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Ai G, Zhang Y, Guo K, Zhao L, Li Z, Hai H, Jia E, Liu J. The impact of optimizing microbial diagnosis processes on clinical and healthcare economic outcomes in hospitalized patients with bloodstream infections. Eur J Clin Microbiol Infect Dis 2024:10.1007/s10096-024-04928-2. [PMID: 39240272 DOI: 10.1007/s10096-024-04928-2] [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: 06/24/2024] [Accepted: 08/23/2024] [Indexed: 09/07/2024]
Abstract
PURPOSE Bloodstream infections (BSIs) are associated with significant morbidity, mortality and costs, while prolonged blood culture (BC) diagnosis may delay the initiation of targeted therapy. This study evaluates the impact of an optimized microbiology laboratory process on turnaround times, antibiotic use, clinical outcomes and economics for hospitalized BSI patients. METHODS A pre-post study was conducted in a Chinese hospital in which BSI derived BC results before (Oct. 2020- Sep. 2021) and after (Oct. 2021- Sep. 2022) newly implemented microbiology diagnostics and workflow changes were analyzed. Turnaround times, antibiotic initiation, length of stay and in-hospital costs were compared. RESULTS From 213 included patients, 134 were pre-optimization (pre-op) and 79 were post-optimization (post-op) cases. The median time from blood sample collection (BSC) to pathogen identification (ID) decreased from 70.12 to 47.43 h post-op (P < 0.001). The median time from BSC to the first ID report related initiation of pathogen-directed antibiotic use decreased from 88.48 to 47.85 h post-op (P < 0.001). The average hospital stay decreased from 19.54 to 16.79 days and 30-day readmissions declined from 18.7 to 13.9%, while the mean total antimicrobial drug usage costs decreased by 3,889 CNY per patient (P = 0.022) after optimization. CONCLUSIONS Implementing new diagnostics technologies and optimizing laboratory workflows significantly reduced antimicrobial drug usage costs, shortened the time to ID results and improved the timeliness of appropriate antibiotic choices to treat BSIs. Investments in faster testing and process improvements were clearly beneficial for patient outcomes and healthcare economics.
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Affiliation(s)
- Genwei Ai
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China.
| | - Ying Zhang
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - Kunshan Guo
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - Lu Zhao
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - Zhi Li
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - He Hai
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - Erjuan Jia
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
| | - Junying Liu
- Department of Laboratory Medicine, Xuchang Central Hospital, No. 666 Wenxuan Street, Xuchang, 461000, China
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Zhou Y, Du W, Chen Y, Li L, Xiao X, Xu Y, Yang W, Hu X, Wang B, Zhang J, Jiang Q, Wang Y. Pathogen detection via inductively coupled plasma mass spectrometry analysis with nanoparticles. Talanta 2024; 277:126325. [PMID: 38833906 DOI: 10.1016/j.talanta.2024.126325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 04/24/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Infections caused by viruses and bacteria pose a significant threat to global public health, emphasizing the critical importance of timely and precise detection methods. Inductively coupled plasma mass spectrometry (ICP-MS), a contemporary approach for pathogen detection, offers distinct advantages such as high sensitivity, a wide linear range, and multi-index capabilities. This review elucidates the underexplored application of ICP-MS in conjunction with functional nanoparticles (NPs) for the identification of viruses and bacteria. The review commences with an elucidation of the underlying principles, procedures, target pathogens, and NP requirements for this innovative approach. Subsequently, a thorough analysis of the advantages and limitations associated with these techniques is provided. Furthermore, the review delves into a comprehensive examination of the challenges encountered when utilizing NPs and ICP-MS for pathogen detection, culminating in a forward-looking assessment of the potential pathways for advancement in this domain. Thus, this review contributes novel perspectives to the field of pathogen detection in biomedicine by showcasing the promising synergy of ICP-MS and NPs.
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Affiliation(s)
- Yujie Zhou
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Wenli Du
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yuzuo Chen
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lei Li
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Xuanyu Xiao
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yuanyuan Xu
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Wenjuan Yang
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xuefeng Hu
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Baoning Wang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Jieyu Zhang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China.
| | - Qing Jiang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, 29 Wangjiang Road, Chengdu, Sichuan, 610065, China
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Shen H, Xie J, Gao W, Wang L, Chen L, Qian H, Yu S, Feng B, Yang F. Detection limit of FT-IR-based bacterial typing based on optimized sample preparation and typing model. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123633. [PMID: 37952427 DOI: 10.1016/j.saa.2023.123633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Accurate and efficient bacterial typing methods are crucial to microbiology. Fourier transform infrared (FT-IR) spectroscopy enables highly distinguishable fingerprint identification of closely related bacterial strains by producing highly specific fingerprints of bacteria, which is increasingly being considered as an alternative to genotypic methods, such as pulsed field gel electrophoresis (PFGE) and whole genome sequencing (WGS), for bacterial typing. Compared with genotypic methods, FT-IR has significant advantages of convenient operation, fast speed, and low cost. Fundamental research into the detection limit based on optimized analytical conditions for FT-IR bacterial typing, which can avoid excessive bacterial culture time or sampling volume, is particularly important, especially in clinical practice. However, the corresponding parameters have not been fully investigated. In this study, we developed a simplified and reliable procedure for sample preparation, optimized the data analysis procedure, and evaluated the FT-IR detection limit based on the above conditions. In particular, we combined the film mold and calcium fluoride plate for sample preparation. We evaluated the detection limit (about 108 CFU/mL) after parameter optimization using hierarchical cluster analysis (HCA) and artificial neural network (ANN). The optimization and evaluation of these key fundamentals will better promote future application of FT-IR-based bacterial typing.
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Affiliation(s)
- Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Jinghang Xie
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wenjing Gao
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China
| | | | - Heng Qian
- Shanghai University of Finance and Economics, Shanghai 200433, China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
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Peixoto-Rodrigues MC, da Costa GL, Pinto TN, Adesse D, Oliveira MME, Hauser-Davis RA. A novel report on the emerging and zoonotic neurotropic fungus Trichosporon japonicum in the brain tissue of the endangered Brazilian guitarfish (Pseudobatos horkelii) off the southeastern coast of Brazil. BMC Microbiol 2023; 23:367. [PMID: 38017412 PMCID: PMC10685615 DOI: 10.1186/s12866-023-03128-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
Yeast infections have gained significant attention in the field of marine biology in recent years. Among the broad diversity of marine organisms affected by these infections, elasmobranchs (sharks and rays) have emerged as highly susceptible, due to climate change effects, such as increasing water temperatures and pollution, which can alter the composition and abundance of fungal communities. Additionally, injuries, or compromised immune systems resulting from pollution or disease may increase the likelihood of fungal infections in elasmobranchs. Studies are, however, still lacking for this taxonomic group. In this context, this study aimed to screen yeast species in cell cultures obtained from the brain of artisanally captured Pseudobatos horkelii, a cartilaginous fish that, although endangered, is highly captured and consumed worldwide. Fungi were isolated during an attempt to establish primary cultures of elasmobranch neural cells. Culture flasks were swabbed and investigated using morphological, phenotypic, and molecular techniques. Two isolates of the emerging opportunistic pathogen Trichosporon japonicum were identified, with high scores (1.80 and 1.85, respectively) by the MALDI-ToF technique. This is the first report of the basidiomycetous yeast T. japonicum in Pseudobatos horkelii in Brazil. This finding highlights the need for further research to determine the potential impact on elasmobranch health, ecology, as well as on commercial fisheries.
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Affiliation(s)
- Maria Carolina Peixoto-Rodrigues
- Laboratório de Avaliação e Promoção da Saúde Ambiental, IInstituto Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Gisela Lara da Costa
- Laboratório de Taxonomia, Bioquímica e Bioprospecção de Fungos, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Tatiane Nobre Pinto
- Laboratório de Taxonomia, Bioquímica e Bioprospecção de Fungos, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Daniel Adesse
- Laboratório de Biologia Estrutural, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, IInstituto Oswaldo Cruz, Rio de Janeiro, Brazil.
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Roytrakul S, Sangprasert P, Jaresitthikunchai J, Phaonakrop N, Arpornsuwan T. Peptide barcode of multidrug-resistant strains of Neisseria gonorrhoeae isolated from patients in Thailand. PLoS One 2023; 18:e0289308. [PMID: 37535640 PMCID: PMC10399818 DOI: 10.1371/journal.pone.0289308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/14/2023] [Indexed: 08/05/2023] Open
Abstract
The emergence of multidrug-resistant strains of Neisseria gonorrhoeae constitutes a serious threat to public health. The present study aimed to investigate peptidome-based biomarkers of multidrug-resistant N. gonorrhoeae, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography tandem mass spectrometry (LC-MS). The peptide barcode database of multidrug resistant N. gonorrhoeae was generated from the whole-cell peptides of 93 N. gonorrhoeae isolated from patients in Thailand. The dendrogram of 93 independent isolates of antibiotic-resistant N. gonorrhoeae revealed five distinct clusters including azithromycin resistance group (AZ), ciprofloxacin resistance group (C), ciprofloxacin and penicillin resistance group (CP), ciprofloxacin and tetracycline resistance group (CT), ciprofloxacin, penicillin and tetracycline resistance group (CPT). The peptidomes of all clusters were comparatively analyzed using a high-performance liquid chromatography-mass spectrometry method (LC-MS). Nine peptides derived from 9 proteins were highly expressed in AZ (p value < 0.05). These peptides also played a crucial role in numerous pathways and showed a strong relationship with the antibiotic resistances. In conclusion, this study showed a rapid screening of antibiotic-resistant N. gonorrhoeae using MALDI-TOF MS. Additionally, potential specific peptidome-based biomarker candidates for AZ, C, CP, CT and CPT-resistant N. gonorrhoeae were identified.
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Affiliation(s)
- Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathumthani, Thailand
| | - Pongsathorn Sangprasert
- Graduate Student of Department of Medical Technology, Faculty of Allied Health Sciences, Thammasat University, Khlong Luang, Pathumthani, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathumthani, Thailand
| | - Narumon Phaonakrop
- Functional Proteomics Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathumthani, Thailand
| | - Teerakul Arpornsuwan
- Medical Technology Research and Service Unit, Health Care Service Center, Faculty of Allied Health Sciences, Thammasat University, Khlong Luang, Pathumthani, Thailand
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Song D, Su Q, Jia A, Fu S, Ma X, Li T, Man C, Yang X, Jiang Y. A Method to Directly Identify Cronobacter sakazakii in Liquid Medium by MALDI-TOF MS. Foods 2023; 12:foods12101981. [PMID: 37238798 DOI: 10.3390/foods12101981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/11/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been widely used as an emerging technology for the rapid identification of microorganisms. Cronobacter sakazakii (C. sakazakii) is a food-borne pathogen of particular importance to the powdered infant formula (PIF) processing environment due to its high lethality in infants. However, the traditional solid spotting detection method of pretreating samples for MALDI-TOF MS leads only to qualitative detection of C. sakazakii. We developed a new, low-cost, robust liquid spotting pretreatment method and used a response surface methodology to optimize its parameters. The applicability, accuracy, and quantitative potential were measured for different types of samples. The optimal parameters of this method were as follows: a volume of 70% formic acid of 25 μL, treatment with ultrasound at 350 W for 3 min, and a volume of acetonitrile added of 75 μL. These conditions led to the highest identification score for C. sakazakii (1926.42 ± 48.497). This method was found to detect bacteria accurately and reproducibly. When 70 strains of C. sakazakii isolates were analyzed with this method, the identification accuracy was 100%. The detection limit of C. sakazakii in environmental and PIF samples was 4.1 × 101 cfu/mL and 2.72 × 103 cfu/mL, respectively.
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Affiliation(s)
- Danliangmin Song
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Qunchao Su
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Ai Jia
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Shiqian Fu
- Key Laboratory of Animal Protein Food Deep Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China
| | - Xiaoming Ma
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Tiantian Li
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Chaoxin Man
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
| | - Xinyan Yang
- Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China
| | - Yujun Jiang
- Department of Food Science, Northeast Agricultural University, Harbin 150038, China
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Chirio D, Demonchy E, Le Marechal M, Gaudart A, Lotte R, Carles M, Ruimy R. 24/7 workflow for bloodstream infection diagnostics in microbiology laboratories: the first step to improve clinical management. Clin Chem Lab Med 2023; 61:349-355. [PMID: 36326696 DOI: 10.1515/cclm-2022-0667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVES We aimed to evaluate the impact of an uninterrupted workflow regarding blood cultures on turnaround time and antibiotic prescription. METHODS Monomicrobial episodes of bacteremia were retrospectively evaluated before and after a continuous 24/7 workflow was implemented in our clinical microbiology laboratory (pre- and post-intervention periods; PREIP and POSTIP). Primary outcome was the time from specimen collection to the first change in antibiotic therapy. Secondary outcomes included the time from specimen collection to effective antibiotic therapy and to antibiotic susceptibility testing results (or turnaround time), as well as hospital length of stay and all-cause mortality at 30 days. RESULTS A total of 548 episodes of bacteremia were included in the final analysis. There was no difference in PREIP and POSTIP regarding patient characteristics and causative bacteria. In POSTIP, the mean time to the first change in antibiotic therapy was reduced by 10.4 h (p<0.001). The time to effective antibiotic therapy and the turnaround time were respectively reduced by 4.8 h (p<0.001) and 5.1 h (p=0.006) in POSTIP. There was no difference in mean hospital length of stay or mortality between the two groups. CONCLUSIONS Around the clock processing of blood cultures allows for a reduction in turnaround time, which in turn reduces the delay until effective antibiotic therapy prescription.
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Affiliation(s)
- David Chirio
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Elisa Demonchy
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
| | - Marion Le Marechal
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Département de santé publique, CHU de Nice, Nice, France
| | - Alice Gaudart
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
| | - Romain Lotte
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
| | - Michel Carles
- Service de Maladies infectieuses et Tropicales, Hôpital l'Archet 1, CHU de Nice, Nice, France
- Université Côte d'Azur, Nice, France
| | - Raymond Ruimy
- Université Côte d'Azur, Nice, France
- Laboratoire de Bactériologie, CHU de Nice, Hôpital de l'Archet, Nice, France
- INSERM U1065, C3M, Equipe 6 "Virulence microbienne et signalisation inflammatoire", Bâtiment Universitaire Archimed, Nice, France
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Pan F, Zhao N, Zhao W, Wang C, Sun Y, Zhang H, Qin J, Liu Q, Zhang H. Performance of Two Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of the Viridans Group Streptococci. Infect Drug Resist 2023; 16:2901-2909. [PMID: 37193297 PMCID: PMC10183192 DOI: 10.2147/idr.s407667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 05/18/2023] Open
Abstract
Background Due to similar colony morphology among viridans group streptococci (VGS), the differentiation of VGS species remains difficult in routine clinical microbiology. Recently, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been described as a fast method for identifying various bacteria at species level, and also for the VGS strains. Methods A total of 277 VGS isolates were identified with the two MALDI-TOF MS systems (VITEK MS and Bruker Biotyper). The tuf and rpoB gene sequencing was used as the reference identification method for comparison. Results Based on tuf and rpoB gene sequencing, 84 isolates were S. pneumoniae and 193 strains were other VGS isolates including S. anginosus group (n=91, 47.2%), S. mitis group (n=80, 41.5%), S. bovis group (n=11, 5.7%), S. salivarius group (n=10, 5.2%), and S. mutans group (n=1, 0.5%). VITEK MS and Bruker Biotyper accurately identified 94.6% and 89.9% of all VGS isolates, respectively. VITEK MS showed better identification results than Bruker Biotyper for S. mitis group including S. pneumoniae and S. bovis group, but for other VGS isolates, two MALDI-TOF MS systems showed comparable identification performance. However, VITEK MS was able to identify S. gallolyticus to the subspecies level with high-confidence (S. gallolyticus ssp. pasteurianus), while the Bruker Biotyper system could not. While Bruker Biotyper system could be able to correctly differentiate the subspecies of S. salivarius from S. vestibularis, VITEK MS poorly identify. Conclusion This study demonstrated that two MALDI-TOF MS systems allowed discrimination for most VGS isolates with different identification performance, but Bruker Biotyper could produce more misidentifications and VITEK MS system. It is crucial to be familiar with the performance of MALDI-TOF MS systems used in clinical microbiology.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Wantong Zhao
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Sun
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Haomin Zhang
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Juanxiu Qin
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
- Qian Liu, Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China, Email
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
- Correspondence: Hong Zhang, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, Tel +86 189 1712 8200, Email
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10
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Sánchez-Juanes F, Calvo Sánchez N, Belhassen García M, Vieira Lista C, Román RM, Álamo Sanz R, Muro Álvarez A, Muñoz Bellido JL. Applications of MALDI-TOF Mass Spectrometry to the Identification of Parasites and Arthropod Vectors of Human Diseases. Microorganisms 2022; 10:2300. [PMID: 36422371 PMCID: PMC9695109 DOI: 10.3390/microorganisms10112300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 08/27/2023] Open
Abstract
Arthropod vectors and parasites are identified morphologically or, more recently, by molecular methods. Both methods are time consuming and require expertise and, in the case of molecular methods, specific devices. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of bacteria has meant a major change in clinical microbiology laboratories because of its simplicity, speed and specificity, and its capacity to identify microorganisms, in some cases, directly from the sample (urine cultures, blood cultures). Recently, MALDI-TOF MS has been shown as useful for the identification of some parasites. On the other hand, the identification of vector arthropods and the control of their populations is essential for the control of diseases transmitted by arthropods, and in this aspect, it is crucial to have fast, simple and reliable methods for their identification. Ticks are blood-sucking arthropods with a worldwide distribution, that behave as efficient vectors of a wide group of human and animal pathogens, including bacteria, protozoa, viruses, and even helminths. They are capable of parasitizing numerous species of mammals, birds and reptiles. They constitute the second group of vectors of human diseases, after mosquitoes. MALDI-TOF MS has been shown as useful for the identification of different tick species, such as Ixodes, Rhipicephalus and Amblyomma. Some studies even suggest the possibility of being able to determine, through MALDI-TOF MS, if the arthropod is a carrier of certain microorganisms. Regarding mosquitoes, the main group of vector arthropods, the possibility of using MALDI-TOF MS for the identification of different species of Aedes and Anopheles has also been demonstrated. In this review, we address the possibilities of this technology for the identification of parasites and arthropod vectors, its characteristics, advantages and possible limitations.
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Affiliation(s)
- Fernando Sánchez-Juanes
- Department of Biochemistry and Molecular Biology, University of Salamanca, 37007 Salamanca, Spain
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Noelia Calvo Sánchez
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Moncef Belhassen García
- Department of Medicine-Infectious Diseases, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, 37008 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - Carmen Vieira Lista
- Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, 37008 Salamanca, Spain
| | - Raul Manzano Román
- Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, 37008 Salamanca, Spain
| | - Rufino Álamo Sanz
- Public Health Information Service, Consejería de Sanidad, Junta de Castilla y León, 47007 Valladolid, Spain
| | - Antonio Muro Álvarez
- Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, 37008 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
| | - Juan Luis Muñoz Bellido
- Department of Microbiology, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Universidad de Salamanca, 37008 Salamanca, Spain
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Hospital Universitario de Salamanca, Universidad de Salamanca, CSIC, 37007 Salamanca, Spain
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Eltahawy AMAE, Awad ESAM, Ibrahim AH, Merwad ARMA, Desoky ESM. Integrative application of heavy metal-resistant bacteria, moringa extracts, and nano-silicon improves spinach yield and declines its contaminant contents on a heavy metal-contaminated soil. FRONTIERS IN PLANT SCIENCE 2022; 13:1019014. [PMID: 36457524 PMCID: PMC9705991 DOI: 10.3389/fpls.2022.1019014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Microorganism-related technologies are alternative and traditional methods of metal recovery or removal. We identified and described heavy metal-resistant bacteria isolated from polluted industrial soils collected from various sites at a depth of 0-200 mm. A total of 135 isolates were screened from polluted industrial soil. The three most abundant isolate strains resistant to heavy metals were selected: Paenibacillus jamilae DSM 13815T DSM (LA22), Bacillus subtilis ssp. spizizenii DSM 15029T DSM (MA3), and Pseudomonas aeruginosa A07_08_Pudu FLR (SN36). A test was conducted to evaluate the effect of (1) isolated heavy metal-resistant bacteria (soil application), (2) a foliar spray with silicon dioxide nanoparticles (Si-NPs), and (3) moringa leaf extract (MLE) on the production, antioxidant defense, and physio-biochemical characteristics of spinach grown on heavy metal-contaminated soil. Bacteria and MLE or Si-NPs have been applied in single or combined treatments. It was revealed that single or combined additions significantly increased plant height, shoot dry and fresh weight, leaf area, number of leaves in the plant, photosynthetic pigments content, total soluble sugars, free proline, membrane stability index, ascorbic acid, relative water content, α-tocopherol, glycine betaine, glutathione, and antioxidant enzyme activities (i.e., peroxidase, glutathione reductase, catalase, superoxide dismutase, and ascorbate peroxidase) compared with the control treatment. However, applying bacteria or foliar spray with MLE or Si-NPs significantly decreased the content of contaminants in plant leaves (e.g., Fe, Mn, Zn, Pb, Cd, Ni, and Cu), malondialdehyde, electrolyte leakage, superoxide radical ( O 2 · - ) , and hydrogen peroxide (H2O2). Integrative additions had a more significant effect than single applications. It was suggested in our study that the integrative addition of B. subtilis and MLE as a soil application and as a foliar spray, respectively, is a critical approach to increasing spinach plant performance and reducing its contaminant content under contaminated soil conditions.
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Affiliation(s)
| | - El-Sayed A. M. Awad
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ahmed H. Ibrahim
- Soil Science Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - El-Sayed M. Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Transmission of gram-negative antibiotic-resistant bacteria following differing exposure to antibiotic-resistance reservoirs in a rural community: a modelling study for bloodstream infections. Sci Rep 2022; 12:13488. [PMID: 35931725 PMCID: PMC9356060 DOI: 10.1038/s41598-022-17598-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022] Open
Abstract
Exposure to community reservoirs of gram-negative antibiotic-resistant bacteria (GN-ARB) genes poses substantial health risks to individuals, complicating potential infections. Transmission networks and population dynamics remain unclear, particularly in resource-poor communities. We use a dynamic compartment model to assess GN-ARB transmission quantitatively, including the susceptible, colonised, infected, and removed populations at the community-hospital interface. We used two side streams to distinguish between individuals at high- and low-risk exposure to community ARB reservoirs. The model was calibrated using data from a cross-sectional cohort study (N = 357) in Chile and supplemented by existing literature. Most individuals acquired ARB from the community reservoirs (98%) rather than the hospital. High exposure to GN-ARB reservoirs was associated with 17% and 16% greater prevalence for GN-ARB carriage in the hospital and community settings, respectively. The higher exposure has led to 16% more infections and attributed mortality. Our results highlight the need for early-stage identification and testing capability of bloodstream infections caused by GN-ARB through a faster response at the community level, where most GN-ARB are likely to be acquired. Increasing treatment rates for individuals colonised or infected by GN-ARB and controlling the exposure to antibiotic consumption and GN-ARB reservoirs, is crucial to curve GN-ABR transmission.
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Agarwal AN, Dallas SD, Mais DD. Sensitivity and Specificity of a Novel Colony Characteristic for Determination of Methicillin-Resistant Staphylococcus aureus. Cureus 2022; 14:e26040. [PMID: 35865434 PMCID: PMC9293263 DOI: 10.7759/cureus.26040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Purpose: To assess colony morphology of Staphylococcus aureus isolates for target shape (T1) and its utility in the identification of methicillin-resistant S. aureus (MRSA). Methods: Staphylococcus species isolated from blood cultures were studied for colony morphology characteristics. A polymerase chain reaction (PCR) test was performed on positive blood culture bottles for the detection of S. aureus and methicillin resistance. Colony morphology was read at 24 and 48 hours and defined as follows: target shaped (T1) - an elevated colony center encircled by a pale zone, which is surrounded by a single ring of peripheral enhancement giving a ‘target’ appearance; dome-shaped (T2) with an elevated center lacking the ‘target’ appearance. Results: At 48 hours, 73.7% of MRSA and 59.5% of coagulase-negative staphylococci (CoNS) showed T1 morphology. T1 morphology has a sensitivity of 73.68% and specificity of 93.55% amongst S. aureus for identification of methicillin resistance and a high positive predictive value (95.45%) at 48 hours. Conclusion: T1 morphology has a modest sensitivity with specificity and positive predictive value amongst S. aureus for identification of methicillin resistance at 48 hours. It can be potentially used for the identification of MRSA, especially in resource-limited settings and wherein a molecular test is not repeated if PCR testing has already identified methicillin-sensitive S. aureus (MSSA) on a recent specimen on the same patient.
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Sacchetti B, Travis J, Steed LL, Webb G. Identification of the main contributors to blood culture contamination at a tertiary care academic medical center. Infect Prev Pract 2022; 4:100219. [PMID: 35692894 PMCID: PMC9184864 DOI: 10.1016/j.infpip.2022.100219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
Background Blood culture contamination poses an issue to all hospital systems worldwide because of the associated costs of extended length of stays, unnecessary antibiotic therapy, and additional laboratory testing that are preventable with proper handling and collection techniques. Methods In our study, multiple units, staff, and collection methods were compared to determine the primary culprits of contamination from a tertiary care academic medical center, which includes a pediatric hospital and both adult and pediatric emergency departments. Results Over 33 months, 2,083 out of 88,322 total blood cultures collected were contaminated, with an overall contamination rate of 2.4%. A moderate positive correlation was found between the monthly total number of cultures and monthly contamination rate (r = 0.411 P < .01). The most notable factors associated with contamination were found to be phlebotomy teams (2.7%) (P < .01), peripheral draws (2.3%) (P <.01), adult emergency departments (2.6%) (P < .01), and pediatric intensive care units (2.7%) (P < .01). A positive correlation was present between the number of hospital beds per unit and unit contamination rates (r = 0.429 P < .01). Conclusion Our results were used to make recommendations for decreasing the rate of blood culture contamination in this institution, which includes acknowledgement of an overwhelmed staff and mandatory periodic training on acceptable aseptic technique and contamination awareness. Understanding the factors contributing to blood culture contamination can aid efforts to reduce contamination rates.
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Výrostková J, Regecová I, Zigo F, Semjon B, Gregová G. Antimicrobial Resistance of Staphylococcus sp. Isolated from Cheeses. Animals (Basel) 2021; 12:ani12010036. [PMID: 35011142 PMCID: PMC8749609 DOI: 10.3390/ani12010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary As far as it is known, studies dealing with antimicrobial resistance in certain species of staphylococci, in particular, S. chromogenes and S. simulans, isolated from products made from unpasteurized milk are limited. In addition to that, little attention was paid to the resistance of staphylococcal isolates from regional sheep and goat cheeses. At this level, works are published that focus on the evaluation of resistance from only one sheep product, Bryndza. Other studies are only focused on the evaluation of resistance from raw sheep’s or goat’s milk. The study contributes to the knowledge of the possible spread of antimicrobial resistance from the farm to the final consumer in this area. Abstract S. aureus and some species of coagulase-negative staphylococci, including S. chromogenes and S. simulans, commonly cause intramammary infections. However, little attention was paid to the antimicrobial resistance of these species with respect to their occurrence in dairy products, for example, popular sheep and goat cheeses made from unpasteurized milk. The aim of this study was to investigate such sheep and goat cheeses for the occurrence and antimicrobial resistance of the relevant staphylococci species. The staphylococcal isolates were identified by polymerase chain reaction (130 isolates) and matrix assisted laser desorption/ionization time-of-flight mass spectrometry. The most common species of S. aureus (56 isolates) were identified, as well as S. chromogenes (16 isolates) and S. simulans (10 isolates). Antimicrobial resistance to penicillin, oxacilin, ceftaroline, teicoplanin, gentamicin, erythromycin, tetracycline and ofloxacin was subsequently determined in these species using the agar dilution method. The highest resistance was confirmed in all species, especially to penicillin (91%) and erythromycin (67%). The highest sensitivity was confirmed to ofloxacin (83%). Due to the high incidence of penicillin and oxacilin-resistant staphylococci, the mecA gene was detected by polymerase chain reaction, which was confirmed only in S. aureus isolates (19%). Our study shows that the tested strains (77%) were resistant to more than one antibiotic at a time.
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Affiliation(s)
- Jana Výrostková
- Department of Food Hygiene, Technology and Safety, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Kosice, Slovakia; (J.V.); (B.S.)
| | - Ivana Regecová
- Department of Food Hygiene, Technology and Safety, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Kosice, Slovakia; (J.V.); (B.S.)
- Correspondence:
| | - František Zigo
- Department of Animal Nutrition and Husbandry, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Kosice, Slovakia;
| | - Boris Semjon
- Department of Food Hygiene, Technology and Safety, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Kosice, Slovakia; (J.V.); (B.S.)
| | - Gabriela Gregová
- Department of Public Veterinary Medicine and Animal Welfare, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 041 81 Kosice, Slovakia;
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Performance and Impact on Initial Antibiotic Choice of Direct Identification of Pathogens from Pediatric Blood Culture Bottles Using an In-House MALDI-TOF MS Protocol. Microbiol Spectr 2021; 9:e0190521. [PMID: 34937166 PMCID: PMC8694180 DOI: 10.1128/spectrum.01905-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance and early therapeutic impact of direct identification by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF; DIMT) on pediatric blood culture bottles using in-house-developed methods to obtain microbial pellets for spectrometric analysis have seldom been studied. During a 2-year period (June 2018 to May 2020), DIMT was performed on broths from positive pediatric blood culture bottles using an in-house-developed method. Organism identifications with a score of ≥1.6 were notified to treating clinicians. Therapeutic modifications that occurred after the communication of DIMT were reviewed through the electronic medical records. DIMT was performed on 530 pediatric positive blood culture bottles. Among 505 monomicrobial bottles, identifications from 298 (97.7%) deemed as bloodstream infections (BSI) and 189 (94.5%) as contaminations had DIMT notified to clinicians. All identifications were correct except for one Streptococcus mitis incorrectly reported as Streptococcus pneumoniae. Therapy modifications resulting from DIMT occurred in 27 (8.3%) patients with BSI. Deescalation from effective or ineffective broad-spectrum regimens occurred mainly in Enterococcus faecalis bacteremia, whereas appropriate escalation from an ineffective regimen with narrower spectrum occurred mainly in bacteremia caused by AmpC-β-lactamase-producing Enterobacterales. Escalation therapy was instituted significantly faster than deescalation therapy (median time, 0.75 versus 10.5 h [P = 0.01]). DIMT also enabled clinicians to confirm contamination in nearly one-half of patients with contaminated blood cultures. Our DIMT method applied to positive pediatric blood culture bottles demonstrated reliable performance for the rapid identification of pathogens. Our DIMT approach allowed therapeutic optimization in BSI, especially involving microorganisms with intrinsic antibiotic resistance, and was helpful in the early identification of likely contaminants. IMPORTANCE We demonstrate the performance and early impact on the antimicrobial management of bloodstream infections of an inexpensive, in-house preparation method for direct identification of bloodstream pathogens in pediatric blood culture bottles by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry.
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Kondori N, Kurtovic A, Piñeiro-Iglesias B, Salvà-Serra F, Jaén-Luchoro D, Andersson B, Alves G, Ogurtsov A, Thorsell A, Fuchs J, Tunovic T, Kamenska N, Karlsson A, Yu YK, Moore ERB, Karlsson R. Mass Spectrometry Proteotyping-Based Detection and Identification of Staphylococcus aureus, Escherichia coli, and Candida albicans in Blood. Front Cell Infect Microbiol 2021; 11:634215. [PMID: 34381737 PMCID: PMC8350517 DOI: 10.3389/fcimb.2021.634215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Bloodstream infections (BSIs), the presence of microorganisms in blood, are potentially serious conditions that can quickly develop into sepsis and life-threatening situations. When assessing proper treatment, rapid diagnosis is the key; besides clinical judgement performed by attending physicians, supporting microbiological tests typically are performed, often requiring microbial isolation and culturing steps, which increases the time required for confirming positive cases of BSI. The additional waiting time forces physicians to prescribe broad-spectrum antibiotics and empirically based treatments, before determining the precise cause of the disease. Thus, alternative and more rapid cultivation-independent methods are needed to improve clinical diagnostics, supporting prompt and accurate treatment and reducing the development of antibiotic resistance. In this study, a culture-independent workflow for pathogen detection and identification in blood samples was developed, using peptide biomarkers and applying bottom-up proteomics analyses, i.e., so-called "proteotyping". To demonstrate the feasibility of detection of blood infectious pathogens, using proteotyping, Escherichia coli and Staphylococcus aureus were included in the study, as the most prominent bacterial causes of bacteremia and sepsis, as well as Candida albicans, one of the most prominent causes of fungemia. Model systems including spiked negative blood samples, as well as positive blood cultures, without further culturing steps, were investigated. Furthermore, an experiment designed to determine the incubation time needed for correct identification of the infectious pathogens in blood cultures was performed. The results for the spiked negative blood samples showed that proteotyping was 100- to 1,000-fold more sensitive, in comparison with the MALDI-TOF MS-based approach. Furthermore, in the analyses of ten positive blood cultures each of E. coli and S. aureus, both the MALDI-TOF MS-based and proteotyping approaches were successful in the identification of E. coli, although only proteotyping could identify S. aureus correctly in all samples. Compared with the MALDI-TOF MS-based approaches, shotgun proteotyping demonstrated higher sensitivity and accuracy, and required significantly shorter incubation time before detection and identification of the correct pathogen could be accomplished.
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Affiliation(s)
- Nahid Kondori
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Amra Kurtovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Francisco Salvà-Serra
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Björn Andersson
- Bioinformatics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Gelio Alves
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Aleksey Ogurtsov
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Annika Thorsell
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johannes Fuchs
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Timur Tunovic
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nina Kamenska
- Norra-Älvsborgs-Länssjukhus (NÄL), Trollhättan, Sweden
| | | | - Yi-Kuo Yu
- National Center for Biotechnology Information (NCBI), Bethesda, MD, United States
| | - Edward R. B. Moore
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy of the University of Gothenburg, Gothenburg, Sweden
| | - Roger Karlsson
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Nanoxis Consulting AB, Gothenburg, Sweden
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Chaiden C, Jaresitthikunchai J, Kerdsin A, Meekhanon N, Roytrakul S, Nuanualsuwan S. Streptococcus suis serotyping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. PLoS One 2021; 16:e0249682. [PMID: 33945547 PMCID: PMC8096114 DOI: 10.1371/journal.pone.0249682] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 01/01/2023] Open
Abstract
Streptococcus suis, particularly S. suis serotype 2 (SS2), is an important zoonotic pathogen causing meningitis in humans worldwide. Although the proper classification of the causative and pathogenic serotype is salutary for the clinical diagnosis, cross-reactions leading to the indistinguishability of serotypes by the current serotyping methods are significant limitations. In the present study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of extracted peptides was developed to improve the classification of serotype of S. suis. The peptide mass fingerprint (PMFs) database of S. suis was generated from the whole-cell peptides of 32 reference strains of S. suis isolates obtained from pigs. Thirty-two human S. suis isolates from clinical cases in Thailand were used to validate this alternative serotyping method in direct comparison to the multiplex (m)PCR approach. All reference strains, representing 32 serotypes of S. suis, exhibited their individual PMFs patterns, thus allowing differentiation from one another. Highly pathogenic SS2 and SS14 were clearly differentiated from the otherwise serologically closely related SS1/2 and SS1, respectively. The developed MALDI-TOF-MS serotyping method correctly classified the serotype in 68.8% (22/32) of the same serotype isolates generated from the PMFs database; while the validity for the clinical human isolates was 62.5% (20/32). The agreement between the MALDI-TOF-MS and mPCR serotyping was moderate with a Kappa score of 0.522, considering that mPCR could correctly serotype up to 75%. The present study demonstrated that PMFs from the developed MALDI-TOF-MS-based method could successfully discriminate the previously indistinguishable highly pathogenic SS2 and SS14 from SS1/2 and SS1, respectively. Moreover, this serotyping method distinguished pathogenic SS6, and so is an alternative approach of choice to rapidly and reliably serotype clinically pathogenic S. suis isolates.
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Affiliation(s)
- Chadaporn Chaiden
- Department of Veterinary Public Health, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology for Development Agency, Pathum Thani, Thailand
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nattakan Meekhanon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology Laboratory, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology for Development Agency, Pathum Thani, Thailand
| | - Suphachai Nuanualsuwan
- Department of Veterinary Public Health, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand.,Food Risk Hub, Research Unit of Chulalongkorn University, Bangkok, Thailand
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Yoo IY, Han J, Ha SI, Cha YJ, Pil SD, Park YJ. Clinical performance of ASTA SepsiPrep kit in direct bacterial identification and antimicrobial susceptibility test using MicroIDSys Elite and VITEK-2 system. J Clin Lab Anal 2021; 35:e23744. [PMID: 33939213 PMCID: PMC8183931 DOI: 10.1002/jcla.23744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Rapid and accurate microbial identification and antimicrobial susceptibility testing (AST) are essential for timely use of appropriate antimicrobial agents for bloodstream infection. To shorten the time for isolating colonies from the positive blood culture, various preparation methods for direct identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system were developed. Here, we evaluated the SepsiPrep kit (ASTA Corp.) for direct identification of microorganisms and AST from positive blood cultures using MicroIDSys Elite MALDI-TOF MS system (ASTA Corp.) and VITEK-2 system (bioMérieux). METHODS For direct identification, a total of 124 prospective monomicrobial positive blood culture bottles were included. For direct identification, the pellet was prepared by centrifugation and washing twice. For direct AST, the pellet was suspended in 0.45% saline and adjusted to McFarland 0.5. The results from the direct identification and AST using MicroIDSys Elite and VITEK-2 system were compared to those from the conventional method performed with pure colony subcultured on agar plate. RESULTS Compared to the conventional method using pure colony, correct direct identification rate was 96.5% and 98.5% for 57 gram-positive isolates and 67 gram-negative isolates, respectively. For direct AST, among the 55 gram-positive isolates, the categorical agreement (CA) for staphylococci, streptococci, and enterococci was 96.7%, 98.4%, and 94.1%, respectively. For 66 gram-negative isolates, the CA for Enterobacterales and non-fermentative gram-negative rods was 99.0% and 96.6%, respectively. CONCLUSIONS The SepsiPrep kit was easy to use combined with MicroIDSys Elite and VITEK-2 system and also, the correct identification and AST rate were very high.
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Affiliation(s)
- In Young Yoo
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Jayho Han
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Sung Il Ha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Young Jong Cha
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Shin Dong Pil
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
| | - Yeon-Joon Park
- Department of Laboratory Medicine, College of Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea, Seoul, Korea
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Solntceva V, Kostrzewa M, Larrouy-Maumus G. Detection of Species-Specific Lipids by Routine MALDI TOF Mass Spectrometry to Unlock the Challenges of Microbial Identification and Antimicrobial Susceptibility Testing. Front Cell Infect Microbiol 2021; 10:621452. [PMID: 33634037 PMCID: PMC7902069 DOI: 10.3389/fcimb.2020.621452] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022] Open
Abstract
MALDI-TOF mass spectrometry has revolutionized clinical microbiology diagnostics by delivering accurate, fast, and reliable identification of microorganisms. It is conventionally based on the detection of intracellular molecules, mainly ribosomal proteins, for identification at the species-level and/or genus-level. Nevertheless, for some microorganisms (e.g., for mycobacteria) extensive protocols are necessary in order to extract intracellular proteins, and in some cases a protein-based approach cannot provide sufficient evidence to accurately identify the microorganisms within the same genus (e.g., Shigella sp. vs E. coli and the species of the M. tuberculosis complex). Consequently lipids, along with proteins are also molecules of interest. Lipids are ubiquitous, but their structural diversity delivers complementary information to the conventional protein-based clinical microbiology matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based approaches currently used. Lipid modifications, such as the ones found on lipid A related to polymyxin resistance in Gram-negative pathogens (e.g., phosphoethanolamine and aminoarabinose), not only play a role in the detection of microorganisms by routine MALDI-TOF mass spectrometry but can also be used as a read-out of drug susceptibility. In this review, we will demonstrate that in combination with proteins, lipids are a game-changer in both the rapid detection of pathogens and the determination of their drug susceptibility using routine MALDI-TOF mass spectrometry systems.
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Affiliation(s)
- Vera Solntceva
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
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21
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Akgun S, Sayiner HS. Comparison of Rapid and Routine Methods of Identification and Antibiotic Susceptibility Testing of Microorganisms from Blood Culture Bottles. Pol J Microbiol 2021; 69:1-12. [PMID: 32412189 PMCID: PMC7324860 DOI: 10.33073/pjm-2020-019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/15/2020] [Accepted: 03/29/2020] [Indexed: 11/28/2022] Open
Abstract
Reporting of the results of routine laboratory blood culture tests to clinicians is vital to the patients’ early treatment. This study aimed to perform identification and antibiotic susceptibility tests of the blood cultures showing positive signals of microbial growth in the first 12 hours of incubation by using centrifugation and Gram staining of 5 ml of liquid from the vial, thus achieving faster results. This study included 152 consecutively incubated blood culture samples showing positive microbial growth signals in the first 12 hours. The samples were centrifuged and then categorized into two groups (Gram-positive and Gram-negative) using Gram staining. Identification and antibiotic susceptibility tests were performed using an automated culture antibiogram device. For routine processing, media inoculated with positive blood culture were kept in the incubator for at least 24 hours. To compare the two methods in terms of the bacteria identification, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of the growing colony was studied. By Gram staining, the same bacterial strains were obtained for 138 (92%) of the 152 samples, similar to the results of the procedures mentioned earlier. With the samples tested with both methods, the antibiotic susceptibility profiles were compared using the antibiogram results for 1,984 samples that underwent the antibiotic testing. A 97.4% (for 1,934 antibiotic susceptibility assays) agreement was observed between the two methods. Comparing the results of the post-centrifugation Gram staining to those obtained for the specimens using routine procedures, the clinicians reported a high success rate (approximately 97%).
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Affiliation(s)
- Sadik Akgun
- Adiyaman University , Faculty of Medicine , Department of Medical Microbiology , Adiyaman , Turkey
| | - Hakan Sezgin Sayiner
- Adiyaman University , Faculty of Medicine , Department of Infectious Diseases and Clinical Microbiology , Adiyaman , Turkey
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22
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Ceballos-Garzón A, Cabrera E, Cortes-Fraile GC, León A, Aguirre-Guataqui K, Linares-Linares MY, Ariza B, Valderrama-Beltrán S, Parra-Giraldo CM. In-house protocol and performance of MALDI-TOF MS in the early diagnosis of bloodstream infections in a fourth-level hospital in Colombia: Jumping to full use of this technology. Int J Infect Dis 2020; 101:85-89. [PMID: 33011284 DOI: 10.1016/j.ijid.2020.09.1469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Bloodstream infections (BSIs) are a major cause of mortality in hospitalized patients. Rapid diagnosis is crucial because any delay in the antimicrobial treatment is associated with an increase in adverse patient outcomes. The application of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology directly to blood cultures permits earlier identification of BSIs and facilitates treatment management. METHODS A total of 470 positive blood cultures from patient samples were analyzed using Standard Aerobic/F and Anaerobic/F blood culture media. Isolates were identified using conventional identification methods and by the direct method using the MALDI-TOF MS system. RESULTS In 470 blood cultures, the direct method showed good identification results (420/470, 89%); specifically, accurate species and genus identification in 283/470 (60%), and only correct genus identification in 137/470 (29%). The direct protocol had better performance for Gram-negative compared to Gram-positive bacteria (97% vs 76%) and was unable to identify the positive blood cultures for both yeasts and some bacteria, mostly Gram-positive (50/470). CONCLUSIONS The protocol used here gave good and reliable results, being available up to 24 h earlier, while also leading to better use of MALDI-TOF.
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Affiliation(s)
- Andrés Ceballos-Garzón
- Unidad de Proteomica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia; Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia.
| | - Erika Cabrera
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá D.C, Colombia.
| | - Gloria Cecilia Cortes-Fraile
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá D.C, Colombia; Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia.
| | - Aura León
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá D.C, Colombia.
| | - Katherine Aguirre-Guataqui
- Unidad de Proteomica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - Melva Y Linares-Linares
- Unidad de Proteomica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia; Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia.
| | - Beatriz Ariza
- Laboratorio Clínico, Área de Microbiología, Hospital Universitario San Ignacio, Bogotá D.C, Colombia; Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia.
| | - Sandra Valderrama-Beltrán
- Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia; Unidad de Infectología, Departamento de Medicina Interna, Facultad de Medicina, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, Bogotá D.C, Colombia.
| | - Claudia M Parra-Giraldo
- Unidad de Proteomica y Micosis Humanas, Grupo de Investigación en Enfermedades Infecciosas, Departamento de Microbiología, Pontificia Universidad Javeriana, Bogotá, Colombia; Grupo de Investigación en Enfermedades Infecciosas, Hospital Universitario San Ignacio, Colombia.
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23
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Weaver AJ, Brandenburg KS, Sanjar F, Wells AR, Peacock TJ, Leung KP. Clinical Utility of PNA-FISH for Burn Wound Diagnostics: A Noninvasive, Culture-Independent Technique for Rapid Identification of Pathogenic Organisms in Burn Wounds. J Burn Care Res 2020; 40:464-470. [PMID: 30893424 PMCID: PMC6587406 DOI: 10.1093/jbcr/irz047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Burn injury results in an immediate compromised skin state, which puts the affected patient at an immediate risk for infection, including sepsis. For burn patients that develop infections, it is critical to rapidly identify the etiology so that an appropriate treatment can be administered. Current clinical standards rely heavily on culture-based methods for local and systemic infection testing, which can often take days to complete. While more advanced methods (ie, MALDI or NAAT) have improved turnaround times, they may still suffer from either the need for pure culture or sensitivity and specificity issues. Peptide nucleic acid fluorescent in situ hybridization (PNA-FISH) offers a way to reduce this time from days to hours and provide species-specific identification. While PNA-FISH has had great utility in research, its use in clinical microbiology diagnostics has been minimal (including burn wound diagnostics). This work describes a nonculture-based identification technique using commercial available U.S. FDA-approved PNA-FISH probes for the identification of common clinical pathogens, Pseudomonas aeruginosa and Staphylococcus aureus, present in burn wound infections. Additionally, calcofluor white was included for identification of Candida albicans. All three pathogens were identified from a tri-species infected deep-partial thickness rat burn wound model. These species were clearly identifiable in swab and tissue samples that were collected, with minimal autofluorescence from any species. Although autofluorescence of the tissue was present, it did not interfere or was otherwise minimized through sample preparation and analysis. The methodology developed was done so with patient care and diagnostic laboratories in mind that it might be easily transferred to the clinical setting.
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Affiliation(s)
- Alan J Weaver
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, United States Army Institute of Surgical Research, JBSA, Fort Sam Houston, Texas
| | - Kenneth S Brandenburg
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, United States Army Institute of Surgical Research, JBSA, Fort Sam Houston, Texas
| | - Fatemeh Sanjar
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, United States Army Institute of Surgical Research, JBSA, Fort Sam Houston, Texas
| | - Adrienne R Wells
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, United States Army Institute of Surgical Research, JBSA, Fort Sam Houston, Texas
| | | | - Kai P Leung
- Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, United States Army Institute of Surgical Research, JBSA, Fort Sam Houston, Texas
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Weis C, Jutzeler C, Borgwardt K. Machine learning for microbial identification and antimicrobial susceptibility testing on MALDI-TOF mass spectra: a systematic review. Clin Microbiol Infect 2020; 26:1310-1317. [DOI: 10.1016/j.cmi.2020.03.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 01/12/2023]
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25
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Cui ZH, Zheng ZJ, Tang T, Zhong ZX, Cui CY, Lian XL, Fang LX, He Q, Wang XR, Chen C, He B, Wang MG, Liu YH, Liao XP, Sun J. Rapid Detection of High-Level Tigecycline Resistance in Tet(X)-Producing Escherichia coli and Acinetobacter spp. Based on MALDI-TOF MS. Front Cell Infect Microbiol 2020; 10:583341. [PMID: 33102258 PMCID: PMC7545121 DOI: 10.3389/fcimb.2020.583341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/17/2020] [Indexed: 12/11/2022] Open
Abstract
The emergence and spread of the novel mobile Tet(X) tetracycline destructases confer high-level tigecycline and eravacycline resistance in Escherichia coli and Acinetobacter spp. and pose serious threats to human and animal health. Therefore, a rapid and robust Tet(X) detection assay was urgently needed to monitor the dissemination of tigecycline resistance. We developed a rapid and simple assay to detect Tet(X) producers in Gram-negative bacteria based on matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). This MALDITet(X) test was based on the inactivation of tigecycline by a Tet(X)-producing strain after a 3-h incubation of bacterial cultures with tigecycline. Culture supernatants were analyzed using MALDI-TOF MS to identify peaks corresponding to tigecycline (586 ± 0.2 m/z) and a tigecycline metabolite (602 ± 0.2 m/z). The results were calculated using the MS ratio [metabolite/(metabolite + tigecycline)]. The sensitivity of the MALDITet(X) test with all 216 test strains was 99.19%, and specificity was 100%. The test can be completed within 3 h. Overall, the MALDITet(X) test is an accurate, rapid, cost-effective method for the detection of Tet(X)-producing E. coli and Acinetobacter spp. by determining the unique peak of an oxygen-modified derivative of tigecycline.
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Affiliation(s)
- Ze-Hua Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Zi-Jian Zheng
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Tian Tang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Zi-Xing Zhong
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Chao-Yue Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xin-Lei Lian
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Qian He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Xi-Ran Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Chong Chen
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Bing He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Min-Ge Wang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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26
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Rodríguez-Sánchez B, Cercenado E, Coste AT, Greub G. Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696525 PMCID: PMC6351997 DOI: 10.2807/1560-7917.es.2019.24.4.1800193] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction MALDI-TOF MS represents a new technological era for microbiology laboratories. Improved sample processing and expanded databases have facilitated rapid and direct identification of microorganisms from some clinical samples. Automated analysis of protein spectra from different microbial populations is emerging as a potential tool for epidemiological studies and is expected to impact public health. Aim To demonstrate how implementation of MALDI-TOF MS has changed the way microorganisms are identified, how its applications keep increasing and its impact on public health and hospital hygiene. Methods A review of the available literature in PubMED, published between 2009 and 2018, was carried out. Results Of 9,709 articles retrieved, 108 were included in the review. They show that rapid identification of a growing number of microorganisms using MALDI-TOF MS has allowed for optimisation of patient management through prompt initiation of directed antimicrobial treatment. The diagnosis of Gram-negative bacteraemia directly from blood culture pellets has positively impacted antibiotic streamlining, length of hospital stay and costs per patient. The flexibility of MALDI-TOF MS has encouraged new forms of use, such as detecting antibiotic resistance mechanisms (e.g. carbapenemases), which provides valuable information in a reduced turnaround time. MALDI-TOF MS has also been successfully applied to bacterial typing. Conclusions MALDI-TOF MS is a powerful method for protein analysis. The increase in speed of pathogen detection enables improvement of antimicrobial therapy, infection prevention and control measures leading to positive impact on public health. For antibiotic susceptibility testing and bacterial typing, it represents a rapid alternative to time-consuming conventional techniques.
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Affiliation(s)
- Belén Rodríguez-Sánchez
- These authors contributed equally to this work.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alix T Coste
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland.,Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.,These authors contributed equally to this work
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Desoky ESM, Merwad ARM, Semida WM, Ibrahim SA, El-Saadony MT, Rady MM. Heavy metals-resistant bacteria (HM-RB): Potential bioremediators of heavy metals-stressed Spinacia oleracea plant. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 198:110685. [PMID: 32387845 DOI: 10.1016/j.ecoenv.2020.110685] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/19/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
Microorganism technologies can provide a potential alternative to traditional methods of removing heavy metals to conserve agricultural soils. This study aimed to identify and characterize heavy metals-resistant bacteria (HM-RB) isolated from industry-affected soil and their desired impact as bioremediators of heavy metals-stressed spinach plants. Three of 135 isolates were selected based on a high level of resistance to heavy metals. Based on morphological and biochemical characteristics, the selected isolates were identified as Bacillus subtilis subsp. spizizenii DSM 15029 T DSM (MA3), Paenibacillus jamilae DSM 13815 T DSM (LA22), or Pseudomonas aeruginosa DSM 1117 DSM (SN36). Experiments were implemented to investigate the three isolated HM-RB ability on improving attributes of growth, physio-biochemistry, and components of the antioxidant defense system of spinach plant exposed to the stress of cadmium (Cd2+; 2 mM), lead (Pb2+; 2 mM) or 2 mM Cd2++2 mM Pb2+. Compared to control, Cd2+ or Pb2+ stress markedly lowered plant fresh and dry weights, leaf contents of chlorophylls and carotenoids, rates of transpiration (Tr), net photosynthesis (Pn) and stomatal conductance (gs), relative water content (RWC), and membrane stability index (MSI). In contrast, contents of α.tochopherol (α.TOC), ascorbic acid (AsA), glutathione (GSH), proline, soluble sugars, Cd2+, and Pb2+, as well as activities of enzymatic and non-enzymatic antioxidants were markedly elevated. The application of HM-RB promoted the tolerance to heavy metal stress in spinach plants by improving Tr, Pn, gs, RWC, and MSI, while activities of enzymatic and non-enzymatic antioxidants were suppressed. These results reflected positively in promoting plant growth under heavy metal stress. Therefore, the application of HM-RB as potential bioremediators may be a promising strategy for promoting plant growth and productivity under heavy metal stress.
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Affiliation(s)
- El-Sayed M Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Abdel-Rahman M Merwad
- Soil Science Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Wael M Semida
- Horticulture Department, Faculty of Agriculture, Fayoum University, 63514, Fayoum, Egypt
| | - Seham A Ibrahim
- Botany Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Mohamed T El-Saadony
- Microbiology Department, Faculty of Agriculture, Zagazig University, 44511, Zagazig, Egypt
| | - Mostafa M Rady
- Botany Department, Faculty of Agriculture, Fayoum University, 63514, Fayoum, Egypt.
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28
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Mizusawa M. Updates on Rapid Diagnostic Tests in Infectious Diseases. MISSOURI MEDICINE 2020; 117:328-337. [PMID: 32848269 PMCID: PMC7431065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the last two decades there have been dramatic advances in development of rapid diagnostic tests. Turnaround time of the assays have significantly been shortened which led to reductions in time to appropriate antimicrobial therapy and improvement of patient clinical outcomes. Molecular-based assays generally have better sensitivity than conventional methods, but the cost is higher. The results need to be interpreted cautiously as detection of colonized organisms, pathogen detection in asymptomatic patients, and false negative/positive can occur. Indications and cost-effectiveness need to be considered for appropriate utilization of rapid diagnostic tests.
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Affiliation(s)
- Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri - Kansas City, Kansas City, Missouri
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29
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Integrating Bacterial Identification and Susceptibility Testing: A Simple and Rapid Approach to Reduce the Turnaround Time in the Management of Blood Cultures. BIOMED RESEARCH INTERNATIONAL 2020; 2019:8041746. [PMID: 31687399 PMCID: PMC6794959 DOI: 10.1155/2019/8041746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 08/15/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022]
Abstract
We evaluated a rapid bacterial identification (rID) and a rapid antimicrobial susceptibility testing by disk diffusion (rAST) from positive blood culture to overcome the limitations of the conventional methods and reduce the turnaround time in bloodstream infection diagnostics. The study included hemocultures flagged as positive by bacT/ALERT®, identification by MALDI-TOF MS, and rAST. The results were compared to identification and antimicrobial susceptibility testing (AST) results by current standard methods, after 24 h incubation. For rAST categorical agreement (CA), very major errors (VME), major errors (ME), and minor errors (mE) were calculated. A total of 524 bacterial samples isolated from blood cultures were obtained, including 246 Gram-negative (GN) and 278 Gram-positive (GP) aerobes. The overall concordance of rID was 88.6%, and it was highest among GN (96%). A total of 2196 and 1476 antimicrobial agent comparisons were obtained for GN and GP, respectively. Evaluation of rAST, CA, VME, ME, and mE disclosed 97.7, 0.7, 0.5, and 1.1% for GN and 98.0, 0.5, 0.7, and 0.8% for GP, respectively. Meropenem CA, VME, and ME were 98.3, 0.5, and 0.5%, respectively; mE was not observed. Oxacillin CA, ME, and mE were 97.4, 1.6, and 0.6%, respectively; VME was not observed. Overall, kappa scores of the results of the comparisons demonstrated the high agreement between rAST and the standard method. Identification and AST of aerobic bacteria from positive blood cultures after a short period of incubation on solid blood agar is a fast and reliable method that may improve the management of bloodstream infections.
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30
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Nix ID, Idelevich EA, Storck LM, Sparbier K, Drews O, Kostrzewa M, Becker K. Detection of Methicillin Resistance in Staphylococcus aureus From Agar Cultures and Directly From Positive Blood Cultures Using MALDI-TOF Mass Spectrometry-Based Direct-on-Target Microdroplet Growth Assay. Front Microbiol 2020; 11:232. [PMID: 32117194 PMCID: PMC7033577 DOI: 10.3389/fmicb.2020.00232] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 11/26/2022] Open
Abstract
Matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS)-based direct-on-target microdroplet growth assay (DOT-MGA) was recently described as a novel method of phenotypic antimicrobial susceptibility testing (AST). Here, we developed the application of MALDI-TOF MS-based DOT-MGA for Gram-positive bacteria including AST from agar cultures and directly from positive blood cultures (BCs) using the detection of methicillin resistance as example. Consecutively collected, a total of 14 methicillin-resistant Staphylococcus aureus (MRSA) and 14 methicillin-susceptible S. aureus (MSSA) clinical isolates were included. Furthermore, a collection of MRSA challenge strains comprising different SCCmec types, mec genes, and spa types was tested. Blood samples were spiked with MRSA and MSSA and positive BC broth processed by three different methods: serial dilution of BC broth, lysis/centrifugation, and differential centrifugation. Processed BC broth was directly used for rapid AST using DOT-MGA. Droplets of 6 μl with and without cefoxitin at the EUCAST breakpoint concentration were spotted in triplicates onto the surface of a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard as a quality control (QC). Spectra were acquired and evaluated using MALDI Biotyper software. First, tests were considered as valid, if the growth control achieved an identification score of ≥1.7. For valid tests, same score criterion was used for resistant isolates when incubated with cefoxitin. An identification score <1.7 after incubation with cefoxitin defined susceptible isolates. On-target protein extraction using formic acid considerably improved detection of methicillin resistance in S. aureus and DOT-MGA showed feasible results for AST from agar cultures after 4 h incubation time. Comparing the different processing methods of positive BC broth, lysis/centrifugation method with a final dilution step 10–1 of the 0.5 McFarland suspension resulted in best test performance after 4 h incubation time. Overall, 96.4% test validity, 100% sensitivity, and 100% specificity were achieved for detection of methicillin resistance in clinical isolates. All strains of the MRSA challenge collection were successfully tested as methicillin-resistant. This first study on Gram-positive organisms showed feasibility and accuracy of MALDI-TOF MS-based DOT-MGA for rapid AST of S. aureus from agar cultures and directly from positive BCs.
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Affiliation(s)
- Ilka D Nix
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Evgeny A Idelevich
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Luise M Storck
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | | | | | | | - Karsten Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.,Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
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Abstract
The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory. After reviewing this chapter, the reader will be able to:List key considerations for specimen collection for microbiology testing. Discuss the advantages and limitations of automation in the clinical microbiology laboratory. Describe the evolution of microorganism identification methods. Discuss the benefits and limitations of molecular microbiology point-of-care testing. Summarize currently available multiplex molecular microbiology testing options.
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Rosa NM, Agnoletti F, Lollai S, Tola S. Comparison of PCR-RFLP, API® 20 Strep and MALDI-TOF MS for identification of Streptococcus spp. collected from sheep and goat milk samples. Small Rumin Res 2019. [DOI: 10.1016/j.smallrumres.2019.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Drees C, Vautz W, Liedtke S, Rosin C, Althoff K, Lippmann M, Zimmermann S, Legler TJ, Yildiz D, Perl T, Kunze-Szikszay N. GC-IMS headspace analyses allow early recognition of bacterial growth and rapid pathogen differentiation in standard blood cultures. Appl Microbiol Biotechnol 2019; 103:9091-9101. [DOI: 10.1007/s00253-019-10181-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/02/2019] [Accepted: 10/09/2019] [Indexed: 01/14/2023]
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Sierra E, Maldonado N, Arroyave B, Robledo C, Robledo J. Identificación directa de microorganismos a partir de muestras de orina y hemocultivos utilizando MALDI-TOF. INFECTIO 2019. [DOI: 10.22354/in.v23i4.812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objetivo: evaluar la utilidad de la identificación directa de microorganismos en muestras de orina y hemocultivos empleando la tecnología MALDI-TOF MS, mediante el análisis de concordancia en la identificación, tiempo necesario para la obtención de un resultado y costos asociados a cada método de identificación.Materiales y métodos: estudio descriptivo de febrero de 2017 a octubre de 2017. Se seleccionaron a conveniencia 180 muestras de orinas y 129 hemocultivos de pacientes de la Clínica El Rosario, Medellín, se realizó identificación del microorganismo directamente de la muestra y a partir del cultivo por MALDI-TOF (Vitek® MS‚ bioMérieux). Se analizaron los costos y tiempo, para determinar la utilidad de esta tecnología en los procesos del laboratorio de microbiología.Resultados: En el 79,6% de las orinas positivas y en el 76% de los hemocultivos se obtuvo una identificación de microorganismos directamente por MALDI-TOF MS. El tiempo de identificación directa tuvo una media de 6 horas y por cultivo una media de 29 horas. El costo total por aislamiento identificado de forma directa (sin incluir el valor del equipo) fue de $8.200 (2,58 USD) en muestras de orina y de $9.720 (3,06 USD) en hemocultivos positivos. El equipo introduce un costo variable en cada identificación de acuerdo con el número de identificaciones que se realicen en el laboratorio.Conclusiones: Estos resultados confirman la utilidad del MALDI-TOF MS para generar identificaciones más rápidas cuando se utiliza directamente en muestras clínicas, sin embargo, tiene un bajo desempeño en la identificación directa de bacterias gram positivas, siendo necesario evaluar otros protocolos que mejoren la identificación directa. El costo de los consumibles es bajo, pero la adquisición de esta tecnología introduce un costo variable que depende del volumen de muestras identificadas en el laboratorio.
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Comparison of rapid BACpro® II, Sepsityper® kit and in-house preparation methods for direct identification of bacteria from blood cultures by MALDI-TOF MS with and without Sepsityper® module analysis. Eur J Clin Microbiol Infect Dis 2019; 38:2133-2143. [PMID: 31494828 PMCID: PMC6800852 DOI: 10.1007/s10096-019-03654-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/21/2019] [Indexed: 01/24/2023]
Abstract
There are several approaches available for purifying microorganisms prior to matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, rapid BACpro® II (Nittobo Medical Co., Ltd., Tokyo, Japan), a new application, has been compared with Sepsityper® kit (Bruker Daltonics, Billerica, USA) and an in-house method. Samples were also tested with two modules, standard and Sepsityper®, identified in the Bruker MALDI-TOF MS. The bottles having monomicrobial growth were included in the study according to Gram staining results. In total, two hundred blood culture bottles were included but there was no growth in one of the subcultures so 199 blood culture bottles were studied prospectively. With the standard MALDI-TOF MS analysis, rapid BACpro® II could successfully identify microorganisms in 174/199 (87.4%) of the bottles where Sepsityper® kit and in-house method were successful in 136/199 (68.3%) and 114/199 (57.3%), respectively. When the MALDI-TOF MS data were analysed by Sepsityper® module, the identification rates were increased to 94.4%, 82.1% and 69.8% (p < 0.001), respectively. In the Sepsityper® module, 72/73 (98.6%) of Gram-negative and 97/106 (91.5%) of Gram-positive microorganisms were detected by rapid BACpro® II method. The present study shows that rapid BACpro® II is a reliable preparation procedure and has higher rates of identification compared with Sepsityper® kit and in-house method. The use of the Sepsityper® module in blood cultures increases the chance of identification for all three methods studied.
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Ratiu IA, Railean Plugaru V, Pomastowski P, Milanowski M, Mametov R, Bocos-Bintintan V, Buszewski B. Temporal influence of different antibiotics onto the inhibition of Escherichia coli bacterium grown in different media. Anal Biochem 2019; 585:113407. [PMID: 31449777 DOI: 10.1016/j.ab.2019.113407] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 01/08/2023]
Abstract
Escherichia coli (E. coli) is a Gram-negative bacterium commonly found in the lower intestine of warm-blooded organisms, including humans. Although the majority of the strains are considerably harmless, some serotypes are pathogenic, frequently causing diarrhea and other illnesses outside the intestinal tract. The standard antidote against bacteria is the use of antibiotics. Depending on their type, the antibiotics have various mechanisms of action on bacteria. Moreover, in case of in-vitro cultivation of bacteria, the used growth media plays a crucial role, since it influences bacterial inhibition as well. In the present study, we emphasize the importance of cultivability in bacterial inhibition under the treatment with five different antibiotics belonging to different classes. Consequently, E. coli was cultivated in three different growth media: trypcase soy broth (TSB), Mueller Hinton (MH), and minimal salts (M9) enriched with glucose, respectively. MALDI-TOF MS (matrix-assisted laser desorption ionization time-of-flight mass spectrometry) analyses, that were used for fast characterization of changes that occur in ribosomal protein profiles, revealed differentiation and similarities between investigated cases, while flow cytometry (FCM) tests better explained the given changes that occurred in the analyzed samples after 3, 24 and 48 h of experimental campaign.
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Affiliation(s)
- Ileana Andreea Ratiu
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland; Babeş-Bolyai University, Faculty of Chemistry and Chemical Engineering, 11 Arany Janos Str., RO, 400028, Cluj-Napoca, Romania.
| | - Viorica Railean Plugaru
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Pawel Pomastowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Maciej Milanowski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland
| | - Radik Mametov
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland
| | - Victor Bocos-Bintintan
- Faculty of Environmental Science and Engineering, Babeş-Bolyai University, 30 Fântânele Str., RO, 400294, Cluj-Napoca, Romania
| | - Boguslaw Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100, Toruń, Poland; Interdisciplinary Centre of Modern Technologies, Nicolaus Copernicus University, 4 Wileńska Str., 87-100, Toruń, Poland.
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Pahlow S, Lehniger L, Hentschel S, Seise B, Braun SD, Ehricht R, Berg A, Popp J, Weber K. Rapid Isolation and Identification of Pneumonia-Associated Pathogens from Sputum Samples Combining an Innovative Sample Preparation Strategy and Array-Based Detection. ACS OMEGA 2019; 4:10362-10369. [PMID: 31460130 PMCID: PMC6648014 DOI: 10.1021/acsomega.9b00904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/27/2019] [Indexed: 05/04/2023]
Abstract
With this study, an innovative and convenient enrichment and detection strategy for eight clinically relevant pneumonia pathogens, namely, Acinetobacter baumannii, Escherichia coli, Haemophilus influenzae, Klebsiella pneumoniae, Moraxella catarrhalis, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae is introduced. Bacteria were isolated from sputum samples with amine-modified particles exploiting pH-dependent electrostatic interactions between bacteria and the functionalized particle surface. Following this, an asymmetric polymerase chain reaction as well as subsequent stringent array-based hybridization with specific complementary capture probes were performed. Finally, results were visualized by an enzyme-induced silver nanoparticle deposition, providing stable endpoint signals and consequently an easy detection possibility. The assay was optimized using spiked samples of artificial sputum with different strains of the abovementioned bacterial species. Furthermore, actual patient sputum samples with S. pneumoniae were successfully analyzed. The presented approach offers great potential for the urgent need of a fast, specific, and reliable isolation and identification platform for important pneumonia pathogens, covering the complete process chain from sample preparation up to array-based detection within only 4 h.
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Affiliation(s)
- Susanne Pahlow
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
| | - Lydia Lehniger
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Stefanie Hentschel
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Barbara Seise
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Sascha D. Braun
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Ralf Ehricht
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Abbott
(Alere Technologies GmbH), Research and Development, Loebstedter Str. 103-105, 07749 Jena, Germany
| | - Albrecht Berg
- INNOVENT
e.V. Jena, Prüssingstraße
27 B, 07745 Jena, Germany
| | - Jürgen Popp
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Karina Weber
- Friedrich
Schiller University Jena, Institute of Physical Chemistry, Abbe Center of Photonics, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics
Research Campus Jena, Centre for Applied
Research, Philosophenweg
7, 07743 Jena, Germany
- Leibniz
Institute of Photonic Technology—Member of the Research Alliance
“Leibniz Health Technologies”, Albert-Einstein-Straße 9, 07745 Jena, Germany
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Freimann S, Shapira M, Athamna A. Serum separator tube method for matrix-assisted laser desorption/ionization time-of-flight analysis. Access Microbiol 2019; 1:e000011. [PMID: 32974509 PMCID: PMC7470352 DOI: 10.1099/acmi.0.000011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/08/2019] [Indexed: 01/13/2023] Open
Abstract
Background Without appropriate treatment, bloodstream infections have a high mortality rate. Quicker identification of the microbial pathogen allows the clinician to develop an initial strategy of antimicrobial therapy. Sample preparation protocols for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS; Bruker Daltonics for Microflex LT spectrometer) technology were evaluated in an attempt to identify pathogens directly from positive blood culture bottles and thus shorten the time to identify them. This application requires preparatory processing because blood culture bottles contain undesirable proteins. This study aimed to evaluate two methods for microbial preparation for identification by MALDI-ToF MS. Methods This study evaluated two methods for microbial preparation from 200 positive blood culture samples, half prepared by the differential centrifugation method and half with the serum separator tube method for identification by MALDI-ToF MS. Both methods were compared to conventional methods such as VITEK II and ChromAgar culture plates. Results All Gram-negative bacteria tested were identified correctly by MALDI-ToF MS compared to conventional methods, regardless of the preparation method. However, more Gram-positive bacteria were identified when the serum separator tube method was used (83.3%) compared with the differential centrifugation method (65.3 %). Moreover, the serum separator tube protocol requires 12–15 min, while the differential centrifugation protocol requires 30–45 min. Conclusions Sample preparation using the serum separator tube method is easy to perform, fast and reliable for accurate microbial identification by MALDI-ToF MS technology.
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Affiliation(s)
- Sarit Freimann
- Clinical Microbiology Laboratory, Hillel Yaffe Medical Center, Hadera, Israel
| | - Maanit Shapira
- Laboratory Division, Hillel Yaffe Medical Center, Hadera, Israel
| | - Abed Athamna
- Clinical Microbiology Laboratory, Hillel Yaffe Medical Center, Hadera, Israel
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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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Abstract
Matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS), adapted for use in clinical microbiology laboratories, challenges current standards of microbial detection and identification. This article summarizes the capabilities of MALDI-TOF MS in diagnostic clinical microbiology laboratories and describes the underpinnings of the technology, highlighting topics such as sample preparation, spectral analysis, and accuracy. The use of MALDI-TOF MS in the clinical microbiology laboratory is growing, and, when properly deployed, can accelerate diagnosis and improve patient care.
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Affiliation(s)
- Donna M Wolk
- Clinical Microbiology, Department of Laboratory Medicine, Diagnostic Medicine Institute, Geisinger Health, 100 North Academy Avenue, Danville, PA 17822-1930, USA.
| | - Andrew E Clark
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA
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Accelerated bacterial detection in blood culture by enhanced acoustic flow cytometry (AFC) following peptide nucleic acid fluorescence in situ hybridization (PNA-FISH). PLoS One 2019; 14:e0201332. [PMID: 30735489 PMCID: PMC6368374 DOI: 10.1371/journal.pone.0201332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/16/2019] [Indexed: 11/23/2022] Open
Abstract
Bacteraemia is a risk factor for subsequent clinical deterioration and death. Current reliance on culture-based methods for detection of bacteraemia delays identification and assessment of this risk until after the optimal period for positively impacting treatment decisions has passed. Therefore, a method for rapid detection and identification of bacterial infection in the peripheral bloodstream in acutely ill patients is crucial for improved patient survival through earlier targeted antibiotic treatment. The turnaround time for current clinical laboratory methods ranges from 12 to 48 hours, emphasizing the need for a faster diagnostic test. Here we describe a novel assay for accelerated generic detection of bacteria in blood culture (BC) using peptide nucleic acid fluorescence in situ hybridization enhanced acoustic flow cytometry (PNA-FISH-AFC). For assay development, we used simulated blood cultures (BCs) spiked with one of three bacterial species at a low starting concentration of 10 CFU/mL: Escherichia coli, Klebsiella pneumoniae or Pseudomonas aeruginosa. Under current clinical settings, it takes a minimum of 12 hours incubation to reach positivity on the BacTEC system, corresponding to a bacterial concentration of 107−109 CFU/mL optimal for further analyses. In contrast, our PNA-FISH-AFC assay detected 103–104 CFU/mL bacteria in BC following a much shorter culture incubation of 5 to 10 hours. Using either PCR-based FilmArray assay or MALDI-TOF for bacterial detection, it took 7–10 and 12–24 hours of incubation, respectively, to reach the positive result. These findings indicate a potential time advantage of PNA-FISH-AFC assay for rapid bacterial detection in BC with significantly improved turnaround time over currently used laboratory techniques.
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Diagnosis and treatment of catheter-related bloodstream infection: Clinical guidelines of the Spanish Society of Infectious Diseases and Clinical Microbiology and (SEIMC) and the Spanish Society of Spanish Society of Intensive and Critical Care Medicine and Coronary Units (SEMICYUC). Med Intensiva 2019; 42:5-36. [PMID: 29406956 DOI: 10.1016/j.medin.2017.09.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/29/2017] [Accepted: 09/29/2017] [Indexed: 12/14/2022]
Abstract
Catheter-related bloodstream infections (CRBSI) constitute an important cause of hospital-acquired infection associated with morbidity, mortality, and cost. The aim of these guidelines is to provide updated recommendations for the diagnosis and management of CRBSI in adults. Prevention of CRBSI is excluded. Experts in the field were designated by the two participating Societies (the Spanish Society of Infectious Diseases and Clinical Microbiology and [SEIMC] and the Spanish Society of Spanish Society of Intensive and Critical Care Medicine and Coronary Units [SEMICYUC]). Short-term peripheral venous catheters, non-tunneled and long-term central venous catheters, tunneled catheters and hemodialysis catheters are covered by these guidelines. The panel identified 39 key topics that were formulated in accordance with the PICO format. The strength of the recommendations and quality of the evidence were graded in accordance with ESCMID guidelines. Recommendations are made for the diagnosis of CRBSI with and without catheter removal and of tunnel infection. The document establishes the clinical situations in which a conservative diagnosis of CRBSI (diagnosis without catheter removal) is feasible. Recommendations are also made regarding empirical therapy, pathogen-specific treatment (coagulase-negative staphylococci, Staphylococcus aureus, Enterococcus spp., Gram-negative bacilli, and Candida spp.), antibiotic lock therapy, diagnosis and management of suppurative thrombophlebitis and local complications.
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Pellegrino FLPC, Chagas TPG, Alves MS, Carvalho-Assef APD, Chapeaurouge A, Asensi MD. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Applications in Bacteriology: brazilian contributions. HU REVISTA 2018. [DOI: 10.34019/1982-8047.2017.v43.2859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Among its innumerous applications in Bacteriology, the Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) technique is evolving as a powerful tool for bacterial identification and antimicrobial resistance investigation. Publications have evaluated the MALDI-TOF MS performance in the identification of a series of bacterial pathogens, including the most common severe infectious agents, emergent pathogens involved with outbreaks of healthcare-associated infections, rare pathogens, and those whose isolation in culture media is difficult. As compared to conventional methods of bacterial identification, MALDI-TOF MS has proven to be a fast, accurate and cost-effective technique. Currently, MALDI-TOF MS has been used in antimicrobial resistance studies, since it has shown to be an efficient tool in detecting specific resistance mechanisms in bacteria, such as beta-lactamases production, for example. Here, we describe the advances in this growing field of mass spectrometry applied to Bacteriology, including Brazilian contributions.
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Ashikawa S, Tarumoto N, Imai K, Sakai J, Kodana M, Kawamura T, Ikebuchi K, Murakami T, Mitsutake K, Maesaki S, Maeda T. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer. J Med Microbiol 2018; 67:1589-1595. [PMID: 30311873 DOI: 10.1099/jmm.0.000855] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Bloodstream infections are major causes of morbidity and mortality that lead to prolonged hospital stays and higher medical costs. In this study, we aimed to evaluate the MinION nanopore sequencer for the identification of the most dominant pathogens in positive blood culture bottles. METHODOLOGY 16S and ITS1-5.8S-ITS2 rRNA genes were amplified by PCR reactions with barcoded primers using nine clinical isolates obtained from positive blood bottles and 11 type strains, including five types of Candida species. Barcoded amplicons were mixed, and multiplex sequencing with the MinION sequencer was performed. In addition, barcoded PCR amplicons were sequenced by Sanger sequencing to validate the performance of the MinION. RESULTS The bacterial and Candida spp. identified by MinION sequencing, based on the highest homology of reference sequences from the NCBI gene databases, agreed with the matrix-assisted laser desorption ionization time of flight mass spectrometry results, excepting the closely related species Streptococcusand Escherichia coli. The 'pass' reads obtained within about 10 min of sequencing were sufficient to identify the pathogens. The average values of sequence identities with 1D2 chemistry and the R9.5 flow cell were around 99 %; thus, frequent sequence errors did not affect species identification based on amplicon sequencing. CONCLUSION We have established a rapid, portable and economical technique for the identification of pathogens in positive blood culture bottles through a novel MinION nanopore sequencer amplicon sequencing scheme, which replaces traditional Sanger sequencing.
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Affiliation(s)
- Sae Ashikawa
- 1School of Medical Technology, Faculty of Health and Medical Care, Saitama Medical University, Saitama, Japan
| | - Norihito Tarumoto
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Kazuo Imai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Jun Sakai
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Masahiro Kodana
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Toru Kawamura
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Kenji Ikebuchi
- 4Clinical Laboratory Medicine, Saitama Medical University Hospital, Saitama, Japan
| | - Takashi Murakami
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
| | - Kotaro Mitsutake
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,6Department of Infectious Diseases and Infection Control, International Medical Center, Saitama Medical University, Saitama, Japan
| | - Shigefumi Maesaki
- 2Department of Infectious Disease and Infection Control, Saitama Medical University, Saitama, Japan.,3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan
| | - Takuya Maeda
- 3Center for Clinical Infectious Diseases and Research, Saitama Medical University, Saitama, Japan.,5Department of Microbiology, Saitama Medical University, Saitama, Japan
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Identification of Neisseria meningitidis by MALDI-TOF MS may not be reliable. Clin Microbiol Infect 2018; 25:717-722. [PMID: 30287414 DOI: 10.1016/j.cmi.2018.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 02/02/2023]
Abstract
OBJECTIVES The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) technique is increasingly used in hospital laboratories for routine identification of microorganisms. However, its performance is variable, particularly for highly variable species such as Neisseria meningitidis. Reliable identification of N. meningitidis is crucial for the management of invasive meningococcal disease by rapid implementation of treatment and preventive measures among close contacts. We assessed and improved N. meningitidis identification by MALDI-TOF MS by enriching the databases with reference strains identified using whole genome sequencing (WGS) as a reference standard. METHODS We first built a collection of 24 strains from several species of the Neisseria genus that we characterized by WGS. This collection was added to the available database to test by MALDI-TOF MS another collection of 32 clinical isolates received between 2015 and 2017 at the French National Reference Laboratory for Meningococci. RESULTS Using the commercially available library of mass spectrometry profiles, only 67% (95% confidence interval (CI), 47-82) concordance was observed at the species level between MALDI-TOF MS and WGS characterization. However, when the new enriched reference collection was used on the second subset of isolates, the identification of N. meningitidis was significantly improved (p 0.0016), showing 92% (95% CI, 75-98) specificity while that of the manufacturer's database alone was 52% (95% CI, 34-70). CONCLUSIONS Our data highlight the need to update the available MALDI-TOF MS database with high-quality references to enhance the identification of N. meningitidis and avoid unwarranted preventive measures or missing identification.
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Ruiz-Aragón J, Ballestero-Téllez M, Gutiérrez-Gutiérrez B, de Cueto M, Rodríguez-Baño J, Pascual Á. Direct bacterial identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry: A systematic review and meta-analysis. Enferm Infecc Microbiol Clin 2018; 36:484-492. [DOI: 10.1016/j.eimc.2017.08.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/24/2017] [Accepted: 08/25/2017] [Indexed: 11/16/2022]
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Luethy PM, Johnson JK. The Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogens Causing Sepsis. J Appl Lab Med 2018; 3:675-685. [PMID: 31639735 DOI: 10.1373/jalm.2018.027318] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Sepsis is a life-threatening condition with high rates of morbidity and mortality; effective and appropriate antibiotic therapy is essential for ensuring patient improvement. To aid in the diagnosis of sepsis, blood cultures are drawn and sent to the microbiology laboratory for pathogen growth, identification, and susceptibility testing. The clinical microbiology laboratory can assist the medical team by providing timely identification of the pathogen(s) causing the bloodstream infection through the use of rapid diagnostic technology. One of these rapid diagnostic technologies, MALDI-TOF MS, has been proven to reduce the time required for appropriate antibiotic therapy when used to identify pathogens grown in culture. This technology has also been used to identify pathogens directly from the positive blood cultures with great success. CONTENT In this minireview, we summarize the different methods that have been developed to directly identify pathogens from positive blood cultures by use of MALDI-TOF MS and the effect of this technology on patient outcomes. Additionally, we touch on current research in the field, including the identification of antimicrobial resistance directly from positive blood cultures by MALDI-TOF MS. SUMMARY Rapid identification of pathogens is important in the survival of patients undergoing a septic event. MALDI-TOF MS technology has played an important role in rapid identification, which has led to a reduction in the time to appropriate antibiotic therapy and contributed to the improvement of patient outcomes. The high sensitivity and specificity of MALDI-TOF MS identification, in combination with MALDI-TOF's rapid function and reduced labor costs, make this technology an attractive choice for clinical laboratories.
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Affiliation(s)
- Paul M Luethy
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD.
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Magarifuchi H, Hamada Y, Oho M, Kusaba K, Urakami T, Aoki Y. Clinical utility of direct application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry and rapid disk diffusion test in presumptive antimicrobial therapy for bacteremia. J Infect Chemother 2018; 24:881-886. [PMID: 30139692 DOI: 10.1016/j.jiac.2018.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVE To study how and to what degree the rapid pathogen identification by MALDI-TOF MS coupled with rapid disk diffusion test improve the current clinical practice of patients with bacteremia in a tertiary teaching hospital with full-time ID consultation service. PATIENTS AND METHODS MALDI-TOF MS and 8H disk diffusion tests were directly applied to the positive blood cultures samples and the results were reflected on antimicrobial therapy (n = 119). The appropriateness of antimicrobial selection through these interventions was verified with conventional culture results in comparison with historical control (n = 129). The mortality of patients between the two periods was also compared. RESULTS The appropriateness of antimicrobial selection was higher (99.2%) in the intervention than in the control group (93.8%) (p 0.024), but there was no difference in 28-day mortality between the two periods (16.8%, 14.8%) (p 0.668). The duration of presumptive antimicrobial therapy with anti-MRSA agents and carbapenem antibiotics did not differ between the two periods indicating that the intervention was not effective in decreasing the unnecessary antibiotics. On the other hand, some bacteremic patients with pathogens whose drug susceptibilities were invariably sensitive to the standard class of antibiotics definitely benefitted from the intervention. CONCLUSION The intervention utilizing MALDI-TOF MS and the rapid disk diffusion test may not demonstrate overall improvement in bacteremia mortality in the institution with full-time infectious disease consultants. Its utility has yet to be evaluated in different setting hospitals.
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Affiliation(s)
- Hiroki Magarifuchi
- Department of Internal Medicine, Imari Arita Kyoritsu Hospital, Saga, Japan.
| | - Yohei Hamada
- Division of Infectious Disease and Hospital Epidemiology, Saga University Hospital, Saga, Japan
| | - Megumi Oho
- Division of Clinical Laboratory, Saga University Hospital, Saga, Japan
| | - Koji Kusaba
- Division of Clinical Laboratory, Saga University Hospital, Saga, Japan
| | - Toshiharu Urakami
- Division of Infectious Disease and Hospital Epidemiology, Saga University Hospital, Saga, Japan
| | - Yosuke Aoki
- Division of Infectious Disease and Hospital Epidemiology, Saga University Hospital, Saga, Japan; Division of Clinical Infectious Diseases, Department of International Medicine, Faculty of Medicine, Saga University, Japan
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Barreiro JR, Gonçalves JL, Grenfell R, Leite RF, Juliano L, Santos MV. Direct identification of bovine mastitis pathogens by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in pre-incubated milk. Braz J Microbiol 2018; 49:801-807. [PMID: 30177270 PMCID: PMC6175725 DOI: 10.1016/j.bjm.2018.04.012] [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: 08/09/2017] [Revised: 02/09/2018] [Accepted: 04/16/2018] [Indexed: 11/21/2022] Open
Abstract
The present study aimed to compare two MALDI-TOF identification methods [(a) direct sample identification after pre-incubation; or (b) use of bacteria isolated on pre-culture)] to standard, traditional bench microbiology. A total of 120 quarter milk samples from 40 Holstein lactating cows were screened based on culture-positive results obtained by microbiological culture (reference method) with the following numbers of quarters positive per cow: 4 cows with 1, 8 cows with 2, 12 cows with 3 and 16 cows with 4 infected quarters per cow. For direct identification method, quarter milk samples (n = 120) were skimmed by centrifugation (10,000 × g/10 min) and pre-incubated at 37 °C for 12 h. After pre-incubation, quarter milk samples were submitted to total bacterial count by flow cytometry and for a preparation protocol for bacterial ribosomal protein extraction followed by MALDI-TOF MS analysis. The direct MALDI-TOF MS identification method compared to microbiological culture correctly identified isolates of coagulase-negative Staphylococci (27.2%), Streptococcus agalactiae (21.8%), Staphylococcus aureus (14.2%), and Streptococcus uberis (5.2%). The pre-incubation protocol of milk samples, associated to the direct identification method by MALDI-TOF MS, did not increase the identification at species level (score >2.0) of pathogens causing subclinical mastitis in comparison to the method without previous incubation.
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Affiliation(s)
- Juliana R Barreiro
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Juliano L Gonçalves
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Rafaella Grenfell
- Universidade Federal de São Paulo, Departamento de Biofísica, São Paulo, SP, Brazil
| | - Renata F Leite
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil
| | - Luiz Juliano
- Universidade Federal de São Paulo, Departamento de Biofísica, São Paulo, SP, Brazil
| | - Marcos V Santos
- Universidade de São Paulo (USP), Faculdade de Medicina Veterinária e Zootecnia, Departamento de Nutrição e Produção animal, Pirassununga, SP, Brazil.
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Alves G, Wang G, Ogurtsov AY, Drake SK, Gucek M, Sacks DB, Yu YK. Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1721-1737. [PMID: 29873019 PMCID: PMC6061032 DOI: 10.1007/s13361-018-1986-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/30/2018] [Accepted: 04/25/2018] [Indexed: 05/30/2023]
Abstract
Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.
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Affiliation(s)
- Gelio Alves
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Guanghui Wang
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David B Sacks
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
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