2] [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: 11/02/2022] [Accepted: 02/07/2023] [Indexed: 06/02/2023] Open
Abstract
The world is heading towards an era of intractable and impending untreatable N. gonorrhoeae, thereby underlining the significance of rapid and accurate prediction of drug resistance as an indispensable need of the hour. In the present study, we optimized and evaluated a stable isotope labeling-based approach using the MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry) for rapid and reliable detection of ciprofloxacin and azithromycin resistance in N. gonorrhoeae. All the isolates were cultured under three varied condition setups viz. medium supplemented with normal lysine, heavy lysine (isotope), and heavy lysine along with the antibiotics (ciprofloxacin/azithromycin), respectively. After incubation, spectra were acquired using the MALDI-TOF MS which were further screened for unique patterns (media-specific spectra) to differentiate drug-susceptible and resistant isolates. The results of the stable isotope labeling assay were comparable to the results of phenotypic methods used for susceptibility testing.
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Affiliation(s)
- Rajneesh Dadwal
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - Saikat Paul
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - Parakriti Gupta
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - Rakesh Yadav
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - Seema Sood
- Department of Microbiology, AIIMS, New Delhi, India
| | - A K Ghosh
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - M R Shivaprakash
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India
| | - Shalini Gainder
- Department of Obstetrics and Gynaecology, PGIMER, Chandigarh, 160012, India
| | - Sunil Sethi
- Department of Medical Microbiology, PGIMER, Chandigarh, 160012, India.
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3
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Zhu Y, Girault HH. Algorithms push forward the application of MALDI–TOF mass fingerprinting in rapid precise diagnosis. VIEW 2023. [DOI: 10.1002/viw.20220042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Yingdi Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences Hangzhou China
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
| | - Hubert H. Girault
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne Lausanne Switzerland
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4
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Chen C, Zhou Z, Cong L, Shan M, Zhu Z, Li Y. Rapid identification of methicillin-resistant Staphylococcus aureus by MALDI-TOF MS: A meta-analysis. Biotechnol Appl Biochem 2022. [PMID: 36575908 DOI: 10.1002/bab.2433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 12/17/2022] [Indexed: 12/29/2022]
Abstract
Invasive infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are associated with high mortality and morbidity. The sooner the pathogen is determined, the better it is beneficial to patient. However, routine laboratory inspections are time-consuming and laborious. A thorough research was conducted in PubMed and Web of Science (until June 2021) to identify studies evaluating the accuracy of MRSA identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). STATA 15.0 software was used to analyze the pooled results of sensitivity, specificity, and 95% confidence intervals (CI). The summary receiver operating characteristic curves (SROC) and area under the curve (AUC) were utilized to show the overall performance of MALDI-TOF MS. Fifteen studies involving 2471 isolates were included in this study after the final selection in this meta-analysis. Using the random effects model forest plot to summarize the overall statistics, the sensitivity of MALDI-TOF MS for identifying MRSA was 92% (95% CI: 81%-97%), and the specificity was 97% (95% CI: 89%-99%). In the SROC curve, the AUC reached 0.99 (95% CI: 97%-99%). Deeks' test showed no significant publication bias in this meta-analysis. Compared with clinical reference methods, MALDI-TOF MS identification of MRSA shows a higher degree of sensitivity and specificity.
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Affiliation(s)
- Chaoqun Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Zheng Zhou
- Department of Clinical Laboratory, Shandong Provincial Public Health Clinical Center, Shandong University Affiliated Hospital, Jinan, Shandong, People's Republic of China
| | - Liu Cong
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Mingzhu Shan
- Department of Clinical Laboratory, The Central Hospital of Xuzhou City, Xuzhou, Jiangsu, People's Republic of China
| | - Zuobin Zhu
- Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Ying Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
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5
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Wang H, Zhang W, Tang YW. Clinical Microbiology in Detection and Identification of Emerging Microbial Pathogens: Past, Present and Future. Emerg Microbes Infect 2022; 11:2579-2589. [PMID: 36121351 PMCID: PMC9639501 DOI: 10.1080/22221751.2022.2125345] [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] [Indexed: 11/21/2022]
Abstract
Clinical microbiology has possessed a marvellous past, an important present and a bright future. Western medicine modernization started with the discovery of bacterial pathogens, and from then, clinical bacteriology became a cornerstone of diagnostics. Today, clinical microbiology uses standard techniques including Gram stain morphology, in vitro culture, antigen and antibody assays, and molecular biology both to establish a diagnosis and monitor the progression of microbial infections. Clinical microbiology has played a critical role in pathogen detection and characterization for emerging infectious diseases as evidenced by the ongoing COVID-19 pandemic. Revolutionary changes are on the way in clinical microbiology with the application of “-omic” techniques, including transcriptomics and metabolomics, and optimization of clinical practice configurations to improve outcomes of patients with infectious diseases.
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Affiliation(s)
- Hui Wang
- Department of Laboratory Medicine, Peking University People's Hospital, Beijing 100044, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Fudan University Huashan Hospital, Shanghai 200040, China
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform China/Cepheid, Shanghai 200325, China
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6
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Wu X, Tan G, Yang J, Guo Y, Huang C, Sha W, Yu F. Prediction of Mycobacterium tuberculosis drug resistance by nucleotide MALDI-TOF-MS. Int J Infect Dis 2022; 121:47-54. [PMID: 35523300 DOI: 10.1016/j.ijid.2022.04.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES To evaluate the performance of nucleotide matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) in predicting the drug resistance of Mycobacterium tuberculosis. METHODS A total of 115 rifampin-resistant and 53 rifampin-susceptible tuberculosis (TB) clinical isolates were randomly selected from TB strains stored at -80℃ in the clinical laboratory of Shanghai Pulmonary Hospital. Nucleotide MALDI-TOF-MS was performed to predict the drug resistance using phenotypic susceptibility as the gold standard. RESULTS The overall assay sensitivities and specificities of nucleotide MALDI-TOF-MS were 92.2% and 100.0% for rifampin, 90.9% and 98.6% for isoniazid, 71.4% and 81.2% for ethambutol, 85.1% and 93.1% for streptomycin, 94.0% and 100.0% for amikacin, 77.8% and 99.3% for kanamycin, 75.0% and 93.3% for ofloxacin, and 75.0% and 93.3% for moxifloxacin. The concordances between nucleotide MALDI-TOF-MS antimicrobial susceptibility testing (AST) and phenotypic AST were 94.6% (rifampin), 90.1% (isoniazid), 79.2% (ethambutol), 89.9% (streptomycin), 99.4% (amikacin), 97.0% (kanamycin), 88.1% (ofloxacin), and 88.0% (moxifloxacin). CONCLUSION Nucleotide MALDI-TOF-MS could be a promising tool for rapid detection of Mycobacterium tuberculosis drug sensitivity to rifampin, isoniazid, ethambutol, streptomycin, amikacin, kanamycin, ofloxacin, and moxifloxacin.
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Affiliation(s)
- Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guangkun Tan
- Department of Clinical Laboratory, Shanghai University of Traditional Chinese Medical Attached Shuguang Hospital, Shanghai, China
| | - Jinghui Yang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | - Wei Sha
- Department of Tuberculosis, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China.
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7
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Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods. Antibiotics (Basel) 2022; 11:antibiotics11040427. [PMID: 35453179 PMCID: PMC9024665 DOI: 10.3390/antibiotics11040427] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.
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8
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Lin H, Hu Z, Wu J, Lu Y, Chen J, Wu W. Methodology Establishment and Application of VITEK Mass Spectrometry to Detect Carbapenemase-Producing Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:761328. [PMID: 35223536 PMCID: PMC8873529 DOI: 10.3389/fcimb.2022.761328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
The ability of VITEK mass spectrometry (MS) in detection of bacterial resistance is currently under exploration and evaluation. In this study, we developed and validated a VITEK MS method to rapidly test carbapenemase-producing Klebsiella pneumoniae (CPKP). Solvents, antibiotic concentrations, crystal conditions and times, centrifugation speeds, and other factors were optimized to design a rapid sample pretreatment process for CPKP detection by VITEK MS. The related parameters of the mass spectrum were adjusted on the instrument to establish an CPKP detection mode. 133 clinically isolated strains of CPKP in the microbiology laboratory at the Shenzhen People’s Hospital from 2004 to 2017 were selected for accuracy evaluation. The fresh suspected strains from the microbiology laboratory in 2020 were used to complete the clinical verification. Two antibiotics, meropenem (MEM) and imipenem (IPM), were used as substrates. These two substrates were incubated with suspected CPKP, and the results were obtained by VITEK MS detection. Using this method, different types of CPKP showed different detection results and all the CPKP strains producing KPC-2 and IMP-4 carbapenemase were detected by VITEK MS. Thus, VITEK MS can be used for rapid detection of CPKP, especially for some common types of CPKP. This method provides high accuracy and speed of detection. Combined with its cost advantages, it can be intensely valuable in clinical microbiology laboratories after the standard operating procedures are determined.
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9
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Shortening the Time of the Identification and Antimicrobial Susceptibility Testing on Positive Blood Cultures with MALDI-TOF MS. Diagnostics (Basel) 2021; 11:diagnostics11081514. [PMID: 34441448 PMCID: PMC8391154 DOI: 10.3390/diagnostics11081514] [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: 07/12/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
The current processes used in clinical microbiology laboratories take ~24 h for incubation to identify the bacteria after the blood culture has been confirmed as positive and fa further ~24 h to report the results of antimicrobial susceptibility tests (ASTs). Patients with suspected bloodstream infection are treated with empiric broad-spectrum antibiotics but delayed targeted antimicrobial therapy. This study aimed to develop a method with a significantly shortened turnaround time for clinical application by identifying the optimal incubation period of a subculture. A total of 188 positive blood culture samples obtained from Nov. 2019 to Aug. 2020 were included. Compared to the conventional 24-h incubation for bacterial identification, our approach achieved 96.1% and 97.4% identification accuracy after shortening the incubation time to 4.5 and 3.5 h for gram-positive (GP) and gram-negative (GN) bacterial samples, respectively. Samples from short-term incubation without any intermediate step or process were directly subjected to analysis with the Phoenix M50 AST. Compared to the conventional disk diffusion AST, the category agreements for GP (excluding Streptococcus spp.), Streptococcus spp., and GN bacterial samples were 91.8%, 97.5%, and 92.7%, respectively. Our approach significantly reduced the average turnaround time from 48 h to 28 h for reporting bacterial identity and decreased average AST from 72 h to 50.3 h compared to the conventional methods. Accordingly, this approach allows a physician to prescribe the appropriate antibiotic(s) ~21.7 h earlier, thereby improving patient outcomes.
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11
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Yoon EJ, Jeong SH. MALDI-TOF Mass Spectrometry Technology as a Tool for the Rapid Diagnosis of Antimicrobial Resistance in Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10080982. [PMID: 34439032 PMCID: PMC8388893 DOI: 10.3390/antibiotics10080982] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022] Open
Abstract
Species identification by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a routine diagnostic process for infectious diseases in current clinical settings. The rapid, low-cost, and simple to conduct methodology is expanding its application in clinical microbiology laboratories to diagnose the antimicrobial resistance (AMR) in microorganisms. Primarily, antimicrobial susceptibility testing is able to be carried out either by comparing the area under curve of MALDI spectra of bacteria grown in media with antimicrobial drugs or by identifying the shift peaks of bacteria grown in media including 13C isotope with antimicrobial drugs. Secondly, the antimicrobial resistance is able to be determined through identifying (i) the antimicrobial-resistant clonal groups based on the fingerprints of the clone, (ii) the shift peak of the modified antimicrobial drug, which is inactivated by the resistance determinant, (iii) the shift peak of the modified antimicrobial target, (iv) the peak specific for the antimicrobial determinant, and (v) the biomarkers that are coproduced proteins with AMR determinants. This review aims to present the current usage of the MALDI-TOF MS technique for diagnosing antimicrobial resistance in bacteria, varied approaches for AMR diagnostics using the methodology, and the future applications of the methods for the accurate and rapid identification of AMR in infection-causing bacterial pathogens.
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Affiliation(s)
- Eun-Jeong Yoon
- Division of Antimicrobial Resistance, Center for Infectious Diseases, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Korea;
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul 06273, Korea
- Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul 06273, Korea
- Correspondence:
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12
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Abstract
The advent of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has dramatically improved the accuracy and speed of diagnostics. However, this progress has mainly been limited to the identification of microorganisms, whereas the practical improvement of antimicrobial susceptibility testing (AST) still lags behind. MALDI-TOF MS-based approaches include the detection of selected resistance mechanisms and the universal phenotypic AST. This minireview focuses on the discussion of those MALDI-TOF MS methods that allow universal growth-based phenotypic AST. The method of minimal profile change concentrations (MPCC) is based on detecting proteome modification in presence of an antimicrobial. Using stable-isotope labeling, characteristic mass shifts in the presence of an antimicrobial indicate the incorporation of the isotopic labels, and, thus, the viability and resistance of the microorganism. For MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA), microorganisms are incubated with or without an antimicrobial, followed by cell lysis, protein extraction, and transfer of the cell lysate onto a MALDI target plate. Using the internal standard, peak intensities are correlated to the amount of microbial proteins, and the relative microbial growth is calculated. Most recent development in the field is the direct-on-target microdroplet growth assay (DOT-MGA). Here, incubation of microorganisms with antimicrobials takes place directly on spots of a MALDI target in form of microdroplets. After incubation, nutrient medium is removed by dabbing with absorptive material. Resistant microorganisms grow despite the presence of antimicrobial, and their amplified biomass is detected by MALDI-TOF MS. Finally, an outlook is provided for further assay improvements.
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Recent Development of Rapid Antimicrobial Susceptibility Testing Methods through Metabolic Profiling of Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10030311. [PMID: 33803002 PMCID: PMC8002737 DOI: 10.3390/antibiotics10030311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/17/2022] Open
Abstract
Due to the inappropriate use and overuse of antibiotics, the emergence and spread of antibiotic-resistant bacteria are increasing and have become a major threat to human health. A key factor in the treatment of bacterial infections and slowing down the emergence of antibiotic resistance is to perform antimicrobial susceptibility testing (AST) of infecting bacteria rapidly to prescribe appropriate drugs and reduce the use of broad-spectrum antibiotics. Current phenotypic AST methods based on the detection of bacterial growth are generally reliable but are too slow. There is an urgent need for new methods that can perform AST rapidly. Bacterial metabolism is a fast process, as bacterial cells double about every 20 to 30 min for fast-growing species. Moreover, bacterial metabolism has shown to be related to drug resistance, so a comparison of differences in microbial metabolic processes in the presence or absence of antimicrobials provides an alternative approach to traditional culture for faster AST. In this review, we summarize recent developments in rapid AST methods through metabolic profiling of bacteria under antibiotic treatment.
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14
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Blake KS, Choi J, Dantas G. Approaches for characterizing and tracking hospital-associated multidrug-resistant bacteria. Cell Mol Life Sci 2021; 78:2585-2606. [PMID: 33582841 PMCID: PMC8005480 DOI: 10.1007/s00018-020-03717-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/26/2020] [Accepted: 11/17/2020] [Indexed: 12/24/2022]
Abstract
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.
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Affiliation(s)
- Kevin S Blake
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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15
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Rentschler S, Kaiser L, Deigner HP. Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance. Int J Mol Sci 2021; 22:E456. [PMID: 33466437 PMCID: PMC7796476 DOI: 10.3390/ijms22010456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.
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Affiliation(s)
- Simone Rentschler
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057 Rostock, Germany
- Faculty of Science, Tuebingen University, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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16
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Florio W, Baldeschi L, Rizzato C, Tavanti A, Ghelardi E, Lupetti A. Detection of Antibiotic-Resistance by MALDI-TOF Mass Spectrometry: An Expanding Area. Front Cell Infect Microbiol 2020; 10:572909. [PMID: 33262954 PMCID: PMC7686347 DOI: 10.3389/fcimb.2020.572909] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/22/2020] [Indexed: 01/21/2023] Open
Abstract
Several MALDI-TOF MS-based methods have been proposed for rapid detection of antimicrobial resistance. The most widely studied methods include assessment of β-lactamase activity by visualizing the hydrolysis of the β-lactam ring, detection of biomarkers responsible for or correlated with drug-resistance/non-susceptibility, and the comparison of proteomic profiles of bacteria incubated with or without antimicrobial drugs. Antimicrobial-resistance to a number of antibiotics belonging to different classes has been successfully tested by MALDI-TOF MS in a variety of clinically relevant bacterial species including members of Enterobacteriaceae family, non-fermenting Gram-negative bacteria, Gram-positive cocci, anaerobic bacteria and mycobacteria, opening this field to further clinically important developments. Early detection of drug-resistance by MALDI-TOF MS can be particularly helpful for clinicians to streamline the antibiotic therapy for a better outcome of patients with systemic infection, in all cases where a prompt and effective antibiotic treatment is essential to preserve organ function and/or patient survival.
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Affiliation(s)
- Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Lelio Baldeschi
- Department of Ophthalmology, Université Catholique de Louvain, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Cosmeri Rizzato
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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17
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Takei S, Ihara H, Togo S, Nakamura A, Fujimoto Y, Watanabe J, Kurokawa K, Shibayama K, Sumiyoshi I, Ochi Y, Iwai M, Okabe T, Chonan M, Misawa S, Ohsaka A, Takahashi K. The synergetic effect of Imipenem-clarithromycin combination in the Mycobacteroides abscessus complex. BMC Microbiol 2020; 20:316. [PMID: 33076820 PMCID: PMC7574464 DOI: 10.1186/s12866-020-02000-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/09/2020] [Indexed: 12/05/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are ubiquitous organisms and the incidence of NTM infections has been increasing in recent years. Mycobacteroides abscessus (M. abscessus) is one of the most antimicrobial-resistant NTM; however, no reliable antibiotic regimen can be officially advocated. We evaluated the efficacy of clarithromycin in combination with various antimicrobial agents against the M. abscessus complex. Results Twenty-nine clinical strains of M. abscessus were isolated from various clinical samples. Of the isolates, 10 (34.5%) were of M. abscessus subsp. abscessus, 18 (62.1%) of M. abscessus subsp. massiliense, and 1 (3.4%) of M. abscessus subsp. bolletii. MICs of three antimicrobial agents (amikacin, imipenem, and moxifloxacin) were measured with or without clarithromycin. The imipenem-clarithromycin combination significantly reduced MICs compared to clarithromycin and imipenem monotherapies, including against resistant strains. The association between susceptibility of the M. abscessus complex and each combination of agents was significant (p = 0.001). Adjusted residuals indicated that the imipenem-clarithromycin combination had the synergistic effect (adjusted residual = 3.1) and suppressed the antagonistic effect (adjusted residual = − 3.1). In subspecies of M. abscessus complex, the association with susceptibility of M. abscessus subsp. massiliense was similarly statistically significant (p = 0.036: adjusted residuals of synergistic and antagonistic effect respectively: 2.6 and − 2.6). The association with susceptibility of M. abscessus subsp. abscessus also showed a similar trend but did not reach statistical significance. Conclusion Our data suggest that the imipenem-clarithromycin combination could be the recommended therapeutic choice for the treatment of M. abscessus complex owing to its ability to restore antimicrobial susceptibility.
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Affiliation(s)
- Satomi Takei
- Department of Clinical Laboratory, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Hiroaki Ihara
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. .,Koto Hospital, Tokyo, Japan.
| | - Shinsaku Togo
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan. .,Research Institute for Diseases of Old Ages, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan.
| | - Ayako Nakamura
- Juntendo Tokyo Koto Geriatric Medical Center, Tokyo, Japan
| | - Yuichi Fujimoto
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Junko Watanabe
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Kana Kurokawa
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Kohei Shibayama
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Issei Sumiyoshi
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Yusuke Ochi
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Moe Iwai
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.,Research Institute for Diseases of Old Ages, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Takahiro Okabe
- Leading Center for the Development and Research of Cancer Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Masayoshi Chonan
- Department of Clinical Laboratory, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Shigeki Misawa
- Department of Clinical Laboratory, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Akimichi Ohsaka
- Department of Transfusion Medicine and Stem Cell Regulation, Juntendo University, Faculty of Medicine & Graduate School of Medicine, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University, Faculty of Medicine & Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
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18
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Horseman TS, Lustik MB, Fong KSK. Rapid qualitative antibiotic resistance characterization using VITEK MS. Diagn Microbiol Infect Dis 2020; 97:115093. [PMID: 32569920 DOI: 10.1016/j.diagmicrobio.2020.115093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 01/27/2023]
Abstract
Development and standardization of simple, timely, and cost-effective antibiotic susceptibility assays are much needed to address the emergence of global resistance. The use of matrix-assisted laser desorption/ionization time of flight mass spectrometry is routine for bacterial identification. This study evaluated 2 assays using the VITEK MS for rapid detection and accurate differentiation of bacterial antibiotic susceptibility. We describe an extraction method and direct-on-target microdroplet growth assay (DOT-MGA). Non-susceptible and susceptible strains of Staphylococcus aureus, Enterococcus species, Escherichia coli, and Klebsiella pneumoniae were tested. The liquid extraction method and DOT-MGA proved to be reliable assays providing consistent differentiation between non-susceptible and susceptible strains. Results from this study support VITEK MS and these assays as rapid and accurate tools to augment traditional susceptibility testing. If implemented clinically, these assays can reduce the cost of patient care and the time to deliver critically needed treatment.
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Affiliation(s)
- Timothy S Horseman
- Department of Clinical Investigation, Tripler Army Medical Center, 1 Jarrett White Rd, Building 40, Honolulu, HI, USA.
| | - Michael B Lustik
- Department of Clinical Investigation, Tripler Army Medical Center, 1 Jarrett White Rd, Building 40, Honolulu, HI, USA
| | - Keith S K Fong
- Department of Clinical Investigation, Tripler Army Medical Center, 1 Jarrett White Rd, Building 40, Honolulu, HI, USA
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Mizusawa M, Carroll KC. Novel strategies for rapid identification and susceptibility testing of MRSA. Expert Rev Anti Infect Ther 2020; 18:759-778. [PMID: 32329637 DOI: 10.1080/14787210.2020.1760842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Methicillin-resistant Staphylococcus aureus (MRSA) is associated with adverse clinical outcomes and increased morbidity, mortality, length of hospital stay, and health-care costs. Rapid diagnosis of MRSA infections has been associated with positive impact on clinical outcomes. AREAS COVERED We searched relevant papers in PubMed for the last 10 years. In major papers, we scanned the bibliographies to ensure that important articles were included. This review describes screening and diagnostic test methods for MRSA and their analytical performances with a focus on rapid molecular-based assays including those that are on the horizon. Future novel technologies will allow more rapid detection of phenotypic resistance. In the case of whole-genome sequencing, detection of mutations may predict resistance, transmission, and virulence. EXPERT OPINION Currently there are many diagnostic options for the detection of MRSA in surveillance and clinical samples. In general, these are highly accurate and have resulted in improvements in targeted management and reduction in hospital or intensive care unit length of stay for both MSSA and MRSA. Impact on mortality has been variable. Promising novel technologies will not only accurately identify pathogens and detect their resistance markers but will allow discovery of virulence determinants that might further affect patient management.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri , Kansas, MO, USA
| | - Karen C Carroll
- Department of Pathology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine , Baltimore, MD, USA
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20
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Kittel M, Findeisen P, Ghebremedhin B, Miethke T, Grundt A, Ahmad-Nejad P, Neumaier M. Rapid susceptibility testing of multi-drug resistant Escherichia coli and Klebsiella by glucose metabolization monitoring. Clin Chem Lab Med 2020; 57:1271-1279. [PMID: 30763260 DOI: 10.1515/cclm-2018-1178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/16/2019] [Indexed: 11/15/2022]
Abstract
Background The increasing number of multi-drug resistant (MDR) bacteria provides enormous challenges for choosing an appropriate antibiotic therapy in the early phase of sepsis. While bacterial identification has been greatly accelerated by the introduction of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), the antibiotic susceptibility testing (AST) remains time-consuming. Here, we present a rapid susceptibility testing method for testing Gram-negative bacteria, exemplarily validated for Escherichia coli and Klebsiella spp. Methods Gram-negative isolates (E. coli and Klebsiella spp.) were either taken as single colonies from agar plates (n=136) or directly extracted and identified from positive blood cultures (n=42) using MALDI-TOF MS. Bacteria were incubated in glucose-supplemented Luria broths (LBs) each containing one antibiotic (ceftazidime, piperacillin, imipenem and ciprofloxacin), routinely used to classify Gram-negative bacteria in Germany. To determine susceptibility the dynamics of glucose utilization in bacterial suspensions were quantitatively measured in the presence or absence of antibiotics designated liquid-AST (L-AST). Results The L-AST can be run on clinical-chemistry analyzers and integrated into laboratory routines. It yields critical resistance information within 90-150 min downstream of a MS-based identification. The results showed a high concordance with routine susceptibility testing, with less than 1% very major errors (VME) and 3.51% major errors (ME) for 178 assessed isolates. Analysis of turnaround time (TAT) for 42 clinical samples indicated that L-AST results could be obtained 34 h earlier than the routine results. Conclusions As exemplified for E. coli and Klebsiella spp., L-AST provides substantial acceleration of susceptibility testing following MALDI-TOF MS identification. The assay is a simple and low-cost method that can be integrated into clinical laboratory to allow for 24/7 AST. This approach could improve antibiotic therapy.
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Affiliation(s)
- Maximilian Kittel
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Beniam Ghebremedhin
- Institute for Medical Laboratory Diagnostics, Center for Clinical and Translational Research, HELIOS Klinikum Wuppertal, Witten/Herdecke University, Witten, Germany
| | - Thomas Miethke
- Institute for Medical Microbiology and Hygiene, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Alexander Grundt
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany
| | - Parviz Ahmad-Nejad
- Institute for Medical Laboratory Diagnostics, Center for Clinical and Translational Research, HELIOS Klinikum Wuppertal, Witten/Herdecke University, Witten, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim of Heidelberg University, Mannheim, Germany, Phone: +49 - 621 383 2222, Fax: +49 - 621 383 3819
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21
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Maus A, Bisha B, Fagerquist C, Basile F. Detection and identification of a protein biomarker in antibiotic-resistant Escherichia coli using intact protein LC offline MALDI-MS and MS/MS. J Appl Microbiol 2019; 128:697-709. [PMID: 31715076 DOI: 10.1111/jam.14507] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/15/2019] [Accepted: 11/04/2019] [Indexed: 11/29/2022]
Abstract
AIMS The identification and differentiation of antibiotic-resistant bacteria by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) profiling remains a challenge due to the difficulty in detecting unique protein biomarkers associated with this trait. To expand the detectable proteome in antibiotic-resistant bacteria, we describe a method implementing offline LC protein separation/fractionation prior to MALDI-ToF-MS and top-down MALDI-ToF/ToF-MS (tandem MS or MS/MS) for the analysis of several antibiotic-resistant Escherichia coli isolates. METHODS AND RESULTS Coupling offline LC with MALDI-ToF-MS increased the number of detected protein signals in the typically analyzed mass regions (m/z 3000-20 000) by a factor of 13. Using the developed LC-MALDI-ToF-MS protocol in conjunction with supervised principal components analysis, we detected a protein biomarker at m/z 9355 which correlated to β-lactam resistance among the E. coli bacteria tested. Implementing a top-down MALDI-ToF/ToF-MS approach, the prefractionated protein biomarker was inferred as a DNA-binding HU protein, likely translated from the blaCMY-2 gene (encoding AmpC-type β-lactamase) in the incompatibility plasmid complex A/C (IncA/C). CONCLUSIONS Our results demonstrate the utility of LC-MALDI-MS and MS/MS to extend the number of proteins detected and perform MALDI-accessible protein biomarker discovery in microorganisms. SIGNIFICANCE AND IMPACT OF THE STUDY This outcome is significant since it expands the detectable bacterial proteome via MALDI-ToF-MS.
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Affiliation(s)
- A Maus
- Department of Chemistry, University of Wyoming, Laramie, WY, USA
| | - B Bisha
- Department of Animal Science, University of Wyoming, Laramie, WY, USA
| | - C Fagerquist
- U.S. Department of Agriculture, Western Regional Research Center, Agricultural Research Service, Albany, CA, USA
| | - F Basile
- Department of Chemistry, University of Wyoming, Laramie, WY, USA
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22
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Welker M, van Belkum A. One System for All: Is Mass Spectrometry a Future Alternative for Conventional Antibiotic Susceptibility Testing? Front Microbiol 2019; 10:2711. [PMID: 31849870 PMCID: PMC6901965 DOI: 10.3389/fmicb.2019.02711] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/08/2019] [Indexed: 12/20/2022] Open
Abstract
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely – still, the same was true for routine microbial identification a mere 15 years ago.
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Affiliation(s)
- Martin Welker
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
| | - Alex van Belkum
- Microbiology Research Unit, BioMérieux SA, La Balme-les-Grottes, France
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23
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Axelsson C, Rehnstam-Holm AS, Nilson B. Rapid detection of antibiotic resistance in positive blood cultures by MALDI-TOF MS and an automated and optimized MBT-ASTRA protocol for Escherichia coli and Klebsiella pneumoniae. Infect Dis (Lond) 2019; 52:45-53. [PMID: 31661349 DOI: 10.1080/23744235.2019.1682658] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Introduction: For fast and effective antibiotic therapy of serious infections like sepsis, it is crucial with rapid information about antibiotic susceptibility, especially in a time when the number of infections caused by multi resistant bacteria has escalated in the world.Methods: Here, we have used a semi-quantitative MALDI-TOF-MS based method for antibiotic resistance detection, MBT-ASTRA™, which is based on the comparison of growth rate of the bacteria cultivated with and without antibiotics. We demonstrate a new protocol where several parameters have been optimized and automated leading to reduced hands-on time and improved capacity to simultaneously analyse multiple clinical samples and antibiotics.Results: Ninety minutes of incubation at 37 °C with agitation was sufficient to differentiate the susceptible and resistant strains of E. coli and K. pneumoniae, for the antibiotics cefotaxime, meropenem and ciprofloxacin. In total, 841 positive blood culture analyses of 14 reference strains were performed. The overall sensitivity was 99%, specificity 99% and the accuracy 97%. The assay gave no errors for cefotaxime (n = 263) or meropenem (n = 289) for sensitive and resistant strains, whilst ciprofloxacin (n = 289) gave six (0.7%) major errors (false resistance) and four (0.5%) very major errors (false susceptibility). The intermediate strains showed a larger variety compared to the E-test MIC values.Conclusions: The hands-on time and the analysis time to detect antibiotic resistance of clinical blood samples can be substantially reduced and the sample capacity can be increased by using automation and this improved protocol.
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Affiliation(s)
- Carolina Axelsson
- Faculty of Natural Science, Kristianstad University, Kristianstad, Sweden.,Faculty of Medicine, Lund University, Lund, Sweden
| | - Ann-Sofi Rehnstam-Holm
- Faculty of Natural Science, Kristianstad University, Kristianstad, Sweden.,Faculty of Medicine, Lund University, Lund, Sweden
| | - Bo Nilson
- Department of Clinical Microbiology, Labmedicin, Lund, Sweden.,Department of Laboratory Medicine Lund, Faculty of Medicine, Division of Medical Microbiology, Lund University, Lund, Sweden
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24
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Idelevich EA, Reischl U, Becker K. New Microbiological Techniques in the Diagnosis of Bloodstream Infections. DEUTSCHES ARZTEBLATT INTERNATIONAL 2019; 115:822-832. [PMID: 30678752 DOI: 10.3238/arztebl.2018.0822] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/04/2017] [Accepted: 10/12/2018] [Indexed: 01/12/2023]
Abstract
BACKGROUND When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment. METHODS This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience. RESULTS A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS. CONCLUSION The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.
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25
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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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26
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Hou TY, Chiang-Ni C, Teng SH. Current status of MALDI-TOF mass spectrometry in clinical microbiology. J Food Drug Anal 2019; 27:404-414. [PMID: 30987712 PMCID: PMC9296205 DOI: 10.1016/j.jfda.2019.01.001] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Mass spectrometry (MS) is a type of analysis used to determine what molecules make up a sample, based on the mass spectrum that are created by the ions. Mass spectrometers are able to perform traditional target analyte identification and quantitation; however, they may also be used within a clinical setting for the rapid identification of bacteria. The causative agent in sepsis is changed over time, and clinical decisions affecting the management of infections are often based on the outcomes of bacterial identification. Therefore, it is essential that such identifications are performed quickly and interpreted correctly. Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer is one of the most popular MS instruments used in biology, due to its rapid and precise identification of genus and species of an extensive range of Gram-negative and-positive bacteria. Microorganism identification by Mass spectrometry is based on identifying a characteristic spectrum of each species and then matched with a large database within the instrument. The present review gives a contemporary perspective on the challenges and opportunities for bacterial identification as well as a written report of how technological innovation has advanced MS. Future clinical applications will also be addressed, particularly the use of MALDI-TOF MS in the field of microbiology for the identification and the analysis of antibiotic resistance.
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Affiliation(s)
- Tsung-Yun Hou
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei,
Taiwan
- Division of Allergy, Immunology and Rheumatology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei,
Taiwan
- Division of Rheumatology/Immunology/Allergy, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei,
Taiwan
| | - Chuan Chiang-Ni
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
| | - Shih-Hua Teng
- Bruker Taiwan Co., Ltd., Taipei,
Taiwan
- Corresponding author. 4F, 107 Yanshou Street, Songshan District, Taipei City 105, Taiwan. Fax: +886 2 2761 5335. E-mail address: (S.-H. Teng)
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27
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Hernández Egido S, Luis Reboredo AD, García Señán A, Gil González AB, Muñoz Bellido JL, González Buitrago JM, Sánchez-Juanes F. Summation of peaks and L34 ribosomal protein in the presence and absence of antibiotics enables susceptibility testing using MALDI-TOF mass spectrometry in 2 h from Escherichia coli-positive blood cultures. Enferm Infecc Microbiol Clin 2019; 37:244-250. [DOI: 10.1016/j.eimc.2018.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/18/2018] [Accepted: 06/04/2018] [Indexed: 11/28/2022]
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28
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Paul S, Singh S, Chakrabarti A, Rudramurthy SM, Ghosh AK. Stable isotope labelling: an approach for MALDI-TOF MS-based rapid detection of fluconazole resistance in Candida tropicalis. J Antimicrob Chemother 2019; 74:1269-1276. [DOI: 10.1093/jac/dkz019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/19/2018] [Accepted: 01/04/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Saikat Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
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Correa-Martínez CL, Idelevich EA, Sparbier K, Kostrzewa M, Becker K. Rapid Detection of Extended-Spectrum β-Lactamases (ESBL) and AmpC β-Lactamases in Enterobacterales: Development of a Screening Panel Using the MALDI-TOF MS-Based Direct-on-Target Microdroplet Growth Assay. Front Microbiol 2019; 10:13. [PMID: 30733710 PMCID: PMC6353820 DOI: 10.3389/fmicb.2019.00013] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/07/2019] [Indexed: 11/13/2022] Open
Abstract
Introduction: Antibiotic resistant bacteria are a growing concern worldwide. Extended-spectrum β-lactamases (ESBL) represent the most common resistance mechanism of Gram-negative bacteria against β-lactams, underlining the need for adequate diagnostic methods that provide reliable information in the shortest time possible. AmpC, a less prevalent but increasingly relevant class of β-lactamases, pose an additional challenge as their detection is complex. Here, we present an ESBL and AmpC screening panel employing the MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA). Materials and Methods: Four reference strains recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) were used to develop the panel, which was further validated on 50 clinical Enterobacterales isolates resistant to third generation cephalosporins. The panel relies on the synergistic effect between ESBL and/or AmpC β-lactamase inhibitors and cephalosporins, which indicates β-lactamase production. Microdroplets containing the tested microorganism, cephalosporins in different concentrations and inhibitors were pipetted onto an MBT Biotarget and incubated for 3 or 4 h at 35 ± 1°C. Afterward, the liquid medium was removed and the material adhered to the spots was analyzed by MALDI-TOF MS. Synergy was detected by determining and comparing the minimum inhibitory concentrations of the tested cephalosporins with and without β-lactamase inhibitors. Data were interpreted following a diagnostic algorithm proposed by EUCAST in order to establish a final diagnosis. In comparison, PCR, broth microdilution (BMD) and combination disk tests (CDT) were performed. Results: Compared to the PCR results, the following positive and negative percent agreement values (PPA/NPA) were obtained for each resistance mechanism: ESBL, 94.44/100%; AmpC, 94.44/93.75% and ESBL+AmpC, 100/100%. These results, obtained after 4 h of incubation, were comparable with those of BMD and showed a higher accuracy than CDT. Discussion: We propose a novel phenotypic method for detection of ESBL and AmpC β-lactamases in Enterobacterales that provides reliable results in a short time, representing a promising alternative to the diagnostic techniques currently available. This easy-to-perform approach has potential for being implemented in routine laboratories, contributing to the further diversification of mass spectrometry technology into other fields such as antibiotic resistance testing.
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Affiliation(s)
| | - Evgeny A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | | | | | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
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Paul S, Singh P, A S S, Rudramurthy SM, Chakrabarti A, Ghosh AK. Rapid detection of fluconazole resistance in Candida tropicalis by MALDI-TOF MS. Med Mycol 2018; 56:234-241. [PMID: 28992333 DOI: 10.1093/mmy/myx042] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/04/2017] [Indexed: 01/11/2023] Open
Abstract
With the changing epidemiology and emergence of antifungal resistance among Candida species, rapid antifungal susceptibility testing (AFST) is crucial for optimization of antifungal therapy. This study was conducted to standardize a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI -TOF MS) based AFST method (ms-AFST) for susceptibility of Candida tropicalis isolates. Clinical isolates of C. tropicalis were confirmed for fluconazole resistance by the CLSI (M27-A3) method. The incubation period and drug concentration were optimized to determine the minimal profile change concentration (MPCC) by MALDI-TOF MS. The data were analyzed first by direct visual observation of the spectra followed by composite correlation index (CCI) matrix analysis, virtual gel analysis, and cluster analysis for confirmation. Finally, the correlation between minimum inhibitory concentrations (MICs) and MPCCs was evaluated. A total of 15 fluconazole resistant (MICs ranging from 16 to 128 μg/ml) and 19 fluconazole susceptible C. tropicalis isolates (MIC ≤1 μg/ml) were included in this study. All C. tropicalis isolates had significant spectral changes after 4h incubation with fluconazole. Of 34 isolates, MPCCs and MICs were equivalent for 16 isolates, and the MPCC was one dilution lower than the respective MIC in the remaining 18 isolates. This finding was further supported by visual analysis, CCI matrix analysis, virtual gel and principal component analysis dendrogram analysis. The correlation between MPCC and MIC was significant (P < .05). Therefore, a MALDI-TOF MS based AFST assay may be used as a rapid screening technique for fluconazole resistance in C. tropicalis.
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Affiliation(s)
- Saikat Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Pankaj Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Shamanth A S
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh 160012, India
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Cassu-Corsi D, Martins WM, Nicoletti AG, Almeida LG, Vasconcelos AT, Gales AC. Characterisation of plasmid-mediated rmtB-1 in Enterobacteriaceae clinical isolates from São Paulo, Brazil. Mem Inst Oswaldo Cruz 2018; 113:e180392. [PMID: 30540076 PMCID: PMC6287189 DOI: 10.1590/0074-02760180392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/14/2018] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES The emergence of 16S rRNA methyltranferases (16 RMTAses) has jeopardised the clinical use of aminoglycosides. RmtB is one of the most frequently reported in Gram-negatives worldwide. In this study, we aimed to estimate the frequency of 16S RMTAses encoding genes in Enterobacteriaceae isolated in a three-month period from a tertiary Brazilian hospital. METHODS All Gram-negatives classified as resistant to amikacin, gentamicin, and tobramycin by agar screening were selected for analysis. The presence of 16SRMTases encoding genes was verified by polymerase chain reaction (PCR). Antimicrobial susceptible profile was determined by broth microdilution. The genetic relationship among these isolates was accessed by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Selected RmtB-producing isolates were characterised by whole genome sequencing (WGS) analysis. RESULTS Twenty-two of 1,052 (2.1%) Enterobacteriaceae were detected as producers of RmtB-1 [Klebsiella pneumoniae (n = 21) and Proteus mirabilis (n = 1)]. blaKPC-2 was identified among 20 RmtB-1-producing K. pneumoniae isolates that exhibited an identical PFGE and MLST (ST258) patterns. Two K. pneumoniae isolates, the A64216 (not harboring blaKPC-2), A64477 (harboring blaKPC-2) and one P. mirabilis isolate (A64421) were selected for WGS. rmtB-1 and blaKPC-2 genes were carried by distinct plasmids. While a plasmid belonging to the IncFIIk group harbored rmtB-1 in K. pneumoniae, this gene was carried by a non-typable plasmid in P. mirabilis. In the three analysed plasmids, rmtB-1 was inserted on a transposon, downstream a Tn2. CONCLUSION Our findings suggested that the rmtB-1 was harbored by plasmids distinct from those previously reported in Bolivia and China. It suggests that multiple mobilization events might have occurred in South America.
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Affiliation(s)
- Dandara Cassu-Corsi
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Interna, Divisão de Doenças Infecciosas, Laboratório Alerta, São Paulo, SP, Brasil
| | - Willames Mbs Martins
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Interna, Divisão de Doenças Infecciosas, Laboratório Alerta, São Paulo, SP, Brasil
| | - Adriana G Nicoletti
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Interna, Divisão de Doenças Infecciosas, Laboratório Alerta, São Paulo, SP, Brasil
| | - Luiz Gp Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brasil
| | | | - Ana C Gales
- Universidade Federal de São Paulo, Escola Paulista de Medicina, Departamento de Medicina Interna, Divisão de Doenças Infecciosas, Laboratório Alerta, São Paulo, SP, Brasil
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Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for the Rapid Detection of Antimicrobial Resistance Mechanisms and Beyond. Clin Microbiol Rev 2018; 32:32/1/e00037-18. [PMID: 30487165 DOI: 10.1128/cmr.00037-18] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied in recent years for first-line identification of pathogens in clinical microbiology because it is simple to use, rapid, and accurate and has economic benefits in hospital management. The range of clinical applications of MALDI-TOF MS for bacterial isolates is increasing constantly, from species identification to the two most promising applications in the near future: detection of antimicrobial resistance and strain typing for epidemiological studies. The aim of this review is to outline the contribution of previous MALDI-TOF MS studies in relation to detection of antimicrobial resistance and to discuss potential future challenges in this field. Three main approaches are ready (or almost ready) for clinical use, including the detection of antibiotic modifications due to the enzymatic activity of bacteria, the detection of antimicrobial resistance by analysis of the peak patterns of bacteria or mass peak profiles, and the detection of resistance by semiquantification of bacterial growth in the presence of a given antibiotic. This review provides an expert guide for MALDI-TOF MS users to new approaches in the field of antimicrobial resistance detection, especially possible applications as a routine diagnostic tool in microbiology laboratories.
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Leonard H, Colodner R, Halachmi S, Segal E. Recent Advances in the Race to Design a Rapid Diagnostic Test for Antimicrobial Resistance. ACS Sens 2018; 3:2202-2217. [PMID: 30350967 DOI: 10.1021/acssensors.8b00900] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Even with advances in antibiotic therapies, bacterial infections persistently plague society and have amounted to one of the most prevalent issues in healthcare today. Moreover, the improper and excessive administration of antibiotics has led to resistance of many pathogens to prescribed therapies, rendering such antibiotics ineffective against infections. While the identification and detection of bacteria in a patient's sample is critical for point-of-care diagnostics and in a clinical setting, the consequent determination of the correct antibiotic for a patient-tailored therapy is equally crucial. As a result, many recent research efforts have been focused on the development of sensors and systems that correctly guide a physician to the best antibiotic to prescribe for an infection, which can in turn, significantly reduce the instances of antibiotic resistance and the evolution of bacteria "superbugs." This review details the advantages and shortcomings of the recent advances (focusing from 2016 and onward) made in the developments of antimicrobial susceptibility testing (AST) measurements. Detection of antibiotic resistance by genomic AST techniques relies on the prediction of antibiotic resistance via extracted bacterial DNA content, while phenotypic determinations typically track physiological changes in cells and/or populations exposed to antibiotics. Regardless of the method used for AST, factors such as cost, scalability, and assay time need to be weighed into their design. With all of the expansive innovation in the field, which technology and sensing systems demonstrate the potential to detect antimicrobial resistance in a clinical setting?
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Affiliation(s)
- Heidi Leonard
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa, Israel 3200003
| | - Raul Colodner
- Laboratory of Clinical Microbiology, Emek Medical Center, Afula, Israel 18101
| | - Sarel Halachmi
- Department of Urology, Bnai Zion Medical Center, Haifa, Israel 3104800
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion − Israel Institute of Technology, Haifa, Israel 3200003
- The Russell Berrie Nanotechnology Institute, Technion − Israel Institute of Technology, Haifa, Israel, 3200003
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Li P, Xin W, Xia S, Luo Y, Chen Z, Jin D, Gao S, Yang H, Ji B, Wang H, Yan Y, Kang L, Wang J. MALDI-TOF mass spectrometry-based serotyping of V. parahaemolyticus isolated from the Zhejiang province of China. BMC Microbiol 2018; 18:185. [PMID: 30424744 PMCID: PMC6234682 DOI: 10.1186/s12866-018-1328-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/29/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is as an important food-borne pathogen circulating in China. Since 1996, the core serotype has become O3:K6, which has specific genetic markers. This serotype causes the majority of outbreaks worldwide. Until now, nearly 21 serotypes were considered as serovariants of O3:K6. Among these, O4:K68, O1:K25 and O1:KUT have caused pandemic outbreaks. O4:K8, a serovariant of O3:K6, has become the second most dominant serotype circulating in China after O3:K6. In this study, we report the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze and characterize 146 V. parahaemolyticus isolates belonging to 23 serotypes. RESULTS Upon mass spectral analysis, isolates belonging to O4:K8 formed a distinct group among the five main pandemic groups (O3:K6, O4:K8, O4:K68, O1:K25 and O1:KUT). Two major protein peaks (m/z 4383 and 4397) were significantly different between serotype O4:K8 and the four other pandemic strains. Both of these peaks were present in 32 out of 36 O4:K8 isolates, but were absent in 105 out of 110 non-O4:K8 isolates. These peaks were also absent in all 74 pandemic serotypes (O3:K6, O4:K68, O1:K25 and O1:KUT). CONCLUSION Our results highlight the threat of O4:K8 forming a distinct group, which differs significantly from pandemic serotypes on the proteomic level. The use of MALDI-TOF MS has not been reported before in a study of this nature. Mass spectrum peaks at m/z 4383 and 4397 may be specific for O4:K8. However, we cannot conclude that MALDI-TOF MS can be used to serotype V. parahaemolyticus.
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Affiliation(s)
- Ping Li
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Wenwen Xin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Susu Xia
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Yun Luo
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Province Center for Disease Control and Prevention, No.3399 Binsheng Road, Hangzhou, 310000, China
| | - Shan Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Hao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Bin Ji
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China
| | - Henghui Wang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, No.486 Wenqiao Road, Nanhu district, Jiaxing, 314050, China
| | - Lin Kang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
| | - Jinglin Wang
- Graduate College, Anhui Medical University, No.81 Meishan Road, Hefei, 230032, Anhui, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.20 Dongdajie, Fengtai, Beijing, 100071, China.
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Rapid antimicrobial susceptibility testing by matrix-assisted laser desorption ionization–time of flight mass spectrometry using a qualitative method in Acinetobacter baumannii complex. J Microbiol Methods 2018; 153:60-65. [DOI: 10.1016/j.mimet.2018.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 08/30/2018] [Accepted: 09/04/2018] [Indexed: 11/24/2022]
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Proof of Concept for MBT ASTRA, a Rapid Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS)-Based Method To Detect Caspofungin Resistance in Candida albicans and Candida glabrata. J Clin Microbiol 2018; 56:JCM.00420-18. [PMID: 30021820 DOI: 10.1128/jcm.00420-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/28/2018] [Indexed: 11/20/2022] Open
Abstract
The incidence of candidemia caused by Candida albicans and Candida glabrata is constantly increasing and is accompanied by the rising use of the few available antifungals. The widespread use of echinocandins and azoles for the treatment of invasive candidemia has enhanced the development of antifungal resistance, resulting in an increasing health care problem. Hence, the rapid detection of resistant strains is required. This study aimed to evaluate the detection of C. albicans and C. glabrata strains resistant to caspofungin by the matrix-assisted laser desorption ionization Biotyper antibiotic susceptibility test rapid assay (MBT ASTRA). This novel semiquantitative technique facilitates the detection of caspofungin-resistant strains within 6 h. MBT ASTRA results were compared to the data obtained by the use of Clinical and Laboratory Standards Institute (CLSI) guidelines. Clinical isolates of C. albicans (n = 58) and C. glabrata (n = 57) were analyzed by MBT ASTRA and the CLSI microdilution method. Antifungal susceptibility testing against caspofungin by the CLSI microdilution method classified the C. albicans isolates into 36 susceptible and 22 resistant strains and the C. glabrata isolates into 5 susceptible, 33 resistant, and 19 intermediate strains. For C. albicans, the comparison of MBT ASTRA and the CLSI method revealed an excellent categorical agreement of 100%. A sensitivity and a specificity between MBT ASTRA and the CLSI microdilution method of 94% and 80%, respectively, were detected for C. glabrata strains, based on categorical agreement. In conclusion, the results obtained by MBT ASTRA indicate that this is a very promising approach for the rapid detection of Candida isolates resistant to caspofungin.
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Burckhardt I, Zimmermann S. Susceptibility Testing of Bacteria Using Maldi-Tof Mass Spectrometry. Front Microbiol 2018; 9:1744. [PMID: 30127772 PMCID: PMC6088204 DOI: 10.3389/fmicb.2018.01744] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/12/2018] [Indexed: 11/13/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was introduced into the microbiological routine more than 10 years ago. Since then it has almost replaced biochemical identification. It is unrivaled in terms of accuracy and cost. From a laboratory's perspective it would be an ideal method to replace classic susceptibility testing, that is Kirby-Baur agardiffusion or determination of minimal inhibitory concentrations (MICs). First reports on possible assays for susceptibility testing are more than 10 years old. However, the developments during the last 5 years were substantial. This review focuses with some exceptions on the progress, which was achieved during the last decade.
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Affiliation(s)
- Irene Burckhardt
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Stefan Zimmermann
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
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Poole S, Kidd SP, Saeed K. A review of novel technologies and techniques associated with identification of bloodstream infection etiologies and rapid antimicrobial genotypic and quantitative phenotypic determination. Expert Rev Mol Diagn 2018; 18:543-555. [PMID: 29790810 DOI: 10.1080/14737159.2018.1480369] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION The antimicrobial aspect of management of patients with blood stream infections (BSI) and sepsis is time critical. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility is crucial to direct therapy early in the course of illness. Molecular techniques offer a potential solution to this. Areas covered: In the present review the authors have discussed a number of novel solutions utilizing a variety of molecular techniques for pathogen detection, identification and antimicrobial susceptibility. The review is not designed to be an exhaustive literature review covering all diagnostic solutions ever developed, instead the authors have focused on what they have had experience using, evaluating or currently view as new and exciting with potential to revolutionize BSI diagnosis. The authors searched PubMed (Medline) and Google Scholar with terms: BSI, Bacteraemia, Candidaemia, Diagnostics, AST, Rapid, AMR, Novel and Blood Culture. The authors attended recent clinical microbiology technology congresses. Expert commentary: There are multiple exciting novel technologies at differing stages of development with potential to revolutionize diagnosis of BSI. More work is needed as well as a standardized assessment of different platforms in order to better understand the clinical and financial impacts these will have in clinical microbiology laboratories.
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Affiliation(s)
- Stephen Poole
- a Hampshire Hospitals NHS Foundation Trust , Department of Microbiology , Basingstoke and Winchester , UK
| | - Stephen P Kidd
- a Hampshire Hospitals NHS Foundation Trust , Department of Microbiology , Basingstoke and Winchester , UK
| | - Kordo Saeed
- a Hampshire Hospitals NHS Foundation Trust , Department of Microbiology , Basingstoke and Winchester , UK.,b University of Southampton , School of medicine , Southampton , UK
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Vrioni G, Tsiamis C, Oikonomidis G, Theodoridou K, Kapsimali V, Tsakris A. MALDI-TOF mass spectrometry technology for detecting biomarkers of antimicrobial resistance: current achievements and future perspectives. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:240. [PMID: 30069442 PMCID: PMC6046294 DOI: 10.21037/atm.2018.06.28] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The laboratory diagnosis of infections is based on pathogen identification and antimicrobial susceptibility determination. The gold standard of cultivation, isolation and susceptibility testing is a time-consuming procedure and in some cases this can be threatening for patients' outcome. In the current review the applications of mass spectrometry in pathogen identification and especially in detecting biomarkers of antimicrobial resistance are analyzed. MALDI-TOF (matrix-assisted laser desorption/ionization time-of-flight) mass spectrometry is a new technology that has revolutionized pathogen identification and has also proven to accelerate detection of antimicrobial resistance compared to the traditional antibiotic susceptibility tests (AST) as well as DNA amplification methodologies. The technology has incorporated up to know four different methodologies: (I) the detection of differences of mass spectra of susceptible and resistant isolates of a given microorganism using the classical strain typing methodology; (II) the analysis of bacterial induced hydrolysis of β-lactam antibiotics; (III) the detection of stable (non-radioactive) isotope-labeled amino acids; and (IV) the analysis of bacterial growth in the presence and absence of antibiotics using an internal standard. The implementation of MALDI-TOF methodologies has improved detection of resistance in aerobic, Gram-positive and Gram-negative bacteria, mycobacteria, anaerobic bacteria, fungi and viruses. The MALDI-TOF is an easy to use, rapid, reliable, economical, and environmentally friendly methodology. However, this technology needs further development of research protocols that will be validated for routine application.
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Affiliation(s)
- Georgia Vrioni
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Constantinos Tsiamis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - George Oikonomidis
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kalliopi Theodoridou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Violeta Kapsimali
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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Florio W, Tavanti A, Barnini S, Ghelardi E, Lupetti A. Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:1097. [PMID: 29896172 PMCID: PMC5986882 DOI: 10.3389/fmicb.2018.01097] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 05/08/2018] [Indexed: 12/25/2022] Open
Abstract
Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. A rapid diagnosis also allows for early streamlining of empirical antimicrobial therapies, thus contributing to limit the emergence and spread of antimicrobial resistance. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. Compared to currently used identification methods, MALDI-TOF MS has the advantage of identifying bacteria and yeasts directly from colonies grown on culture plates for primary isolation in a few minutes and with considerable material and labor savings. The reliability and accuracy of MALDI-TOF MS in identification of clinically relevant bacteria and yeasts has been demonstrated by several studies showing that the performance of MALDI-TOF MS is comparable or superior to phenotypic methods currently in use in clinical microbiology laboratories, and can be further improved by database updates and analysis software upgrades. Besides microbial identification from isolated colonies, new perspectives are being explored for MALDI-TOF MS, such as identification of pathogens directly from positive blood cultures, sub-species typing, and detection of drug resistance determinants. In this review, we summarize the state of the art in routine identification of microbial pathogens by MALDI-TOF MS, and highlight recent advancements of this technology in special applications, such as strain typing, assessment of drug susceptibility, and detection of virulence factors.
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Affiliation(s)
- Walter Florio
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | | | | | - Emilia Ghelardi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy
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van Belkum A, Welker M, Pincus D, Charrier JP, Girard V. Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry in Clinical Microbiology: What Are the Current Issues? Ann Lab Med 2018; 37:475-483. [PMID: 28840984 PMCID: PMC5587819 DOI: 10.3343/alm.2017.37.6.475] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 06/20/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microbial species in clinical microbiology laboratories. MALDI-TOF-MS has swiftly become the new gold-standard method owing to its key advantages of simplicity and robustness. However, as with all new methods, adoption of the MALDI-TOF MS approach is still not widespread. Optimal sample preparation has not yet been achieved for several applications, and there are continuing discussions on the need for improved database quality and the inclusion of additional microbial species. New applications such as in the field of antimicrobial susceptibility testing have been proposed but not yet translated to the level of ease and reproducibility that one should expect in routine diagnostic systems. Finally, during routine identification testing, unexpected results are regularly obtained, and the best methods for transmitting these results into clinical care are still evolving. We here discuss the success of MALDI-TOF MS in clinical microbiology and highlight fields of application that are still amenable to improvement.
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Affiliation(s)
- Alex van Belkum
- Scientific Office, bioMérieux, La Balme Les Grottes, France.
| | - Martin Welker
- Scientific Office, bioMérieux, La Balme Les Grottes, France
| | - David Pincus
- Scientific Office, bioMérieux, La Balme Les Grottes, France
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42
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Kostrzewa M. Application of the MALDI Biotyper to clinical microbiology: progress and potential. Expert Rev Proteomics 2018; 15:193-202. [DOI: 10.1080/14789450.2018.1438193] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Markus Kostrzewa
- Microbiology and Diagnostics, Bruker Daltonik GmbH, Bremen, Germany
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43
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Zhu Y, Gasilova N, Jović M, Qiao L, Liu B, Lovey LT, Pick H, Girault HH. Detection of antimicrobial resistance-associated proteins by titanium dioxide-facilitated intact bacteria mass spectrometry. Chem Sci 2018; 9:2212-2221. [PMID: 29719694 PMCID: PMC5897883 DOI: 10.1039/c7sc04089j] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/18/2018] [Indexed: 01/05/2023] Open
Abstract
Titanium dioxide-modified target plates were developed to enhance intact bacteria analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The plates were designed to photocatalytically destroy the bacterial envelope structure and improve the ionization efficiency of intracellular components, thereby promoting the measurable mass range and the achievable detection sensitivity. Accordingly, a method for rapid detection of antimicrobial resistance-associated proteins, conferring bacterial resistance against antimicrobial drugs, was established by mass spectrometric fingerprinting of intact bacteria without the need for any sample pre-treatment. With this method, the variations in resistance proteins' expression levels within bacteria were quickly measured from the relative peak intensities. This approach of resistance protein detection directly from intact bacteria by mass spectrometry is useful for fast discrimination of antimicrobial-resistant bacteria from their non-resistant counterparts whilst performing species identification. Also, it could be used as a rapid and convenient way for initial determination of the underlying resistance mechanisms.
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Affiliation(s)
- Yingdi Zhu
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
| | - Natalia Gasilova
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland . .,ISIC-GE-VS , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland
| | - Milica Jović
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
| | - Liang Qiao
- Department of Chemistry , Fudan University , Handan Road 220 , 200433 Shanghai , China
| | - Baohong Liu
- Department of Chemistry , Fudan University , Handan Road 220 , 200433 Shanghai , China
| | | | - Horst Pick
- Laboratoire de Chimie Biophysique des Macromolécules , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Hubert H Girault
- Laboratoire d'Electrochimie Physique et Analytique , École Polytechnique Fédérale de Lausanne , Rue de l'industrie 17 , CH-1951 Sion , Switzerland .
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44
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Florio W, Morici P, Ghelardi E, Barnini S, Lupetti A. Recent advances in the microbiological diagnosis of bloodstream infections. Crit Rev Microbiol 2017; 44:351-370. [PMID: 29185372 DOI: 10.1080/1040841x.2017.1407745] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Rapid identification (ID) and antimicrobial susceptibility testing (AST) of the causative agent(s) of bloodstream infections (BSIs) are essential for the prompt administration of an effective antimicrobial therapy, which can result in clinical and financial benefits. Immediately after blood sampling, empirical antimicrobial therapy, chosen on clinical and epidemiological data, is administered. When ID and AST results are available, the clinician decides whether to continue or streamline the antimicrobial therapy, based on the results of the in vitro antimicrobial susceptibility profile of the pathogen. The aim of the present study is to review and discuss the experimental data, advantages, and drawbacks of recently developed technological advances of culture-based and molecular methods for the diagnosis of BSI (including mass spectrometry, magnetic resonance, PCR-based methods, direct inoculation methods, and peptide nucleic acid fluorescence in situ hybridization), the understanding of which could provide new perspectives to improve and fasten the diagnosis and treatment of septic patients. Although blood culture remains the gold standard to diagnose BSIs, newly developed methods can significantly shorten the turnaround time of reliable microbial ID and AST, thus substantially improving the diagnostic yield.
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Affiliation(s)
- Walter Florio
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Paola Morici
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Emilia Ghelardi
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
| | - Simona Barnini
- b U.O. Microbiologia Universitaria Azienda Ospedaliero-Universitaria Pisana , Pisa , Italy
| | - Antonella Lupetti
- a Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia , Università di Pisa , Pisa , Italy
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45
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Martins WMBS, Narciso AC, Cayô R, Santos SV, Fehlberg LCC, Ramos PL, da Cruz JB, Gales AC. SPM-1-producing Pseudomonas aeruginosa ST277 clone recovered from microbiota of migratory birds. Diagn Microbiol Infect Dis 2017; 90:221-227. [PMID: 29224710 DOI: 10.1016/j.diagmicrobio.2017.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 02/02/2023]
Abstract
The production of São Paulo metallo-β-lactamase (SPM-1) is the most common carbapenem resistance mechanism detected among multidrug-resistant Pseudomonas aeruginosa clinical isolates in Brazil. Dissemination of SPM-1-producing P. aeruginosa has been restricted to the nosocomial settings, with sporadic reports of environmental isolates due to contamination by hospital sewage. Herein, we described the detection and molecular characterization of SPM-1-producing P. aeruginosa recovered from the microbiota of migratory birds in Brazil. Three hundred gram-negative bacilli were recovered from cloacal and choanal swabs of Dendrocygna viduata during a surveillance study for detection of carbapenem-resistant isolates. All isolates were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. MICs were determined by agar dilution, except for polymyxin B. Antibiotic resistance genes were detected by polymerase chain reaction (PCR) followed by DNA sequencing. Transcriptional levels of oprD and efflux system encoding genes were also carried out by quantitative real-time PCR. Nine imipenem-resistant P. aeruginosa isolates were recovered with 7 of them carrying blaSPM-1. Additional resistance genes (rmtD-1, blaOXA-56,aacA4, and aac(6')-Ib-cr) were also detected in all 9 isolates. The SPM-1-producing isolates showed high MICs for all β-lactams, fluoroquinolones, and aminoglycosides, being susceptible only to polymyxin B. Interestingly, all isolates showed the same PFGE pattern and belonged to ST277. Overexpression of MexXY-OprM and MexAB-OprM was observed in those isolates that did not harbor blaSPM-1. Our results suggest that migratory birds might have played a role in the dissemination of SPM-1-producing P. aeruginosa within the Brazilian territory.
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Affiliation(s)
- Willames M B S Martins
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil.
| | - Ana Clara Narciso
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Rodrigo Cayô
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Stéfanie Vanessa Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Lorena C C Fehlberg
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
| | - Patrícia Locosque Ramos
- Departamento de Pesquisas Aplicadas, Fundação Parque Zoológico de São Paulo, São Paulo, SP, Brazil
| | | | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo-UNIFESP, São Paulo, Brazil
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46
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Hombach M, Jetter M, Blöchliger N, Kolesnik-Goldmann N, Böttger EC. Fully automated disc diffusion for rapid antibiotic susceptibility test results: a proof-of-principle study. J Antimicrob Chemother 2017; 72:1659-1668. [PMID: 28333189 DOI: 10.1093/jac/dkx026] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/17/2017] [Indexed: 11/14/2022] Open
Abstract
Background Antibiotic resistance poses a significant threat to patients suffering from infectious diseases. Early readings of antibiotic susceptibility test (AST) results could be of critical importance to ensure adequate treatment. Disc diffusion is a well-standardized, established and cost-efficient AST procedure; however, its use in the clinical laboratory is hampered by the many manual steps involved, and an incubation time of 16-18 h, which is required to achieve reliable test results. Methods We have evaluated a fully automated system for its potential for early reading of disc diffusion diameters after 6-12 h of incubation. We assessed availability of results, methodological precision, categorical agreement and interpretation errors as compared with an 18 h standard. In total, 1028 clinical strains (291 Escherichia coli , 272 Klebsiella pneumoniae , 176 Staphylococcus aureus and 289 Staphylococcus epidermidis ) were included in this study. Disc diffusion plates were streaked, incubated and imaged using the WASPLab TM automation system. Results and conclusions Our results demonstrate that: (i) early AST reading is possible for important pathogens; (ii) methodological precision is not hampered at early timepoints; and (iii) species-specific reading times must be selected. As inhibition zone diameters change over time and are phenotype/drug combination dependent, specific cut-offs and expert rules will be essential to ensure reliable interpretation and reporting of early susceptibility testing results.
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Affiliation(s)
- Michael Hombach
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Schweiz
| | - Marion Jetter
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Schweiz
| | - Nicolas Blöchliger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Schweiz
| | | | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Schweiz
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47
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Maxson T, Taylor-Howell CL, Minogue TD. Semi-quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus aureus. PLoS One 2017; 12:e0183899. [PMID: 28859120 PMCID: PMC5578647 DOI: 10.1371/journal.pone.0183899] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/14/2017] [Indexed: 11/18/2022] Open
Abstract
Antibiotic resistant bacterial infections are a significant problem in the healthcare setting, in many cases requiring the rapid administration of appropriate and effective antibiotic therapy. Diagnostic assays capable of quickly and accurately determining the pathogen resistance profile are therefore crucial to initiate or modify care. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a standard method for species identification in many clinical microbiology laboratories and is well positioned to be applied towards antimicrobial susceptibility testing. One recently reported approach utilizes semi-quantitative MALDI-TOF MS for growth rate analysis to provide a resistance profile independent of resistance mechanism. This method was previously successfully applied to Gram-negative pathogens and mycobacteria; here, we evaluated this method with the Gram-positive pathogen Staphylococcus aureus. Specifically, we used 35 strains of S. aureus and four antibiotics to optimize and test the assay, resulting in an overall accuracy rate of 95%. Application of the optimized assay also successfully determined susceptibility from mock blood cultures, allowing both species identification and resistance determination for all four antibiotics within 3 hours of blood culture positivity.
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Affiliation(s)
- Tucker Maxson
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland, United States of America
| | - Cheryl L. Taylor-Howell
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland, United States of America
| | - Timothy D. Minogue
- Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland, United States of America
- * E-mail:
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48
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Popović NT, Kazazić SP, Strunjak-Perović I, Čož-Rakovac R. Differentiation of environmental aquatic bacterial isolates by MALDI-TOF MS. ENVIRONMENTAL RESEARCH 2017; 152:7-16. [PMID: 27741451 DOI: 10.1016/j.envres.2016.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 09/20/2016] [Accepted: 09/24/2016] [Indexed: 05/20/2023]
Abstract
Identification of bacteria in aquatic and environmental applications, for monitoring purposes and research, for health assessments and therapy considerations of farmed and free-living aquatic organisms, still relies on conventional phenotypic and biochemical protocols. Although molecular techniques based on DNA amplification and sequencing are finding ways into diagnostic laboratories, they are time-consuming, costly and difficult in the case of multiplex assays. Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is a rapid and accurate proteomic method reliable for identification of unknown bacteria to the genus and species level. Upon extension of databases, it will certainly find its position in environmental sciences. The paper presents an overview of the principle of the method, its effectiveness in comparison with conventional and molecular identification procedures, and applicability on environmental and aquatic isolates, discussing its advantages and shortcomings, as well as possible future implementations.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry, Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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49
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Wieser A, Schubert S. MALDI-TOF MS entering the microbiological diagnostic laboratory – from fast identification to resistance testing. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.05.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Sanguinetti M, Posteraro B. Mass spectrometry applications in microbiology beyond microbe identification: progress and potential. Expert Rev Proteomics 2016; 13:965-977. [DOI: 10.1080/14789450.2016.1231578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Brunella Posteraro
- Institute of Public Health (Section of Hygiene), Università Cattolica del Sacro Cuore, Rome, Italy
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